iOpener Workbench: Tools for rapid understanding of scientific literature - Dunne,C.; Shneiderman, Ben; Dorr, Bonnie J; Klavans,J. (Human-Computer Interaction Lab 27th Annual Symposium, University of Maryland, College Park, MD, 2010)

On k-Column Sparse Packing Programs - Bansal,Nikhil; Korula,Nitish; Nagarajan,Viswanath; Srinivasan, Aravind (Integer Programming and Combinatorial OptimizationInteger Programming and Combinatorial Optimization, 2010)
We consider the class of packing integer programs (PIPs) that are column sparse, where there is a specified upper bound k on the number of constraints that each variable appears in. We give an improved (ek + o(k))-approximation algorithm for k-column sparse PIPs. Our algorithm is based on a linear programming relaxation, and involves randomized rounding combined with alteration. We also show that the integrality gap of our LP relaxation is at least 2k − 1; it is known that even special cases of k-column sparse PIPs are (klogk)-hard to approximate.We generalize our result to the case of maximizing monotone submodular functions over k-column sparse packing constraints, and obtain an e2ke−1+o(k) -approximation algorithm. In obtaining this result, we prove a new property of submodular functions that generalizes the fractionally subadditive property, which might be of independent interest.

Lineage processing over correlated probabilistic databases - Kanagal,Bhargav; Deshpande, Amol (Proceedings of the 2010 international conference on Management of data, 2010)
In this paper, we address the problem of scalably evaluating conjunctive queries over correlated probabilistic databases containing tuple or attribute uncertainties. Like previous work, we adopt a two-phase approach where we first compute lineages of the output tuples, and then compute the probabilities of the lineage formulas. However unlike previous work, we allow for arbitrary and complex correlations to be present in the data, captured via a forest of junction trees. We observe that evaluating even read-once (tree structured) lineages (e.g., those generated by hierarchical conjunctive queries), polynomially computable over tuple independent probabilistic databases, is #P-complete for lightly correlated probabilistic databases like Markov sequences. We characterize the complexity of exact computation of the probability of the lineage formula on a correlated database using a parameter called lwidth (analogous to the notion of treewidth). For lineages that result in low lwidth, we compute exact probabilities using a novel message passing algorithm, and for lineages that induce large lwidths, we develop approximate Monte Carlo algorithms to estimate the result probabilities. We scale our algorithms to very large correlated probabilistic databases using the previously proposed INDSEP data structure. To mitigate the complexity of lineage evaluation, we develop optimization techniques to process a batch of lineages by sharing computation across formulas, and to exploit any independence relationships that may exist in the data. Our experimental study illustrates the benefits of using our algorithms for processing lineage formulas over correlated probabilistic databases.
Keywords: conjunctive queries; Indexing; junction trees; lineage; Probabilistic databases

Making sense of archived e‐mail: Exploring the Enron collection with NetLens - Kang,Hyunmo; Plaisant, Catherine; Elsayed,Tamer; Oard, Douglas (Journal of the American Society for Information Science and Technology, 2010)
Informal communications media pose new challenges for information-systems design, but the nature of informal interaction offers new opportunities as well. This paper describes NetLens-E-mail, a system designed to support exploration of the content-actor network in large e-mail collections. Unique features of NetLens-E-mail include close coupling of orientation, specification, restriction, and expansion, and introduction and incorporation of a novel capability for iterative projection between content and actor networks within the same collection. Scenarios are presented to illustrate the intended employment of NetLens-E-mail, and design walkthroughs with two domain experts provide an initial basis for assessment of the suitability of the design by scholars and analysts.

Mesh saliency and human eye fixations - Kim,Youngmin; Varshney, Amitabh; Jacobs, David W.; Guimbretière,François (ACM Transactions on Applied Perception (TAP), 2010)
Mesh saliency has been proposed as a computational model of perceptual importance for meshes, and it has been used in graphics for abstraction, simplification, segmentation, illumination, rendering, and illustration. Even though this technique is inspired by models of low-level human vision, it has not yet been validated with respect to human performance. Here, we present a user study that compares the previous mesh saliency approaches with human eye movements. To quantify the correlation between mesh saliency and fixation locations for 3D rendered images, we introduce the normalized chance-adjusted saliency by improving the previous chance-adjusted saliency measure. Our results show that the current computational model of mesh saliency can model human eye movements significantly better than a purely random model or a curvature-based model.
Keywords: eye-tracker; mesh saliency; Visual perception

Mixing type checking and symbolic execution - Khoo,Y.P.; Chang,B.Y.E.; Foster, Jeffrey S. (ACM SIGPLAN Notices, 2010)

Natural language annotations for the Semantic Web - Katz,B.; Jimmy Lin; Quan,D. (On the Move to Meaningful Internet Systems 2002: CoopIS, DOA, and ODBASE, 2010)

New forms of Human-Computer Interaction for Visualizing Information - Reiterer,H.; Kerren,A.; Plaisant, Catherine; Stasko,J.T. (Information Visualization, 2010)
The Graphical User Interface (GUI) – although developed in research laboratories in the late 1970s – is still the dominant interaction paradigm in Information Visualization. We propose a new interaction paradigm called Blended Interaction. It combines ideas of Embodied Cognition, Multimodal Interaction, Reality-Based Interaction & Ubiquitous Computing. This is intended to stress that a single increase in the reality aspect of the interaction cannot go far enough. The particular challenge – and from the user's standpoint, the key advantage – lies in a meaningful marriage between the tested real-world options and the digital world. As a minimum this marriage must exist on the levels of the interaction, communication, of the way we solve problems with conventional tools (workflows), and of the design of the space or the architecture of buildings and places. The digital world often offers entirely new possibilities and takes the form of interactive devices of various shapes but also of intelligent everyday objects (e.g. the 'Internet of things'). In our view, interaction concepts can indeed offer a new quality of interaction, but only when the design of the interaction includes all these domains at the same time and with equal weighting. We test the suitability of our ideas of Blended Interaction concepts by using specific application examples that are being worked on as part of current research projects. Our experiences show that this new interaction paradigm has also great potential for interacting with visualization. For example, we have developed multi-touch scatter plots & facet maps for tangible user interfaces supporting the searching & browsing in Digital Libraries. We have embedded different visualizations into a Zoomable Object-oriented Information Landscape (ZOIL), which supports our vision of using visualizations on different displays of different size at the same time. We have developed specific kind of search tokens that supports collaborative search activities. For example, we try to address the following research questions: * How can future interactive InfoVis tools look like, especially in the light of the idea Blended Interaction? * How can future interactive InfoVis tools benefit from Multi-Displays & Multimodal environments used by Multiple Users? * What are the specific design requirements for multi-touch visualizations? * How can we support the collaborative use visualization tools?

A new framework for efficient password-based authenticated key exchange - Groce,Adam; Katz, Jonathan (Proceedings of the 17th ACM conference on Computer and communications security, 2010)
Protocols for password-based authenticated key exchange (PAKE) allow two users who share only a short, low-entropy password to agree on a cryptographically strong session key. The challenge in designing such protocols is that they must be immune to off-line dictionary attacks in which an eavesdropping adversary exhaustively enumerates the dictionary of likely passwords in an attempt to match a password to the set of observed transcripts. To date, few general frameworks for constructing PAKE protocols in the standard model are known. Here, we abstract and generalize a protocol by Jiang and Gong to give a new methodology for realizing PAKE without random oracles, in the common reference string model. In addition to giving a new approach to the problem, the resulting construction off ers several advantages over prior work. We also describe an extension of our protocol that is secure within the universal composability (UC) framework and, when instantiated using El Gamal encryption, is more efficient than a previous protocol of Canetti et al.
Keywords: exchange; key; password-based

A New Framework for Password-Based Authenticated Key Exchange - Groce,Adam; Katz, Jonathan (ACM CCCS 2010, 2010)
Protocols for password-based authenticated key exchange (PAKE) allowtwo users who share only a short, low-entropy password to agree on a cryptographically strong session key. The challenge in designing such protocols is that they must be immune to off-line dictionary attacks in which an eavesdropping adversary exhaustively enumerates the dictionary of likely passwords in an attempt to match a password to the set of observed transcripts. To date, few general frameworks for constructing PAKE protocols in the standard model are known. Here, we abstract and generalize a protocol by Jiang and Gong to give a new methodology for realizing PAKE without random oracles, in the common reference string model. In addition to giving a new approach to the problem, the resulting construction offers several advantages over prior work. We also describe an extension of our protocol that is secure within the universal composability~(UC) framework and, when instantiated using El Gamal encryption, is more efficient than a previous protocol of Canetti et al.
Keywords: Cryptographic protocols; password-based key exchange

Nfsight: netflow-based network awareness tool - Berthier,R.; Michel Cukier; Hiltunen,M.; Kormann,D.; Vesonder,G.; Sheleheda,D. (2010)
Network awareness is highly critical for network and se-curity administrators. It enables informed planning and management of network resources, as well as detection and a comprehensive understanding of malicious activ- ity. It requires a set of tools to efficiently collect, process, and represent network data. While many such tools al- ready exist, there is no flexible and practical solution for visualizing network activity at various granularities, and quickly gaining insights about the status of network as- sets. To address this issue, we developed Nfsight, a Net- Flow processing and visualization application designed to offer a comprehensive network awareness solution. Nfsight constructs bidirectional flows out of the unidi- rectional NetFlow flows and leverages these bidirectional flows to provide client/server identification and intrusion detection capabilities. We present in this paper the in- ternal architecture of Nfsight, the evaluation of the ser- vice, and intrusion detection algorithms. We illustrate the contributions of Nfsight through several case studies conducted by security administrators on a large univer- sity network.

Overcoming the Hole in the Bucket: Public-Key Cryptography Resilient to Continual Memory Leakage - Brakerski,Z.; Kalai,Y.T.; Katz, Jonathan; Vaikuntanathan,V. (Foundations of Computer Science (FOCS), 2010 51st Annual IEEE Symposium on, 2010)
In recent years, there has been a major effort to design cryptographic schemes that remain secure even when arbitrary information about the secret key is leaked (e.g., via side-channel attacks). We explore the possibility of achieving security under emphcontinual leakage from the emphentire secret key by designing schemes in which the secret key is updated over time. In this model, we construct public-key encryption schemes, digital signatures, and identity-based encryption schemes that remain secure even if an attacker can leak a constant fraction of the secret memory (including the secret key) in each time period between key updates. We also consider attackers who may probe the secret memory during the updates themselves. We stress that we allow unrestricted leakage, without the assumption that “only computation leaks information”. Prior to this work, constructions of public-key encryption schemes secure under continual leakage were not known even under this assumption.
Keywords: continual; cryptography; cryptography; public-key; encryption; key; key; digital; leakage; cryptographic; memory; schemes; digital; schemes; public-key; schemes; secret; signatures; identity-based; signatures; public

Parallel and concurrent security of the HB and HB+ protocols - Katz, Jonathan; Shin,J. S; Smith,A. (Journal of cryptology, 2010)
Hopper and Blum (Asiacrypt 2001) and Juels and Weis (Crypto 2005) recently proposed two shared-key authentication protocols—HB and HB+, respectively—whose extremely low computational cost makes them attractive for low-cost devices such as radio-frequency identification (RFID) tags. The security of these protocols is based on the conjectured hardness of the “learning parity with noise” (LPN) problem, which is equivalent to the problem of decoding random binary linear codes. The HB protocol is proven secure against a passive (eavesdropping) adversary, while the HB+ protocol is proven secure against active attacks.

