An Initial Characterization of Industrial Graphical User Interface Systems - Brooks,P.A.; Robinson,B.P.; Memon, Atif M. (Software Testing Verification and Validation, 2009. ICST '09. International Conference on, 2009)
To date we have developed and applied numerous model-based GUI testing techniques; however, we are unable to provide definitive improvement schemes to real-world GUI test planners, as our data was derived from open source applications, small compared to industrial systems. This paper presents a study of three industrial GUI-based software systems developed at ABB, including data on classified defects detected during late-phase testing and customer usage, test suites, and source code change metrics. The results show that (1) 50% of the defects found through the GUI are categorized as data access and handling, control flow and sequencing, correctness, and processing defects, (2) system crashes exposed defects 12-19% of the time, and (3) GUI and non-GUI components are constructed differently, in terms of source code metrics.
Keywords: Graphical user interfaces; GUI-based software systems; industrial graphical user interface systems; model-based GUI testing techniques; program testing; software metrics; source code change metrics

The Ins and Outs of Home Networking: The Case for Useful and Usable Domestic Networking - Grinter, Rebecca E.; Edwards, W. Keith; Marshini Chetty; Poole, Erika S.; Sung, Ja-Young; Yang, Jeonghwa; Crabtree, Andy; Tolmie, Peter; Rodden, Tom; Greenhalgh, Chris; Benford, Steve (ACM Trans. Comput.-Hum. Interact., 2009)
Householders are increasingly adopting home networking as a solution to the demands created by the presence of multiple computers, devices, and the desire to access the Internet. However, current network solutions are derived from the world of work (and initially the military) and provide poor support for the needs of the home. We present the key findings to emerge from empirical studies of home networks in the UK and US. The studies reveal two key kinds of work that effective home networking relies upon: one, the technical work of setting up and maintaining the home network, and the other, the collaborative and socially organized work of the home which the network is embedded in and supports. The two are thoroughly intertwined and rely upon one another for their realization, yet neither is adequately supported by current networking technologies and applications. Explication of the “work to make the home network work” opens up the design space for the continued integration of the home network in domestic life and elaboration of future support. Key issues for development include the development of networking facilities that do not require advanced networking knowledge, that are flexible and support the local social order of the home and the evolution of its routines, and which ultimately make the home network visible and accountable to household members.
Keywords: home networking; Human computer interaction

Interlingual annotation of multilingual text corpora and FrameNet - Farwell,David; Dorr, Bonnie J; Habash,Nizar; Helmreich,Stephen; Hovy,Eduard; Green,Rebecca; Levin,Lori; Miller,Keith; Mitamura,Teruko; Rambow,Owen; Reeder,Flo; Siddharthan,Advaith (Multilingual FrameNets in Computational LexicographyMultilingual FrameNets in Computational Lexicography, 2009)

Learning Facial Aging Models: A Face Recognition Perspective - Ramanathan,N.; Chellapa, Rama (Biometrics: theory, methods, and applications, 2009)

More than words: Syntactic packaging and implicit sentiment - Greene,S.; Resnik, Philip (Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics, 2009)

Multi-label prediction via sparse infinite CCA - Rai,P.; Daumé, Hal (Advances in Neural Information Processing Systems, 2009)

Off-Line Loop Investigation for Handwriting Analysis - Steinherz,T.; David Doermann; Rivlin,E.; Intrator,N. (IEEETransactions on Pattern Analysis and Machine Intelligence, 2009)

An oscillatory hebbian network model of short-term memory - Winder,R. K; Reggia, James A.; Weems,S. A; Bunting,M. F (Neural computation, 2009)

Participatory simulation as a tool for agent-based simulation - Berland,M.; Rand, William (Proceedings of the International Conference on Agents and Artificial Intelligence (ICAART-09), 2009)
Participatory simulation, as described by Wilensky & Stroup (1999c), is a form of agent-based simulation inwhich multiple humans control or design individual agents in the simulation. For instance, in a participatory simulation of an ecosystem, fifty participants might each control the intake and output of one agent, such that the food web emerges from the interactions of the human-controlled agents. We argue that participatory simulation has been under-utilized outside of strictly educational contexts, and that it provides myriad benefits to designers of traditional agent-based simulations. These benefits include increased robustness of the model, increased comprehensibility of the findings, and simpler design of individual agent behaviors. To make this argument, we look to recent research such as that from crowdsourcing (von Ahn, 2005) and the reinforcement learning of autonomous agent behavior (Abbeel, 2008).

Predicate Privacy in Encryption Systems - Shen, Emily; Elaine Shi; Waters,Brent (Theory of Cryptography, 2009)
Predicate encryption is a new encryption paradigm which gives a master secret key owner fine-grained control over access to encrypted data. The master secret key owner can generate secret key tokens corresponding to predicates. An encryption of data x can be evaluated using a secret token corresponding to a predicate f ; the user learns whether the data satisfies the predicate, i.e., whether f ( x ) = 1. Prior work on public-key predicate encryption has focused on the notion of data or plaintext privacy, the property that ciphertexts reveal no information about the encrypted data to an attacker other than what is inherently revealed by the tokens the attacker possesses. In this paper, we consider a new notion called predicate privacy , the property that tokens reveal no information about the encoded query predicate. Predicate privacy is inherently impossible to achieve in the public-key setting and has therefore received little attention in prior work. In this work, we consider predicate encryption in the symmetric-key setting and present a symmetric-key predicate encryption scheme which supports inner product queries. We prove that our scheme achieves both plaintext privacy and predicate privacy.
Keywords: Computer science

Pushing Enterprise Security Down the Network Stack - Clark,R.; Feamster, Nick; Nayak,A.; Reimers,A. (Georgia Institute of Technology, 2009)
Network security is typically reactive: Networks provide connectivity and subsequently alter this connectivity according to various security policies, as implemented in middleboxes, or at higher layers. This approach gives rise to complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. In this paper, we propose a proactive approach to securing networks, whereby security-related actions (e.g., dropping or redirecting traffic) are embedded into the network fabric itself, leaving only a fixed set of actions to higher layers. We explore this approach in the context of network access control. Our design uses programmable switches to manipulate traffic at lower layers; these switches interact with policy and monitoring at higher layers. We apply our approach to Georgia Tech’s network access control system, show how the new design can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.

Rate-Invariant Recognition of Humans and Their Activities - Veeraraghavan,A.; Srivastava, A.; Roy-Chowdhury, A.K.; Chellapa, Rama (Image Processing, IEEE Transactions on, 2009)
Pattern recognition in video is a challenging task because of the multitude of spatio-temporal variations that occur in different videos capturing the exact same event. While traditional pattern-theoretic approaches account for the spatial changes that occur due to lighting and pose, very little has been done to address the effect of temporal rate changes in the executions of an event. In this paper, we provide a systematic model-based approach to learn the nature of such temporal variations (time warps) while simultaneously allowing for the spatial variations in the descriptors. We illustrate our approach for the problem of action recognition and provide experimental justification for the importance of accounting for rate variations in action recognition. The model is composed of a nominal activity trajectory and a function space capturing the probability distribution of activity-specific time warping transformations. We use the square-root parameterization of time warps to derive geodesics, distance measures, and probability distributions on the space of time warping functions. We then design a Bayesian algorithm which treats the execution rate function as a nuisance variable and integrates it out using Monte Carlo sampling, to generate estimates of class posteriors. This approach allows us to learn the space of time warps for each activity while simultaneously capturing other intra- and interclass variations. Next, we discuss a special case of this approach which assumes a uniform distribution on the space of time warping functions and show how computationally efficient inference algorithms may be derived for this special case. We discuss the relative advantages and disadvantages of both approaches and show their efficacy using experiments on gait-based person identification and activity recognition.
Keywords: Automated; Video Recording; Bayesian algorithm; Monte Carlo sampling; action recognition; activity-specific time warping transformations; computationally efficient inference algorithms; distance measures; execution rate function; function space; gait-based person identification; geodesics; no; Statistical; Monte Carlo Method; Movement; Pattern Recognition

Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians - Qasim,Atif N; Metkus,Thomas S; Tadesse,Mahlet; Lehrke,Michael; Restine,Stephanie; Wolfe,Megan L; Hannenhalli, Sridhar; Cappola,Thomas; Rader,Daniel J; Reilly,Muredach P (Clinical Endocrinology, 2009)
Objective  Resistin causes insulin resistance and diabetes in mice whereas in humans it is linked to inflammation and atherosclerosis. Few human genetic studies of resistin in inflammation and atherosclerosis have been performed. We hypothesized that the –420C>G putative gain-of-function resistin variant would be associated with inflammatory markers and atherosclerosis but not with metabolic syndrome or adipokines in humans.Design and methods  We examined the association of three resistin polymorphisms, –852A>G, –420C>G and +157C>T, and related haplotypes with plasma resistin, cytokines, C-reactive protein (CRP), adipokines, plasma lipoproteins, metabolic syndrome and coronary artery calcification (CAC) in nondiabetic Caucasians (n = 851). Results  Resistin levels were higher, dose-dependently, with the –420G allele (CC 5·9 ± 2·7 ng/ml, GC 6·5 ± 4·0 ng/ml and GG 7·2 ± 4·8 ng/ml, trend P = 0·04) after age and gender adjustment [fold higher for GC + GG vs. CC; 1·07 (1·00–1·15), P < 0·05)]. The –852A>G single nucleotide polymorphism (SNP) was associated with higher soluble tumour necrosis factor-receptor 2 (sol-TNFR2) levels in fully adjusted models [1·06 (95% CI 1·01–1·11), P = 0·01)]. The estimated resistin haplotype (GGT) was associated with sol-TNFR2 (P = 0·04) and the AGT haplotype was related to CRP (P = 0·04) in the fully adjusted models. Resistin SNPs and haplotypes were not associated with body mass index (BMI), fasting glucose, insulin resistance, metabolic syndrome, adipokines or CAC scores. Conclusions  Despite modest associations with plasma resistin and inflammatory biomarkers, resistin 5′ variants were not associated with metabolic parameters or coronary calcification. This suggests that resistin is an inflammatory cytokine in humans but has little influence on adiposity, metabolic syndrome or atherosclerosis.

Resonance: dynamic access control for enterprise networks - Nayak,Ankur Kumar; Reimers,Alex; Feamster, Nick; Clark,Russ (Proceedings of the 1st ACM workshop on Research on enterprise networking, 2009)
Enterprise network security is typically reactive, and it relies heavily on host security and middleboxes. This approach creates complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. We argue that imbuing the network layer with mechanisms for dynamic access control can remedy these ills. We propose Resonance, a system for securing enterprise networks, where the network elements themselves enforce dynamic access control policies based on both flow-level information and real-time alerts. Resonance uses programmable switches to manipulate traffic at lower layers; these switches take actions (e.g., dropping or redirecting traffic) to enforce high-level security policies based on input from both higherlevel security policies and distributed monitoring and inference systems. We describe the design of Resonance, apply it to Georgia Tech's network access control system, show how it can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.
Keywords: Access control; enterprise networks; programmable networks

RNA Colony Blot Hybridization Method for Enumeration of Culturable Vibrio Cholerae and Vibrio Mimicus Bacteria - Grim,Christopher J.; Zo,Young-Gun; Hasan,Nur A.; Ali,Afsar; Chowdhury,Wasimul B.; Islam,Atiqul; Rashid,Mohammed H.; Alam,Munirul; Morris,J. Glenn; Huq,Anwar; Rita R Colwell (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2009)
A species-specific RNA colony blot hybridization protocol was developed for enumeration of culturable Vibrio cholerae and Vibrio mimicus bacteria in environmental water samples. Bacterial colonies on selective or nonselective plates were lysed by sodium dodecyl sulfate, and the lysates were immobilized on nylon membranes. A fluorescently labeled oligonucleotide probe targeting a phylogenetic signature sequence of 16S rRNA of V. cholerae and V. mimicus was hybridized to rRNA molecules immobilized on the nylon colony lift blots. The protocol produced strong positive signals for all colonies of the 15 diverse V. cholerae-V. mimicus strains tested, indicating 100% sensitivity of the probe for the targeted species. For visible colonies of 10 nontarget species, the specificity of the probe was calculated to be 90% because of a weak positive signal produced by Grimontia (Vibrio) hollisae, a marine bacterium. When both the sensitivity and specificity of the assay were evaluated using lake water samples amended with a bioluminescent V. cholerae strain, no false-negative or false-positive results were found, indicating 100% sensitivity and specificity for culturable bacterial populations in freshwater samples when G. hollisae was not present. When the protocol was applied to laboratory microcosms containing V. cholerae attached to live copepods, copepods were found to carry approximately 10,000 to 50,000 CFU of V. cholerae per copepod. The protocol was also used to analyze pond water samples collected in an area of cholera endemicity in Bangladesh over a 9-month period. Water samples collected from six ponds demonstrated a peak in abundance of total culturable V. cholerae bacteria 1 to 2 months prior to observed increases in pathogenic V. cholerae and in clinical cases recorded by the area health clinic. The method provides a highly specific and sensitive tool for monitoring the dynamics of V. cholerae in the environment. The RNA blot hybridization protocol can also be applied to detection of other gram-negative bacteria for taxon-specific enumeration.

Running memory span: A comparison of behavioral capacity limits with those of an attractor neural network - Weems,Scott A.; Winder,Ransom K.; Bunting,Michael; Reggia, James A. (Cognitive Systems Research, 2009)
We studied a computational model of short term memory capacity that performs a simulated running memory span task using Hebbian learning and rapid decay of connection strengths to keep recent items active for later recall. This model demonstrates recall performance similar to humans performing the same task, with a capacity limit of approximately three items and a prominent recency effect. The model also shows that this capacity depends on decay to release the model from accumulating interference. Model findings are compared with data from two behavioral experiments that used varying task demands to tax memory capacity limits. Following additional theoretical predictions from the computational model, behavioral data support that when task demands require attention to be spread too thin to keep items available for later recall, capacity limits suffer. These findings are important both for understanding the mechanisms underlying short term memory capacity, and also to memory researchers interested in the role of attention in capacity limitations.
Keywords: Attractor neural network; Computational model; Running span; Short term memory; Working memory capacity

Simple, Black-Box Constructions of Adaptively Secure Protocols - Choi, Seung Geol; Dana Dachman-Soled; Malkin, Tal; Wee, Hoeteck (Theory of Cryptography, 2009)
We present a compiler for transforming an oblivious transfer (OT) protocol secure against an adaptive semi-honest adversary into one that is secure against an adaptive malicious adversary. Our compiler achieves security in the universal composability framework, assuming access to an ideal commitment functionality, and improves over previous work achieving the same security guarantee in two ways: it uses black-box access to the underlying protocol and achieves a constant multiplicative overhead in the round complexity. As a corollary, we obtain the first constructions of adaptively secure protocols in the stand-alone model using black-box access to a low-level primitive.
Keywords: Algorithm Analysis and Problem Complexity; computers and society; Data Encryption; Discrete Mathematics in Computer Science; Management of Computing and Information Systems; Systems and Data Security

Streamed learning: one-pass SVMs - Rai,P.; Daumé, Hal; Venkatasubramanian,S. (Proceedings of the 21st international jont conference on Artifical intelligence, 2009)

Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13 - Zhang,Naixia; Wang,Qinghua; Ehlinger,Aaron; Randles,Leah; Lary,Jeffrey W.; Kang,Yang; Haririnia,Aydin; Storaska,Andrew J.; Cole,James L.; Fushman, David; Walters,Kylie J. (Molecular Cell, 2009)
SummaryDegradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of one ubiquitin subunit (the “proximal” one) is covalently bonded to G76 of the other (the “distal” subunit). We demonstrate that S5a's UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains.
Keywords: Proteins

Surface reconstruction from gradient fields via gradient transformations - Agrawal,A.; Raskar, R.; Chellapa, Rama (International Journal of Computer Vision, 2009)

Temporal Summaries: Supporting Temporal Categorical Searching, Aggregation and Comparison - Wang,T. D; Plaisant, Catherine; Shneiderman, Ben; Spring, Neil; Roseman,D.; Marchand,G.; Mukherjee,V.; Smith,M. (Visualization and Computer Graphics, IEEE Transactions on, 2009)
When analyzing thousands of event histories, analysts often want to see the events as an aggregate to detect insights and generate new hypotheses about the data. An analysis tool must emphasize both the prevalence and the temporal ordering of these events. Additionally, the analysis tool must also support flexible comparisons to allow analysts to gather visual evidence. In a previous work, we introduced align, rank, and filter (ARF) to accentuate temporal ordering. In this paper, we present temporal summaries, an interactive visualization technique that highlights the prevalence of event occurrences. Temporal summaries dynamically aggregate events in multiple granularities (year, month, week, day, hour, etc.) for the purpose of spotting trends over time and comparing several groups of records. They provide affordances for analysts to perform temporal range filters. We demonstrate the applicability of this approach in two extensive case studies with analysts who applied temporal summaries to search, filter, and look for patterns in electronic health records and academic records.
Keywords: Automated; Thrombocytopenia; Time Factors; Computerized; Pattern Recognition; Factual; Heparin; Humans; Medical Records Systems; interactive visualization technique; temporal categorical searching; temporal ordering; temporal summaries; data visualisation; human computer interaction; Computational Biology; Computer Graphics; Databases

Temporal Summaries: Supporting Temporal Categorical Searching, Aggregation and Comparison - Wang,T. D; Plaisant, Catherine; Shneiderman, Ben; Spring, Neil; Roseman,D.; Marchand,G.; Mukherjee,V.; Smith,M. (IEEE Transactions on Visualization and Computer Graphics, 2009)
When analyzing thousands of event histories, analysts often want to see the events as an aggregate to detect insights and generate new hypotheses about the data. An analysis tool must emphasize both the prevalence and the temporal ordering of these events. Additionally, the analysis tool must also support flexible comparisons to allow analysts to gather visual evidence. In a previous work, we introduced align, rank, and filter (ARF) to accentuate temporal ordering. In this paper, we present temporal summaries, an interactive visualization technique that highlights the prevalence of event occurrences. Temporal summaries dynamically aggregate events in multiple granularities (year, month, week, day, hour, etc.) for the purpose of spotting trends over time and comparing several groups of records. They provide affordances for analysts to perform temporal range filters. We demonstrate the applicability of this approach in two extensive case studies with analysts who applied temporal summaries to search, filter, and look for patterns in electronic health records and academic records.
Keywords: Aggregates; Collaborative work; Computational Biology; Computer Graphics; Data analysis; data visualisation; Data visualization; Databases, Factual; Displays; Event detection; Filters; Heparin; History; Human computer interaction; Human-computer interaction; HUMANS; Information Visualization; Interaction design; interactive visualization technique; Medical Records Systems, Computerized; Pattern Recognition, Automated; Performance analysis; Springs; temporal categorical data visualization; temporal categorical searching; temporal ordering; temporal summaries; Thrombocytopenia; Time factors

Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. - Ward, Naomi L; Challacombe, Jean F; Janssen, Peter H; Henrissat, Bernard; Coutinho, Pedro M; Wu, Martin; Xie, Gary; Haft, Daniel H; Sait, Michelle; Badger, Jonathan; Barabote, Ravi D; Bradley, Brent; et al. (Appl Environ Microbiol, 2009)
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
Keywords: Anti-Bacterial Agents; bacteria; Biological Transport; Carbohydrate Metabolism; Cyanobacteria; DNA, Bacterial; Fungi; Genome, Bacterial; Macrolides; Molecular Sequence Data; Nitrogen; Phylogeny; Proteobacteria; Sequence Analysis, DNA; sequence homology; Soil Microbiology

Together, Rpn10 and Dsk2 Can Serve as a Polyubiquitin Chain-Length Sensor - Zhang,Daoning; Chen,Tony; Ziv,Inbal; Rosenzweig,Rina; Matiuhin,Yulia; Bronner,Vered; Glickman,Michael H.; Fushman, David (Molecular Cell, 2009)
SummaryAs a signal for substrate targeting, polyubiquitin meets various layers of receptors upstream to the 26S proteasome. We obtained structural information on two receptors, Rpn10 and Dsk2, alone and in complex with (poly)ubiquitin or with each other. A hierarchy of affinities emerges with Dsk2 binding monoubiquitin tighter than Rpn10 does, whereas Rpn10 prefers the ubiquitin-like domain of Dsk2 to monoubiquitin, with increasing affinities for longer polyubiquitin chains. We demonstrated the formation of ternary complexes of both receptors simultaneously with (poly)ubiquitin and found that, depending on the ubiquitin chain length, the orientation of the resulting complex is entirely different, providing for alternate signals. Dynamic rearrangement provides a chain-length sensor, possibly explaining how accessibility of Dsk2 to the proteasome is limited unless it carries a properly tagged cargo. We propose a mechanism for a malleable ubiquitin signal that depends both on chain length and combination of receptors to produce tetraubiquitin as an efficient signal threshold.
Keywords: Proteins; signaling

Topological ordering of function words in hierarchical phrase-based translation - Setiawan,H.; Kan,M.Y.; Li,H.; Resnik, Philip (Proceedings of the Joint Conference of the 47th Annual Meeting of the ACL and the 4th International Joint Conference on Natural Language Processing of the AFNLP: Volume 1-Volume 1, 2009)

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study - Regier,J. C; Zwick,A.; Cummings, Michael P.; Kawahara,A. Y; Cho,S.; Weller,S.; Roe,A.; Baixeras,J.; Brown,J. W; Parr,C.; Davis,DR; Epstein,M; et al. (BMC Evol Biol, 2009)
BACKGROUND: In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis. RESULTS: Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P < or = 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data. CONCLUSION: Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.