Partial fairness in secure two-party computation - Gordon,S.; Katz, Jonathan (Advances in Cryptology–EUROCRYPT 2010, 2010)
A seminal result of Cleve (STOC ’86) is that complete fairness is impossible to achieve in two-party computation. In light of this, various techniques for obtaining partial fairness have been suggested in the literature. We propose a definition of partial fairness within the standard real-/ideal-world paradigm that addresses deficiencies of prior definitions. We also show broad feasibility results with respect to our definition: partial fairness is possible for any (randomized) functionality f:X ×Y →Z 1 ×Z 2 at least one of whose domains or ranges is polynomial in size. Our protocols are always private, and when one of the domains has polynomial size our protocols also simultaneously achieve the usual notion of security with abort. In contrast to some prior work, we rely on standard assumptions only.We also show that, as far as general feasibility is concerned, our results are optimal (with respect to our definition).

Perturbing the Ubiquitin Pathway Reveals How Mitosis Is Hijacked to Denucleate and Regulate Cell Proliferation and Differentiation In Vivo - Caceres,Andrea; Shang,Fu; Wawrousek,Eric; Liu,Qing; Avidan,Orna; Cvekl,Ales; Yang,Ying; Haririnia,Aydin; Storaska,Andrew; Fushman, David; Kuszak,Jer; Dudek,Edward; et al. (PLoS ONEPLoS ONE, 2010)
BackgroundThe eye lens presents a unique opportunity to explore roles for specific molecules in cell proliferation, differentiation and development because cells remain in place throughout life and, like red blood cells and keratinocytes, they go through the most extreme differentiation, including removal of nuclei and cessation of protein synthesis. Ubiquitination controls many critical cellular processes, most of which require specific lysines on ubiquitin (Ub). Of the 7 lysines (K) least is known about effects of modification of K6. Methodology and Principal Findings We replaced K6 with tryptophan (W) because K6 is the most readily modified K and W is the most structurally similar residue to biotin. The backbone of K6W-Ub is indistinguishable from that of Wt-Ub. K6W-Ub is effectively conjugated and deconjugated but the conjugates are not degraded via the ubiquitin proteasome pathways (UPP). Expression of K6W-ubiquitin in the lens and lens cells results in accumulation of intracellular aggregates and also slows cell proliferation and the differentiation program, including expression of lens specific proteins, differentiation of epithelial cells into fibers, achieving proper fiber cell morphology, and removal of nuclei. The latter is critical for transparency, but the mechanism by which cell nuclei are removed has remained an age old enigma. This was also solved by expressing K6W-Ub. p27kip, a UPP substrate accumulates in lenses which express K6W-Ub. This precludes phosphorylation of nuclear lamin by the mitotic kinase, a prerequisite for disassembly of the nuclear membrane. Thus the nucleus remains intact and DNAseIIβ neither gains entry to the nucleus nor degrades the DNA. These results could not be obtained using chemical proteasome inhibitors that cannot be directed to specific tissues. Conclusions and Significance K6W-Ub provides a novel, genetic means to study functions of the UPP because it can be targeted to specific cells and tissues. A fully functional UPP is required to execute most stages of lens differentiation, specifically removal of cell nuclei. In the absence of a functional UPP, small aggregate prone, cataractous lenses are formed.

The power of protein interaction networks for associating genes with diseases - Navlakha,S.; Kingsford, Carl (Bioinformatics, 2010)

Public-Key Cryptography - Katz, Jonathan (Handbook of Information and Communication Security, 2010)
Public-key cryptography ensures both secrecy and authenticity of communication using public-key encryption schemes and digital signatures, respectively. Following a brief introduction to the public-key setting (and a comparison with the classical symmetric-key setting), we present rigorous definitions of security for public-key encryption and digital signature schemes, introduce some number-theoretic primitives used in their construction, and describe various practical instantiations.

Rapid prototyping for digital signal processing systems using Parameterized Synchronous Dataflow graphs - Wu, Hsiang-Huang; Kee, Hojin; Sane, N.; Plishker,W.; Bhattacharyya, Shuvra S. (2010 21st IEEE International Symposium on Rapid System Prototyping (RSP), 2010)
Parameterized Synchronous Dataflow (PSDF) has been used previously for abstract scheduling and as a model for architecting embedded software and FPGA implementations. PSDF has been shown to be attractive for these purposes due to its support for flexible dynamic reconfiguration, and efficient quasi-static scheduling. To apply PSDF techniques more deeply into the design flow, support for comprehensive functional simulation and efficient hardware mapping is important. By building on the DIF (Dataflow Interchange Format), which is a design language and associated software package for developing and experimenting with dataflow-based design techniques for signal processing systems, we have developed a tool for functional simulation of PSDF specifications. This simulation tool allows designers to model applications in PSDF and simulate their functionality, including use of the dynamic parameter reconfiguration capabilities offered by PSDF. Based on this simulation tool, we also present a systematic design methodology for applying PSDF to the design and implementation of digital signal processing systems, with emphasis on FPGA-based systems for signal processing. We demonstrate capabilities for rapid and accurate prototyping offered by our proposed design methodology, along with its novel support for PSDF-based FPGA system implementation.
Keywords: abstract scheduling; Computational modeling; Computer architecture; data flow graphs; dataflow based design; dataflow interchange format; design flow; design language; Digital signal processing; digital signal processing systems; dynamic parameter reconfiguration; Dynamic scheduling; efficient hardware mapping; efficient quasistatic scheduling; Embedded software; embedded systems; Field programmable gate arrays; flexible dynamic reconfiguration; FPGA based systems; FPGA implementations; functional simulation; Hardware; parameterized synchronous dataflow graphs; rapid prototyping; Schedules; scheduling; semantics; simulation tool; software package; systematic design methodology

REPORTS AI Theory and Practice: A Discussion on Hard Challenges and Opportunities Ahead - Horvitz,E.; Getoor, Lise; Guestrin,C.; Hendler,J.; Kautz,H.; Konstan,J.; Subramanian,D.; Wellman,M. (AI Magazine, 2010)

Resource-Aware Compiler Prefetching for Many-Cores - Caragea,G.C.; Tzannes,A.; Keceli,F.; Barua,R.; Vishkin, Uzi (Parallel and Distributed Computing (ISPDC), 2010 Ninth International Symposium on, 2010)
Super-scalar, out-of-order processors that can have tens of read and write requests in the execution window place significant demands on Memory Level Parallelism (MLP). Multi-and many-cores with shared parallel caches further increase MLP demand. Current cache hierarchies however have been unable to keep up with this trend, with modern designs allowing only 4-16 concurrent cache misses. This disconnect is exacerbated by recent highly parallel architectures (e.g. GPUs) where power and area per-core budget favor lighter cores with less resources. Support for hardware and software prefetch increase MLP pressure since these techniques overlap multiple memory requests with existing computation. In this paper, we propose and evaluate a novel Resource-Aware Prefetching (RAP) compiler algorithm that is aware of the number of simultaneous prefetches supported, and optimized for the same. We show that in situations where not enough resources are available to issue prefetch instructions for all references in a loop, it is more beneficial to decrease the prefetch distance and prefetch for as many references as possible, rather than use a fixed prefetched distance and skip prefetching for some references, as in current approaches. We implemented our algorithm in a GCC-derived compiler and evaluated its performance using an emerging fine-grained many-core architecture. Our results show that the RAP algorithm outperforms a well-known loop prefetching algorithm by up to 40.15% and the state-of-the art GCC implementation by up to 34.79%. Moreover, we compare the RAP algorithm with a simple hardware prefetching mechanism, and show improvements of up to 24.61%.
Keywords: algorithm; memory; architecture; hardware-software; architectures; parallel; architectures; resource; aware; caches; super-scalar; compiler; compiler; Multicore; compilers; parallel; GCC-derived; level; management; many-core; memories; storage; out-of-order; Parallel; parallelism; parallel; prefetch; loop; prefetching; prefetching; shared; processor; fine-grained; processors; multiprocessing; systems; optimising

Scalable representation of dataflow graph structures using topological patterns - Sane, N.; Kee, Hojin; Seetharaman, G.; Bhattacharyya, Shuvra S. (2010 IEEE Workshop on Signal Processing Systems (SIPS), 2010)
Tools for designing signal processing systems with their semantic foundation in dataflow modeling often use high-level graphical user interface (GUI) or text based languages that allow specifying applications as directed graphs. Such graphical representations serve as an initial reference point for further analysis and optimizations that lead to platform-specific implementations. For large-scale applications, the underlying graphs often consist of smaller substructures that repeat multiple times. To enable more concise representation and direct analysis of such substructures in the context of high level DSP specification languages and design tools, we develop the modeling concept of topological patterns, and propose ways for supporting this concept in a high-level language. We augment the DIF language - a language for specifying DSP-oriented dataflow graphs - with constructs for supporting topological patterns, and we show how topological patterns can be effective in various aspects of embedded signal processing design flows using specific application examples.
Keywords: arrays; data flow graphs; Dataflow graphs; DIF language; Digital signal processing; directed graphs; DSP specification languages; embedded signal processing design flows; embedded systems; Field programmable gate arrays; graphical user interface; Graphical user interfaces; High-level languages; modelbased design; optimisation; optimizations; scalable dataflow graph structures representation; semantics; Signal processing; Signal processing systems; Specification languages; text based languages; Topological patterns; Topology; Transform coding

Secure network coding over the integers - Gennaro,R.; Katz, Jonathan; Krawczyk,H.; Rabin,T. (Public Key Cryptography–PKC 2010, 2010)
Network coding offers the potential to increase throughput and improve robustness without any centralized control. Unfortunately, network coding is highly susceptible to “pollution attacks” in which malicious nodes modify packets improperly so as to prevent message recovery at the recipient(s); such attacks cannot be prevented using standard end-to-end cryptographic authentication because network coding mandates that intermediate nodes modify data packets in transit.Specialized “network coding signatures” addressing this problem have been developed in recent years using homomorphic hashing and homomorphic signatures. We contribute to this area in several ways: • We show the first homomorphic signature scheme based on the RSA assumption (in the random oracle model). • We give a homomorphic hashing scheme that is more efficient than existing schemes, and which leads to network coding signatures based on the hardness of factoring (in the standard model). • We describe variants of existing schemes that reduce the communication overhead for moderate-size networks, and improve computational efficiency (in some cases quite dramatically – e.g., we achieve a 20-fold speedup in signature generation at intermediate nodes). Underlying our techniques is a modified approach to random linear network coding where instead of working in a vector space over a field, we work in a module over the integers (with small coefficients).