The University of Maryland statistical machine translation system for the Fourth Workshop on Machine Translation - Dyer,C.; Setiawan,H.; Marton,Y.; Resnik, Philip (Proceedings of the Fourth Workshop on Statistical Machine Translation, 2009)

An unsupervised learning method for representing simple sentences - Monner,D.; Reggia, James A. (Neural Networks, 2009. IJCNN 2009. International Joint Conference on, 2009)

Using citations to generate surveys of scientific paradigms - Mohammad,Saif; Dorr, Bonnie J; Egan,Melissa; Hassan,Ahmed; Muthukrishan,Pradeep; Qazvinian,Vahed; Radev,Dragomir; Zajic, David (Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics, 2009)
The number of research publications in various disciplines is growing exponentially. Researchers and scientists are increasingly finding themselves in the position of having to quickly understand large amounts of technical material. In this paper we present the first steps in producing an automatically generated, readily consumable, technical survey. Specifically we explore the combination of citation information and summarization techniques. Even though prior work (Teufel et al., 2006) argues that citation text is unsuitable for summarization, we show that in the framework of multi-document survey creation, citation texts can play a crucial role.

Using Satellite Images of Environmental Changes to Predict Infectious Disease Outbreaks - Ford,Timothy E.; Rita R Colwell; Rose,Joan B.; Morse,Stephen S.; Rogers,David J.; Yates,Terry L. (Emerging Infectious DiseasesEmerg Infect Dis, 2009)
A strong global satellite imaging system is essential for predicting outbreaks., Recent events clearly illustrate a continued vulnerability of large populations to infectious diseases, which is related to our changing human-constructed and natural environments. A single person with multidrug-resistant tuberculosis in 2007 provided a wake-up call to the United States and global public health infrastructure, as the health professionals and the public realized that today’s ease of airline travel can potentially expose hundreds of persons to an untreatable disease associated with an infectious agent. Ease of travel, population increase, population displacement, pollution, agricultural activity, changing socioeconomic structures, and international conflicts worldwide have each contributed to infectious disease events. Today, however, nothing is larger in scale, has more potential for long-term effects, and is more uncertain than the effects of climate change on infectious disease outbreaks, epidemics, and pandemics. We discuss advances in our ability to predict these events and, in particular, the critical role that satellite imaging could play in mounting an effective response.

Validating Automotive Control Software Using Instrumentation-Based Verification - Ray,Arnab; Morschhaeuser,Iris; Ackermann,Chris; Cleaveland, Rance; Shelton,Charles; Martin,Chris (Automated Software Engineering, International Conference on, 2009)
This paper discusses the results of an application of a formally based verification technique, called Instrumentation-Based Verification (IBV), to a production automotive lighting controller. The goal of the study is to assess, from both a tools as well as a methodological perspective, the performance of IBV in an industrial setting. The insights obtained as a result of the project include a refinement of a previously developed architecture for requirements specifications; observations about changes to model-based design workflows; insights into the role of requirements during development; and the capability of automated verification to detect inconsistencies among requirements as well as between requirements and design models.

Visual overviews for discovering key papers and influences across research fronts - Aris,Aleks; Shneiderman, Ben; Qazvinian,Vahed; Radev,Dragomir (Journal of the American Society for Information Science and Technology, 2009)
Gaining a rapid overview of an emerging scientific topic, sometimes called research fronts, is an increasingly common task due to the growing amount of interdisciplinary collaboration. Visual overviews that show temporal patterns of paper publication and citation links among papers can help researchers and analysts to see the rate of growth of topics, identify key papers, and understand influences across subdisciplines. This article applies a novel network-visualization tool based on meaningful layouts of nodes to present research fronts and show citation links that indicate influences across research fronts. To demonstrate the value of two-dimensional layouts with multiple regions and user control of link visibility, we conducted a design-oriented, preliminary case study with 6 domain experts over a 4-month period. The main benefits were being able (a) to easily identify key papers and see the increasing number of papers within a research front, and (b) to quickly see the strength and direction of influence across related research fronts.

Web Monitoring 2.0: Crossing Streams to Satisfy Complex Data Needs - Roitman,H.; Gal,A.; Raschid, Louiqa (IEEE 25th International Conference on Data Engineering, 2009. ICDE '09, 2009)
Web monitoring 2.0 supports the complex information needs of clients who probe multiple information sources and generate mashups by integrating across these volatile streams. A proxy that aims at satisfying multiple customized client profiles will face a scalability challenge in trying to maximize the number of clients served while at the same time fully satisfying complex client needs. In this paper, we introduce an abstraction of complex execution intervals, a combination of time intervals and information streams, to capture complex client needs. Given some budgetary constraints (e.g., bandwidth), we present offline algorithmic solutions for the problem of maximizing completeness of capturing complex profiles.
Keywords: Bandwidth; complex client information need; Data Delivery; Data engineering; database management systems; Educational institutions; Internet; Mashups; mashups generation; Monitoring; multiple information source; offline algorithmic solution; Portals; PROBES; Profiles; Query processing; scalability; scheduling; volatile information stream; Web 2.0; Web Monitoring

Within epsilon of optimal play in the cultaptation social learning game - Carr,Ryan; Raboin,Eric; Parker,Austin; Nau, Dana S. (International Foundation for Autonomous Agents and Multiagent Systems, 2009)
Social learning, in which members of a society learn by observing the behavior of others, is an important foundation for human culture, and is observed in many other species as well. It seems natural to assume that social learning evolved due to the inherent superiority of copying others' success rather than learning on one's own via trial-and-error innovation. However, there has also been substantial work questioning this intuition [3, 5, 1, 6, 4]. For example, blindly copying information from others is not useful if the information is wrong---or if it once was right but has since become outdated. Under what conditions does social learning outperform trial-and-error learning, and what kinds of social-learning strategies are likely to perform well?

The acl anthology reference corpus: A reference dataset for bibliographic research in computational linguistics - Bird,S.; Dale,R.; Dorr, Bonnie J; Gibson,B.; Joseph,M.T.; Kan,M.Y.; Lee,D.; Powley,B.; Radev,D.R.; Tan,Y.F. (Proc. of the 6th International Conference on Language Resources and Evaluation Conference (LREC’08), 2008)
The ACL Anthology is a digital archive of conference and journal papers in natural language processing and computational linguistics.Its primary purpose is to serve as a reference repository of research results, but we believe that it can also be an object of study and a platform for research in its own right. We describe an enriched and standardized reference corpus derived from the ACL Anthology that can be used for research in scholarly document processing. This corpus, which we call the ACL Anthology Reference Corpus (ACL ARC), brings together the recent activities of a number of research groups around the world. Our goal is to make the corpus widely available, and to encourage other researchers to use it as a standard testbed for experiments in both bibliographic and bibliometric research.

Activity representation using 3D shape models - Abdelkader,Mohamed F.; Roy-Chowdhury,Amit K.; Chellapa, Rama; Akdemir,Umut (J. Image Video Process., 2008)
We present a method for characterizing human activities using 3D deformable shape models. The motion trajectories of points extracted from objects involved in the activity are used to build models for each activity, and these models are used for classification and detection of unusual activities. The deformable models are learnt using the factorization theorem for nonrigid 3D models. We present a theory for characterizing the degree of deformation in the 3D models from a sequence of tracked observations. This degree, termed as deformation index (DI), is used as an input to the 3D model estimation process. We study the special case of ground plane activities in detail because of its importance in video surveillance applications. We present results of our activity modeling approach using videos of both high-resolution single individual activities and ground plane surveillance activities.

Affinity Makes the Difference: Nonselective Interaction of the UBA Domain of Ubiquilin-1 with Monomeric Ubiquitin and Polyubiquitin Chains - Zhang,Daoning; Raasi,Shahri; Fushman, David (Journal of Molecular Biology, 2008)
Ubiquilin/PLIC proteins belong to the family of UBL–UBA proteins implicated in the regulation of the ubiquitin-dependent proteasomal degradation of cellular proteins. A human presenilin-interacting protein, ubiquilin-1, has been suggested as potential therapeutic target for treating Huntington's disease. Ubiquilin's interactions with mono- and polyubiquitins are mediated by its UBA domain, which is one of the tightest ubiquitin binders among known ubiquitin-binding domains. Here we report the three-dimensional structure of the UBA domain of ubiquilin-1 (UQ1-UBA) free in solution and in complex with ubiquitin. UQ1-UBA forms a compact three-helix bundle structurally similar to other known UBAs, and binds to the hydrophobic patch on ubiquitin with a Kd of 20 μM. To gain structural insights into UQ1-UBA's interactions with polyubiquitin chains, we have mapped the binding interface between UQ1-UBA and Lys48- and Lys63-linked di-ubiquitins and characterized the strength of UQ1-UBA binding to these chains. Our NMR data show that UQ1-UBA interacts with the individual ubiquitin units in both chains in a mode similar to its interaction with mono-ubiquitin, although with an improved binding affinity for the chains. Our results indicate that, in contrast to UBA2 of hHR23A that has strong binding preference for Lys48-linked chains, UQ1-UBA shows little or no binding selectivity toward a particular chain linkage or between the two ubiquitin moieties in the same chain. The structural data obtained in this study provide insights into the possible structural reasons for the diversity of polyubiquitin chain recognition by UBA domains.
Keywords: polyubiquitin; protein–protein interaction; UBA domain; ubiquilin; ubiquitin

Applying automatically generated semantic knowledge: A case study in machine translation - Madnani,N.; Resnik, Philip; Dorr, Bonnie J; Schwartz,R. (NSF Symposium on Semantic Knowledge Discovery, Organization and Use, 2008)
In this paper, we discuss how we apply automatically generated semantic knowledge to benefit statisticalmachine translation (SMT). Currently, almost all statistical machine translation systems rely heavily on memorizing translations of phrases. Some systems attempt to go further and generalize these learned phrase translations into templates using empirically derived information about word alignments and a small amount of syntactic information, if at all. There are several issues in a SMT pipeline that could be addressed by the application of semantic knowledge, if such knowledge were easily available. One such issue, an important one, is that of reference sparsity. The fundamental problem that translation systems have to face is that there is no such thing as the correct translation for any sentence. In fact, any given source sentence can often be translated into the target language in many valid ways. Since there can be many “correct answers,” almost all models employed by SMT systems require, in addition to a large bitext, a held-out development set comprised of multiple high-quality, human-authored reference translations in the target language in order to tune their parameters relative to a translation quality metric.1 There are several reasons that this requirement is not an easy one to satisfy. First, with a few exceptions—notably NIST’s annual MT evaluations—most new MT research data sets are provided with only a single reference translation. Second, obtaining multiple reference translations in rapid development, low-density source language scenarios (e.g. (Oard, 2003)) is likely to be severely limited (or made entirely impractical) by limitations of time, cost, and ready availability of qualified translators.

Are multiple reference translations necessary? investigating the value of paraphrased reference translations in parameter optimization - Madnani,N.; Resnik, Philip; Dorr, Bonnie J; Schwartz,R. (Proceedings of the Eighth Conference of the Association for Machine Translation in the Americas, October, 2008)
Most state-of-the-art statistical machine trans-lation systems use log-linear models, which are defined in terms of hypothesis features and weights for those features. It is standard to tune the feature weights in order to maxi- mize a translation quality metric, using held- out test sentences and their corresponding ref- erence translations. However, obtaining refer- ence translations is expensive. In our earlier work (Madnani et al., 2007), we introduced a new full-sentence paraphrase technique, based on English-to-English decoding with an MT system, and demonstrated that the resulting paraphrases can be used to cut the number of human reference translations needed in half. In this paper, we take the idea a step further, asking how far it is possible to get with just a single good reference translation for each item in the development set. Our analysis suggests that it is necessary to invest in four or more hu- man translations in order to significantly im- prove on a single translation augmented by monolingual paraphrases.

Authenticated out-of-band communication over social links - Ramachandran,Anirudh V.; Feamster, Nick (Proceedings of the first workshop on Online social networks, 2008)
Many existing host-based applications rely on their own authentication mechanisms and peer discovery services. Although social networking sites already provide mechanisms for users both to discover other users (e.g., by logging on to the social network Web site) and to communicate securely with each other (e.g., using instant messages within the social networking site), today's applications have no way to exploit the relationships and trust that are inherent in these networks. This paper proposes Authenticatr, a framework that allows applications to use the authentication and peer discovery mechanisms inherent in social networking sites to bootstrap their own authenticated communication channels. We describe motivating applications, detail the interface that Authenticatr exposes to applications, and discuss practical considerations and security threats.
Keywords: Authentication; Security; social networks

Automated design of distributed control rules for the self-assembly of prespecified artificial structures - Grushin,Alexander; Reggia, James A. (Robotics and Autonomous Systems, 2008)
The self-assembly problem involves the design of agent-level control rules that will cause the agents to form some desired, target structure, subject to environmental constraints. This paper describes a fully automated rule generation procedure that allows structures to successfully self-assemble in a simulated environment with constrained, continuous motion. This environment implicitly imposes ordering constraints on the self-assembly process, where certain parts of the target structure must be assembled before others, and where it may be necessary to assemble (and subsequently disassemble) temporary structures such as staircases. A provably correct methodology is presented for computing a partial order on the self-assembly process, and for generating rules that enforce this order at runtime. The assembly and disassembly of structures is achieved by generating another set of rules, which are inspired by construction behavior among certain species of social insects. Computational experiments verify the effectiveness of the approach on a diverse set of target structures.
Keywords: Collective problem solving; Coordination; Self-assembly; Stigmergy; Swarm intelligence

Automatic online tuning for fast Gaussian summation - Morariu,V.; Srinivasan,B.V.; Raykar,V.C.; Duraiswami, Ramani; Davis, Larry S. (Advances in Neural Information Processing Systems, 2008)
Many machine learning algorithms require the summation of Gaussian kernelfunctions, an expensive operation if implemented straightforwardly. Several meth- ods have been proposed to reduce the computational complexity of evaluating such sums, including tree and analysis based methods. These achieve varying speedups depending on the bandwidth, dimension, and prescribed error, making the choice between methods difficult for machine learning tasks. We provide an algorithm that combines tree methods with the Improved Fast Gauss Transform (IFGT). As originally proposed the IFGT suffers from two problems: (1) the Taylor series expansion does not perform well for very low bandwidths, and (2) parameter se- lection is not trivial and can drastically affect performance and ease of use. We address the first problem by employing a tree data structure, resulting in four eval- uation methods whose performance varies based on the distribution of sources and targets and input parameters such as desired accuracy and bandwidth. To solve the second problem, we present an online tuning approach that results in a black box method that automatically chooses the evaluation method and its parameters to yield the best performance for the input data, desired accuracy, and bandwidth. In addition, the new IFGT parameter selection approach allows for tighter error bounds. Our approach chooses the fastest method at negligible additional cost, and has superior performance in comparisons with previous approaches.

AVA: Adjective-Verb-Adverb Combinations for Sentiment Analysis - V.S. Subrahmanian; Reforgiato,Diego (Intelligent Systems, IEEE, 2008)
Most research on determining the strength of subjective expressions in a sentence or document uses single, specific parts of speech such as adjectives, adverbs, or verbs. To date, almost no research covers the development of a single comprehensive framework in which we can analyze sentiment that takes all three into account. The authors propose the AVA (adjective verb adverb) framework for identifying opinions on any given topic. In AVA, a user can select any topic t of interest and any document d. AVA will return a score that d expresses topic t. The score is expressed on a #x02013;1 (maximally negative) to +1 (maximally positive) scale.

Bandwidth-constrained queries in sensor networks - Deligiannakis,A.; Kotidis,Y.; Roussopoulos, Nick (The VLDB Journal, 2008)

Budgeted Allocations in the Full-Information Setting - Srinivasan, Aravind (Approximation, Randomization and Combinatorial Optimization. Algorithms and TechniquesApproximation, Randomization and Combinatorial Optimization. Algorithms and Techniques, 2008)
We build on the work of Andelman & Mansour and Azar, Birnbaum, Karlin, Mathieu & Thach Nguyen to show that the full-information (i.e., offline) budgeted-allocation problem can be approximated to within 4/3: we conduct a rounding of the natural LP relaxation, for which our algorithm matches the known lower-bound on the integrality gap.

Capturing Approximated Data Delivery Tradeoffs - Roitman,H.; Gal,A.; Raschid, Louiqa (Data Engineering, 2008. ICDE 2008. IEEE 24th International Conference on, 2008)
This paper presents a middleware data delivery setting with a proxy that is required to maximize the completeness of captured updates, specified in its clients' profiles, while minimizing at the same time the delay in delivering the updates to clients. The two objectives may conflict when the monitoring budget is limited. Therefore, any solution should consider this tradeoff in satisfying both objectives. We term this problem the "proxy dilemma" and formalize it as a biobjective optimization problem. Such problem occurs in many contemporary applications, such as mobile and sensor networks, and poses scalability challenges in delivering up-to-date data from remote resources to meet client specifications. We present a Pareto set as a formal solution to the proxy dilemma. We discuss the complexity of generating a Pareto set for the proxy dilemma and suggest an approximation scheme to this problem.
Keywords: approximation scheme; approximation theory; biobjective optimization problem; Middleware; middleware data delivery tradeoffs; mobile networks; Pareto optimisation; Pareto set; proxy dilemma problem; sensor networks

Compressed sensing for multi-view tracking and 3-D voxel reconstruction - Reddy, D.; Sankaranarayanan,A. C; Cevher, V.; Chellapa, Rama (Image Processing, 2008. ICIP 2008. 15th IEEE International Conference on, 2008)
Compressed sensing (CS) suggests that a signal, sparse in some basis, can be recovered from a small number of random projections. In this paper, we apply the CS theory on sparse background-subtracted silhouettes and show the usefulness of such an approach in various multi-view estimation problems. The sparsity of the silhouette images corresponds to sparsity of object parameters (location, volume etc.) in the scene. We use random projections (compressed measurements) of the silhouette images for directly recovering object parameters in the scene coordinates. To keep the computational requirements of this recovery procedure reasonable, we tessellate the scene into a bunch of non-overlapping lines and perform estimation on each of these lines. Our method is scalable in the number of cameras and utilizes very few measurements for transmission among cameras. We illustrate the usefulness of our approach for multi-view tracking and 3-D voxel reconstruction problems.
Keywords: 3D; background-subtracted; coding; Estimation; image; problems; multi-view; projections; silhouette; reconstruction; CS; reconstruction; video; sensing; multi-view; silhouettes; image; sparsity; sparse; theory; compressed; tracking; random; voxel

Compressive sensing for background subtraction - Cevher, V.; Sankaranarayanan, A.; Duarte, M.; Reddy, D.; Baraniuk, R.; Chellapa, Rama (Computer Vision–ECCV 2008, 2008)
Compressive sensing (CS) is an emerging field that provides a framework for image recovery using sub-Nyquist sampling rates. The CS theory shows that a signal can be reconstructed from a small set of random projections, provided that the signal is sparse in some basis, e.g., wavelets. In this paper, we describe a method to directly recover background subtracted images using CS and discuss its applications in some communication constrained multi-camera computer vision problems. We show how to apply the CS theory to recover object silhouettes (binary background subtracted images) when the objects of interest occupy a small portion of the camera view, i.e., when they are sparse in the spatial domain. We cast the background subtraction as a sparse approximation problem and provide different solutions based on convex optimization and total variation. In our method, as opposed to learning the background, we learn and adapt a low dimensional compressed representation of it, which is sufficient to determine spatial innovations; object silhouettes are then estimated directly using the compressive samples without any auxiliary image reconstruction. We also discuss simultaneous appearance recovery of the objects using compressive measurements. In this case, we show that it may be necessary to reconstruct one auxiliary image. To demonstrate the performance of the proposed algorithm, we provide results on data captured using a compressive single-pixel camera. We also illustrate that our approach is suitable for image coding in communication constrained problems by using data captured by multiple conventional cameras to provide 2D tracking and 3D shape reconstruction results with compressive measurements.