Secure text processing with applications to private DNA matching - Katz, Jonathan; Malka,Lior (Proceedings of the 17th ACM conference on Computer and communications security, 2010)
Motivated by the problem of private DNA matching, we consider the design of efficient protocols for secure text processing. Here, informally, a party P1 holds a text T and a party P2 holds a pattern p and some additional information y, and P2 wants to learn {f(T,j,y)} for all locations j where p is found as a substring in T. (In particular, this generalizes the basic pattern matching problem.) We aim for protocols with full security against a malicious P2 that also preserve privacy against a malicious P1 (i.e., one-sided security). We show how to modify Yao's garbled circuit approach to obtain a protocol where the size of the garbled circuit is linear in the number of occurrences of p in T (rather than linear in $|T|$). Along the way we show a new keyword search protocol that may be of independent interest.
Keywords: COMPUTATION; secure

Special Section on Distributed Camera Networks: Sensing, Processing, Communication, and Implementation - Chellapa, Rama; Heinzelman, W.; Konrad, J.; Schonfeld, D.; Wolf, M. (Image Processing, IEEE Transactions on, 2010)
The eight papers in this special section span across theoretical and practical considerations of various aspects of distributed camera networks, including adaptive sensing, distributed processing, efficient communications, and versatile implementations.

The state of visual analytics: Views on what visual analytics is and where it is going - May,R.; Hanrahan,P.; Keim,D. A; Shneiderman, Ben; Card,S. (2010 IEEE Symposium on Visual Analytics Science and Technology (VAST), 2010)
In the 2005 publication "Illuminating the Path" visual analytics was defined as "the science of analytical reasoning facilitated by interactive visual interfaces." A lot of work has been done in visual analytics over the intervening five years. While visual analytics started in the United States with a focus on security, it is now a worldwide research agenda with a broad range of application domains. This is evidenced by efforts like the European VisMaster program and the upcoming Visual Analytics and Knowledge Discovery (VAKD) workshop, just to name two.There are still questions concerning where and how visual analytics fits in the large body of research and applications represented by the VisWeek community. This panel will present distinct viewpoints on what visual analytics is and its role in understanding complex information in a complex world. The goal of this panel is to engender discussion from the audience on the emergence and continued advancement of visual analytics and its role relative to fields of related research. Four distinguished panelists will provide their perspective on visual analytics focusing on what it is, what it should be, and thoughts about a development path between these two states. The purpose of the presentations is not to give a critical review of the literature but rather to give a review on the field and to provide a contextual perspective based on the panelists' years of experience and accumulated knowledge.
Keywords: analytical reasoning; Data analysis; data mining; data visualisation; European VisMaster program; interactive visual interfaces; knowledge discovery; United States; visual analytics; VisWeek community

Strategy generation in multi-agent imperfect-information pursuit games - Raboin,Eric; Nau, Dana S.; Kuter,Ugur; Gupta, Satyandra K.; Svec,Petr (International Foundation for Autonomous Agents and Multiagent Systems, 2010)
We describe a formalism and algorithms for game-tree search in partially-observable Euclidean space, and implementation and tests in a scenario where a multi-agent team, called tracking agents, pursues a target agent that wants to evade the tracking agents. Our contributions include--- • A formalism that combines geometric elements (agents' locations and trajectories and observable regions, and obstacles that restrict mobility and observability) with game-theoretic elements (information sets, utility functions, and strategies). • A recursive formula for information-set minimax values based on our formalism, and a implementation of the formula in a game-tree search algorithm. • A heuristic evaluation function for use at the leaf nodes of the game-tree search. It works by doing a quick lookahead search of its own, in a relaxed version of the problem. • Experimental results in 500 randomly generated trials. With the strategies generated by our heuristic, the tracking agents were more than twice as likely to know the target agent's location at the end of the game than with the strategies generated by heuristics that compute estimates of the target's possible locations.
Keywords: game tree search; multi-agent planning; visibility-based pursuit-evasion games

Summary of the first ACM SIGKDD workshop on knowledge discovery from uncertain data (U'09) - Pei,Jian; Getoor, Lise; de Keijzer,Ander (ACM SIGKDD Explorations Newsletter, 2010)

Transit portal: BGP connectivity as a service - Valancius,Vytautas; Kim,Hyojoon; Feamster, Nick (ACM SIGCOMM Computer Communication Review, 2010)
Keywords: bgp-mux; transit portal

Using a Social Orientation Model for the Evolution of Cooperative Societies - Cheng,K. L.; Zuckerman,I.; Kuter,U.; Nau, Dana S. (2010)
We utilize evolutionary game theory to studythe evolution of cooperative societies and the behaviors of individual agents (i.e., players) in such societies. We present a novel player model based upon empirical evidence from the social and behavioral sciences stating that: (1) an individual’s behavior may often be motivated not only by self-interest but also by the consequences for others, and (2) individuals vary in their interpersonal social tendencies, which reflect stable personal orientations that influence their choices. Alongside the formal player model we provide an analysis that considers possible interactions between different types of individuals and identifies five general steady-state behavioral patterns. We present evolutionary simulations that ratify previous findings on evolution of cooperation, and provide new insights on the evolutionary process of cooperative behavior in a society as well as on the emergence of cooperative societies. Our main experimental result demonstrates that in contrast to previous common knowledge, increasing mutual reward or mutual punishment in the Prisoner’s dilemma game does not result in the same type of cooperative society: while increasing reward does increase the society’s cooperativeness level, increasing mutual punishment does not.

Using friendship ties and family circles for link prediction - Zheleva,E.; Getoor, Lise; Golbeck,J.; Kuter,U. (Advances in Social Network Mining and Analysis, 2010)
Social networks can capture a variety of relationships among the participants. Both friendship and family ties are commonly studied, but most existing work studies them in isolation. Here, we investigate how these networks can be overlaid, and propose a feature taxonomy for link prediction. We show that when there are tightly-knit family circles in a social network, we can improve the accuracy of link prediction models. This is done by making use of the family circle features based on the likely structural equivalence of family members. We investigated the predictive power of overlaying friendship and family ties on three real-world social networks. Our experiments demonstrate significantly higher prediction accuracy (between 15% and 30% more accurate) compared to using more traditional features such as descriptive node attributes and structural features. The experiments also show that a combination of all three types of attributes results in the best precision-recall trade-off.

VAST 2010 Challenge: Arms dealings and pandemics - Grinstein,G.; Konecni,S.; Scholtz,J.; Whiting,M.; Plaisant, Catherine (Visual Analytics Science and Technology (VAST), 2010 IEEE Symposium on, 2010)
The 5th VAST Challenge consisted of three mini-challenges that involved both intelligence analysis and bioinformatics. Teams could solve one, two or all three mini-challenges and assess the overall situation to enter the Grand Challenge. Mini-challenge one involved text reports about people and events giving information about arms dealers, situations in various countries and linkages between different countries. Mini-challenge two involved hospital admission and death records from various countries providing information about the spread of a world wide pandemic. Mini-challenge three involved genetic data to be used to identify the origin of the pandemic and the most dangerous viral mutations. The Grand Challenge was to determine how these various mini-challenges were connected. As always the goal was to analyze the data and provide novel interactive visualizations useful in the analytic process. We received 58 submissions in total and gave 15 awards.
Keywords: 2010; administrative; admission; intelligence; analysis; interactive; analysis; medical; challenge; arms; challenge; hospital; data; data; grand; dealings; bioinformatics; dangerous; mutations; death; processing; weapons; records; genetic; reports; bioinformatics; data; VAST; viral; visualizations; minichallenge; pandemics; text

Who's Hogging the Bandwidth: The Consequences of Revealing the Invisible in the Home - Marshini Chetty; Banks, Richard; Harper, Richard; Regan, Tim; Sellen, Abigail; Gkantsidis, Christos; Karagiannis, Thomas; Key, Peter (SIGCHI '10, 2010)
As more technologies enter the home, householders are burdened with the task of digital housekeeping-managing and sharing digital resources like bandwidth. In response to this, we created and evaluated a domestic tool for bandwidth management called Home Watcher. Our field trial showed that when resource contention amongst different household members is made visible, people's understanding of bandwidth changes and household politics are revealed. In this paper, we describe the consequences of showing real time resource usage in a home, and how this varies depending on the social make up of the household.
Keywords: bandwidth monitoring; home broadband; home networks

Why Did the Person Cross the Road (There)? Scene Understanding Using Probabilistic Logic Models and Common Sense Reasoning - Kembhavi,Aniruddha; Tom Yeh; Davis, Larry S. (Computer Vision – ECCV 2010, 2010)
We develop a video understanding system for scene elements, such as bus stops, crosswalks, and intersections, that are characterized more by qualitative activities and geometry than by intrinsic appearance. The domain models for scene elements are not learned from a corpus of video, but instead, naturally elicited by humans, and represented as probabilistic logic rules within a Markov Logic Network framework. Human elicited models, however, represent object interactions as they occur in the 3D world rather than describing their appearance projection in some specific 2D image plane. We bridge this gap by recovering qualitative scene geometry to analyze object interactions in the 3D world and then reasoning about scene geometry, occlusions and common sense domain knowledge using a set of meta-rules. The effectiveness of this approach is demonstrated on a set of videos of public spaces.

Young Proteins Experience More Variable Selection Pressures Than Old Proteins - Vishnoi,Anchal; Kryazhimskiy,Sergey; Bazykin,Georgii A; Hannenhalli, Sridhar; Plotkin,Joshua B. (Genome ResearchGenome Res., 2010)
It is well known that young proteins tend to experience weaker purifying selection and evolve more quickly than old proteins. Here, we show that, in addition, young proteins tend to experience more variable selection pressures over time than old proteins. We demonstrate this pattern in three independent taxonomic groups: yeast, Drosophila, and mammals. The increased variability of selection pressures on young proteins is highly significant even after controlling for the fact that young proteins are typically shorter and experience weaker purifying selection than old proteins. The majority of our results are consistent with the hypothesis that the function of a young gene tends to change over time more readily than that of an old gene. At the same time, our results may be caused in part by young genes that serve constant functions over time, but nevertheless appear to evolve under changing selection pressures due to depletion of adaptive mutations. In either case, our results imply that the evolution of a protein-coding sequence is partly determined by its age and origin, and not only by the phenotypic properties of the encoded protein. We discuss, via specific examples, the consequences of these findings for understanding of the sources of evolutionary novelty.

2009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates - Kingsford, Carl; Nagarajan,Niranjan; Salzberg,Steven L. (PLoS ONEPLoS ONE, 2009)
In April 2009, novel swine-origin influenza viruses (S-OIV) were identified in patients from Mexico and the United States. The viruses were genetically characterized as a novel influenza A (H1N1) strain originating in swine, and within a very short time the S-OIV strain spread across the globe via human-to-human contact.We conducted a comprehensive computational search of all available sequences of the surface proteins of H1N1 swine influenza isolates and found that a similar strain to S-OIV appeared in Thailand in 2000. The earlier isolates caused infections in pigs but only one sequenced human case, A/Thailand/271/2005 (H1N1). Differences between the Thai cases and S-OIV may help shed light on the ability of the current outbreak strain to spread rapidly among humans.

An architectural level design methodology for smart camera applications - Saha,S.; Kianzad,V.; Schlessman,J.; Aggarwal,G.; Bhattacharyya, Shuvra S.; Chellapa, Rama; Wolf,W. (International Journal of Embedded Systems, 2009)
Today's embedded computing applications are characterised by increased functionality, and hence increased design complexity and processing requirements. The resulting design spaces are vast and designers are typically able to evaluate only small subsets of solutions due to lack of efficient design tools. In this paper, we propose an architectural level design methodology that provides a means for a comprehensive design space exploration for smart camera applications and enable designers to select higher quality solutions and provides substantial savings on the overall cost of the system. We present efficient, accurate and intuitive models for performance estimation and validate them with experiments.

Attacking cryptographic schemes based on "perturbation polynomials" - Albrecht,Martin; Gentry,Craig; Halevi,Shai; Katz, Jonathan (Proceedings of the 16th ACM conference on Computer and communications security, 2009)
We show attacks on several cryptographic schemes that have recently been proposed for achieving various security goals in sensor networks. Roughly speaking, these schemes all use "perturbation polynomials" to add "noise" to polynomialbased systems that offer information-theoretic security, in an attempt to increase the resilience threshold while maintaining efficiency. We show that the heuristic security arguments given for these modified schemes do not hold, and that they can be completely broken once we allow even a slight extension of the parameters beyond those achieved by the underlying information-theoretic schemes. Our attacks apply to the key predistribution scheme of Zhang et al. (MobiHoc 2007), the access-control schemes of Subramanian et al. (PerCom 2007), and the authentication schemes of Zhang et al. (INFOCOM 2008). Our results cast doubt on the viability of using "perturbation polynomials" for designing secure cryptographic schemes.
Keywords: pairwise key establishment; random perturbation polynomial; sensor network security

On black-box constructions of predicate encryption from trapdoor permutations - Katz, Jonathan; Yerukhimovich,A. (Advances in Cryptology–ASIACRYPT 2009, 2009)
Predicate encryption is a recent generalization of identity-based encryption (IBE), broadcast encryption, attribute-based encryption, and more. A natural question is whether there exist black-box constructions of predicate encryption based on generic building blocks, e.g., trapdoor permutations. Boneh et al. (FOCS 2008) recently gave a negative answer for the specific case of IBE.We show both negative and positive results. First, we identify a combinatorial property on the sets of predicates/attributes and show that, for any sets having this property, no black-box construction of predicate encryption from trapdoor permutations (or even CCA-secure encryption) is possible. Our framework implies the result of Boneh et al. as a special case, and also rules out, e.g., black-box constructions of forward-secure encryption and broadcast encryption (with many excluded users). On the positive side, we identify conditions under which predicate encryption schemes can be constructed based on any CPA-secure (standard) encryption scheme.

Collusion-free multiparty computation in the mediated model - Alwen,J.; Katz, Jonathan; Lindell,Y.; Persiano,G.; Shelat,A.; Visconti,I. (Advances in Cryptology-CRYPTO 2009, 2009)
Collusion-free protocols prevent subliminal communication (i.e., covert channels) between parties running the protocol. In the standard communication model, if one-way functions exist, then protocols satisfying any reasonable degree of privacy cannot be collusion-free. To circumvent this impossibility, Alwen, shelat and Visconti (CRYPTO 2008) recently suggested the mediated model where all communication passes through a mediator. The goal is to design protocols where collusion-freeness is guaranteed as long as the mediator is honest, while standard security guarantees hold if the mediator is dishonest. In this model, they gave constructions of collusion-free protocols for commitments and zero-knowledge proofs in the two-party setting.We strengthen the definition of Alwen et al., and resolve the main open questions in this area by showing a collusion-free protocol (in the mediated model) for computing any multi-party functionality.

Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae - Chun,J.; Grim,C. J.; Hasan,N. A.; Lee,J. H.; Choi,S. Y.; Haley,B. J.; Taviani,E.; Jeon,Y. S.; Kim,D.W.; Lee,J. H.; Rita R Colwell (Proceedings of the National Academy of Sciences, 2009)
Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a “shift” between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a “drift” between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.

Complete fairness in multi-party computation without an honest majority - Gordon,S.; Katz, Jonathan (Theory of Cryptography, 2009)
Gordon et al. recently showed that certain (non-trivial) functions can be computed with complete fairness in the two-party setting. Motivated by their results, we initiate a study of complete fairness in the multi-party case and demonstrate the first completely-fair protocols for non-trivial functions in this setting. We also provide evidence that achieving fairness is “harder” in the multi-party setting, at least with regard to round complexity.

Complete Genome Sequence of Aggregatibacter (Haemophilus) Aphrophilus NJ8700 - Di Bonaventura,Maria Pia; DeSalle,Rob; Pop, Mihai; Nagarajan,Niranjan; Figurski,David H; Fine,Daniel H; Kaplan,Jeffrey B; Planet,Paul J (Journal of BacteriologyJ. Bacteriol., 2009)
We report the finished and annotated genome sequence of Aggregatibacter aphrophilus strain NJ8700, a strain isolated from the oral flora of a healthy individual, and discuss characteristics that may affect its dual roles in human health and disease. This strain has a rough appearance, and its genome contains genes encoding a type VI secretion system and several factors that may participate in host colonization.

Composability and on-line deniability of authentication - Dodis,Y.; Katz, Jonathan; Smith,A.; Walfish,S. (Theory of Cryptography, 2009)
Protocols for deniable authentication achieve seemingly paradoxical guarantees: upon completion of the protocol the receiver is convinced that the sender authenticated the message, but neither party can convince anyone else that the other party took part in the protocol. We introduce and study on-line deniability, where deniability should hold even when one of the parties colludes with a third party during execution of the protocol. This turns out to generalize several realistic scenarios that are outside the scope of previous models.We show that a protocol achieves our definition of on-line deniability if and only if it realizes the message authentication functionality in the generalized universal composability framework; any protocol satisfying our definition thus automatically inherits strong composability guarantees. Unfortunately, we show that our definition is impossible to realize in the PKI model if adaptive corruptions are allowed (even if secure erasure is assumed). On the other hand, we show feasibility with respect to static corruptions (giving the first separation in terms of feasibility between the static and adaptive setting), and show how to realize a relaxation termed deniability with incriminating abort under adaptive corruptions.

Computational linguistics for metadata building (CLiMB): using text mining for the automatic identification, categorization, and disambiguation of subject terms for image metadata - Klavans,J. L; Sheffield,C.; Abels,E.; Jimmy Lin; Passonneau,R.; Sidhu,T.; Soergel,D. (Multimedia Tools and Applications, 2009)
In this paper, we present a system using computational linguistic techniques to extract metadata for image access. We discuss the implementation, functionality and evaluation of an image catalogers’ toolkit, developed in the Computational Linguistics for Metadata Building (CLiMB) research project. We have tested components of the system, including phrase finding for the art and architecture domain, functional semantic labeling using machine learning, and disambiguation of terms in domain-specific text vis a vis a rich thesaurus of subject terms, geographic and artist names. We present specific results on disambiguation techniques and on the nature of the ambiguity problem given the thesaurus, resources, and domain-specific text resource, with a comparison of domain-general resources and text. Our primary user group for evaluation has been the cataloger expert with specific expertise in the fields of painting, sculpture, and vernacular and landscape architecture.

On Computing Compression Trees for Data Collection in Sensor Networks - Li,Jian; Deshpande, Amol; Khuller, Samir (arXiv:0907.5442, 2009)
We address the problem of efficiently gathering correlated data from a wired or a wireless sensor network, with the aim of designing algorithms with provable optimality guarantees, and understanding how close we can get to the known theoretical lower bounds. Our proposed approach is based on finding an optimal or a near-optimal {\em compression tree} for a given sensor network: a compression tree is a directed tree over the sensor network nodes such that the value of a node is compressed using the value of its parent. We consider this problem under different communication models, including the {\em broadcast communication} model that enables many new opportunities for energy-efficient data collection. We draw connections between the data collection problem and a previously studied graph concept, called {\em weakly connected dominating sets}, and we use this to develop novel approximation algorithms for the problem. We present comparative results on several synthetic and real-world datasets showing that our algorithms construct near-optimal compression trees that yield a significant reduction in the data collection cost.
Keywords: Computer Science - Information Theory; Computer Science - Networking and Internet Architecture

Conceptual modeling: past, present and the continuum of the future - Roussopoulos, Nick; Karagiannis,D. (Conceptual Modeling: Foundations and Applications, 2009)

A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing - Lapizco-Encinas,G.; Kingsford, Carl; Reggia, James A. (IEEE Swarm Intelligence Symposium, 2009. SIS '09, 2009)
Particle Swarm Optimization (PSO) is a well-known, competitive technique for numerical optimization with real-parameter representation. This paper introduces CCPSO, a new Cooperative Particle Swarm Optimization algorithm for combinatorial problems. The cooperative strategy is achieved by splitting the candidate solution vector into components, where each component is optimized by a particle. Particles move throughout a continuous space, their movements based on the influences exerted by static particles that then get feedback based on the fitness of the candidate solution. Here, the application of this technique to side-chain packing (a proteomics optimization problem) is investigated. To verify the efficiency of the proposed CCPSO algorithm, we test our algorithm on three side-chain packing problems and compare our results with the provably optimal result. Computational results show that the proposed algorithm is very competitive, obtaining a conformation with an energy value within 1% of the provably optimal solution in many proteins.
Keywords: Algorithm design and analysis; Amino acids; combinatorial mathematics; cooperative combinatorial particle swarm optimization algorithm; Design optimization; Encoding; Feedback; numerical optimization; Optimization methods; particle swarm optimisation; Particle swarm optimization; Partitioning algorithms; Proteins; proteomics; proteomics optimization; Robustness; side-chain packing

Design guidelines for agent based model visualization - Kornhauser,D.; Wilensky,U.; Rand, William (Journal of Artificial Societies and Social Simulation, 2009)
In the field of agent-based modeling (ABM), visualizations play an important role in identifying, communicating and understanding important behavior of the modeled phenomenon. However, many modelers tend to create ineffective visualizations of Agent Based Models (ABM) due to lack of experience with visual design. This paper provides ABM visualization design guidelines in order to improve visual design with ABM toolkits. These guidelines will assist the modeler in creating clear and understandable ABM visualizations. We begin by introducing a non-hierarchical categorization of ABM visualizations. This categorization serves as a starting point in the creation of an ABM visualization. We go on to present well-known design techniques in the context of ABM visualization. These techniques are based on Gestalt psychology, semiology of graphics, and scientific visualization. They improve the visualization design by facilitating specific tasks, and providing a common language to critique visualizations through the use of visual variables. Subsequently, we discuss the application of these design techniques to simplify, emphasize and explain an ABM visualization. Finally, we illustrate these guidelines using a simple redesign of a NetLogo ABM visualization. These guidelines can be used to inform the development of design tools that assist users in the creation of ABM visualizations.