Cross-language parser adaptation between related languages - Zeman,D.; Resnik, Philip (NLP for Less Privileged Languages, 2008)

CrossNet: a framework for crossover with network-based chromosomal representations - Stonedahl,Forrest; Rand, William; Wilensky,Uri (Proceedings of the 10th annual conference on Genetic and evolutionary computation, 2008)
We propose a new class of crossover operators for genetic algorithms (CrossNet) which use a network-based (or graph-based) chromosomal representation. We designed CrossNet with the intent of providing a framework for creating crossover operators that take advantage of domain-specific knowledge for solving problems. Specifically, GA users supply a network which defines the epistatic relationships between genes in the genotype. CrossNet-based crossover uses this information with the goal of improving linkage. We performed two experiments that compared CrossNet-based crossover with one-point and uniform crossover. The first experiment involved the density classification problem for cellular automata (CA), and the second experiment involved fitting two randomly generated hyperplane-defined functions (hdf's). Both of these exploratory experiments support the hypothesis that CrossNet-based crossover can be useful, although performance improvements were modest. We discuss the results and remain hopeful about the successful application of CrossNet to other domains. We conjecture that future work with the CrossNet framework will provide a useful new perspective for investigating linkage and chromosomal representations.
Keywords: crossover; Genetic algorithms; graphs; linkage; NETWORKS; recombination

CrossTalk: The Journal of Defense Software Engineering. Volume 21, Number 10, October 2008 - Basili, Victor R.; Dangle,K.; Esker,L.; Marotta,F.; Rus,I.; Brosgol,B. M; Jamin,S.; Arthur,J. D; Ravichandar,R.; Wisnosky,D. E (DTIC Document, 2008)

Detecting botnet membership with dnsbl counterintelligence - Ramachandran,A.; Feamster, Nick; Dagon,D. (Botnet Detection, 2008)

A Dynamic Reputation Service for Spotting Spammers - Ramachandran,A.; Hao,S.; Khandelwal,H.; Feamster, Nick; Vempala,S. (School of Computer Science, Georgia Tech, 2008)
This paper presents the design, implementation, evalu-ation, and initial deployment of SpamSpotter, the first open, large-scale, real-time reputation system for filtering spam. Existing blacklists (e.g., SpamHaus) have trouble keeping pace with spammers’ increasing ability to send spam from “fresh” IP addresses, and filters based purely on content are easily evadable. In contrast, SpamSpotter dynamically classifies email senders in real time based on their global sending behavior, rather than based on ephemeral features such as an IP address or the content of the message. In implementing SpamSpotter, we address significant challenges involving both dynamism (i.e., de- termining when to “retrain” our dynamic classification algorithms) and scale (i.e., maintaining fast, accurate per- formance in the face of tremendous email message vol- ume). We have evaluated the performance and accuracy of SpamSpotter using traces from a large email-hosting provider and a spam appliance vendor that receives 300 million messages a day. Our evaluation shows that SpamSpotter is scalable, fast, and accurate. SpamSpotter is also operational today: it will currently answer queries from existing spam filtering software (e.g., SpamAssas- sin) with only minor configuration changes.

Efficient Kriging via Fast Matrix-Vector Products - Memarsadeghi,N.; Raykar,V.C.; Duraiswami, Ramani; Mount, Dave (Aerospace Conference, 2008 IEEE, 2008)
Interpolating scattered data points is a problem of wide ranging interest. Ordinary kriging is an optimal scattered data estimator, widely used in geosciences and remote sensing. A generalized version of this technique, called cokriging, can be used for image fusion of remotely sensed data. However, it is computationally very expensive for large data sets. We demonstrate the time efficiency and accuracy of approximating ordinary kriging through the use of fast matrix-vector products combined with iterative methods. We used methods based on the fast Multipole methods and nearest neighbor searching techniques for implementations of the fast matrix-vector products.
Keywords: cokriging technique; fast matrix-vector products; fast multipole methods; geophysical techniques; image fusion; Interpolation; iterative methods; nearest neighbor searching; optimal scattered data estimator; Remote sensing; remotely sensed data; scattered data points; sensor fusion; time efficiency

Efficient Kriging via Fast Matrix-Vector Products - Memarsadeghi,N.; Raykar,V.C.; Duraiswami, Ramani; Mount, Dave (Aerospace Conference, 2008 IEEE, 2008)
Interpolating scattered data points is a problem of wide ranging interest. Ordinary kriging is an optimal scattered data estimator, widely used in geosciences and remote sensing. A generalized version of this technique, called cokriging, can be used for image fusion of remotely sensed data. However, it is computationally very expensive for large data sets. We demonstrate the time efficiency and accuracy of approximating ordinary kriging through the use of fast matrix-vector products combined with iterative methods. We used methods based on the fast Multipole methods and nearest neighbor searching techniques for implementations of the fast matrix-vector products.
Keywords: cokriging; data; data; scattered; efficiency; geophysical; estimator; remotely; fusion; fusion; interpolation; iterative; matrix-vector; methods; image; methods; nearest; methods; remote; multipole; neighbor; points; time; products; fast; scattered; searching; optimal; sensed; sensing; sensor; technique; fast; techniques; iterative

Enhancements in robust feature matching - Ratanasanya,S.; Mount, Dave; Netanyahu,N. S; Achalakul,T. (Electrical Engineering/Electronics, Computer, Telecommunications and Information Technology, 2008. ECTI-CON 2008. 5th International Conference on, 2008)
We present in this paper a number of new enhancements to a branch-and-bound algorithm given by Mount, Netanyahu, and Le Moigne [8] for feature matching. We introduce a new distance measure, which is more robust to the presence of outliers than the previously used measure, as well as a new variant of the search algorithm and a new search strategy. We also present experimental results, which show that these enhancements offer significant tangible improvements in performance.
Keywords: branch-and-bound algorithm; distance measure; Image Enhancement; Image matching; robust feature matching; tree searching

Executable Specifications for Real-Time Distributed Systems - Ray,Arnab; Cleaveland, Rance (Electronic Notes in Theoretical Computer Science, 2008)
One of the challenges in designing distributed, embedded systems is the paucity of formal, executable specification notations that provide support for both real-time and asynchronous communication. This paper describes a timed architecture design language (Timed Architecture Interaction Diagrams or TAID) that, by virtue of its formal, executable semantics, combines the benefits of synchronous specification notations with the advantages of traditional architecture description languages. In addition, TAID provides support for a variety of temporal inter-process communication (IPC) primitives as a native feature of the language, so that the encapsulated communication behavior (captured by real-time â€œbusesâ€ in TAID) may be re-used across designs and serve as specifications for more detailed model implementations.
Keywords: distributed systems; Formal Methods; real-time; Simulations; Software architecture

Experiences with building an intrusion-tolerant group communication system - Ramasamy,HariGovind V.; Pandey,Prashant; Michel Cukier; Sanders,William H. (Software: Practice and Experience, 2008)
There are many group communication systems (GCSs) that provide consistent group membership and reliable, ordered multicast properties in the presence of crash faults. However, relatively few GCS implementations are able to provide these properties in the presence of malicious faults resulting from intrusions. We describe the systematic transformation of a crash-tolerant GCS, namely C-Ensemble, into an intrusion-tolerant GCS, the ITUA GCS. To perform the transformation, we devised intrusion-tolerant versions of key group communication protocols. We then inserted implementations of the protocols into C-Ensemble and made significant changes to the rest of the C-Ensemble protocol stack to make the stack intrusion tolerant. We quantify the cost of providing intrusion-tolerant group communication in two ways. First, we quantify the implementation effort by presenting a detailed analysis of the amount of change required to the original C-Ensemble system. In doing so, we provide insight into the choice of building an intrusion-tolerant GCS from scratch versus building one by leveraging a crash-tolerant implementation. Second, we quantify the run-time performance cost of tolerating intrusions by presenting results from an experimental evaluation of the main intrusion-tolerant microprotocols. The results are analyzed to identify the parts that contribute the most overhead while providing intrusion tolerance during both normal operation and recovery from intrusions. Copyright © 2007 John Wiley & Sons, Ltd.
Keywords: distributed protocols; experimental evaluation; Fault tolerance; Group communication; intrusion tolerance

Exploiting ontology structure and patterns of annotation to mine significant associations between pairs of controlled vocabulary terms - Lee,W. J; Raschid, Louiqa; Sayyadi,H.; Srinivasan,P. (Data Integration in the Life Sciences, 2008)

Exurbia from the bottom-up: Confronting empirical challenges to characterizing a complex system - Brown,Daniel G.; Robinson,Derek T.; An,Li; Nassauer,Joan I.; Zellner,Moira; Rand, William; Riolo,Rick; Page,Scott E.; Low,Bobbi; Wang,Zhifang (Geoforum, 2008)
We describe empirical results from a multi-disciplinary project that support modeling complex processes of land-use and land-cover change in exurban parts of Southeastern Michigan. Based on two different conceptual models, one describing the evolution of urban form as a consequence of residential preferences and the other describing land-cover changes in an exurban township as a consequence of residential preferences, local policies, and a diversity of development types, we describe a variety of empirical data collected to support the mechanisms that we encoded in computational agent-based models. We used multiple methods, including social surveys, remote sensing, and statistical analysis of spatial data, to collect data that could be used to validate the structure of our models, calibrate their specific parameters, and evaluate their output. The data were used to investigate this system in the context of several themes from complexity science, including have (a) macro-level patterns; (b) autonomous decision making entities (i.e., agents); (c) heterogeneity among those entities; (d) social and spatial interactions that operate across multiple scales and (e) nonlinear feedback mechanisms. The results point to the importance of collecting data on agents and their interactions when producing agent-based models, the general validity of our conceptual models, and some changes that we needed to make to these models following data analysis. The calibrated models have been and are being used to evaluate landscape dynamics and the effects of various policy interventions on urban land-cover patterns.
Keywords: Ecological effects; Land-cover change; Land-use change; spatial modeling; Urban sprawl

A Fast Algorithm for Learning a Ranking Function from Large-Scale Data Sets - Raykar,V.C.; Duraiswami, Ramani; Krishnapuram,B. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2008)
We consider the problem of learning a ranking function that maximizes a generalization of the Wilcoxon-Mann-Whitney statistic on the training data. Relying on an e-accurate approximation for the error function, we reduce the computational complexity of each iteration of a conjugate gradient algorithm for learning ranking functions from O(m2) to O(m), where m is the number of training samples. Experiments on public benchmarks for ordinal regression and collaborative filtering indicate that the proposed algorithm is as accurate as the best available methods in terms of ranking accuracy, when the algorithms are trained on the same data. However, since it is several orders of magnitude faster than the current state-of-the-art approaches, it is able to leverage much larger training data sets.
Keywords: Automated; Factual; Information Storage and Retrieval; Likelihood Functions; Models; Statistical; Pattern Recognition; Wilcoxon-Mann-Whitney statistics; collaborative filtering; error function; gradient algorithm; large-scale data sets; learning ranking functions; ranking function; training data; computational complexity; error analysis; learning (artificial intelligence); regressio

Fast monitoring of traffic subpopulations - Ramachandran,Anirudh; Seetharaman,Srinivasan; Feamster, Nick; Vazirani,Vijay (Proceedings of the 8th ACM SIGCOMM conference on Internet measurement, 2008)
Network accounting, forensics, security, and performance monitoring applications often need to examine detailed traces from subsets of flows ("subpopulations"), where the application desires flexibility in specifying the subpopulation (e.g., to detect a portscan, the application must observe many packets between a source and a destination with one packet to each port). However, the dynamism and volume of network traffic on many high-speed links necessitates traffic sampling, which adversely affects subpopulation monitoring: because many subpopulations of interest to operators are low-volume flows, conventional sampling schemes (e.g., uniform random sampling) miss much of the subpopulation's traffic. Today's routers and network devices provide scant support for monitoring specific traffic subpopulations. This paper presents the design, implementation, and evaluation of FlexSample, a traffic monitoring engine that dynamically extracts traffic from subpopulations that operators define using conditions on packet header fields. FlexSample uses a fast, flexible counter array to provide rough estimates of packets' membership in respective subpopulations. Based on these coarse estimates, FlexSample then makes per-packet sampling decisions to sample proportionately from each subpopulation (as specified by a network operator), subject to an overall sampling constraint. We apply FlexSample to extract subpopulations such as port scans and traffic to high-degree nodes and find that it is able to capture significantly more packets from these subpopulations than conventional approaches.
Keywords: counters; flexsample; sampling; traffic statistics; traffic subpopulations

Figaro: A Novel Statistical Method for Vector Sequence Removal - White,James Robert; Roberts,Michael; Yorke,James A.; Pop, Mihai (Bioinformatics, 2008)
Motivation: Sequences produced by automated Sanger sequencing machines frequently contain fragments of the cloning vector on their ends. Software tools currently available for identifying and removing the vector sequence require knowledge of the vector sequence, specific splice sites and any adapter sequences used in the experiment—information often omitted from public databases. Furthermore, the clipping coordinates themselves are missing or incorrectly reported. As an example, within the ∼1.24 billion shotgun sequences deposited in the NCBI Trace Archive, as many as ∼735 million (∼60%) lack vector clipping information. Correct clipping information is essential to scientists attempting to validate, improve and even finish the increasingly large number of genomes released at a ‘draft’ quality level.Results: We present here Figaro, a novel software tool for identifying and removing the vector from raw sequence data without prior knowledge of the vector sequence. The vector sequence is automatically inferred by analyzing the frequency of occurrence of short oligo-nucleotides using Poisson statistics. We show that Figaro achieves 99.98% sensitivity when tested on ∼1.5 million shotgun reads from Drosophila pseudoobscura. We further explore the impact of accurate vector trimming on the quality of whole-genome assemblies by re-assembling two bacterial genomes from shotgun sequences deposited in the Trace Archive. Designed as a module in large computational pipelines, Figaro is fast, lightweight and flexible. Availability: Figaro is released under an open-source license through the AMOS package (http://amos.sourceforge.net/Figaro). Contact: mpop@umiacs.umd.edu

Fishing for Phishing from the Network Stream - Ramachandran,A.; Feamster, Nick; Krishnamurthy,B.; Spatscheck,O.; Van der Merwe,J. (Georgia Institute of Technology, 2008)
Phishing is an increasingly prevalent social-engineering attack that attempts identity theft using spoofed Web pages of legitimate organizations. Unfortunately, current phishing detection methods are neither complete nor responsive because they rely on user reports, and many also require clientside software. Anti-phishing techniques could be more effective if they (1) could detect phishing attacks automatically from the network traffic; (2) could operate without cooperation from end-users. This paper performs a preliminary study to determine the feasibility of detecting phishing attacks in real-time, from the network traffic stream itself. We develop a model to identify the stages where in-network phishing detection is feasible and the data sources that can be analyzed to provide relevant information at each stage. Based on this model, we develop and evaluate a detection method based on features that exist in the network traffic it- self and are correlated with confirmed phishing attacks.

Generalizing Word Lattice Translation - Dyer,Christopher; Muresan,Smaranda; Resnik, Philip (Instititue for Advanced Computer Studies, Univ of Maryland, College Park, 2008)
Word lattice decoding has proven useful in spoken language translation; we argue that it provides a compelling model for translation of text genres, as well. We extend lattice decoding to hierarchical phrase-based models, providing a unified treatment with phrase-based decoding by treating lattices as a case of weighted finite-state automata. In the process, we resolve a significant complication that lattice representations introduce in reordering models. Our experiments evaluating the approach demonstrate substantial gains for Chinese-English and Arabic-English translation.
Keywords: *MACHINE TRANSLATION; *STATISTICAL MACHINE TRANSLATION; *WORD LATTICE TRANSLATION; grammars; HIERARCHICAL PHRASE-BASED MODELS; linguistics; MODELS; STATISTICAL PROCESSES

GoGoBot: group collaboration, multi-agent modeling, and robots - Rand, William; Blikstein,Paulo; Wilensky,Uri (Proceedings of the 7th international joint conference on Autonomous agents and multiagent systems: demo papers, 2008)
Multi-agent simulation is a powerful technique used to encode real-world simple rules in virtual agents and then simulate their interactions [1]. Participatory simulations are similar to multi-agent simulation except individuals play the role of virtual agents, sometimes in combination with these virtual agents [2]. Finally, the bifocal modeling framework has enabled the examination of agents embodied in physical entities using sensors and actuators [3]. All three of these technologies are concerned with the creation, manipulation, and development of agents in one form or another. Thus combining these three disparate systems in to one unified platform would be useful. Multi-agent simulation platforms, participatory simulations, and bifocal modeling have all been demonstrated separately in the past. However many extant systems are difficult if not impossible to integrate.
Keywords: multi-agent simulation; participatory simulation; ROBOTICS

High Performance Computing Algorithms for Land Cover - Dynamics Using Remote; Satya Kalluri; Bader,David A.; John Townshend; JaJa, Joseph F.; Zengyan Zhang; Fallah-adl,Hassan (CiteSeerX, 2008)
Global and regional land cover studies require the ability to apply complex models on selected subsets of large amounts of multi-sensor and multi-temporal data sets that have been derived from raw instrument measurements using widely accepted pre-processing algorithms. The computational and storage requirements of most such studies far exceed what is possible on a single workstation environment. We have been pursuing a new approach that couples scalable and open distributed heterogeneous hardware with the development of high performance software for processing, indexing, and organizing remotely sensed data. Hierarchical data management tools are used to ingest raw data, create metadata, and organize the archived data so as to automatically achieve computational load balancing among the available nodes and minimize I/O overheads. We illustrate our approach with four specific examples. The first is the development of the first fast operational scheme for the atmospheric correction of Landsat TM scenes, while the second example focuses on image segmentation using a novel hierarchical connected components algorithm. Retrieval of global BRDF (Bidirectional Reflectance Distribution Function) in the red and near infrared wavelengths using four years (1983 to 1986) of Pathfinder AVHRR Land (PAL) data set is the focus of our third example. The fourth example is the development of a hierarchical data organization scheme that allows on-demand processing and retrieval of regional and global AVHRR data sets. Our results show that substantial improvements in computational times can be achieved by using the high performance computing technology.

Hosting virtual networks on commodity hardware - Bhatia,S.; Motiwala,M.; Muhlbauer,W.; Valancius,V.; Bavier,A.; Feamster, Nick; Peterson,L.; Rexford,J. (Georgia Institute of Technology, 2008)
This paper describes Trellis, a software platform for hostingmultiple virtual networks on shared commodity hardware. Trellis allows each virtual network to define its own topol- ogy, control protocols, and forwarding tables, which low- ers the barrier for deploying custom services on an isolated, reconfigurable, and programmable network, while amor- tizing costs by sharing the physical infrastructure. Trellis synthesizes two container-based virtualization technologies, VServer and NetNS, as well as a new tunneling mechanism, EGRE, into a coherent platform that enables high-speed vir- tual networks. We describe the design and implementation, of Trellis, including kernel-level performance optimizations, and evaluate its supported packet-forwarding rates against other virtualization technologies. We are in the process of upgrading the VINI facility to use Trellis. We also plan to release Trellis as part of MyVINI, a standalone software dis- tribution that allows researchers and application developers to deploy their own virtual network hosting platforms.

LEARNING STRUCTURED BAYESIAN NETWORKS: COMBINING ABSTRACTION HIERARCHIES AND TREE‐STRUCTURED CONDITIONAL PROBABILITY TABLES - desJardins, Marie; Rathod,Priyang; Getoor, Lise (Computational Intelligence, 2008)
Context-specific independence representations, such as tree-structured conditional probability distributions, capture local independence relationships among the random variables in a Bayesian network (BN). Local independence relationships among the random variables can also be captured by using attribute-value hierarchies to find an appropriate abstraction level for the values used to describe the conditional probability distributions. Capturing this local structure is important because it reduces the number of parameters required to represent the distribution. This can lead to more robust parameter estimation and structure selection, more efficient inference algorithms, and more interpretable models. In this paper, we introduce Tree-Abstraction-Based Search (TABS), an approach for learning a data distribution by inducing the graph structure and parameters of a BN from training data. TABS combines tree structure and attribute-value hierarchies to compactly represent conditional probability tables. To construct the attribute-value hierarchies, we investigate two data-driven techniques: a global clustering method, which uses all of the training data to build the attribute-value hierarchies, and can be performed as a preprocessing step; and a local clustering method, which uses only the local network structure to learn attribute-value hierarchies. We present empirical results for three real-world domains, finding that (1) combining tree structure and attribute-value hierarchies improves the accuracy of generalization, while providing a significant reduction in the number of parameters in the learned networks, and (2) data-derived hierarchies perform as well or better than expert-provided hierarchies.
Keywords: abstraction hierarchies; background knowledge; Bayesian networks; clustering; machine learning; MDL

A Logic Framework for Sports Video Summarization Using Text-Based Semantic Annotation - Refaey,M.A.; Abd-Almageed, Wael; Davis, Larry S. (Semantic Media Adaptation and Personalization, 2008. SMAP '08. Third International Workshop on, 2008)
Detection of semantic events in sports videos is an essential step towards video summarization. A large volume of research has been conducted for automatic semantic event detection and summarization of sports videos. In this paper we present a novel sports video summarization framework using a combination of text, video and logic analysis. Parse trees are used to analyze structured and free-style text webcasting of sports games and extract the game¿s semantic events, such as goals and penalties in soccer games. Semantic events are then hierarchically arranged before being passed to a logic processing engine. The logic engine receives the summary preferences from the user and subsequently parses the event hierarchy to generate the game¿s summary according to the user¿s preferences. The proposed framework was applied to both soccer and basketball videos. We achieved an average accuracy of 98.6% and 100% on soccer and basketball videos, respectively.
Keywords: (mathematics); video; analysis; trees; annotation; Internet; broadcasting; sport; text; AUTOMATIC; detection; logic; engine; parse; event; PROCESSING; processing; semantic; signal; summarization; text; trees; sports; video; Webcasting; text-based

The marine environment and human health: the cholera model - Rita R Colwell (Global Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease EmergenceGlobal Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease Emergence, 2008)