Detecting spammers with SNARE: spatio-temporal network-level automatic reputation engine - Hao,Shuang; Syed,Nadeem Ahmed; Feamster, Nick; Gray,Alexander G.; Krasser,Sven (Proceedings of the 18th conference on USENIX security symposium, 2009)
Users and network administrators need ways to filter email messages based primarily on the reputation of the sender. Unfortunately, conventional mechanisms for sender reputation--notably, IP blacklists--are cumbersome to maintain and evadable. This paper investigates ways to infer the reputation of an email sender based solely on network-level features, without looking at the contents of a message. First, we study first-order properties of network-level features that may help distinguish spammers from legitimate senders. We examine features that can be ascertained without ever looking at a packet's contents, such as the distance in IP space to other email senders or the geographic distance between sender and receiver. We derive features that are lightweight, since they do not require seeing a large amount of email from a single IP address and can be gleaned without looking at an email's contents--many such features are apparent from even a single packet. Second, we incorporate these features into a classification algorithm and evaluate the classifier's ability to automatically classify email senders as spammers or legitimate senders. We build an automated reputation engine, SNARE, based on these features using labeled data from a deployed commercial spam-filtering system. We demonstrate that SNARE can achieve comparable accuracy to existing static IP blacklists: about a 70%detection rate for less than a 0.3%false positive rate. Third, we show how SNARE can be integrated into existing blacklists, essentially as a first-pass filter.

Detection of toxigenic Vibrio cholerae O1 in freshwater lakes of the former Soviet Republic of Georgia - Grim,Christopher J.; Jaiani,Ekaterina; Whitehouse,Chris A.; Janelidze,Nino; Kokashvili,Tamuna; Tediashvili,Marina; Rita R Colwell; Huq,Anwar (Environmental Microbiology Reports, 2009)
Three freshwater lakes, Lisi Lake, Kumisi Lake and Tbilisi Sea, near Tbilisi, Georgia, were studied from January 2006 to December 2007 to determine the presence of Vibrio cholerae employing both bacteriological culture method and direct detection methods, namely PCR and direct fluorescent antibody (DFA). For PCR, DNA extracted from water samples was tested for presence of V. cholerae and genes coding for selected virulence factors. Vibrio cholerae non-O1/non-O139 was routinely isolated by culture from all three lakes; whereas V. cholerae O1 and O139 were not. Water samples collected during the summer months from Lisi Lake and Kumisi Lake were positive for both V. cholerae and V. cholerae ctxA, tcpA, zot, ompU and toxR by PCR. Water samples collected during the same period from both Lisi and Kumisi Lake were also positive for V. cholerae serogroup O1 by DFA. All of the samples were negative for V. cholerae serotype O139. The results of this study provide evidence for an environmental presence of toxigenic V. cholerae O1, which may represent a potential source of illness as these lakes serve as recreational water in Tbilisi, Georgia.

Directing JavaScript with arrows - Khoo,Yit Phang; Hicks, Michael W.; Foster, Jeffrey S.; Sazawal,Vibha (Proceedings of the 5th symposium on Dynamic languages, 2009)
JavaScript programmers make extensive use of event-driven programming to help build responsive web applications. However, standard approaches to sequencing events are messy, and often lead to code that is difficult to understand and maintain. We have found that arrows, a generalization of monads, are an elegant solution to this problem. Arrows allow us to easily write asynchronous programs in small, modular units of code, and flexibly compose them in many different ways, while nicely abstracting the details of asynchronous program composition. In this paper, we present Arrowlets, a new JavaScript library that offers arrows to the everyday JavaScript programmer. We show how to use Arrowlets to construct a variety of state machines, including state machines that branch and loop. We also demonstrate how Arrowlets separate computation from composition with examples such as a drag-and-drop handler and a bubblesort animation.
Keywords: arrowlets; arrows; events; javascript; web programming

Distributed Strategies for Channel Allocation and Scheduling in Software-Defined Radio Networks - Han,Bo; Kumar,V. S.A; Marathe,M. V; Parthasarathy,S.; Srinivasan, Aravind (IEEE INFOCOM 2009, 2009)
Equipping wireless nodes with multiple radios can significantly increase the capacity of wireless networks, by making these radios simultaneously transmit over multiple non-overlapping channels. However, due to the limited number of radios and available orthogonal channels, designing efficient channel assignment and scheduling algorithms in such networks is a major challenge. In this paper, we present provably-good distributed algorithms for simultaneous channel allocation of individual links and packet-scheduling, in software-defined radio (SDR) wireless networks. Our distributed algorithms are very simple to implement, and do not require any coordination even among neighboring nodes. A novel access hash function or random oracle methodology is one of the key drivers of our results. With this access hash function, each radio can know the transmitters' decisions for links in its interference set for each time slot without introducing any extra communication overhead between them. Further, by utilizing the inductive-scheduling technique, each radio can also backoff appropriately to avoid collisions. Extensive simulations demonstrate that our bounds are valid in practice.
Keywords: access hash function; Channel allocation; channel assignment algorithm; channel capacity; collision avoidance; Computer science; cryptography; distributed algorithm; distributed algorithms; Educational institutions; inductive-scheduling technique; Interference; interference set; packet scheduling algorithm; Peer to peer computing; Radio network; radio networks; radiofrequency interference; random oracle methodology; scheduling; Scheduling algorithm; simultaneous channel allocation; software radio; software-defined radio wireless network capacity; telecommunication congestion control; telecommunication security; Throughput; wireless channels; Wireless networks

Dynamic Provable Data Possession - Erway, Chris; Küp\ccü, Alptekin; Charalampos Papamanthou; Tamassia, Roberto (CCS '09 Proceedings of the 16th ACM Conference on Computer and Communications Security, 2009)
We consider the problem of efficiently proving the integrity of data stored at untrusted servers. In the provable data possession (PDP) model, the client preprocesses the data and then sends it to an untrusted server for storage, while keeping a small amount of meta-data. The client later asks the server to prove that the stored data has not been tampered with or deleted (without downloading the actual data). However, the original PDP scheme applies only to static (or append-only) files. We present a definitional framework and efficient constructions for dynamic provable data possession (DPDP), which extends the PDP model to support provable updates to stored data. We use a new version of authenticated dictionaries based on rank information. The price of dynamic updates is a performance change from O(1) to O(logn) (or O(nεlog n), for a file consisting of n blocks, while maintaining the same (or better, respectively) probability of misbehavior detection. Our experiments show that this slowdown is very low in practice (e.g. 415KB proof size and 30ms computational overhead for a 1GB file). We also show how to apply our DPDP scheme to outsourced file systems and version control systems (e.g. CVS).
Keywords: authenticated data structures; Authentication; integrity checking; outsourced storage; proof of retrievability; provable data possession; skip list

Dynamics of online scam hosting infrastructure - Konte,M.; Feamster, Nick; Jung,J. (Passive and Active Network Measurement, 2009)
This paper studies the dynamics of scam hosting infrastructure, with an emphasis on the role of fast-flux service networks. By monitoring changes in DNS records of over 350 distinct spam-advertised domains collected from URLs in 115,000 spam emails received at a large spam sinkhole, we measure the rates and locations of remapping DNS records, and the rates at which “fresh” IP addresses are used. We find that, unlike the short-lived nature of the scams themselves, the infrastructure that hosts these scams has relatively persistent features that may ultimately assist detection.

Ef?cient Query Evaluation over Temporally Correlated Probabilistic Streams - Kanagal,B.; Deshpande, Amol (IEEE 25th International Conference on Data Engineering, 2009. ICDE '09, 2009)
In this paper, we address the problem of efficient query evaluation over highly correlated probabilistic streams. We observe that although probabilistic streams tend to be strongly correlated in space and time, the correlations are usually quite structured (i.e., the same set of dependencies and independences repeat across time) and Markovian (i.e., the state at time "t+1" is independent of the states at previous times given the state at time "t"). We exploit this observation to compactly encode probabilistic streams by decoupling the correlation structure (the set of dependencies) from the actual probability values. We develop novel stream processing operators that can efficiently and incrementally process new data items; our operators are based on the previously proposed framework of viewing probabilistic query evaluation as inference over probabilistic graphical models (PGMs) [P. Sen and A. Deshpande, 2007]. We develop a query planning algorithm that constructs efficient query plans that are executable in polynomial-time whenever possible, and we characterize queries for which such plans are not possible. Finally we conduct an extensive experimental evaluation that illustrates the advantages of exploiting the structured nature of correlations in probabilistic streams.
Keywords: Birds; Computerized monitoring; correlated probabilistic streams; correlation structure; Data engineering; data mining; Databases; Event detection; Graphical models; inference mechanisms; Markov processes; polynomial time; probabilistic database; probabilistic graphical model; probabilistic query evaluation; query evaluation; query planning algorithm; query plans; Query processing; Random variables; stream processing operator; Streaming media

Efficient and secure authenticated key exchange using weak passwords - Katz, Jonathan; Ostrovsky,Rafail; Yung,Moti (Journal of the ACM (JACM), 2009)
Mutual authentication and authenticated key exchange are fundamental techniques for enabling secure communication over public, insecure networks. It is well known how to design secure protocols for achieving these goals when parties share high-entropy cryptographic keys in advance of the authentication stage. Unfortunately, it is much more common for users to share weak, low-entropy passwords which furthermore may be chosen from a known space of possibilities (say, a dictionary of English words). In this case, the problem becomes much more difficult as one must ensure that protocols are immune to off-line dictionary attacks in which an adversary exhaustively enumerates all possible passwords in an attempt to determine the correct one. We propose a 3-round protocol for password-only authenticated key exchange, and provide a rigorous proof of security for our protocol based on the decisional Diffie-Hellman assumption. The protocol assumes only public parameters—specifically, a “common reference string”—which can be “hard-coded” into an implementation of the protocol; in particular, and in contrast to some previous work, our protocol does not require either party to pre-share a public key. The protocol is also remarkably efficient, requiring computation only (roughly) 4 times greater than “classical” Diffie-Hellman key exchange that provides no authentication at all. Ours is the first protocol for password-only authentication that is both practical and provably-secure using standard cryptographic assumptions.
Keywords: Authentication; cryptography; passwords

Electromagnetic Analysis of Plasmon-Resonance Based All-Optical Magnetic Recording - Mayergoyz, Issak D; Zhang,Zhenyu; McAvoy,P.; Bowen,D.; Krafft,C. (Magnetics, IEEE Transactions on, 2009)
The electromagnetic analysis of plasmon-resonance-based all-optical magnetic recording is performed. This analysis is based on the treatment of plasmon resonances as an eigenvalue problem for specific boundary integral equations. The plasmon modes which can be excited in circular nanoholes and cylindrical nanoshells by circularly polarized light are theoretically and numerically studied. Dramatic enhancement of circularly polarized light intensity on the nanoscale through the excitation of specific plasmon modes in uniaxial nanostructures is demonstrated.
Keywords: Ag; boundary; all-optical; analysis; magnetization; and; based; effects; nanoparticles; silver; surface; eigenfunctions; magnetic; equations; circular; equations; eigenvalues; integral; intensity; cylindrical; light; magnetic; modes; plasmon-resonance; nanoholes; circularly; nanoshells; eigenvalue; nanostructures; boundary; plasmon; polarized; problem; electromagnetic; recording; magnetisation; recording; silver; uniaxial; resonance; reversal; magneto-optical; reversals; nanoparticle; plasmon

Energy loss in MEMS resonators and the impact on inertial and RF devices - Weinberg,M.; Candler,R.; Chandorkar,S.; Varsanik,J.; Kenny,T.; Duwel,A. (2009)
In this paper, we review the current understanding of energy loss mechanisms in micromachined (MEMS and NEMS) devices. We describe the importance of high quality factor (Q) to the performance of MEMS gyros and MEMS resonators used in radio-frequency applications.
Keywords: energy loss; gyroscopes; inertial devices; MEMS gyros; MEMS resonators; micromachined devices; micromechanical resonators; NEMS devices; Q-factor; quality factor; radiofrequency applications; RF devices

Enhancing Testing Technologies for Globalization of Software Engineering and Productivity - Khan,A.H.; Memon, Atif M. (Handbook of Research on Software Engineering and Productivity Technologies: Implications of GlobalizationHandbook of Research on Software Engineering and Productivity Technologies: Implications of Globalization, 2009)

The evolution of Fox genes and their role in development and disease - Hannenhalli, Sridhar; Kaestner,Klaus H. (Nature reviews. GeneticsNat Rev Genet, 2009)
The forkhead box (Fox) family of transcription factors, which originated in unicellular eukaryotes, has expanded over time through multiple duplication events, and sometimes through gene loss, to over 40 members in mammals. Fox genes have evolved to acquire a specialized function in many key biological processes. Mutations in Fox genes have a profound effect on human disease, causing phenotypes as varied as cancer, glaucoma and language disorders. We summarize the salient features of the evolution of the Fox gene family and highlight the diverse contribution of various Fox subfamilies to developmental processes, from organogenesis to speech acquisition.

On expected constant-round protocols for Byzantine agreement - Katz, Jonathan; Koo,Chiu-Yuen (Journal of Computer and System Sciences, 2009)
In a seminal paper, Feldman and Micali show an n-party Byzantine agreement protocol in the plain model that tolerates t < n / 3 malicious parties and runs in expected constant rounds. Here, resolving a question that had been open since their work, we show an expected constant-round protocol for authenticated Byzantine agreement assuming honest majority (i.e., t < n / 2 ), and relying only on the existence of signature schemes and a public-key infrastructure. Combined with existing results, this gives the first expected constant-round protocol for secure computation with honest majority in a point-to-point network under the same assumptions. Our key technical tool — a new primitive we introduce called moderated VSS — also yields a simpler proof of the Feldman–Micali result.In addition, we show a simple technique for sequential composition of Byzantine agreement protocols that do not achieve simultaneous termination, something that is inherent for protocols using o ( t ) rounds.
Keywords: broadcast; cryptography; Distributed computing; secure computation

Finding Biologically Accurate Clusterings in Hierarchical Decompositions Using the Variation of Information - Navlakha,S.; White,J. R.; Nagarajan,N.; Pop, Mihai; Kingsford, Carl (Lecture Notes in Computer Science: Research in Computational Molecular Biology, 2009)

Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information - Navlakha,Saket; White,James; Nagarajan,Niranjan; Pop, Mihai; Kingsford, Carl (Research in Computational Molecular Biology, 2009)
Hierarchical clustering is a popular method for grouping together similar elements based on a distance measure between them. In many cases, annotations for some elements are known beforehand, which can aid the clustering process. We present a novel approach for decomposing a hierarchical clustering into the clusters that optimally match a set of known annotations, as measured by the variation of information metric. Our approach is general and does not require the user to enter the number of clusters desired. We apply it to two biological domains: finding protein complexes within protein interaction networks and identifying species within metagenomic DNA samples. For these two applications, we test the quality of our clusters by using them to predict complex and species membership, respectively. We find that our approach generally outperforms the commonly used heuristic methods.

Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo - Shah,Rachana; Lu,Yun; Hinkle,Christine C; McGillicuddy,Fiona C; Kim,Roy; Hannenhalli, Sridhar; Cappola,Thomas P.; Heffron,Sean; Wang,XingMei; Mehta,Nehal N; Putt,Mary; Reilly,Muredach P (DiabetesDiabetes, 2009)
OBJECTIVE Adipose inflammation plays a central role in obesity-related metabolic and cardiovascular complications. However, few human adipose-secreted proteins are known to mediate these processes. We hypothesized that microarray mRNA profiling of human adipose during evoked inflammation could identify novel adipocytokines.RESEARCH DESIGN AND METHODS Healthy human volunteers (n = 14) were treated with intravenous endotoxin (3 ng/kg lipopolysaccharide [LPS]) and underwent subcutaneous adipose biopsies before and after LPS. On Affymetrix U133Plus 2.0 arrays, adipose mRNAs modulated >1.5-fold (with P < 0.00001) were selected. SignalP 3.0 and SecretomeP 2.0 identified genes predicted to encode secreted proteins. Of these, 86 candidates were chosen for validation in adipose from an independent human endotoxemia protocol (N = 7, with 0.6 ng/kg LPS) and for exploration of cellular origin in primary human adipocytes and macrophages in vitro. RESULTS Microarray identified 776 adipose genes modulated by LPS; 298 were predicted to be secreted. Of detectable prioritized genes, 82 of 85 (96% [95% CI 90–99]) were upregulated (fold changes >1.0) during the lower-dose (LPS 0.6 ng/kg) validation study and 51 of 85 (59% [49–70]) were induced greater than 1.5-fold. Treatment of primary adipocytes with LPS and macrophage polarization to M1 proinflammatory phenotype increased expression by 1.5-fold for 58 and 73% of detectable genes, respectively. CONCLUSIONS We demonstrate that evoked inflammation of human adipose in vivo modulated expression of multiple genes likely secreted by adipocytes and monocytes. These included established adipocytokines and chemokines implicated in recruitment and activation of lymphocytes, adhesion molecules, antioxidants, and several novel genes with unknown function. Such candidates may represent biomarkers and therapeutic targets for obesity-related complications.

Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains - Brettin,Thomas S[Los Alamos National Laboratory; Bruce,David C[Los Alamos National Laboratory; Challacombe,Jean F[Los Alamos National Laboratory; Detter,John C[Los Alamos National Laboratory; Han,Cliff S[Los Alamos National Laboratory; Munik,A. C[Los Alamos National Laboratory; Chertkov,Olga[Los Alamos National Laboratory; Meincke,Linda[Los Alamos National Laboratory; Saunders,Elizabeth[Los Alamos National Laboratory; Choi,Seon Y[SEOUL NATL UNIV; Haley,Bradd J[U MARYLAND; Taviani,Elisa[U MARYLAND; et al. (Nature, 2009)
Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the 6th and the current 7th pandemics, respectively. Cholera researchers continually face newly emerging and re-emerging pathogenic clones carrying combinations of new serogroups as well as of phenotypic and genotypic properties. These genotype and phenotype changes have hampered control of the disease. Here we compare the complete genome sequences of 23 strains of V. cholerae isolated from a variety of sources and geographical locations over the past 98 years in an effort to elucidate the evolutionary mechanisms governing genetic diversity and genesis of new pathogenic clones. The genome-based phylogeny revealed 12 distinct V. cholerae phyletic lineages, of which one, designated the V. cholerae core genome (CG), comprises both O1 classical and EI Tor biotypes. All 7th pandemic clones share nearly identical gene content, i.e., the same genome backbone. The transition from 6th to 7th pandemic strains is defined here as a 'shift' between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages within the CG clade. In contrast, transition among clones during the present 7th pandemic period can be characterized as a 'drift' between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V.cholerae serogroup O139 and V.cholerae O1 El Tor hybrid clones that produce cholera toxin of classical biotype. Based on the comprehensive comparative genomics presented in this study it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.
Keywords: 59; CHOLERA; GENES; GENETICS; GENOTYPE; ISLANDS; ORIGIN; PHENOTYPE; PUBLIC HEALTH; RECOMBINATION; STRAINS; TOXINS

GrouPeer: Dynamic clustering of P2P databases - Kantere,Verena; Tsoumakos,Dimitrios; Sellis,Timos; Roussopoulos, Nick (Information Systems, 2009)
Sharing structured data in a P2P network is a challenging problem, especially in the absence of a mediated schema. The standard practice of answering a consecutively rewritten query along the propagation path often results in significant loss of information. On the opposite, the use of mediated schemas requires human interaction and global agreement, both during creation and maintenance. In this paper we present GrouPeer, an adaptive, automated approach to both issues in the context of unstructured P2P database overlays. By allowing peers to individually choose which rewritten version of a query to answer and evaluate the received answers, information-rich sources left hidden otherwise are discovered. Gradually, the overlay is restructured as semantically similar peers are clustered together. Experimental results show that our technique produces very accurate answers and builds clusters that are very close to the optimal ones by contacting a very small number of nodes in the overlay.
Keywords: Peer-to-Peer databases; Query reformulation in P2P databases; Semantics in P2P query answering; Structured data in unstructured P2P overlays

Hat guessing games - Butler,S.; Hajiaghayi, Mohammad T.; Kleinberg,R. D; Leighton,T. (SIAM review, 2009)

High-Fidelity Data Embedding for Image Annotation - He,Shan; Kirovski,D.; M. Wu (Image Processing, IEEE Transactions on, 2009)
High fidelity is a demanding requirement for data hiding, especially for images with artistic or medical value. This correspondence proposes a high-fidelity image watermarking for annotation with robustness to moderate distortion. To achieve the high fidelity of the embedded image, we introduce a visual perception model that aims at quantifying the local tolerance to noise for arbitrary imagery. Based on this model, we embed two kinds of watermarks: a pilot watermark that indicates the existence of the watermark and an information watermark that conveys a payload of several dozen bits. The objective is to embed 32 bits of metadata into a single image in such a way that it is robust to JPEG compression and cropping. We demonstrate the effectiveness of the visual model and the application of the proposed annotation technology using a database of challenging photographic and medical images that contain a large amount of smooth regions.
Keywords: Automated; Product Labeling; Reproducibility of Results; Sensitivity and Specificity; Signal Processing; Computer-Assisted; Computer-Assisted; Information Storage and Retrieval; Pattern Recognition; JPEG compression; JPEG cropping; arbitrary imagery; data hiding; high-fidelity data embedding; image annotation; image watermarking; medical images; photographic images; data compression; image coding; watermarking; Algorithms; Computer Graphics; Documentation; Image En

Human detection using partial least squares analysis - Schwartz,William Robson; Kembhavi,Aniruddha; Harwood,David; Davis, Larry S. (Computer Vision, 2009 IEEE 12th International Conference on, 2009)
Significant research has been devoted to detecting people in images and videos. In this paper we describe a human detection method that augments widely used edge-based features with texture and color information, providing us with a much richer descriptor set. This augmentation results in an extremely high-dimensional feature space (more than 170,000 dimensions). In such high-dimensional spaces, classical machine learning algorithms such as SVMs are nearly intractable with respect to training. Furthermore, the number of training samples is much smaller than the dimensionality of the feature space, by at least an order of magnitude. Finally, the extraction of features from a densely sampled grid structure leads to a high degree of multicollinearity. To circumvent these data characteristics, we employ Partial Least Squares (PLS) analysis, an efficient dimensionality reduction technique, one which preserves significant discriminative information, to project the data onto a much lower dimensional subspace (20 dimensions, reduced from the original 170,000). Our human detection system, employing PLS analysis over the enriched descriptor set, is shown to outperform state-of-the-art techniques on three varied datasets including the popular INRIA pedestrian dataset, the low-resolution gray-scale DaimlerChrysler pedestrian dataset, and the ETHZ pedestrian dataset consisting of full-length videos of crowded scenes.