The Maryland Large-Scale Integrated Neurocognitive Architecture - Reggia, James A.; Tagamets,M.; Contreras-Vidal,J.; Jacobs, David W.; Weems,S.; Naqvi,W.; Yang,C. (University of Maryland College Park, 2008)
Recent progress in neural computation, high performance computing, neuroscience and cognitive science suggests that an effort to produce a general-purpose, adaptive machine intelligence is likely to yield a qualitatively more powerful system than those currently existing. Here we outline our progress in developing a framework for creating such a large-scale machine intelligence, or neurocognitive architecture that is based on the modularity, dynamics and plasticity of the human brain. We successfully implemented three intermediate-scale parts of such a system, and these are described. Based on this experience, we concluded that for the short term, optimal results would be obtained by using a hybrid design including neural, symbolic AI, and artificial life methods. We propose a three-tiered architecture that integrates these different methods, and describe a prototype mini-Roboscout that we implemented and evaluated based on this architecture. We also examined, via computational experiments, the effectiveness of genetic programming as a design tool for recurrent neural networks, and the speed-up obtained for adaptive neural networks when they are executed on a graphical processing unit. We conclude that the implementation of a large-scale neurocognitive architecture is feasible, and outline a roadmap for proceeding.
Keywords: *COMPUTATIONS; *HYBRID SYSTEMS; *NEURAL NETS; *NEUROCOGNITIVE ARCHITECTURE; ADAPTIVE SYSTEMS; Artificial intelligence; BRAIN; Cognition; COMPUTER PROGRAMMING; COMPUTER PROGRAMMING AND SOFTWARE; HYBRID AI; Machine intelligence; MECHANICAL ORGANS; MODULAR CONSTRUCTION; NERVOUS SYSTEM; PE61101E; PLASTIC PROPERTIES; PROCESSING EQUIPMENT; RECURRENT NEURAL NETWORK

Matchmaking and implementation issues for a P2P desktop grid - Marsh,M.; Kim,Jik-Soo; Nam,Beomseok; Jaehwan Lee; Ratanasanya,S.; Bhattacharjee, Bobby; Keleher,P.; Richardson,D.; Wellnitz,D. (Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on, 2008)
We present some recent and ongoing work in our decentralized desktop computing grid project. Specifically, we discuss matching jobs with compute nodes in a peer-to-peer grid of heterogeneous platforms, and the implementation of our algorithms in a concrete system.
Keywords: computing; computing; computing; peer-to-peer; desktop; grid; decentralized; grid; grid; grid; peer-to-peer; P2P

Measures and Risk Indicators for Early Insight into Software Safety. Development of Fault-Tolerant Systems - Basili, Victor R.; Marotta,Frank; Dangle,Kathleen; Esker,Linda; Rus,Ioana (ABERDEEN TEST CENTER MD, 2008)
Software contributes an ever-increasing level of functionality and control in today's systems. This increased use of software can dramatically increase the complexity and time needed to evaluate the safety of a system. Although the actual system safety cannot be verified during its development, measures can reveal early insights into potential safety problems and risks. An approach for developing early software safety measures is presented in this article. The approach and the example software measures presented are based on experience working with the safety engineering group on a large Department of Defense program.
Keywords: *SOFTWARE ENGINEERING; *SYSTEM SAFETY; COMPUTER PROGRAMMING AND SOFTWARE; fault tolerant computing; INDICATORS; measurement; REPRINTS; risk; SAFETY ENGINEERING

Method and System for Detecting and Responding to Attacking Networks - Dagon,David; Feamster, Nick; Lee,Weake; Edmonds,Robert; Lipton,Richard; Ramachandran,Anirudh (2008)
A system and method for detecting a first network of compromised computers in a second network of computers, comprising: collecting Domain Name System (DNS) data for the second network; examining the collected data relative to DNS data from known comprised and/or uncompromised computers in the second network; and determining the existence of the first network and/or the identity of compromised computers in the second network based on the examination.

Model Based Design Verification: A Monitor Based Approach - Ackermann,Chris; Ray,Arnab; Cleaveland, Rance; Heit,Jürgen; Martin,Christopher; Shelton,Charles (SAE International, 2008)
This paper assesses the utility of an automated functional verification methodology in the design of a body electronics application. The use of design models as detailed specifications for software is gaining steady acceptance in the automotive industry because of the advantages it offers in terms of rapid system prototyping and automatic code generation. This paper argues that such modeling effort can also be used to provide support for design verification, so that errors may be pinpointed before they find their way into code, when they become much harder and more expensive to isolate, diagnose and repair.

Modeling shape and textural variations in aging faces - Ramanathan,N.; Chellapa, Rama (Automatic Face Gesture Recognition, 2008. FG '08. 8th IEEE International Conference on, 2008)
We propose a two fold approach towards modeling facial aging in adults. Firstly, we develop a shape transformation model that is formulated as a physically-based parametric muscle model that captures the subtle deformations facial features undergo with age. The model implicitly accounts for the physical properties and geometric orientations of the individual facial muscles. Next, we develop an image gradient based texture transformation function that characterizes facial wrinkles and other skin artifacts often observed during different ages. Facial growth statistics (both in terms of shape and texture) play a crucial role in developing the aforementioned transformation models. From a database that comprises of pairs of age separated face images of many individuals, we extract age-based facial measurements across key fiducial features and further, study textural variations across ages. We present experimental results that illustrate the applications of the proposed facial aging model in tasks such as face recognition and facial appearance prediction across aging.
Keywords: Aging; analysis; faces; image; function; face; gradient; modeling; model; textural; recognition; image; shape; shape; texture; statistical; transformation; variations; texture

Multi-agent learning with a distributed genetic algorithm - Stonedahl,F.; Rand, William; Wilensky,U. (AAMAS 2008: ALAMAS + ALAg Workshop, 2008)
Lightweight agents distributed in space have the potential to solve many complex problems. In this paper, we examine a model where agents represent individuals in a genetic algorithm (GA) solving a shared problem. We examine two questions: (1) How does the network density of connections between agents affect the performance of the systems? (2) How does the interaction topology aaffect the performance of the system? In our model, agents exist in either a random network topology with long-distance communication, or a location-based topology, where agents only communicate with near neighbors. We examine both fixed and dynamic networks. Within the context of our investigation, our initial results indicate that relatively low network density achievesthe same results as a panmictic, or fully connected, population. Additionally, we find that dynamic networks outperform fixed networks, and that random network topologies outperform proximity-based network topologies. We conclude by showing how this model can be useful not only for multi-agent learning, but also for genetic algorithms, agent-based simulation and models of diffusion of innovation.

Multi-biometric cohort analysis for biometric fusion - Aggarwal,G.; Ratha,N. K; Bolle, R.M.; Chellapa, Rama (Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on, 2008)
Biometric matching decisions have traditionally been made based solely on a score that represents the similarity of the query biometric to the enrolled biometric(s) of the claimed identity. Fusion schemes have been proposed to benefit from the availability of multiple biometric samples (e.g., multiple samples of the same fingerprint) or multiple different biometrics (e.g., face and fingerprint). These commonly adopted fusion approaches rarely make use of the large number of non-matching biometric samples available in the database in the form of other enrolled identities or training data. In this paper, we study the impact of combining this information with the existing fusion methodologies in a cohort analysis framework. Experimental results are provided to show the usefulness of such a cohort-based fusion of face and fingerprint biometrics.
Keywords: (access; analysis; biometrics; biometric; biometrics; fingerprint; biometrics; multi-biometric; cohort; control); face; data; decisions; face; fusion; biometric; identification; security; MATCHING; of; recognition; fingerprint

Multi-resolution Tracking in Space and Time - Roy,S.D.; Tran,S.D.; Davis, Larry S.; Vikram,B.S. (Computer Vision, Graphics Image Processing, 2008. ICVGIP '08. Sixth Indian Conference on, 2008)
This paper proposes efficient and robust methods for tracking a moving object at multiple spatial and temporal resolution levels. The efficiency comes from optimising the amounts of spatial and temporal data processed. The robustness results from multi-level coarse-to-fine state-space searching. Tracking across resolution levels incurs an accuracy-versus-speed trade-off. For example, tracking at higher resolutions incurs greater processing cost, while maintaining higher accuracy in estimating the position of the moving object. We propose a novel spatial multi-scale tracker that tracks at the optimal accuracy-versus-speed operating point. Next, we relax this requirement to propose a multi-resolution tracker that operates at a minimum acceptable performance level. Finally, we extend these ideas to a multi-resolution spatio-temporal tracker. We show results of extensive experimentation in support of the proposed approaches.
Keywords: analysis; image; coarse-to-fine; detection; estimation; spatial; MOTION; moving; multiscale; object; resolution; object; searching; multiresolution; state-space; tracker; image; tracker; spatio-temporal; tracking; multilevel; tracking; position

A Non-generative Approach for Face Recognition Across Aging - Biswas,S.; Aggarwal,G.; Ramanathan,N.; Chellapa, Rama (Biometrics: Theory, Applications and Systems, 2008. BTAS 2008. 2nd IEEE International Conference on, 2008)
Human faces undergo a lot of change in appearance as they age. Though facial aging has been studied for decades, it is only recently that attempts have been made to address the problem from a computational point of view. Most of these early efforts follow a simulation approach in which matching is performed by synthesizing face images at the target age. Given the innumerable different ways in which a face can potentially age, the synthesized aged image may not be similar to the actual aged image. In this paper, we bypass the synthesis step and directly analyze the drifts of facial features with aging from a purely matching perspective. Our analysis is based on the observation that facial appearance changes in a coherent manner as people age. We provide measures to capture this coherency in feature drifts. Illustrations and experimental results show the efficacy of such an approach for matching faces across age progression.
Keywords: appearance; nongenerative; approach; face; Face; image; matching; recognition; facial; recognition; image; synthesis; face

Packets with provenance - Ramachandran,A.; Bhandankar,K.; Tariq,M.B.; Feamster, Nick (Georgia Institute of Technology, 2008)
Traffic classification and distinction allows network operators to provision resources, enforce trust, control unwanted traffic, and traceback unwanted traffic to its source. Today’s classification mechanisms rely primarily on IP addresses and port numbers; unfortunately, these fields are often too coarse and ephemeral, and moreover, they do not reflect traffic’s provenance, associated trust, or relationship to other processes or hosts. This paper presents the design, analysis, user-space implementation, and evaluation of Pedigree, which consists of two components: a trusted tagger that resides on hosts and tags packets with information about their provenance (i.e., identity and history of potential input from hosts and resources for the process that generated them), and an arbiter, which decides what to do with the traffic that carries certain tags. Pedigree allows operators to write traffic classification policies with expressive semantics that reflect properties of the actual process that generated the traffic. Beyond offering new function and flexibility in traffic classification, Pedigree represents a new and interesting point in the design space between filtering and capabilities, and it allows network operators to leverage host-based trust models to decide treatment of network traffic.

Readability of scanned books in digital libraries - Quinn,A.J.; Hu,C.; Arisaka,T.; Rose,A.; Bederson, Benjamin B. (Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems, 2008)

Reciprocity between the cerebellum and the cerebral cortex: Nonlinear dynamics in microscopic modules for generating voluntary motor commands - Wang,Jun; Dam,Gregory; Yildirim,Sule; Rand, William; Wilensky,Uri; Houk,James C. (Complexity, 2008)
The cerebellum and basal ganglia are reciprocally connected with the cerebral cortex, forming many loops that function as distributed processing modules. Here we present a detailed model of one microscopic loop between the motor cortex and the cerebellum, and we show how small arrays of these microscopic loops (CB modules) can be used to generate biologically plausible motor commands for controlling movement. A fundamental feature of CB modules is the presence of positive feedback loops between the cerebellar nucleus and the motor cortex. We use nonlinear dynamics to model one microscopic loop and to investigate its bistable properties. Simulations demonstrate an ability to program a motor command well in advance of command generation and an ability to vary command duration. However, control of command intensity is minimal, which could interfere with the control of movement velocity. To assess these hypotheses, we use a minimal nonlinear model of the neuromuscular (NM) system that translates motor commands into actual movements. Simulations of the combined CB-NM modular model indicate that movement duration is readily controlled, whereas velocity is poorly controlled. We then explore how an array of eight CB-NM modules can be used to control the direction and endpoint of a planar movement. In actuality, thousands of such microscopic loops function together as an array of adjustable pattern generators for programming and regulating the composite motor commands that control limb movements. We discuss the biological plausibility and limitations of the model. We also discuss ways in which an agent-based representation can take advantage of the modularity in order to model this complex system. © 2008 Wiley Periodicals, Inc. Complexity, 2008
Keywords: agent‐based modeling; cerebellum; equilibrium point control; motor command; motor cortex; Movement; neural network; nonlinear dynamics

Residual periodograms for choosing regularization parameters for ill-posed problems - Rust,Bert W.; O'Leary, Dianne P. (Inverse Problems, 2008)
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. 32 333–47 ), 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.

Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence - Regier,J. C; Shultz,J. W; Ganley,A. R.D; Hussey,A.; Shi,D.; Ball,B.; Zwick,A.; Stajich,J. E; Cummings, Michael P.; Martin,J. W; Cunningham,CW (Syst Biol, 2008)
This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations–first codon positions encoding leucine and arginine, which were also compositionally heterogeneous–yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned–fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow or intermediate categories, whereas groups supported only by a single gene region tended to be from genes of the fast category, arguing that fast genes provide a less consistent signal. (2) A sensitivity analysis was performed in which increasing numbers of genes were excluded, beginning with the fastest. The number of strongly supported nodes increased up to a point and then decreased slightly. Recovery of Hexapoda required removal of fast genes. Support for Mandibulata (Pancrustacea + Myriapoda) also increased, at times to "strong" levels, with removal of the fastest genes. (3) Concordance selection was evaluated by clustering genes according to their ability to recover Pancrustacea, Euchelicerata, or Myriapoda and analyzing the three clusters separately. All clusters of genes recovered the three concordance clades but were at times inconsistent in the relationships recovered among and within these clades, a result that indicates that the a priori concordance criteria may bias phylogenetic signal in unexpected ways. In a further attempt to increase support of taxonomic relationships, sequence data from 49 additional taxa for three slow genes (i.e., EF-1 alpha, EF-2, and Pol II) were combined with the various 13-taxon data sets. The 62-taxon analyses supported the results of the 13-taxon analyses and provided increased support for additional pancrustacean clades found in an earlier analysis including only EF-1 alpha, EF-2, and Pol II.

Satisfying Complex Data Needs using Pull-Based Online Monitoring of Volatile Data Sources - Roitman,Haggai; Gal,Avigdor; Raschid, Louiqa (Data Engineering, International Conference on, 2008)
Emerging applications on the Web require better management of volatile data in pull-based environments. In a pull based setting, data may be periodically removed from the server. Data may also become obsolete, no longer serving client needs. In both cases, we consider such data to be volatile. To model such constraints on data usability, and support complex user needs we define profiles to specify which data sources are to be monitored and when. Using a novel abstraction of execution intervals we model complex profiles that access simultaneously several servers to gain from the used data. Given some budgetary constraints (e.g., bandwidth), the paper formalizes the problem of maximizing completeness.

Scaffolding and Validation of Bacterial Genome Assemblies Using Optical Restriction Maps - Nagarajan,Niranjan; Read,Timothy D.; Pop, Mihai (Bioinformatics, 2008)
Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of the complete sequence of a genome is complicated by specific features of these new sequencing technologies, such as the short length of the sequencing reads and absence of mate-pair information. In this article we propose methods to overcome such limitations by incorporating information from optical restriction maps.Results: We demonstrate the robustness of our methods to sequencing and assembly errors using extensive experiments on simulated datasets. We then present the results obtained by applying our algorithms to data generated from two bacterial genomes Yersinia aldovae and Yersinia kristensenii. The resulting assemblies contain a single scaffold covering a large fraction of the respective genomes, suggesting that the careful use of optical maps can provide a cost-effective framework for the assembly of genomes. Availability: The tools described here are available as an open-source package at ftp://ftp.cbcb.umd.edu/pub/software/soma Contact: mpop@umiacs.umd.edu

SCALABLE CATALOG INFRASTRUCTURE FOR MANAGING ACCESS COSTS AND SOURCE SELECTION IN WIDE AREA NETWORKS - Zadorozhny,V.; Raschid, Louiqa; Gal,A. (International Journal of Cooperative Information Systems, 2008)

Searching Electronic Health Records for Temporal Patterns in Patient Histories: A Case Study with Microsoft Amalga - Plaisant, Catherine; Lam,Stanley; Shneiderman, Ben; Smith,Mark S.; Roseman,David; Marchand,Greg; Gillam,Michael; Feied,Craig; Handler,Jonathan; Rappaport,Hank (AMIA Annual Symposium ProceedingsAMIA Annu Symp Proc, 2008)
As electronic health records (EHR) become more widespread, they enable clinicians and researchers to pose complex queries that can benefit immediate patient care and deepen understanding of medical treatment and outcomes. However, current query tools make complex temporal queries difficult to pose, and physicians have to rely on computer professionals to specify the queries for them. This paper describes our efforts to develop a novel query tool implemented in a large operational system at the Washington Hospital Center (Microsoft Amalga, formerly known as Azyxxi). We describe our design of the interface to specify temporal patterns and the visual presentation of results, and report on a pilot user study looking for adverse reactions following radiology studies using contrast.

Searching the world’s herbaria: A system for visual identification of plant species - Belhumeur,P.; Chen,D.; Feiner,S.; Jacobs, David W.; Kress,W.; Ling,H.; Lopez,I.; Ramamoorthi,R.; Sheorey,S.; White,S. (Computer Vision–ECCV 2008, 2008)
We describe a working computer vision system that aids in the identification of plant species. A user photographs an isolated leaf on a blank background, and the system extracts the leaf shape and matches it to the shape of leaves of known species. In a few seconds, the system displays the top matching species, along with textual descriptions and additional images. This system is currently in use by botanists at the Smithsonian Institution National Museum of Natural History. The primary contributions of this paper are: a description of a working computer vision system and its user interface for an important new application area; the introduction of three new datasets containing thousands of single leaf images, each labeled by species and verified by botanists at the US National Herbarium; recognition results for two of the three leaf datasets; and descriptions throughout of practical lessons learned in constructing this system.

Securing enterprise networks using traffic tainting - Ramachandran,A.; Mundada,Y.; Tariq,M.B.; Feamster, Nick (Special Interest Group on Data Communication, 2008)
Enterprise networks are vulnerable to attacks ranging from dataleaks to the spread of malware to insider threats. Previous defenses have largely focused on securing hosts; unfortunately, when hosts are compromised, these defenses become ineffective. Rather than attempting to harden the host against every possible attack (which is impractical) or constraining the software that can run on a host (which is inconvenient), we place a small amount of trusted code on the host to assist with tracking the provenance of network traf- fic, moving the rest of the trust and function to the network. We present Pedigree, a system that tracks information flow across pro- cesses and hosts within a network by annotating traffic with taints that reflect the process that generated the traffic and the inputs that process has taken (we call this function traffic tainting). A tagger on the host annotates network traffic with information about the “taints” that the sending process has acquired. Network devices act as arbiters to take appropriate actions (e.g., blocking) based on the taints associated with the traffic and the enterprise network’s secu- rity policy. We have implemented Pedigree’s host-based tagger as a Linux kernel module and the arbiter using the OpenFlow platform. This demonstration presents a prototype deployment of Pedigree that identifies and prevents both sensitive data leaks and the spread of malware in a typical enterprise network setting. The demon- stration will show that Pedigree can defend against these attacks without significant overhead at the host or the filtering device.

Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure - Fermin,David R.; Barac,Ana; Lee,Sangjin; Polster,Sean P.; Hannenhalli, Sridhar; Bergemann,Tracy L.; Grindle,Suzanne; Dyke,David B.; Pagani,Francis; Miller,Leslie W.; Tan,Sarah; dos Remedios,Cris; et al. (Circulation: Cardiovascular Genetics, 2008)
Background— We report the first comprehensive analysis of gene expression differences by sex and age in left ventricular samples from 102 patients with dilated cardiomyopathy.Methods and Results— Gene expression data (HG-U133A gene chip, Affymetrix) were analyzed from 30 females and 72 males from 3 separate centers. More than 1800 genes displayed sexual dimorphism in the heart (adjusted P value <0.05). A significant number of these genes were highly represented in gene ontology pathways involved in ion transport and G-protein-coupled receptor signaling. Localization of these genes revealed enrichment on both the sex chromosomes as well as chromosomes 3, 4, and 14. The second goal of this study was to determine the effect of age on gene expression. Within the female cohort, >140 genes were differentially expressed in the <55 years age group compared with the >55 years age group. These genes were highly represented in gene ontology pathways involved in DNA damage. In contrast, zero genes in the male cohort <55 years met statistical significance when compared with the >55 years age group.Conclusions— Gene expression in dilated cardiomyopathy displayed evidence of sexual dimorphism similar to other somatic tissues and age dimorphism within the female cohort.

Soft syntactic constraints for hierarchical phrased-based translation - Marton,Y.; Resnik, Philip (Proceedings of ACL-08: HLT, 2008)

Trellis: a platform for building flexible, fast virtual networks on commodity hardware - Bhatia,Sapan; Motiwala,Murtaza; Muhlbauer,Wolfgang; Mundada,Yogesh; Valancius,Vytautas; Bavier,Andy; Feamster, Nick; Peterson,Larry; Rexford,Jennifer (Proceedings of the 2008 ACM CoNEXT Conference, 2008)
We describe Trellis, a platform for hosting virtual networks on shared commodity hardware. Trellis allows each virtual network to define its own topology, control protocols, and forwarding tables, while amortizing costs by sharing the physical infrastructure. Trellis synthesizes two container-based virtualization technologies, VServer and NetNS, as well as a new tunneling mechanism, EGRE, into a coherent platform that enables high-speed virtual networks. We describe the design and implementation of Trellis and evaluate its packet-forwarding rates relative to other virtualization technologies and native kernel forwarding performance.