Improved approximation algorithms for prize-collecting Steiner tree and TSP - Archer,A.; Bateni,M. H; Hajiaghayi, Mohammad T.; Karloff,H. (2009 50th Annual IEEE Symposium on Foundations of Computer Science, 2009)

Improving recommendation accuracy by clustering social networks with trust - DuBois,T.; Golbeck,J.; Kleint,J.; Srinivasan, Aravind (Recommender Systems & the Social Web, 2009)
Social trust relationships between users in social networksspeak to the similarity in opinions between the users, both in general and in important nuanced ways. They have been used in the past to make recommendations on the web. New trust metrics allow us to easily cluster users based on trust. In this paper, we investigate the use of trust clusters as a new way of improving recommendations. Previous work on the use of clusters has shown the technique to be relatively un- successful, but those clusters were based on similarity rather than trust. Our results show that when trust clusters are integrated into memory-based collaborative filtering algo- rithms, they lead to statistically significant improvements in accuracy. In this paper we discuss our methods, experi- ments, results, and potential future applications of the tech- nique.

Improving the round complexity of VSS in point-to-point networks - Katz, Jonathan; Koo,Chiu-Yuen; Kumaresan,Ranjit (Information and Computation, 2009)
We revisit the following question: what is the optimal round complexity of verifiable secret sharing (VSS)? We focus here on the case of perfect VSS where the number of corrupted parties t satisfies t < n / 3 , with n the total number of parties. Work of Gennaro et al. (STOC 2001) and Fitzi et al. (TCC 2006) shows that, assuming a broadcast channel, three rounds are necessary and sufficient for efficient VSS. Existing protocols, however, treat the broadcast channel as being available “for free” and do not attempt to minimize its usage. This approach leads to relatively poor round complexity when such protocols are compiled to run over a point-to-point network.We show here a VSS protocol that is simultaneously optimal in terms of both the number of rounds and the number of invocations of broadcast. Our protocol also satisfies a certain “2-level sharing” property that makes it useful for constructing protocols for general secure computation.

Incremental Multiple Kernel Learning for object recognition - Kembhavi,Aniruddha; Siddiquie,Behjat; Miezianko,Roland; McCloskey,Scott; Davis, Larry S. (Computer Vision, 2009 IEEE 12th International Conference on, 2009)
A good training dataset, representative of the test images expected in a given application, is critical for ensuring good performance of a visual categorization system. Obtaining task specific datasets of visual categories is, however, far more tedious than obtaining a generic dataset of the same classes. We propose an Incremental Multiple Kernel Learning (IMKL) approach to object recognition that initializes on a generic training database and then tunes itself to the classification task at hand. Our system simultaneously updates the training dataset as well as the weights used to combine multiple information sources. We demonstrate our system on a vehicle classification problem in a video stream overlooking a traffic intersection. Our system updates itself with images of vehicles in poses more commonly observed in the scene, as well as with image patches of the background, leading to an increase in performance. A considerable change in the kernel combination weights is observed as the system gathers scene specific training data over time. The system is also seen to adapt itself to the illumination change in the scene as day transitions to night.

Indexing correlated probabilistic databases - Kanagal,Bhargav; Deshpande, Amol (Proceedings of the 35th SIGMOD international conference on Management of data, 2009)
With large amounts of correlated probabilistic data being generated in a wide range of application domains including sensor networks, information extraction, event detection etc., effectively managing and querying them has become an important research direction. While there is an exhaustive body of literature on querying independent probabilistic data, supporting efficient queries over large-scale, correlated databases remains a challenge. In this paper, we develop efficient data structures and indexes for supporting inference and decision support queries over such databases. Our proposed hierarchical data structure is suitable both for in-memory and disk-resident databases. We represent the correlations in the probabilistic database using a junction tree over the tuple-existence or attribute-value random variables, and use tree partitioning techniques to build an index structure over it. We show how to efficiently answer inference and aggregation queries using such an index, resulting in orders of magnitude performance benefits in most cases. In addition, we develop novel algorithms for efficiently keeping the index structure up-to-date as changes (inserts, updates) are made to the probabilistic database. We present a comprehensive experimental study illustrating the benefits of our approach to query processing in probabilistic databases.
Keywords: caching; Indexing; inference queries; junction trees; Probabilistic databases

Interacting with eHealth: towards grand challenges for HCI - André,P.; White,R.; Tan,D.; Berners-Lee,T.; Consolvo,S.; Jacobs,R.; Kohane,I.; Le Dantec,C.A.; Mamykina,L.; Marsden,G. (Proceedings of the 27th international conference extended abstracts on Human factors in computing systems, 2009)
While health records are increasingly stored electronically, we, as citizens, have little access to this data about ourselves. We are not used to thinking of these official records either as ours or as useful to us. We increasingly turn to the Web, however, to query any ache, pain or health goal we may have before consulting with health care professionals. Likewise, for proactive health care such as nutrition or fitness, or to find fellow-sufferers for post diagnosis support, we turn to online resources. There is a potential disconnect between points at which professional and lay eHealth data and resources intersect for preventative or proactive health care. Such gaps in information sharing may have direct impact on practices we decide to take up, the care we seek, or the support professionals offer. In this panel, we consider several places within proactive, preventative health care in particular HCI has a role towards enhancing health knowledge discovery and health support interaction. Our goal is to demonstrate how now is the time for eHealth to come to the forefront of the HCI research agenda.

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays - Bloom, Joshua S.; Zia Khan; Kruglyak, Leonid; Singh, Mona; Caudy, Amy A. (BMC Genomics, 2009)
Background High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression. Results Consequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of S. cerevisiae. Conclusion Using a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of S. cerevisiae that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.
Keywords: Animal Genetics and Genomics; Life Sciences, general; Microarrays; Microbial Genetics and Genomics; Plant Genetics & Genomics; proteomics

Microbial oceanography in a sea of opportunity - Bowler,Chris; Karl,David M.; Rita R Colwell (Nature, 2009)
Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean's response to climate change, improving the predictive power of climate models.
Keywords: Astronomy; astrophysics; Biochemistry; Bioinformatics; Biology; biotechnology; cancer; cell cycle; cell signalling; climate change; Computational Biology; development; developmental biology; DNA; drug discovery; earth science; ecology; environmental science; Evolution; evolutionary biology; functional genomics; Genetics; Genomics; geophysics; immunology; interdisciplinary science; life; marine biology; materials science; medical research; medicine; metabolomics; molecular biology; molecular interactions; nanotechnology; Nature; neurobiology; neuroscience; palaeobiology; pharmacology; Physics; proteomics; quantum physics; RNA; Science; science news; science policy; signal transduction; structural biology; systems biology; transcriptomics

Minimizing Communication Cost in Distributed Multi-query Processing - Li,Jian; Deshpande, Amol; Khuller, Samir (IEEE 25th International Conference on Data Engineering, 2009. ICDE '09, 2009)
Increasing prevalence of large-scale distributed monitoring and computing environments such as sensor networks, scientific federations, Grids etc., has led to a renewed interest in the area of distributed query processing and optimization. In this paper we address a general, distributed multi-query processing problem motivated by the need to minimize the communication cost in these environments. Specifically we address the problem of optimally sharing data movement across the communication edges in a distributed communication network given a set of overlapping queries and query plans for them (specifying the operations to be executed). Most of the problem variations of our general problem can be shown to be NP-Hard by a reduction from the Steiner tree problem. However, we show that the problem can be solved optimally if the communication network is a tree, and present a novel algorithm for finding an optimal data movement plan. For general communication networks, we present efficient approximation algorithms for several variations of the problem. Finally, we present an experimental study over synthetic datasets showing both the need for exploiting the sharing of data movement and the effectiveness of our algorithms at finding such plans.
Keywords: Approximation algorithms; Communication networks; Computer science; Cost function; Data engineering; distributed communication network; distributed databases; distributed multi-query processing; grid computing; Large-scale systems; NP-hard; optimisation; Polynomials; Publish-subscribe; publish-subscribe systems; Query optimization; Query processing; sensor networks; Steiner tree problem; Tree graphs; trees (mathematics)

Modal expansion of HRTFs: Continuous representation in frequency-range-angle - Zhang,Wen; Abhayapala,T.D.; Kennedy,R.A.; Duraiswami, Ramani (Acoustics, Speech and Signal Processing, 2009. ICASSP 2009. IEEE International Conference on, 2009)
This paper proposes a continuous HRTF representation in both 3D spatial and frequency domains. The method is based on the acoustic reciprocity principle and a modal expansion of the wave equation solution to represent the HRTF variations with different variables in separate basis functions. The derived spatial basis modes can achieve HRTF near-field and far-field representation in one formulation. The HRTF frequency components are expanded using Fourier Spherical Bessel series for compact representation. The proposed model can be used to reconstruct HRTFs at any arbitrary position in space and at any frequency point from a finite number of measurements. Analytical simulated and measured HRTFs from a KEMAR are used to validate the model.
Keywords: analysis; signal; bessel; domains; frequency-range-angle; head; expansion; modal; Fourier; function; modal; functions; reconstruction; signal; related; representation; transfer; series; HRTF; frequency; spherical; transfer

Modeling and Testing of Ethernet Transformers - Bowen,D.; Mayergoyz, Issak D; Zhang,Zhenyu; McAvoy,P.; Krafft,C.; Kroop,D. (Magnetics, IEEE Transactions on, 2009)
In this paper, novel techniques for the testing and identification of lumped parameters of equivalent circuits for Ethernet transformers are presented. It is demonstrated experimentally and theoretically that resonance phenomena may occur in the loop formed by leakage inductances and cross-winding capacitance. This resonance may corrupt the pass band of the transformers transfer characteristic for differential-mode signals.
Keywords: area; capacitance; differential-mode; characteristic; local; Ethernet; identification; lumped; inductances; lumped; networks; transformers; PARAMETERS; phenomena; transformers; signals; leakage; testing; resonance; transfer; transformers; cross-winding

New records of phytoplankton for Bangladesh. 9. Some rare and a new species - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Plant Taxonomy, 2009)
Ten taxa belonging to Chlorophyceae, Cyanophyceae, Bacillariophyceae and Euglenophyceae, and one with an uncertain taxonomic position have been described in this paper. Of these, 10 taxa have been found to be globally rare and new records for Bangladesh, whereas Strombomonas islamii Khondker sp. nov. has been described as new to science.