UFO: a resilient layered routing architecture - Zhu,Yaping; Bavier,Andy; Feamster, Nick; Rangarajan,Sampath; Rexford,Jennifer (ACM SIGCOMM Computer Communication Review, 2008)
Conventional wisdom has held that routing protocols cannot achieve both scalability and high availability. Despite scaling relatively well, today's Internet routing system does not react quickly to changing network conditions (e.g., link failures or excessive congestion). Overlay networks, on the other hand, can respond quickly to changing network conditions, but their reliance on aggressive probing does not scale to large topologies. The paper presents a layered routing architecture called UFO (Underlay Fused with Overlays), which achieves the best of both worlds by having the "underlay" provide explicit notification about network conditions to help improve the efficiency and scalability of routing overlays.
Keywords: network monitoring; overlay networks; routing architecture

Using specularities in comparing 3D models and 2D images - Osadchy,Margarita; Jacobs, David W.; Ramamoorthi,Ravi; Tucker,David (Computer Vision and Image Understanding, 2008)
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’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

Video stabilization and mosaicing - Ramachandran, M.; Veeraraghavan,A.; Chellapa, Rama (The Essential Guide to Video Processing,, 2008)

Virtual access points for vehicular networks - Frangiadakis,N.; Câmara,D.; Filali,F.; Loureiro,A. A.F; Roussopoulos, Nick (Proceedings of the 1st international conference on MOBILe Wireless MiddleWARE, Operating Systems, and Applications, 2008)

Adaptive query processing - Deshpande, Amol; Ives,Zachary; Vijayshankar Raman (Foundations and Trends in Databases, 2007)
As the data management field has diversified to consider settings in which queries are increasingly complex, statistics are less available, or data is stored remotely, there has been an acknowledgment that the traditional optimize-then-execute paradigm is insufficient. This has led to a plethora of new techniques, generally placed under the common banner of adaptive query processing, that focus on using runtime feed-back to modify query processing in a way that provides better response time or more efficient CPU utilization.In this survey paper, we identify many of the common issues, themes, and approaches that pervade this work, and the settings in which each piece of work is most appropriate. Our goal with this paper is to be a "value-add" over the existing papers on the material, providing not only a brief overview of each technique, but also a basic framework for understanding the field of adaptive query processing in general. We focus primarily on intra-query adaptivity of long-running, but not full-fledged streaming, queries. We conclude with a discussion of open research problems that are of high importance.

Adaptive query processing: why, how, when, what next? - Deshpande, Amol; Ives,Zachary; Vijayshankar Raman (Proceedings of the 33rd international conference on Very large data bases, 2007)
Adaptive query processing has been the subject of a great deal of recent work, particularly in emerging data management environments such as data integration and data streams. We provide an overview of the work in this area, identifying its common themes, laying out the space of query plans, and discussing open research problems. We discuss why adaptive query processing is needed, how it is being implemented, where it is most appropriately used, and finally, what next, i.e., open research problems.

Archetypal behavior in computer security - Rosenfeld,Shalom N.; Rus,Ioana; Michel Cukier (Journal of Systems and Software, 2007)
The purpose of this study is to understand observed behavior and to diagnose and find solutions to issues encountered in organizational computer security using a systemic approach, namely system archetypes. In this paper we show the feasibility of archetypes application and the benefits of simulation. We developed a model and simulation of some aspects of security based on system dynamics principles. The system dynamics simulation model can be used in support of decision-making, training, and teaching regarding the mitigation of computer security risks. In this paper, we combine two archetypes and show the computer security relevance of such combinations. Presented are instances of the archetypes “Escalation”, in which an organization must continuously increase its efforts to counter additional attacker effort; and “Limits to Growth”, in which the gains from an organization’s security efforts plateau or decline due to its limited capacity for security-related tasks. We describe a scenario where these archetypes (individually and combined) can help in diagnosis and understanding, and present simulation of “what-if” scenarios suggesting how an organization might remedy these problems and maximize its gains from security efforts.
Keywords: Attacks and countermeasures; Escalation; Limits to Growth; Organization computer security; System archetypes; System dynamics; System dynamics modeling and simulation

Association of Vibrio Cholerae O1 El Tor and O139 Bengal with the Copepods Acartia Tonsa and Eurytemora Affinis - Rawlings,Tonya K.; Ruiz,Gregory M.; Rita R Colwell (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2007)
The association of Vibrio cholerae with zooplankton has been suggested as an important factor in transmission of human epidemic cholera, and the ability to colonize zooplankton surfaces may play a role in the temporal variation and predominance of the two different serogroups (V. cholerae O1 El Tor and O139) in the aquatic environment. To date, interactions between specific serogroups and species of plankton remain poorly understood. Laboratory microcosm experiments were carried out to compare quantitatively the colonization of two copepod species, Acartia tonsa and Eurytemora affinis, by each of the epidemic serogroups. V. cholerae O1 consistently achieved higher abundances than V. cholerae O139 in colonizing adults of each copepod species as well as the multiple life stages of E. affinis. This difference in colonization may be significant in the general predominance of V. cholerae O1 in cholera epidemics in rural Bangladesh where water supplies are taken directly from the environment.

Biased data reduce efficiency and effectiveness of conservation reserve networks - Grand,Joanna; Cummings, Michael P.; Rebelo,Tony G; Ricketts,Taylor H; Neel,Maile C (Ecology Letters, 2007)
Complementarity-based reserve selection algorithms efficiently prioritize sites for biodiversity conservation, but they are data-intensive and most regions lack accurate distribution maps for the majority of species. We explored implications of basing conservation planning decisions on incomplete and biased data using occurrence records of the plant family Proteaceae in South Africa. Treating this high-quality database as ‘complete’, we introduced three realistic sampling biases characteristic of biodiversity databases: a detectability sampling bias and two forms of roads sampling bias. We then compared reserve networks constructed using complete, biased, and randomly sampled data. All forms of biased sampling performed worse than both the complete data set and equal-effort random sampling. Biased sampling failed to detect a median of 1–5% of species, and resulted in reserve networks that were 9–17% larger than those designed with complete data. Spatial congruence and the correlation of irreplaceability scores between reserve networks selected with biased and complete data were low. Thus, reserve networks based on biased data require more area to protect fewer species and identify different locations than those selected with randomly sampled or complete data.
Keywords: Bias; biodiversity conservation; complementarity; efficiency; marxan; rarity; reserve networks; reserve selection algorithms; species detection

Bid based scheduler with backfilling for a multiprocessor system - Yahav,I.; Raschid, Louiqa; Andrade,H. (Proceedings of the ninth international conference on Electronic commerce, 2007)

Bilattice-based Logical Reasoning for Human Detection - Shet,V. D; Neumann, J.; Ramesh,V.; Davis, Larry S. (Computer Vision and Pattern Recognition, 2007. CVPR '07. IEEE Conference on, 2007)
The capacity to robustly detect humans in video is a critical component of automated visual surveillance systems. This paper describes a bilattice based logical reasoning approach that exploits contextual information and knowledge about interactions between humans, and augments it with the output of different low level detectors for human detection. Detections from low level parts-based detectors are treated as logical facts and used to reason explicitly about the presence or absence of humans in the scene. Positive and negative information from different sources, as well as uncertainties from detections and logical rules, are integrated within the bilattice framework. This approach also generates proofs or justifications for each hypothesis it proposes. These justifications (or lack thereof) are further employed by the system to explain and validate, or reject potential hypotheses. This allows the system to explicitly reason about complex interactions between humans and handle occlusions. These proofs are also available to the end user as an explanation of why the system thinks a particular hypothesis is actually a human. We employ a boosted cascade of gradient histograms based detector to detect individual body parts. We have applied this framework to analyze the presence of humans in static images from different datasets.
Keywords: automated; detection; parts-based; detectors; static; histograms; human; images; formal; interactions; gradient; logic; image; logical; mechanisms; surveillance; video; processing; reasoning; complex; recognition; inference; signal; Surveillance; systems; bilattice-based; visual

BIPASS: BioInformatics Pipeline Alternative Splicing Services - Legendre,C.; Raschid, Louiqa; Snyder,B. (Nucleic Acids Research, 2007)

Bitstore: An incentive-compatible solution for blocked downloads in bittorrent - Ramachandran,A.; Sarma,A.D.; Feamster, Nick (Proc. Joint Workshop on The Economics of Networked Systems and Incentive-Based Computing (NetEcon), 2007)
As many as 30% of all files shared on public BitTorrentnetworks suffer from the lack of “seeders” (peers that have complete copies of the file being shared); peers attempting to download such a file (“leechers”) may have to wait indef- initely to obtain certain file chunks that are not distributed in the file’s network of peers (the “swarm”). We call this the Blocked Leecher Problem (BLP). To alleviate BLP, we propose BitStore, a larger, secure network of BitTorrent users (not necessarily all sharing the same content) where nodes offer their resources (such as disk space and bandwidth) for public use. Peers sharing any file can use the storage network to maintain replicas for each chunk of the file. Any leecher seeking chunks that are absent from in its own swarm can query the public network, locate the node storing the said chunks, and retrieve them. BitStore also provides robust incentives for nodes contributing re- sources: In return for storing and serving chunks, such nodes can negotiate micropayments using a second-price auction. Peers who receive these credits may later use them to re- trieve blocks they need from the storage network. This paper quantifies the BLP, presents an overview of the BitStore design, and discusses various challenges related to storage management and incentives.

Building a Better Mousetrap - Ramachandran,A.; Seetharaman,S.; Feamster, Nick; Vazirani,V. (Georgia Institute of Technology. College of Computing, 2007)
Routers in the network core are unable to maintain detailed statistics for every packet; thus, traffic statistics are often based on packet sampling, which reduces accuracy. Because tracking large ("heavy-hitter") traffic flows is important both for pricing and for traffic engineering, much attention has focused on maintaining accurate statistics for such flows, often at the expense of small-volume flows. Eradicating these smaller flows makes it difficult to observe communication structure, which is sometimes more important than maintaining statistics about flow sizes. This paper presents FlexSample, a sampling framework that allows network operators to get the best of both worlds: For a fixed sampling budget, FlexSample can capture significantly more small-volume flows for only a small increase in relative error of large traffic flows. FlexSample uses a fast, lightweight counter array that provides a coarse estimate of the size ("class") of each traffic flow; a router then can sample at different rates according to the class of the traffic using any existing sampling strategy. Given a fixed sampling rate and a target fraction of sampled packets to allocate across traffic classes, FlexSample computes packet sampling rates for each class that achieve these allocations online. Through analysis and trace-based experiments, we find that FlexSample captures at least 50% more mouse flows than strategies that do not perform class-dependent packet sampling. We also show how FlexSample can be used to capture unique flows for specific applications.

Caching in Mobile Environments: A New Analysis and the Mobile-Cache System - Frangiadakis,N.; Roussopoulos, Nick (IEEE 18th International Symposium on Personal, Indoor and Mobile Radio Communications, 2007. PIMRC 2007, 2007)
In the near future, we will be surrounded by ubiquitous wireless networks and so information dissemination for mobile users is a key issue. Hybrid push-pull constitutes a very effective and scalable solution. Our contribution is twofold. First we provide a new analysis that takes into account the user mobility. We argue that in a highly mobile setting, analysis and optimization goals discussed in past papers become irrelevant, since the most important aspect of the system is not delay, but rather the ability to answer as many queries as possible. As we show, the optimal pull-push bandwidth ratio depends on the mobility patterns of the users. Second, we use our findings to build Mobile-Cache, a system that can efficiently answer multiple queries over a wireless environment.
Keywords: Bandwidth; Broadcasting; cache storage; Cities and towns; FCC; hybrid push-pull solution; information dissemination; Intelligent networks; Land mobile radio; mobile communication; Mobile computing; mobile environment; mobile radio; mobile-cache system; multiple query answering; pull-push bandwidth ratio; Query processing; Road safety; road vehicles; ubiquitous wireless network; Vehicle safety

CARA: A Cultural-Reasoning Architecture - V.S. Subrahmanian; Albanese,Massimiliano; Martinez,Mar?a Vanina; Nau, Dana S.; Reforgiato,Diego; Simari,Gerardo I.; Sliva,Amy; Udrea,Octavian; Wilkenfeld,Jonathan (IEEE Intelligent Systems, 2007)
The Cognitive Architecture for Reasoning about Adversaries supports methods to gather data about different cultural groups and learn the intensity of those groups' opinions on various topics. It also lets users build and extract models of those groups' behavior and continuously refine those models through shared multiperson learning experiences. Researchers have applied the architecture to develop cultural-reasoning applications for example, a game that teaches soldiers about cultural norms in an Afghan village.
Keywords: cultural reasoning; opinion extraction; opponent modeling

Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus - Hammel,Michal; Sfyroera,Georgia; Pyrpassopoulos,Serapion; Ricklin,Daniel; Ramyar,Kasra X.; Pop, Mihai; Jin,Zhongmin; Lambris,John D.; Geisbrecht,Brian V. (Journal of Biological Chemistry, 2007)
We report here the discovery and characterization of Ehp, a new secreted Staphylococcus aureus protein that potently inhibits the alternative complement activation pathway. Ehp was identified through a genomic scan as an uncharacterized secreted protein from S. aureus, and immunoblotting of conditioned S. aureus culture medium revealed that the Ehp protein was secreted at the highest levels during log-phase bacterial growth. The mature Ehp polypeptide is composed of 80 residues and is 44% identical to the complement inhibitory domain of S. aureus Efb (extracellular fibrinogen-binding protein). We observed preferential binding by Ehp to native and hydrolyzed C3 relative to fully active C3b and found that Ehp formed a subnanomolar affinity complex with these various forms of C3 by binding to its thioester-containing C3d domain. Site-directed mutagenesis demonstrated that Arg75 and Asn82 are important in forming the Ehp·C3d complex, but loss of these side chains did not completely disrupt Ehp/C3d binding. This suggested the presence of a second C3d-binding site in Ehp, which was mapped to the proximity of Ehp Asn63. Further molecular level details of the Ehp/C3d interaction were revealed by solving the 2.7-Å crystal structure of an Ehp·C3d complex in which the low affinity site had been mutationally inactivated. Ehp potently inhibited C3b deposition onto sensitized surfaces by the alternative complement activation pathway. This inhibition was directly related to Ehp/C3d binding and was more potent than that seen for Efb-C. An altered conformation in Ehp-bound C3 was detected by monoclonal antibody C3-9, which is specific for a neoantigen exposed in activated forms of C3. Our results suggest that increased inhibitory potency of Ehp relative to Efb-C is derived from the second C3-binding site in this new protein.

Coevolution of Predators and Prey in a Spatial Model - Ottino-Lofler,J.; Rand, William; Wilensky,U. (Genetic and Evolutionary Computation Conference (GECCO), 2007)

Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei - Djikeng,A.; Raverdy,S.; Foster, Jeffrey S.; Bartholomeu,D.; Zhang,Y.; El‐Sayed, Najib M.; Carlow,C. (Parasitology research, 2007)

Combining outputs from multiple machine translation systems - Rosti,A.V.I.; Ayan,N.F.; Xiang,B.; Matsoukas,S.; Schwartz,R.; Dorr, Bonnie J (Human Language Technologies 2007: The Conference of the North American Chapter of the Association for Computational Linguistics; Proceedings of the Main Conference, 2007)
Currently there are several approaches tomachine translation (MT) based on differ- ent paradigms; e.g., phrasal, hierarchical and syntax-based. These three approaches yield similar translation accuracy despite using fairly different levels of linguistic knowledge. The availability of such a variety of systems has led to a growing interest toward finding better translations by combining outputs from multiple sys- tems. This paper describes three differ- ent approaches to MT system combina- tion. These combination methods oper- ate on sentence, phrase and word level exploiting information from N -best lists, system scores and target-to-source phrase alignments. The word-level combination provides the most robust gains but the best results on the development test sets (NIST MT05 and the newsgroup portion of GALE 2006 dry-run) were achieved by combining all three methods.

Conditionalization: Adapting forward-chaining planners to partially observable environments - Kuter,U.; Nau, Dana S.; Reisner,E.; Goldman,R. (2007)
We provide a general way to take forward-chainingplanners for classical planning domains and condition- alize them, i.e., adapt them to generate policies for partially observable planning domains. For domain-configurable planners such as SHOP2, TLPlan, and TALplanner, our generalization tech- nique preserves the ability to use domain knowledge to achieve highly efficient planning. We demonstrate this experimentally in two problem domains. The experi- ments compare PKS and MBP (two existing planners for partially observable planning) and CondSHOP2, a version of the HTN planner SHOP2 created by apply- ing our conditionalization method. To our surprise, PKS and MBP could solve only the simplest problems in our test domains. In contrast, CondSHOP2 solved all of the test problems quite eas- ily. This suggests that the ability to use domain knowl- edge may be not just desirable but indeed essential for solving large problems in partially observable domains.

Creating a Robust Desktop Grid using Peer-to-Peer Services - Kim,J.-S.; Nam,B.; Marsh,M.; Keleher,P.; Bhattacharjee, Bobby; Richardson,D.; Wellnitz,D.; Sussman, Alan (Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International, 2007)
The goal of the work described in this paper is to design and build a scalable infrastructure for executing grid applications on a widely distributed set of resources. Such grid infrastructure must be decentralized, robust, highly available, and scalable, while efficiently mapping application instances to available resources in the system. However, current desktop grid computing platforms are typically based on a client-server architecture, which has inherent shortcomings with respect to robustness, reliability and scalability. Fortunately, these problems can be addressed through the capabilities promised by new techniques and approaches in peer-to-peer (P2P) systems. By employing P2P services, our system allows users to submit jobs to be run in the system and to run jobs submitted by other users on any resources available in the system, essentially allowing a group of users to form an ad-hoc set of shared resources. The initial target application areas for the desktop grid system are in astronomy and space science simulation and data analysis.
Keywords: allocation; architecture; load; balancing; peer-to-peer; client-server; computing; peer-to-peer; computing; resource; desktop; grid; scalable; infrastructure; client-server; system; robust; systems; grid

The defined cliffs variant in dynamic environments: a case study using the shaky ladder hyperplane-defined functions - Alharbi,Abir; Rand, William; Riolo,Rick (Proceedings of the 9th annual conference on Genetic and evolutionary computation, 2007)
The shaky ladder hyperplane-defined functions (sl-hdfs) are a test suite utilized for exploring the behavior of the genetic algorithm (GA) in dynamic environments. This test suite can generate arbitrary problems with similar levels of difficulty and it provides a platform for systematic controlled observations of the GA in dynamic environments. Previous work has found two factors that contribute to the GA's success on sl-hdfs: (1) short initial building blocks and (2) significantly changing the reward structure during fitness landscape changes. Therefore a test function that combines these two features should facilitate even better GA performance. This has led to the construction of a new sl-hdf variant, "Defined Cliffs," in which we combine short elementary building blocks with sharp transitions in the environment. We examine this variant with two different levels of dynamics, static and regularly changing, using four different metrics. The results show superior GA performance on the Defined Cliffs over all previous variants (Cliffs, Weight, and Smooth). Our observations and conclusions in this variant further the understanding of the GA in dynamic environments.
Keywords: building blocks; dynamic environments; Genetic algorithms; shaky ladder hyperplane-defined functions

Development of in-mold assembly process for realizing mesoscale revolute joints - Ananthanarayanan,A.; Gupta,S.K.; Bruck,H. A.; Yu,Z.; Rajurkar,K. P. (Transactions of North American Manufacturing Research Institution of SME, 2007)
In-mold Assembly process at the mesoscalepresents several manufacturing challenges. Results reported in this paper demonstrate the technical feasibility of creating rigid body mesoscale revolute joints using In-Mold Assembly process. The following new results are reported in this paper. First, we describe a mold design with varying cavity shape to perform In-Mold Assembly. This mold design uses an accurate mold piece positioning method to avoid damage to delicate mesoscale parts during the cavity change step. Second, we describe a mold insert fabrication process for making mold inserts with the desired surface characteristics for mesoscale molding. Finally, we describe methods to limit the adhesion at the interfaces and hence create articulated revolute joint. Using the advances reported in this paper we have successfully molded a mesoscale revolute joint. To the best of our knowledge, this is the first demonstration of In-Mold Assembly process using a varying cavity shape mold to create a mesoscale revolute joint.

Distribution-Free Testing Lower Bounds for Basic Boolean Functions - Dana Dachman-Soled; Servedio, Rocco A. (Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques, 2007)
In the distribution-free property testing model, the distance between functions is measured with respect to an arbitrary and unknown probability distribution \mathcal{D} over the input domain. We consider distribution-free testing of several basic Boolean function classes over {0,1} n , namely monotone conjunctions, general conjunctions, decision lists, and linear threshold functions. We prove that for each of these function classes, Ω((n/logn)1/5) oracle calls are required for any distribution-free testing algorithm. Since each of these function classes is known to be distribution-free properly learnable (and hence testable) using Θ(n) oracle calls, our lower bounds are within a polynomial factor of the best possible.
Keywords: Algorithm Analysis and Problem Complexity; Discrete Mathematics in Computer Science; Numeric Computing

Draft Genome of the Filarial Nematode Parasite Brugia Malayi - Ghedin,Elodie; Wang,Shiliang; Spiro,David; Caler,Elisabet; Zhao,Qi; Crabtree,Jonathan; Allen,Jonathan E; Delcher,Arthur L.; Guiliano,David B; Miranda-Saavedra,Diego; Angiuoli,Samuel V; Creasy,Todd; et al. (Science, 2007)
Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the ∼90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict ∼11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during ∼350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.

Ecotopia: An Ecological Framework for Change Management in Distributed Systems - Tudor Dumitras; Roşu, Daniela; Dan, Asit; Narasimhan, Priya (Architecting Dependable Systems IV, 2007)
Dynamic change management in an autonomic, service-oriented infrastructure is likely to disrupt the critical services delivered by the infrastructure. Furthermore, change management must accommodate complex real-world systems, where dependability and performance objectives are managed across multiple distributed service components and have specific criticality/value models. In this paper, we present Ecotopia, a framework for change management in complex service-oriented architectures (SOA) that is ecological in its intent: it schedules change operations with the goal of minimizing the service-delivery disruptions by accounting for their impact on the SOA environment. The change-planning functionality of Ecotopia is split between multiple objective-advisors and a system-level change-orchestrator component. The objective advisors assess the change-impact on service delivery by estimating the expected values of the Key Performance Indicators (KPIs), during and after change. The orchestrator uses the KPI estimations to assess the per-objective and overall business-value changes over a long time-horizon and to identify the scheduling plan that maximizes the overall business value. Ecotopia handles both external change requests, like software upgrades, and internal changes requests, like fault-recovery actions. We evaluate the Ecotopia framework using two realistic change-management scenarios in distributed enterprise systems.
Keywords: Autonomic Computing; Dynamic Change Management; Fault-Tolerant Architecture; Operating systems; Performability; Service Orchestration; software engineering

Efficient simulation of critical synchronous dataflow graphs - Hsu,C. J; Ko,M. Y; Bhattacharyya, Shuvra S.; Ramasubbu,S.; Pino,J. L (ACM Transactions on Design Automation of Electronic Systems (TODAES), 2007)

Evaluating a cross-cultural children’s online book community: Lessons learned for sociability, usability, and cultural exchange - Komlodi,Anita; Hou,Weimin; Preece,Jenny; Druin, Allison; Golub,Evan; Alburo,Jade; Liao,Sabrina; Elkiss,Aaron; Resnik, Philip (Interacting with Computers, 2007)
The use of computers for human-to-human communication among adults has been studied for many years, but using computer technology to enable children from all over the world to talk to each other has rarely been discussed by researchers. The goal of our research is to fill this gap and explore the design and evaluation of children’s cross-language online communities via a case study of the International Children’s Digital Library Communities (ICDLCommunities). This project supports the development of communities for children (ages 7–11) that form around the International Digital Children’s Library (ICDL) book collection. In this community the children can learn about each others’ cultures and make friends even if they do not speak the same language. They can also read and create stories and ask and answer questions about these. From this evaluation study we learned that: (i) children are very interested in their counterparts in other countries and a remarkable amount of communication takes place even when they do not share a common language; (ii) representing their identity online in many different forms is particularly important to children when communicating in an online community; (iii) children enjoy drawing but representing stories in a sequence of diagrams is challenging and needs support; and (iv) asking and answering questions without language is possible using graphical templates. In this paper we present our findings and make recommendations for designing children’s cross-cultural online communities.
Keywords: children; Cross-cultural; Evaluation and design; International Children’s Digital Library; Online communities

Evolution of genes and genomes on the Drosophila phylogeny - Clark,Andrew G.; Eisen,Michael B.; Smith,Douglas R.; Bergman,Casey M.; Oliver,Brian; Markow,Therese A.; Kaufman,Thomas C.; Kellis,Manolis; Gelbart,William; Iyer,Venky N.; Pollard,Daniel A.; Sackton,Timothy B.; et al. (Nature, 2007)
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.

Evolution of non-uniform cellular automata using a genetic algorithm: diversity and computation - Sondahl,Forrest; Rand, William (Proceedings of the 9th annual conference on Genetic and evolutionary computation, 2007)
We used a genetic algorithm to evaluate the cost / benefit of diversity in evolving sets of rules for non-uniform cellular automata solving the density classification problem.
Keywords: diversity; Genetic algorithms; non-uniform cellular automata; search spaces

Examining Group Behavior and Collaboration using ABM and Robots - Blikstein,P.; Rand, William; Wilensky,Uri (Proc. of Agent, 2007)
Agent-based modeling has been extensively used by scientists to study complex systems.Participatory simulations are similar to agent-based models except that humans play the role of the virtual agents. The Bifocal modeling approach uses sensors to gather data about the real-world phenomena being modeled and uses that information to affect the model. In this work, we are interested in automatically extracting, analyzing and modeling group behaviors in problem solving. Combining these three systems into one unified platform would be useful for those purposes, since it would facilitate a synthesis of their main affordances: understanding the role of locality, mapping human action to emergent behaviors, and controlling embedded physical objects in noisy environments while receiving sensory feedback. We will demonstrate a technological platform based on the NetLogo/HubNet architecture that supports simulated agents, participatory agents and physical agents. We place this platform within a more general framework that we call Human, Embedded and Virtual agents in Mediation (HEV-M). We have run several studies using an instantiation of this platform that consists of a robot-car with four users who navigate a maze. We believe that this tool has potential for three main reasons (1) it facilitates logging of participant’s actions, so as to identify patterns, (2) it offers researchers in the field of computer-supported collaborative learning an easy-to-use tool to design engaging collaborative learning activities and, (3) it foregrounds the role of individual actions within the accomplishment of a collective goal, highlighting the connections between simple individual actions and the resultant macroscopic behaviors of the system.

Experimenting with software testbeds for evaluating new technologies - Lindvall,M.; Rus,I.; Donzelli,P.; Memon, Atif M.; Zelkowitz, Marvin V; Betin-Can,A.; Bultan,T.; Ackermann,C.; Anders,B.; Asgari, S.; Basili, Victor R. (Empirical Software Engineering, 2007)
The evolution of a new technology depends upon a good theoretical basis for developing the technology, as well as upon its experimental validation. In order to provide for this experimentation, we have investigated the creation of a software testbed and the feasibility of using the same testbed for experimenting with a broad set of technologies. The testbed is a set of programs, data, and supporting documentation that allows researchers to test their new technology on a standard software platform. An important component of this testbed is the Unified Model of Dependability (UMD), which was used to elicit dependability requirements for the testbed software. With a collection of seeded faults and known issues of the target system, we are able to determine if a new technology is adept at uncovering defects or providing other aids proposed by its developers. In this paper, we present the Tactical Separation Assisted Flight Environment (TSAFE) testbed environment for which we modeled and evaluated dependability requirements and defined faults to be seeded for experimentation. We describe two completed experiments that we conducted on the testbed. The first experiment studies a technology that identifies architectural violations and evaluates its ability to detect the violations. The second experiment studies model checking as part of design for verification. We conclude by describing ongoing experimental work studying testing, using the same testbed. Our conclusion is that even though these three experiments are very different in terms of the studied technology, using and re-using the same testbed is beneficial and cost effective.

Extended wavelets for multiple measures - Deligiannakis,Antonios; Garofalakis,Minos; Roussopoulos, Nick (ACM Transactions on Database SystemsACM Trans. Database Syst., 2007)

A fast algorithm for learning large scale preference relations - Raykar,V.C.; Duraiswami, Ramani; Krishnapuram,B. (Proceedings of the Eleventh International Conference on Artificial Intelligence and Statistics (AISTATS 2007), 2007)
We consider the problem of learning the rank-ing function that maximizes a generalization of the Wilcoxon-Mann-Whitney statistic on training data. Relying on an ϵ-exact approx- imation for the error-function, we reduce the computational complexity of each iteration of a conjugate gradient algorithm for learn- ing ranking functions from O(m2), to O(m), where m is the size of the training data. Experiments on public benchmarks for ordi- nal regression and collaborative filtering show that the proposed algorithm is as accurate as the best available methods in terms of rank- ing accuracy, when trained on the same data, and is several orders of magnitude faster.

Fast Bilinear SfM with Side Information - Ramachandran, M.; Veeraraghavan,A.; Chellapa, Rama (Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on, 2007)
We study the beneficial effect of side information on the Structure from Motion (SfM) estimation problem. The side information that we consider is measurement of a 'reference vector' and distance from fixed plane perpendicular to that reference vector. Firstly, we show that in the presence of this information, the SfM equations can be rewritten similar to a bilinear form in its unknowns. Secondly, we describe a fast iterative estimation procedure to recover the structure of both stationary scenes and moving objects that capitalizes on this information. We also provide a refinement procedure in order to tackle incomplete or noisy side information. We characterize the algorithm with respect to its reconstruction accuracy, memory requirements and stability. Finally, we describe two classes of commonly occurring real-world scenarios in which this algorithm will be effective: (a) presence of a dominant ground plane in the scene and (b) presence of an inertial measurement unit on board. Experiments using both real data and rigorous simulations show the efficacy of the algorithm.
Keywords: bilinear; Estimation; estimation; estimation; reference; information; image; methods; motion; procedure; motion; procedure; side; reconstruction; iterative; recovery; image; structure; vector; refinement

Fast computation of sums of Gaussians - Raykar,V.C.; Duraiswami, Ramani; Gumerov, Nail A. (Journal of Machine Learning Research (submitted), 2007)
Evaluating sums of multivariate Gaussian kernels is a key computational task in manyproblems in computational statistics and machine learning. The computational cost of the direct evaluation of such sums scales as the product of the number of kernel functions and the evaluation points. The fast Gauss transform proposed by Greengard and Strain (1991) is a ǫ-exact approximation algorithm that reduces the computational complexity of the evaluation of the sum of N Gaussians at M points in d dimensions from O(MN) to O(M + N). However, the constant factor in O(M + N) grows exponentially with increasing dimensionality d, which makes the algorithm impractical for dimensions greater than three. In this paper we present a new algorithm where the constant factor is reduced to asymptotically polynomial order. The reduction is based on a new multivariate Taylor’s series expansion (which can act both as a local as well as a far field expansion) scheme combined with the efficient space subdivision using the k-center algorithm. The proposed method differs from the original fast Gauss transform in terms of a different factorization, efficient space subdivision, and the use of different error bounds for each source point. Algorithm details, error bounds, a procedure to choose the parameters, and numerical experiments are presented. We also compare our algorithm with the dual-tree algorithm of Gray and Moore (2003). As an example we show how the proposed method can be used for very fast ǫ-exact multivariate kernel density estimation.

Fast large scale Gaussian process regression using approximate matrix-vector products - Raykar,V.C.; Duraiswami, Ramani (Learning workshop, 2007)

Fast weighted summation of erfc functions - Raykar,Vikas C.; Duraiswami, Ramani; Krishnapuram,B. (Technical Reports from UMIACS UMIACS-TR-2007-03, 2007)
Abstract: Direct computation of the weighted sum of N complementaryerror functions at M points scales as O(MN). We present a O(M + N) $ε$-exact approximation algorithm to compute the same.
Keywords: Technical Report

Filtering spam with behavioral blacklisting - Ramachandran,Anirudh; Feamster, Nick; Vempala,Santosh (Proceedings of the 14th ACM conference on Computer and communications security, 2007)
Spam filters often use the reputation of an IP address (or IP address range) to classify email senders. This approach worked well when most spam originated from senders with fixed IP addresses, but spam today is also sent from IP addresses for which blacklist maintainers have outdated or inaccurate information (or no information at all). Spam campaigns also involve many senders, reducing the amount of spam any particular IP address sends to a single domain; this method allows spammers to stay "under the radar". The dynamism of any particular IP address begs for blacklisting techniques that automatically adapt as the senders of spam change. This paper presents SpamTracker, a spam filtering system that uses a new technique called behavioral blacklisting to classify email senders based on their sending behavior rather than their identity. Spammers cannot evade SpamTracker merely by using "fresh" IP addresses because blacklisting decisions are based on sending patterns, which tend to remain more invariant. SpamTracker uses fast clustering algorithms that react quickly to changes in sending patterns. We evaluate SpamTracker's ability to classify spammers using email logs for over 115 email domains; we find that SpamTracker can correctly classify many spammers missed by current filtering techniques. Although our current datasets prevent us from confirming SpamTracker's ability to completely distinguish spammers from legitimate senders, our evaluation shows that SpamTracker can identify a significant fraction of spammers that current IP-based blacklists miss. SpamTracker's ability to identify spammers before existing blacklists suggests that it can be used in conjunction with existing techniques (e.g., as an input to greylisting). SpamTracker is inherently distributed and can be easily replicated; incorporating it into existing email filtering infrastructures requires only small modifications to mail server configurations.
Keywords: blacklists; botnets; clustering; Security; spam

Full Spectrum Modeling: From Simplicity to Elaboration and Realism in Urban Pattern Formation - Rand, William; Wilensky,U. (North american association computational social and organization sciences conference (NAACSOS), 2007)
There is a dichotomy between researchers who utilize elaborated and realistic agent-basedmodels and those who prefer simple models. Researchers who use realistic agent-based models (ABMs) argue that their realism makes them more useful, while those who utilize simple models claim that they are more general and provide more global knowledge. We believe that it is better to embrace both of these modeling approaches at the same time. Creating richly, detailed, empirically validated models to explore complex systems at a high level, and at the same time extracting general principles to create simplified models that help explore the most important general principles of the phenomena. We call this approach full spectrum modeling and we examine its use through a particular project concerned with understanding urban pattern formation.

Functional connectivity in fMRI: A modeling approach for estimation and for relating to local circuits - Winder,R.; Cortes,C. R; Reggia, James A.; Tagamets,M. A (Neuroimage, 2007)

GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo - Zhang,Yuzhen; Rath,Nibedita; Hannenhalli, Sridhar; Wang,Zhishan; Cappola,Thomas; Kimura,Shioko; Atochina-Vasserman,Elena; Lu,Min Min; Beers,Michael F.; Morrisey,Edward E. (Development, 2007)
In vitro studies have suggested that members of the GATA and Nkx transcription factor families physically interact, and synergistically activate pulmonary epithelial- and cardiac-gene promoters. However, the relevance of this synergy has not been demonstrated in vivo. We show that Gata6-Titf1 (Gata6-Nkx2.1) double heterozygous (G6-Nkx DH) embryos and mice have severe defects in pulmonary epithelial differentiation and distal airway development, as well as reduced phospholipid production. The defects in G6-Nkx DH embryos and mice are similar to those observed in human neonates with respiratory distress syndromes, including bronchopulmonary dysplasia, and differential gene expression analysis reveals essential developmental pathways requiring synergistic regulation by both Gata6 and Titf1 (Nkx2.1). These studies indicate that Gata6 and Nkx2.1 act in a synergistic manner to direct pulmonary epithelial differentiation and development in vivo, providing direct evidence that interactions between these two transcription factor families are crucial for the development of the tissues in which they are co-expressed.

Geometry and Charge State of Mixed‐Ligand Au13 Nanoclusters - Frenkel, A. I.; Menard, L. D.; Northrup, P.; Rodriguez, J. A.; Zypman, F.; Dana Dachman-Soled; Gao, S.-P.; Xu, H.; Yang, J. C.; Nuzzo, R. G. (X-RAY ABSORPTION FINE STRUCTURE - XAFS13: 13th International Conference, 2007)
The integration of synthetic, experimental and theoretical tools into a self‐consistent data analysis methodology allowed us to develop unique new levels of detail in nanoparticle characterization. We describe our methods using an example of Au 13 monolayer‐protected clusters (MPCs), synthesized by ligand exchange methods. The combination of atom counting methods of scanning transmission electron microscopy and Au L3‐edge EXAFS allowed us to characterize these clusters as icosahedral, with surface strain reduced from 5% (as in ideal, regular icosahedra) to 3%, due to the interaction with ligands. Charge transfer from Au to the thiol and phosphine ligands was evidenced by S and P K‐edge XANES. A comparison of total energies of bare clusters of different geometries was performed by equivalent crystal theory calculations.
Keywords: Atom surface interactions; Charge transfer; Data analysis; Extended X-ray absorption fine structure spectroscopy; Gold; nanoparticles; Scanning transmission electron microscopy; Surface strains; Total energy calculations; X-ray absorption near edge structure

A graph-based approach to vehicle tracking in traffic camera video streams - Shahri,Hamid Haidarian; Namata,Galileo; Navlakha,Saket; Deshpande, Amol; Roussopoulos, Nick (Proceedings of the 4th workshop on Data management for sensor networks: in conjunction with 33rd International Conference on Very Large Data Bases, 2007)
Vehicle tracking has a wide variety of applications from law enforcement to traffic planning and public safety. However, the image resolution of the videos available from most traffic camera systems, make it difficult to track vehicles based on unique identifiers like license plates. In many cases, vehicles with similar attributes are indistinguishable from one another due to image quality issues. Often, network bandwidth and power constraints limit the frame rate, as well. In this paper, we discuss the challenges of performing vehicle tracking queries over video streams from ubiquitous traffic cameras. We identify the limitations of tracking vehicles individually in such conditions and provide a novel graph-based approach using the identity of neighboring vehicles to improve the performance. We evaluate our approach using streaming video feeds from live traffic cameras available on the Internet. The results show that vehicle tracking is feasible, even for low quality and low frame rate traffic cameras. Additionally, exploitation of the attributes of neighboring vehicles significantly improves the performance.

Grow and Know: Understanding Record-keeping Needs for Tracking the Development of Young Children - Kientz, Julie A.; Arriaga, Rosa I.; Marshini Chetty; Hayes, Gillian R.; Richardson, Jahmeilah; Patel, Shwetak N.; Abowd, Gregory D. (SIGCHI '07, 2007)
From birth through age five, children undergo rapid development and learn skills that will influence them their entire lives. Regular visits to the pediatrician and detailed record-keeping can ensure that children are progressing and can identify early warning signs of developmental delay or disability. However, new parents are often overwhelmed with new responsibilities, and we believe there is an opportunity for computing technology to assist in this process. In this paper, we present a qualitative study aimed at uncovering some specific needs for record-keeping and analysis for new parents and their network of caregivers. Through interviews and focus groups, we have confirmed assumptions about the rationales parents have and the functions required for using technology for record-keeping. We also identify new themes, potential prototypes, and design guidelines for this domain.
Keywords: children; design requirements; developmental delay; healthcare; qualitative study

Guest Editorial: Special Issue on Human Detection and Recognition - Bhanu, B.; Ratha,N. K; Kumar, V.; Chellapa, Rama; Bigun, J. (Information Forensics and Security, IEEE Transactions on, 2007)
The 12 regular papers and three correspondences in this special issue focus on human detection and recognition. The papers represent gait, face (3-D, 2-D, video), iris, palmprint, cardiac sounds, and vulnerability of biometrics and protection against the spoof attacks.

Heuristic Search and Information Visualization Methods for School Redistricting - desJardins, Marie; Bulka,Blazej; Carr,Ryan; Jordan,Eric; Rheingans,Penny (AI Magazine, 2007)
We describe an application of AI search and information visualization techniques to the problem of school redistricting, in which students are assigned to home schools within a county or school district. This is a multicriteria optimization problem in which competing objectives, such as school capacity, busing costs, and socioeconomic distribution, must be considered. Because of the complexity of the decision-making problem, tools are needed to help end users generate, evaluate, and compare alternative school assignment plans. A key goal of our research is to aid users in finding multiple qualitatively different redistricting plans that represent different trade-offs in the decision space. We present heuristic search methods that can be used to find a set of qualitatively different plans, and give empirical results of these search methods on population data from the school district of Howard County, Maryland. We show the resulting plans using novel visualization methods that we have developed for summarizing and comparing alternative plans.

How to lease the internet in your spare time - Feamster, Nick; Gao,Lixin; Rexford,Jennifer (SIGCOMM Comput. Commun. Rev., 2007)
Today's Internet Service Providers (ISPs) serve two roles: managing their network infrastructure and providing (arguably limited) services to end users. We argue that coupling these roles impedes the deployment of new protocols and architectures, and that the future Internet should support two separate entities: infrastructure providers (who manage the physical infrastructure) and service providers (who deploy network protocols and offer end-to-end services). We present a high-level design for Cabo, an architecture that enables this separation; we also describe challenges associated with realizing this architecture.

Human Identification using Gait and Face - Chellapa, Rama; Roy-Chowdhury, A.K.; Kale, A. (Computer Vision and Pattern Recognition, 2007. CVPR '07. IEEE Conference on, 2007)
In general the visual-hull approach for performing integrated face and gait recognition requires at least two cameras. In this paper we present experimental results for fusion of face and gait for the single camera case. We considered the NIST database which contains outdoor face and gait data for 30 subjects. In the NIST database, subjects walk along an inverted Sigma pattern. In (A. Kale, et al., 2003), we presented a view-invariant gait recognition algorithm for the single camera case along with some experimental evaluations. In this chapter we present the results of our view-invariant gait recognition algorithm in (A. Kale, et al., 2003) on the NIST database. The algorithm is based on the planar approximation of the person which is valid when the person walks far away from the camera. In (S. Zhou et al., 2003), an algorithm for probabilistic recognition of human faces from video was proposed and the results were demonstrated on the NIST database. Details of these methods can be found in the respective papers. We give an outline of the fusion strategy here.
Keywords: algorithm; visual-hull; analysis; image; approach; cameras; face; approximation; probabilistic; database; camera; face; databases; fusion; face; fusion; human; fusion; probability; video; Gait; identification; planar; NIST; processing; visual; recognition; recognition; gait; recognition; view-invariant; signal

IFISS: A Matlab toolbox for modelling incompressible flow - Elman, Howard; Ramage, A.; Silvester, D. J (ACM Transactions on Mathematical Software, 2007)

The improved fast Gauss transform with applications to machine learning - Raykar,V.C.; Duraiswami, Ramani (Large Scale Kernel Machines, 2007)

Just a cog in the machine: participatory robotics as a tool for understanding collaborative learning and decision-making - Blikstein,Paulo; Rand, William; Wilensky,Uri (Proceedings of the 8th iternational conference on Computer supported collaborative learning, 2007)
We will demonstrate the integration of a software-based multi-agent modeling platform with a participatory simulation environment and a real-time control system for a physical robotic agent. Both real and virtual participants will be able to act collaboratively in a simulation that will control a physical agent. The backbone of this demonstration is a widely used, freely available, mature modeling platform (NetLogo). We posit that this technological platform can be of use for researchers interested in investigating collaborative learning and decision-making, as well as to design collaborative learning activities. We will present preliminary findings from pilot studies with the tool.

Large-scale byzantine fault tolerance: safe but not always live - Rodrigues,Rodrigo; Kouznetsov,Petr; Bhattacharjee, Bobby (Proceedings of the 3rd workshop on on Hot Topics in System Dependability, 2007)
The overall correctness of large-scale systems composed of many groups of replicas executing BFT protocols scales poorly with the number of groups. This is because the probability of at least one group being compromised (more than 1/3 faulty replicas) increases rapidly as the number of groups increases. In this paper we address this problem with a simple modification to Castro and Liskov's BFT replication that allows for arbitrary choice of n (number of replicas) and f (failure threshold). The price to pay is a more restrictive liveness requirement, and we present the design of a large-scale BFT replicated system that obviates this problem.

Making models match: Replicating an agent-based model - Wilensky,U.; Rand, William (Journal of Artificial Societies and Social Simulation, 2007)
Scientists have increasingly employed computer models in their work. Recent years have seen a proliferation of agent-based models in the natural and social sciences. But with the exception of a few "classic" models, most of these models have never been replicated by anyone but the original developer. As replication is a critical component of the scientific method and a core practice of scientists, we argue herein for an increased practice of replication in the agent-based modeling community, and for widespread discussion of the issues surrounding replication. We begin by clarifying the concept of replication as it applies to ABM. Furthermore we argue that replication may have even greater benefits when applied to computational models than when applied to physical experiments. Replication of computational models affects model verification and validation and fosters shared understanding about modeling decisions. To facilitate replication, we must create standards for both how to replicate models and how to evaluate the replication. In this paper, we present a case study of our own attempt to replicate a classic agent-based model. We begin by describing an agent-based model from political science that was developed by Axelrod and Hammond. We then detail our effort to replicate that model and the challenges that arose in recreating the model and in determining if the replication was successful. We conclude this paper by discussing issues for (1) researchers attempting to replicate models and (2) researchers developing models in order to facilitate the replication of their results.

Multimodal Tracking for Smart Videoconferencing and Video Surveillance - Zotkin,Dmitry N; Raykar,V.C.; Duraiswami, Ramani; Davis, Larry S. (Computer Vision and Pattern Recognition, 2007. CVPR '07. IEEE Conference on, 2007)
Many applications require the ability to track the 3-D motion of the subjects. We build a particle filter based framework for multimodal tracking using multiple cameras and multiple microphone arrays. In order to calibrate the resulting system, we propose a method to determine the locations of all microphones using at least five loudspeakers and under assumption that for each loudspeaker there exists a microphone very close to it. We derive the maximum likelihood (ML) estimator, which reduces to the solution of the non-linear least squares problem. We verify the correctness and robustness of the multimodal tracker and of the self-calibration algorithm both with Monte-Carlo simulations and on real data from three experimental setups.
Keywords: (numerical; 3D; algorithm; smart; analysis; least; approximations; particle; arrays; nonlinear; cameras; multiple; Carlo; estimator; multimodal; filter; self-calibration; Filtering; least; likelihood; methods); teleconferencing; video; methods; image; microphone; MOTION; motion; Monte-Carlo; problem; particle; processing; video; signal; simulations; maximum; squares; surveillance; surveillance; Monte; tracking; multiple; videoconferencing; video

Network-Wide Prediction of BGP Routes - Feamster, Nick; Rexford,J. (Networking, IEEE/ACM Transactions on, 2007)
This paper presents provably correct algorithms for computing the outcome of the BGP route-selection process for each router in a network, without simulating the complex details of BGP message passing. The algorithms require only static inputs that can be easily obtained from the routers: the BGP routes learned from neighboring domains, the import policies configured on the BGP sessions, and the internal topology. Solving the problem would be easy if the route-selection process were deterministic and every router received all candidate BGP routes. However, two important features of BGP-the Multiple Exit Discriminator (MED) attribute and route reflectors-violate these properties. After presenting a simple route-prediction algorithm for networks that do not use these features, we present algorithms that capture the effects of the MED attribute and route reflectors in isolation. Then, we explain why the interaction between these two features precludes efficient route prediction. These two features also create difficulties for the operation of BGP itself, leading us to suggest improvements to BGP that achieve the same goals as MED and route reflection without introducing the negative side effects
Keywords: BGP message passing; BGP route-selection process; border gateway protocol; Message passing; multiple exit discriminator attribute; network-wide prediction; route reflectors; route-prediction algorithm; routing protocols; telecommunication network topology

New Trypanosoma cruzi Repeated Element That Shows Site Specificity for Insertion - Souza,Renata T.; Santos,Marcia R. M.; Lima,Fabio M.; El‐Sayed, Najib M.; Myler,Peter J.; Ruiz,Jeronimo C.; da Silveira,Jose Franco (Eukaryotic Cell, 2007)
A new family of site-specific repeated elements identified in Trypanosoma cruzi, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other T. cruzi sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5' end of the element and a sequence domain of [~]500 bp without a well-defined borderline at the 3' end. Northern blot hybridization and reverse transcriptase PCR analyses showed that TcTREZO transcripts are expressed as oligo(A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of [~]0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. TcTREZO transcripts are unspliced and not translated. The copy number of TcTREZO sequences was estimated to be [~]173 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.

Oblivious routing on node-capacitated and directed graphs - Hajiaghayi, Mohammad T.; Kleinberg,R. D; R\äcke,H.; Leighton,T. (ACM Transactions on Algorithms (TALG), 2007)

Optimizing mpf queries - Corrada Bravo, Hector; Ramakrishnan,Raghu (Proceedings of the 2007 ACM SIGMOD international conference on Management of data - SIGMOD '07, 2007)

Pedestrian detection via periodic motion analysis - Ran, Y.; Weiss, I.; Zheng,Q.; Davis, Larry S. (International Journal of Computer Vision, 2007)
We describe algorithms for detecting pedestrians in videos acquired by infrared (and color) sensors. Two approaches are proposed based on gait. The first employs computationally efficient periodicity measurements. Unlike other methods, it estimates a periodic motion frequency using two cascading hypothesis testing steps to filter out non-cyclic pixels so that it works well for both radial and lateral walking directions. The extraction of the period is efficient and robust with respect to sensor noise and cluttered background. In order to integrate shape and motion, we convert the cyclic pattern into a binary sequence by Maximal Principal Gait Angle (MPGA) fitting in the second method. It does not require alignment and continuously estimates the period using a Phase-locked Loop. Both methods are evaluated by experimental results that measure performance as a function of size, movement direction, frame rate and sequence length.

A practical approximation algorithm for the LMS line estimator - Mount, Dave; Netanyahu,Nathan S.; Romanik,Kathleen; Silverman,Ruth; Wu,Angela Y. (Computational Statistics & Data Analysis, 2007)
The problem of fitting a straight line to a finite collection of points in the plane is an important problem in statistical estimation. Robust estimators are widely used because of their lack of sensitivity to outlying data points. The least median-of-squares (LMS) regression line estimator is among the best known robust estimators. Given a set of n points in the plane, it is defined to be the line that minimizes the median squared residual or, more generally, the line that minimizes the residual of any given quantile q, where 0 < q ⩽ 1 . This problem is equivalent to finding the strip defined by two parallel lines of minimum vertical separation that encloses at least half of the points.The best known exact algorithm for this problem runs in O ( n 2 ) time. We consider two types of approximations, a residual approximation, which approximates the vertical height of the strip to within a given error bound ε r ⩾ 0 , and a quantile approximation, which approximates the fraction of points that lie within the strip to within a given error bound ε q ⩾ 0 . We present two randomized approximation algorithms for the LMS line estimator. The first is a conceptually simple quantile approximation algorithm, which given fixed q and ε q > 0 runs in O ( n log n ) time. The second is a practical algorithm, which can solve both types of approximation problems or be used as an exact algorithm. We prove that when used as a quantile approximation, this algorithm's expected running time is O ( n log 2 n ) . We present empirical evidence that the latter algorithm is quite efficient for a wide variety of input distributions, even when used as an exact algorithm.
Keywords: Approximation algorithms; least median-of-squares regression; line arrangements; line fitting; randomized algorithms; robust estimation

Probabilistic wavelet synopses for multiple measures - Deligiannakis,Antonios; Garofalakis,Minos N.; Roussopoulos, Nick (2007)
A technique for building probabilistic wavelet synopses for multi-measure data sets is provided. In the presence of multiple measures, it is demonstrated that the problem of exact probabilistic coefficient thresholding becomes significantly more complex. An algorithmic formulation for probabilistic multi-measure wavelet thresholding based on the idea of partial-order dynamic programming (PODP) is provided. A fast, greedy approximation algorithm for probabilistic multi-measure thresholding based on the idea of marginal error gains is provided. An empirical study with both synthetic and real-life data sets validated the approach, demonstrating that the algorithms outperform naive approaches based on optimizing individual measures independently and the greedy thresholding scheme provides near-optimal and, at the same time, fast and scalable solutions to the probabilistic wavelet synopsis construction problem.

Profiling Attacker Behavior Following SSH Compromises - Ramsbrock,D.; Berthier,R.; Michel Cukier (2007)
This practical experience report presents the results of an experiment aimed at building a profile of attacker behavior following a remote compromise. For this experiment, we utilized four Linux honeypot computers running SSH with easily guessable passwords. During the course of our research, we also determined the most commonly attempted usernames and passwords, the average number of attempted logins per day, and the ratio of failed to successful attempts. To build a profile of attacker behavior, we looked for specific actions taken by the attacker and the order in which they occurred. These actions were: checking the configuration, changing the password, downloading a file, installing/running rogue code, and changing the system configuration.
Keywords: Linux; Linux honeypot computers; profiling attacker behavior; remote compromise; rogue code; security of data; SSH compromises; system configuration

Recognizing Faces Across Age Progression - Ramanathan,Narayanan; Chellapa, Rama (Face Biometrics for Personal IdentificationFace Biometrics for Personal Identification, 2007)

Searching spontaneous conversational speech - Jong,Franciska De; Oard, Douglas; Ordelman,Roeland; Raaijmakers,Stephan (ACM SIGIR Forum, 2007)

Secure lookup without (constrained) flooding - Bhattacharjee, Bobby; Rodrigues,R.; Kouznetsov,P. (WRAITS 2007, 2007)

Sentiment analysis: Adjectives and adverbs are better than adjectives alone - Benamara,F.; Cesarano,C.; Picariello, A.; Reforgiato,D.; V.S. Subrahmanian (Proceedings of the International Conference on Weblogs and Social Media (ICWSM), 2007)
Most past work on determining the strength of subjective expres-sions within a sentence or a document use specific parts of speech such as adjectives, verbs and nouns. To date, there is almost no work on the use of adverbs in sentiment analysis, nor has there been any work on the use of adverb-adjective combinations (AACs). We propose an AAC-based sentiment analysis technique that uses a lin- guistic analysis of adverbs of degree. We define a set of general axioms (based on a classification of adverbs of degree into five cat- egories) that all adverb scoring techniques must satisfy. Instead of aggregating scores of both adverbs and adjectives using simple scor- ing functions, we propose an axiomatic treatment of AACs based on the linguistic classification of adverbs. Three specific AAC scor- ing methods that satisfy the axioms are presented. We describe the results of experiments on an annotated set of 200 news articles (an- notated by 10 students) and compare our algorithms with some exist- ing sentiment analysis algorithms. We show that our results lead to higher accuracy based on Pearson correlation with human subjects.

Some observations on multigrid convergence for convection–diffusion equations - Ramage, A.; Elman, Howard (Computing and Visualization in Science, 2007)

A spatial model of the red queen effect - Ottino-Loffler,Jules; Rand, William; Wilensky,Uri (Proceedings of the 9th annual conference on Genetic and evolutionary computation, 2007)
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 µr and µp 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'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'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's initial poison / resistance will be drawn from a normal distribution with the parent'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 µp; we held µr constant at 25 and varied µp 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 µp is similar to µr then neither species is completely destroyed, but if there is any significant difference between µr and µp then one species will die off. The highest final trait values are found when µp = µr, 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

A Study of Face Recognition as People Age - Ling,Haibin; Soatto,S.; Ramanathan,N.; Jacobs, David W. (Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on, 2007)
In this paper we study face recognition across ages within a real passport photo verification task. First, we propose using the gradient orientation pyramid for this task. Discarding the gradient magnitude and utilizing hierarchical techniques, we found that the new descriptor yields a robust and discriminative representation. With the proposed descriptor, we model face verification as a two-class problem and use a support vector machine as a classifier. The approach is applied to two passport data sets containing more than 1,800 image pairs from each person with large age differences. Although simple, our approach outperforms previously tested Bayesian technique and other descriptors, including the intensity difference and gradient with magnitude. In addition, it works as well as two commercial systems. Second, for the first time, we empirically study how age differences affect recognition performance. Our experiments show that, although the aging process adds difficulty to the recognition task, it does not surpass illumination or expression as a confounding factor.
Keywords: Bayesian; difference; passport; machine; face; machines; magnitude; gradient; orientation; photo; pyramid; hierarchical; recognition; face; recognition; support; representation; face; task; support; technique; discriminative; techniques; intensity; vector; verification; verification; gradient

Super-Resolution of Face Images Using Kernel PCA-Based Prior - Chakrabarti,Ayan; Rajagopalan, AN; Chellapa, Rama (Multimedia, IEEE Transactions on, 2007)
We present a learning-based method to super-resolve face images using a kernel principal component analysis-based prior model. A prior probability is formulated based on the energy lying outside the span of principal components identified in a higher-dimensional feature space. This is used to regularize the reconstruction of the high-resolution image. We demonstrate with experiments that including higher-order correlations results in significant improvements
Keywords: analysis; learning-based; analysis; probability; component; Face; image; method; prior; model; face; principal; probability; recognition; image; reconstruction; image; reconstruction; kernel; resolution; principal; super-resolution; high-resolution

Swarm Intelligence Systems Using Guided Self-Organization for Collective Problem Solving - RodrIGuez,A.; Grushin,A.; Reggia, James A.; HAUPTMAN,AMI; SIPPER,M.; PAN,Z.; Reggia, James A.; GAO,D.; DARABOS,C.; GIACOBINI,M.; others (Advances in Complex Systems, 2007)

System for 802.11 connectivity at high speed - Frangiadakis,Nikolaos; Kuklov,Danila; Roussopoulos, Nick (Instititue for Advanced Computer Studies, Univ of Maryland, College Park, 2007)
Measurements and ongoing research have shown that WLANconnection for moving vehicles is feasible. However none of the previous work suggests a solution addressing a complete array of the challenges in vehicular WLAN communications. To amend this we designed a system that provides wireless connection roaming at high velocities transparent to user level applications, and does not impose additional requirements to existing infrastructures. It offers simple deployment, security, and scalability. It remains efficient under intermittent connectivity conditions and supports heterogeneous network mediums for increased robustness.
Keywords: Technical Report

Understanding the Semantics of the Genetic Algorithm in Dynamic Environments - Alharbi,A.; Rand, William; Riolo,R (Applications of Evolutionary Computing, 2007)
Researchers examining genetic algorithms (GAs) in applied settings rarely have access to anything other than fitness values of the best individuals to observe the behavior of the GA. In particular, researchers do not know what schemata are present in the population. Even when researchers look beyond best fitness values, they concentrate on either performance related measures like average fitness and robustness, or low-level descriptions like bit-level diversity measures. To understand the behavior of the GA on dynamic problems, it would be useful to track what is occurring on the “semantic” level of schemata. Thus in this paper we examine the evolving “content” in terms of schemata, as the GA solves dynamic problems. This allows us to better understand the behavior of the GA in dynamic environments. We finish by summarizing this knowledge and speculate about future work to address some of the new problems that we discovered during these experiments.

Using annotations from controlled vocabularies to find meaningful associations - Lee,W. J; Raschid, Louiqa; Srinivasan,P.; Shah,N.; Rubin,D.; Noy,N. (Proceedings of the 4th international conference on Data integration in the life sciences, 2007)

Using paraphrases for parameter tuning in statistical machine translation - Madnani,N.; Ayan,N.F.; Resnik, Philip; Dorr, Bonnie J (Proceedings of the Second Workshop on Statistical Machine Translation, 2007)

Using paraphrases for parameter tuning in statistical machine translation - Madnani,Nitin; Ayan,Necip Fazil; Resnik, Philip; Dorr, Bonnie J (Proceedings of the Second Workshop on Statistical Machine Translation, 2007)
Most state-of-the-art statistical machine translation systems use log-linear models, which are defined in terms of hypothesis features and weights for those features. It is standard to tune the feature weights in order to maximize a translation quality metric, using held-out test sentences and their corresponding reference translations. However, obtaining reference translations is expensive. In this paper, we introduce a new full-sentence paraphrase technique, based on English-to-English decoding with an MT system, and we demonstrate that the resulting paraphrases can be used to drastically reduce the number of human reference translations needed for parameter tuning, without a significant decrease in translation quality.

An adaptive probabilistic replication method for unstructured p2p networks - Tsoumakos,D.; Roussopoulos, Nick (On the Move to Meaningful Internet Systems 2006: CoopIS, DOA, GADA, and ODBASE, 2006)

Adaptive pull-based policies for wide area data delivery - Bright,L.; Gal,A.; Raschid, Louiqa (ACM Transactions on Database Systems (TODS), 2006)

Annotated rdf - Udrea,O.; Recupero,D.; V.S. Subrahmanian (The Semantic Web: Research and Applications, 2006)
There are numerous extensions of RDF that support temporal reasoning, reasoning about pedigree, reasoning about uncertainty, and so on. In this paper, we present Annotated RDF (or aRDF for short) in which RDF triples are annotated by members of a partially ordered set (with bottom element) that can be selected in any way desired by the user. We present a formal declarative semantics (model theory) for annotated RDF and develop algorithms to check consistency of aRDF theories and to answer queries to aRDF theories. We show that annotated RDF captures versions of all the forms of reasoning mentioned above within a single unified framework. We develop a prototype aRDF implementation and show that our algorithms work very fast indeed – in fact, in just a matter of seconds for theories with over 100,000 nodes.

Approximating the minimal sensor selection for supervisory control - Rohloff,K. R; Khuller, Samir; Kortsarz,G. (Discrete Event Dynamic Systems, 2006)
This paper discusses the problem of selecting a set of sensors of minimum cost that can be used for the synthesis of a supervisory controller. It is shown how this sensor selection problem is related to a type of directed graph st-cut problem that has not been previously discussed in the literature. Approximation algorithms to solve the sensor selection problem can be used to solve the graph cutting problem and vice-versa. Polynomial time algorithms to find good approximate solutions to either problem most likely do not exist (under certain complexity assumptions), but a time efficient approximation algorithm is shown that solves a special case of these problems. It is also shown how to convert the sensor selection problem into an integer programming problem.

An architecture for adaptive intrusion-tolerant applications - Pal,Partha; Rubel,Paul; Atighetchi,Michael; Webber,Franklin; Sanders,William H.; Seri,Mouna; Ramasamy,HariGovind; Lyons,James; Courtney,Tod; Agbaria,Adnan; Michel Cukier; Gossett,Jeanna; et al. (Software: Practice and Experience, 2006)
Applications that are part of a mission-critical information system need to maintain a usable level of key services through ongoing cyber-attacks. In addition to the well-publicized denial of service (DoS) attacks, these networked and distributed applications are increasingly threatened by sophisticated attacks that attempt to corrupt system components and violate service integrity. While various approaches have been explored to deal with DoS attacks, corruption-inducing attacks remain largely unaddressed. We have developed a collection of mechanisms based on redundancy, Byzantine fault tolerance, and adaptive middleware that help distributed, object-based applications tolerate corruption-inducing attacks. In this paper, we present the ITUA architecture, which integrates these mechanisms in a framework for auto-adaptive intrusion-tolerant systems, and we describe our experience in using the technology to defend a critical application that is part of a larger avionics system as an example. We also motivate the adaptive responses that are key to intrusion tolerance, and explain the use of the ITUA architecture to support them in an architectural framework. Copyright © 2006 John Wiley & Sons, Ltd.
Keywords: adaptive defense; adaptive middleware; Byzantine fault tolerance; intrusion tolerance; redundancy; survivability architecture

Can DNS-based blacklists keep up with bots - Ramachandran,A.; Dagon,D.; Feamster, Nick (Conference on email and anti-spam, 2006)

Characterization of the turbulence structure in supersonic boundary layers using DNS data - Ringuette,M. J; Martin, M.P; Smits,A. J.; Wu,M. (AIAA Paper, 2006)

Creativity Support Tools: Report From a U.S. National Science Foundation Sponsored Workshop - Shneiderman, Ben; Fischer,Gerhard; Czerwinski,Mary; Resnick,Mitch; Myers,Brad; Candy,Linda; Edmonds,Ernest; Eisenberg,Mike; Giaccardi,Elisa; Hewett,Tom; Jennings,Pamela; Kules,Bill; et al. (International Journal of Human-Computer Interaction, 2006)
Creativity support tools is a research topic with high risk but potentially very high payoff. The goal is to develop improved software and user interfaces that empower users to be not only more productive but also more innovative. Potential users include software and other engineers, diverse scientists, product and graphic designers, architects, educators, students, and many others. Enhanced interfaces could enable more effective searching of intellectual resources, improved collaboration among teams, and more rapid discovery processes. These advanced interfaces should also provide potent support in hypothesis formation, speedier evaluation of alternatives, improved understanding through visualization, and better dissemination of results. For creative endeavors that require composition of novel artifacts (e.g., computer programs, scientific papers, engineering diagrams, symphonies, artwork), enhanced interfaces could facilitate exploration of alternatives, prevent unproductive choices, and enable easy backtracking. This U.S. National Science Foundation sponsored workshop brought together 25 research leaders and graduate students to share experiences, identify opportunities, and formulate research challenges. Two key outcomes emerged: (a) encouragement to evaluate creativity support tools through multidimensional in-depth longitudinal case studies and (b) formulation of 12 principles for design of creativity support tools.Creativity support tools is a research topic with high risk but potentially very high payoff. The goal is to develop improved software and user interfaces that empower users to be not only more productive but also more innovative. Potential users include software and other engineers, diverse scientists, product and graphic designers, architects, educators, students, and many others. Enhanced interfaces could enable more effective searching of intellectual resources, improved collaboration among teams, and more rapid discovery processes. These advanced interfaces should also provide potent support in hypothesis formation, speedier evaluation of alternatives, improved understanding through visualization, and better dissemination of results. For creative endeavors that require composition of novel artifacts (e.g., computer programs, scientific papers, engineering diagrams, symphonies, artwork), enhanced interfaces could facilitate exploration of alternatives, prevent unproductive choices, and enable easy backtracking. This U.S. National Science Foundation sponsored workshop brought together 25 research leaders and graduate students to share experiences, identify opportunities, and formulate research challenges. Two key outcomes emerged: (a) encouragement to evaluate creativity support tools through multidimensional in-depth longitudinal case studies and (b) formulation of 12 principles for design of creativity support tools.

Cross-Language Access to Recorded Speech in the MALACH Project - Oard, Douglas; Demner-Fushman,Dina; Hajič,Jan; Ramabhadran,Bhuvana; Gustman,Samuel; Byrne,William; Soergel,Dagobert; Dorr, Bonnie J; Resnik, Philip; Picheny,Michael (Text, Speech and DialogueText, Speech and Dialogue, 2006)
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.

Development of a Large-Scale Integrated Neurocognitive Architecture - Part 2: Design and Architecture - Reggia, James A.; Tagamets,M.; Contreras-Vidal,J.; Jacobs, David W.; Weems,S.; Naqvi,W.; Winder,R.; Chabuk,T.; Jung,J.; Yang,C. (Instititue for Advanced Computer Studies, Univ of Maryland, College Park, 2006)
In Part 1 of this report, we outlined a framework for creating an intelligent agentbased upon modeling the large-scale functionality of the human brain. Building on those results, we begin Part 2 by specifying the behavioral requirements of a large-scale neurocognitive architecture. The core of our long-term approach remains focused on creating a network of neuromorphic regions that provide the mechanisms needed to meet these requirements. However, for the short term of the next few years, it is likely that optimal results will be obtained by using a hybrid design that also includes symbolic methods from AI/cognitive science and control processes from the field of artificial life. We accordingly propose a three-tiered architecture that integrates these different methods, and describe an ongoing computational study of a prototype 'mini-Roboscout' based on this architecture. We also examine the implications of some non-standard computational methods for developing a neurocognitive agent. This examination included computational experiments assessing the effectiveness of genetic programming as a design tool for recurrent neural networks for sequence processing, and experiments measuring the speed-up obtained for adaptive neural networks when they are executed on a graphical processing unit (GPU) rather than a conventional CPU. We conclude that the implementation of a large-scale neurocognitive architecture is feasible, and outline a roadmap for achieving this goal.
Keywords: Technical Report

Development of a Large-Scale Integrated Neurocognitive Architecture Part 1: Conceptual Framework - Reggia, James A.; Tagamets,Malle; Contreras-Vidal,Jose; Weems,Scott; Jacobs, David W.; Winder,Ransom; Chabuk,Timur (Instititue for Advanced Computer Studies, Univ of Maryland, College Park, 2006)
The idea of creating a general purpose machine intelligence that capturesmany of the features of human cognition goes back at least to the earliest days of artificial intelligence and neural computation. In spite of more than a half-century of research on this issue, there is currently no existing approach to machine intelligence that comes close to providing a powerful, general-purpose human-level intelligence. However, substantial progress made during recent years in neural computation, high performance computing, neuroscience and cognitive science suggests that a renewed effort to produce a general purpose and adaptive machine intelligence is timely, likely to yield qualitatively more powerful approaches to machine intelligence than those currently existing, and certain to lead to substantial progress in cognitive science, AI and neural computation. In this report, we outline a conceptual framework for the long-term development of a large-scale machine intelligence that is based on the modular organization, dynamics and plasticity of the human brain. Some basic design principles are presented along with a review of some of the relevant existing knowledge about the neurobiological basis of cognition. Three intermediate-scale prototypes for parts of a larger system are successfully implemented, providing support for the effectiveness of several of the principles in our framework. We conclude that a human-competitive neuromorphic system for machine intelligence is a viable long- term goal, but that for the short term, substantial integration with more standard symbolic methods as well as substantial research will be needed to make this goal achievable.
Keywords: Technical Report

Dissemination of compressed historical information in sensor networks - Deligiannakis,Antonios; Kotidis,Yannis; Roussopoulos, Nick (The VLDB JournalThe VLDB Journal, 2006)

Dwarf cube architecture for reducing storage sizes of multidimensional data - Roussopoulos, Nick; Sismanis,John; Deligiannakis,Antonios (2006)
The invention relates to data warehouses and the ability to create and maintain data cubes of multi-dimensional data. More specifically, the invention pertains to data cube architectures that permit significant reduction of storage, exhibit very efficient retrieval and provide a very efficient incremental update of the data cubes.

Edge Suppression by Gradient Field Transformation Using Cross-Projection Tensors - Agrawal,A.; Raskar, R.; Chellapa, Rama (Computer Vision and Pattern Recognition, 2006 IEEE Computer Society Conference on, 2006)
We propose a new technique for edge-suppressing operations on images. We introduce cross projection tensors to achieve affine transformations of gradient fields. We use these tensors, for example, to remove edges in one image based on the edge-information in a second image. Traditionally, edge suppression is achieved by setting image gradients to zero based on thresholds. A common application is in the Retinex problem, where the illumination map is recovered by suppressing the reflectance edges, assuming it is slowly varying. We present a class of problems where edge-suppression can be a useful tool. These problems involve analyzing images of the same scene under variable illumination. Instead of resetting gradients, the key idea in our approach is to derive local tensors using one image and to transform the gradient field of another image using them. Reconstructed image from the modified gradient field shows suppressed edges or textures at the corresponding locations. All operations are local and our approach does not require any global analysis. We demonstrate the algorithm in the context of several applications such as (a) recovering the foreground layer under varying illumination, (b) estimating intrinsic images in non-Lambertian scenes, (c) removing shadows from color images and obtaining the illumination map, and (d) removing glass reflections.

The effect of building block construction on the behavior of the ga in dynamic environments: A case study using the shaky ladder hyperplane-defined functions - Rand, William; Riolo,R (Applications of Evolutionary Computing, 2006)
The shaky ladder hyperplane-defined functions (sl-hdf’s) are a test suite utilized for exploring the behavior of the genetic algorithm (GA) in dynamic environments. We present three ways of constructing the sl-hdf’s by manipulating the way building blocks are constructed, combined, and changed. We examine the effect of the length of elementary building blocks used to create higher building blocks, and the way in which those building blocks are combined. We show that the effects of building block construction on the behavior of the GA are complex. Our results suggest that construction routines which increase the roughness of the changes in the environment allow the GA to perform better by preventing premature convergence. Moreover, short length elementary building blocks permit early rapid progress.

The effect of crossover on the behavior of the GA in dynamic environments: a case study using the shaky ladder hyperplane-defined functions - Rand, William; Riolo,Rick; Holland,John H. (Proceedings of the 8th annual conference on Genetic and evolutionary computation, 2006)
One argument as to why the hyperplane-defined functions (hdf's) are a good testbed for the genetic algorithm (GA) is that the hdf's are built in the same way that the GA works. In this paper we test that hypothesis in a new setting by exploring the GA on a subset of the hdf's which are dynamic---the shaky ladder hyperplane-defined functions (sl-hdf's). In doing so we gain insight into how the GA makes use of crossover during its traversal of the sl-hdf search space. We begin this paper by explaining the sl-hdf's. We then conduct a series of experiments with various crossover rates and various rates of environmental change. Our results show that the GA performs better with than without crossover in dynamic environments. Though these results have been shown on some static functions in the past, they are re-confirmed and expanded here for a new type of function (the hdf) and a new type of environment (dynamic environments). Moreover we show that crossover is even more beneficial in dynamic environments than it is in static environments. We discuss how these results can be used to develop a richer knowledge about the use of building blocks by the GA.
Keywords: crossover; dynamic environments; Genetic algorithms; hyperplane-defined functions; search

An Efficient Computational Method for Predicting Rotational Diffusion Tensors of Globular Proteins Using an Ellipsoid Representation - Ryabov,Yaroslav E.; Geraghty,Charles; Varshney, Amitabh; Fushman, David (Journal of the American Chemical Society, 2006)
We propose a new computational method for predicting rotational diffusion properties of proteins in solution. The method is based on the idea of representing protein surface as an ellipsoid shell. In contrast to other existing approaches this method uses principal component analysis of protein surface coordinates, which results in a substantial increase in the computational efficiency of the method. Direct comparison with the experimental data as well as with the recent computational approach (Garcia de la Torre; et al. J. Magn. Reson. 2000, B147, 138?146), based on representation of protein surface as a set of small spherical friction elements, shows that the method proposed here reproduces experimental data with at least the same level of accuracy and precision as the other approach, while being approximately 500 times faster. Using the new method we investigated the effect of hydration layer and protein surface topography on the rotational diffusion properties of a protein. We found that a hydration layer constructed of approximately one monolayer of water molecules smoothens the protein surface and effectively doubles the overall tumbling time. We also calculated the rotational diffusion tensors for a set of 841 protein structures representing the known protein folds. Our analysis suggests that an anisotropic rotational diffusion model is generally required for NMR relaxation data analysis in single-domain proteins, and that the axially symmetric model could be sufficient for these purposes in approximately half of the proteins.We propose a new computational method for predicting rotational diffusion properties of proteins in solution. The method is based on the idea of representing protein surface as an ellipsoid shell. In contrast to other existing approaches this method uses principal component analysis of protein surface coordinates, which results in a substantial increase in the computational efficiency of the method. Direct comparison with the experimental data as well as with the recent computational approach (Garcia de la Torre; et al. J. Magn. Reson. 2000, B147, 138?146), based on representation of protein surface as a set of small spherical friction elements, shows that the method proposed here reproduces experimental data with at least the same level of accuracy and precision as the other approach, while being approximately 500 times faster. Using the new method we investigated the effect of hydration layer and protein surface topography on the rotational diffusion properties of a protein. We found that a hydration layer constructed of approximately one monolayer of water molecules smoothens the protein surface and effectively doubles the overall tumbling time. We also calculated the rotational diffusion tensors for a set of 841 protein structures representing the known protein folds. Our analysis suggests that an anisotropic rotational diffusion model is generally required for NMR relaxation data analysis in single-domain proteins, and that the axially symmetric model could be sufficient for these purposes in approximately half of the proteins.

Efficient simulation of critical synchronous dataflow graphs - Hsu,C. J; Ramasubbu,S.; Ko,M. Y; Pino,J. L; Bhattacharyya, Shuvra S. (Proceedings of the 43rd annual Design Automation Conference, 2006)

Evolutionary design of neural network architectures using a descriptive encoding language - Jung,J. Y; Reggia, James A. (Evolutionary Computation, IEEE Transactions on, 2006)

Exploring erotics in Emily Dickinson's correspondence with text mining and visual interfaces - Plaisant, Catherine; Rose,James; Yu,Bei; Auvil,Loretta; Kirschenbaum,Matthew G.; Smith,Martha Nell; Clement,Tanya; Lord,Greg (Proceedings of the 6th ACM/IEEE-CS joint conference on Digital libraries, 2006)
This paper describes a system to support humanities scholars in their interpretation of literary work. It presents a user interface and web architecture that integrates text mining, a graphical user interface and visualization, while attempting to remain easy to use by non specialists. Users can interactively read and rate documents found in a digital libraries collection, prepare training sets, review results of classification algorithms and explore possible indicators and explanations. Initial evaluation steps suggest that there is a rationale for "provocational" text mining in literary interpretation.
Keywords: case studies; humanities; literary criticism; text mining; user interface; Visualization

Face Verification Across Age Progression - Ramanathan,N.; Chellapa, Rama (Image Processing, IEEE Transactions on, 2006)
Human faces undergo considerable amounts of variations with aging. While face recognition systems have been proven to be sensitive to factors such as illumination and pose, their sensitivity to facial aging effects is yet to be studied. How does age progression affect the similarity between a pair of face images of an individual? What is the confidence associated with establishing the identity between a pair of age separated face images? In this paper, we develop a Bayesian age difference classifier that classifies face images of individuals based on age differences and performs face verification across age progression. Further, we study the similarity of faces across age progression. Since age separated face images invariably differ in illumination and pose, we propose preprocessing methods for minimizing such variations. Experimental results using a database comprising of pairs of face images that were retrieved from the passports of 465 individuals are presented. The verification system for faces separated by as many as nine years, attains an equal error rate of 8.5%
Keywords: age; Aging; Bayesian; classification; classification; face; classifier; age; difference; effects; preprocessing; Face; image; images; error; methods; Bayes; methods; error; progression; age; rate; face; recognition; recognition; image; separated; statistics; face; systems; face; verification; facial

Fast optimal bandwidth selection for kernel density estimation - Raykar,V.C.; Duraiswami, Ramani (Proceedings of the sixth SIAM International Conference on Data Mining, 2006)
We propose a computationally efficient ϵ−exact approxima-tion algorithm for univariate Gaussian kernel based density derivative estimation that reduces the computational com- plexity from O(MN) to linear O(N +M). We apply the pro- cedure to estimate the optimal bandwidth for kernel density estimation. We demonstrate the speedup achieved on this problem using the ”solve-the-equation plug-in” method, and on exploratory projection pursuit techniques.

Finding Gait in Space and Time - Yang Ran; Chellapa, Rama; Qinfen Zheng (Pattern Recognition, 2006. ICPR 2006. 18th International Conference on, 2006)
We describe an approach to characterize the signatures generated by walking humans in spatio-temporal domain. To describe the computational model for this periodic pattern, we take the mathematical theory of geometry group theory, which is widely used in crystallographic structure research. Both empirical and theoretical analyses prove that spatio-temporal helical patterns generated by legs belong to the Frieze Groups because they can be characterized by a repetitive motif along the direction of walking. The theory is applied to an automatic detection-and-tracking system capable of counting heads and handling occlusion by recognizing such patterns. Experimental results for videos acquired from both static and moving ground sensors are presented. Our algorithm demonstrates robustness to non-rigid human deformation as well as background clutter
Keywords: analysis; analysis; geometry; analysis; group; characterization; occlusion; counting; mathematical; detection-and-tracking; domain; spatiotemporal; Frieze; group; groups; automatic; handling; pattern; helical; humans; computer; MOTION; pattern; spatiotemporal; patterns; walking; recognition; periodic; signature; system; computer; theory; head; theory; image; theory; motion; vision; gait

First Steps Toward an Electronic Field Guide for Plants - Haibin,Gaurav Agarwal; Agarwal,Gaurav; Ling,Haibin; Jacobs, David W.; Shirdhonkar,Sameer; Kress,W. John; Russell,Rusty; Belhumeur,Peter; Dixit,An; Feiner,Steve; Mahajan,Dhruv; Sunkavalli,Kalyan; et al. (Taxon, 2006)
this paper, we will describe our progress towards building a digital collection of the Smithsonian's type specimens, developing recognition algorithms that can match an image of a leaf to the species of plant from which it comes, and designing user interfaces for interacting with an electronic field guide. To start, we are developing a prototype electronic field guide for the flora of Plummers Island, a small, well-studied island in the Potomac River. This prototype system contains multiple images for each of about 130 species of plants on the island, and should soon grow to cover all 200+ species currently recorded (Shetler et al., 2005). Images of full specimens are available, as well as images of isolated leaves of each species. A zoomable user interface allows a user to browse these images, zooming in on ones of interest. Visual recognition algorithms assist a botanist in locating the specimens that are most relevant to identify the species of a plant. The system currently runs on a small hand-held computer. We will describe the components of this prototype, and also describe some of the future challenges we anticipate if we are to provide botanists in the field with all the resources that are now currently available in the world's museums and herbaria. Type Specimen Digital Collection The first challenge in producing our electronic field guide is to create a digital collection covering all of the Smithsonian's 85,000 vascular plant type specimens. For each type specimen, the database should eventually include systematically acquired high-resolution digital images of the specimen, textual descriptions, links to decision trees, images of live plants, and 3D models. Figure 1: On the left, our set-up at the Smithsonian for digitally photographing type specimens. On the...

Fourier analysis of multigrid for a model two-dimensional convection-diffusion equation - Elman, Howard; Ramage, A. (BIT Numerical Mathematics, 2006)

The Function Space of an Activity - Veeraraghavan,A.; Chellapa, Rama; Roy-Chowdhury, A.K. (Computer Vision and Pattern Recognition, 2006 IEEE Computer Society Conference on, 2006)
An activity consists of an actor performing a series of actions in a pre-defined temporal order. An action is an individual atomic unit of an activity. Different instances of the same activity may consist of varying relative speeds at which the various actions are executed, in addition to other intra- and inter- person variabilities. Most existing algorithms for activity recognition are not very robust to intra- and inter-personal changes of the same activity, and are extremely sensitive to warping of the temporal axis due to variations in speed profile. In this paper, we provide a systematic approach to learn the nature of such time warps while simultaneously allowing for the variations in descriptors for actions. For each activity we learn an #145;average #146; sequence that we denote as the nominal activity trajectory. We also learn a function space of time warpings for each activity separately. The model can be used to learn individualspecific warping patterns so that it may also be used for activity based person identification. The proposed model leads us to algorithms for learning a model for each activity, clustering activity sequences and activity recognition that are robust to temporal, intra- and inter-person variations. We provide experimental results using two datasets.

Functional Analysis of Hes-1 in Preadipocytes - Ross,David A; Hannenhalli, Sridhar; Tobias,John W; Cooch,Neil; Shiekhattar,Ramin; Kadesch,Tom (Molecular EndocrinologyMolecular Endocrinology, 2006)
Notch signaling blocks differentiation of 3T3-L1 preadipocytes, and this can be mimicked by constitutive expression of the Notch target gene Hes-1. Although considered initially to function only as a repressor, recent evidence indicates that Hes-1 can also activate transcription. We show here that the domains of Hes-1 needed to block adipogenesis coincide with those necessary for transcriptional repression. HRT1, another basic-helix-loop-helix protein and potential Hes-1 partner, was also induced by Notch in 3T3-L1 cells but did not block adipogenesis, suggesting that Hes-1 functions primarily as a homodimer or possibly as a heterodimer with an unknown partner. Purification of Hes-1 identified the Groucho/transducin-like enhancer of split family of corepressors as the only significant Hes-1 interacting proteins in vivo. An evaluation of global gene expression in preadipocytes identified approximately 200 Hes-1-responsive genes comprising roughly equal numbers of up-regulated and down-regulated genes. However, promoter analyses indicated that the down-regulated genes were significantly more likely to contain Hes-1 binding sites, indicating that Hes-1 is more likely to repress transcription of its direct targets. We conclude that Notch most likely blocks adipogenesis through the induction of Hes-1 homodimers, which repress transcription of key target genes.