Observing Human-Object Interactions: Using Spatial and Functional Compatibility for Recognition - Gupta,A.; Kembhavi,A.; Davis, Larry S. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2009)
Interpretation of images and videos containing humans interacting with different objects is a daunting task. It involves understanding scene or event, analyzing human movements, recognizing manipulable objects, and observing the effect of the human movement on those objects. While each of these perceptual tasks can be conducted independently, recognition rate improves when interactions between them are considered. Motivated by psychological studies of human perception, we present a Bayesian approach which integrates various perceptual tasks involved in understanding human-object interactions. Previous approaches to object and action recognition rely on static shape or appearance feature matching and motion analysis, respectively. Our approach goes beyond these traditional approaches and applies spatial and functional constraints on each of the perceptual elements for coherent semantic interpretation. Such constraints allow us to recognize objects and actions when the appearances are not discriminative enough. We also demonstrate the use of such constraints in recognition of actions from static images without using any motion information.
Keywords: Automated; Recognition (Psychology); Video Recording; Bayesian approach; functional compatibility; human perception; human-object interactions; objects recognition; psychological studies; spatial compatibility; Bayes methods; behavioural sciences; human factors; image recognition; motion estimation; object recognition; A; Biological; Movement; Pattern Recognition; Computer-Assisted; Models

Online allocation of display advertisements subject to advanced sales contracts - Alaei,Saeed; Arcaute,Esteban; Khuller, Samir; Ma,Wenjing; Malekian,Azarakhsh; Tomlin,John (Proceedings of the Third International Workshop on Data Mining and Audience Intelligence for Advertising, 2009)
In this paper we propose a utility model that accounts for both sales and branding advertisers. We first study the computational complexity of optimization problems related to both online and offline allocation of display advertisements. Next, we focus on a particular instance of the online allocation problem, and design a simple online algorithm with provable approximation guarantees. Our algorithm is near optimal as is shown by a matching lower bound. Finally, we report on experiments to establish actual case behavior on some real datasets, with encouraging results.
Keywords: display advertising; modeling; online algorithms; OPTIMIZATION; simulation

Page Rule-Line Removal using Linear Subspaces in Monochromatic Handwritten Arabic Documents - Abd-Almageed, Wael; Kumar,Jayant; David Doermann (Intl. Conf. on Document Analysis and Recognition (ICDAR 09), 2009)
In this paper we present a novel method for removing page rule lines in monochromatic handwritten Arabic documents using subspace methods with minimal effect on the quality of the foreground text. We use moment and histogram properties to extract features that represent the characteristics of the underlying rule lines. A linear subspace is incrementally built to obtain a line model that can be used to identify rule line pixels. We also introduce a novel scheme for evaluating noise removal algorithms in general and we use it to assess the quality of our rule line removal algorithm. Experimental results presented on a data set of 50 Arabic documents, handwritten by different writers, demonstrate the effectiveness of the proposed method.

A phylogenetic mixture model for the evolution of gene expression - Eng,K. H; Corrada Bravo, Hector; Keleş,S. (Molecular biology and evolution, 2009)

Planning for Interactions among Autonomous Agents - Au,Tsz-Chiu; Kuter,Ugur; Nau, Dana S. (Programming Multi-Agent Systems, 2009)
AI planning research has traditionally focused on offline pl- anning for static single-agent environments. In environments where an agent needs to plan its interactions with other autonomous agents, planning is much more complicated, because the actions of the other agents can induce a combinatorial explosion in the number of contingencies that the planner will need to consider. This paper discusses several ways to alleviate the combinatorial explosion, and illustrates their use in several different kinds of multi-agent planning domains.
Keywords: Computer science

A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays - Zia Khan; Bloom, Joshua S.; Kruglyak, Leonid; Singh, Mona (Bioinformatics, 2009)
Motivation: High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences appear in two contexts where high-throughput sequencing will vastly increase the volume of sequence data: (i) seeding alignments of high-throughput reads for genome assembly and (ii) designating anchor points for genome–genome comparisons.Results: We introduce a new algorithm for finding MEMs. The algorithm leverages a sparse suffix array (SA), a text index that stores every K-th position of the text. In contrast to a full text index that stores every position of the text, a sparse SA occupies much less memory. Even though we use a sparse index, the output of our algorithm is the same as a full text index algorithm as long as the space between the indexed suffixes is not greater than a minimum length of a MEM. By relying on partial matches and additional text scanning between indexed positions, the algorithm trades memory for extra computation. The reduced memory usage makes it possible to determine MEMs between significantly longer sequences. Availability: Source code for the algorithm is available under a BSD open source license at http://compbio.cs.princeton.edu/mems. The implementation can serve as a drop-in replacement for the MEMs algorithm in MUMmer 3. Contact: zkhan@cs.princeton.edu;mona@cs.princeton.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Probabilistic graphical models - Gupta,A.; Kembhavi,A.; Davis, Larry S. (IEEE transactions on pattern analysis and machine intelligence, 2009)

Proceedings of the 1st ACM SIGKDD Workshop on Knowledge Discovery from Uncertain Data - Pei,Jian; Getoor, Lise; de Keijzer,Ander (ACM, 2009)
The importance of uncertain data is growing quickly in many essential applications such as environmental surveillance, mobile object tracking and data integration. Recently, storing, collecting, processing, and analyzing uncertain data has attracted increasing attention from both academia and industry. Analyzing and mining uncertain data needs collaboration and joint effort from multiple research communities including reasoning under uncertainty, uncertain databases and mining uncertain data. For example, statistics and probabilistic reasoning can provide support with models for representing uncertainty. The uncertain database community can provide methods for storing and managing uncertain data, while research in mining uncertain data can provide data analysis tasks and methods. It is important to build connections among those communities to tackle the overall problem of analyzing and mining uncertain data. There are many common challenges among the communities. One is to understand the different modeling assumptions made, and how they impact the methods, both in terms of accuracy and efficiency. Different researchers hold different assumptions and this is one of the major obstacles in the research of mining uncertain data. Another is the scalability of proposed management and analysis methods. Finally, to make analysis and mining useful and practical, we need real data sets for testing. Unfortunately, uncertain data sets are often hard to get. The goal of the First ACM SIGKDD Workshop on Knowledge Discovery from Uncertain Data (U'09) is to discuss in depth the challenges, opportunities and techniques on the topic of analyzing and mining uncertain data. The theme of this workshop is to make connections among the research areas of uncertain databases, probabilistic reasoning, and data mining, as well as to build bridges among the aspects of models, data, applications, novel mining tasks and effective solutions. By making connections among different communities, we aim at understanding each other in terms of scientific foundation as well as commonality and differences in research methodology. The workshop program is very stimulating and exciting. We are pleased to feature two invited talks by pioneers in mining uncertain data. Christopher Jermaine will give an invited talk titled "Managing and Mining Uncertain Data: What Might We Do Better?" Matthias Renz will address the topic "Querying and Mining Uncertain Data: Methods, Applications, and Challenges". Moreover, 8 accepted papers in 4 full presentations and 4 concise presentations will cover a bunch of interesting topics and on-going research projects about uncertain data mining.

Proofs of storage from homomorphic identification protocols - Ateniese,G.; Kamara,S.; Katz, Jonathan (Advances in Cryptology–ASIACRYPT 2009, 2009)
Proofs of storage (PoS) are interactive protocols allowing a client to verify that a server faithfully stores a file. Previous work has shown that proofs of storage can be constructed from any homomorphic linear authenticator (HLA). The latter, roughly speaking, are signature/message authentication schemes where ‘tags’ on multiple messages can be homomorphically combined to yield a ‘tag’ on any linear combination of these messages.We provide a framework for building public-key HLAs from any identification protocol satisfying certain homomorphic properties. We then show how to turn any public-key HLA into a publicly-verifiable PoS with communication complexity independent of the file length and supporting an unbounded number of verifications. We illustrate the use of our transformations by applying them to a variant of an identification protocol by Shoup, thus obtaining the first unbounded-use PoS based on factoring (in the random oracle model).

Protein quantification across hundreds of experimental conditions - Zia Khan; Bloom, Joshua S.; Garcia, Benjamin A.; Singh, Mona; Kruglyak, Leonid (Proceedings of the National Academy of Sciences, 2009)
Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than reading quantitative data from a gene expression microarray. To address this problem, we introduce two algorithmic advances in the processing of quantitative proteomics data. First, we use space-partitioning data structures to handle the large size of these datasets. Second, we introduce techniques that combine graph-theoretic algorithms with space-partitioning data structures to collect relative protein abundance data across hundreds of experimental conditions and replicates. We validate these algorithmic techniques by analyzing several datasets and computing both internal and external measures of quantification accuracy. We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates.
Keywords: kd-tree; orthogonal range query; quantitative proteomics; space partitioning data structures; tandem mass spectrometry

Reducing complexity assumptions for statistically-hiding commitment - Haitner,I.; Horvitz,O.; Katz, Jonathan; Koo,C. Y; Morselli,R.; Shaltiel,R. (Journal of cryptology, 2009)
We revisit the following question: what are the minimal assumptions needed to construct statistically-hiding commitment schemes? Naor et al. show how to construct such schemes based on any one-way permutation. We improve upon this by showing a construction based on any approximable preimage-size one-way function. These are one-way functions for which it is possible to efficiently approximate the number of pre-images of a given output. A special case is the class of regular one-way functions where all points in the image of the function have the same (known) number of pre-images.We also prove two additional results related to statistically-hiding commitment. First, we prove a (folklore) parallel composition theorem showing, roughly speaking, that the statistical hiding property of any such commitment scheme is amplified exponentially when multiple independent parallel executions of the scheme are carried out. Second, we show a compiler which transforms any commitment scheme which is statistically hiding against an honest-but-curious receiver into one which is statistically hiding even against a malicious receiver.

Revealing biological modules via graph summarization - Navlakha,S.; Schatz,M. C; Kingsford, Carl (Journal of Computational Biology, 2009)

Ring signatures: Stronger definitions, and constructions without random oracles - Bender,A.; Katz, Jonathan; Morselli,R. (Journal of Cryptology, 2009)
Ring signatures, first introduced by Rivest, Shamir, and Tauman, enable a user to sign a message so that a ring of possible signers (of which the user is a member) is identified, without revealing exactly which member of that ring actually generated the signature. In contrast to group signatures, ring signatures are completely “ad-hoc” and do not require any central authority or coordination among the various users (indeed, users do not even need to be aware of each other); furthermore, ring signature schemes grant users fine-grained control over the level of anonymity associated with any particular signature.This paper has two main areas of focus. First, we examine previous definitions of security for ring signature schemes and suggest that most of these prior definitions are too weak, in the sense that they do not take into account certain realistic attacks. We propose new definitions of anonymity and unforgeability which address these threats, and give separation results proving that our new notions are strictly stronger than previous ones. Second, we show the first constructions of ring signature schemes in the standard model. One scheme is based on generic assumptions and satisfies our strongest definitions of security. Two additional schemes are more efficient, but achieve weaker security guarantees and more limited functionality.

Saliency-guided lighting - Lee,C. H; Kim,Y.; Varshney, Amitabh (IEICE TRANSACTIONS on Information and Systems, 2009)

Scene it or not? incremental multiple kernel learning for object detection - Kembhavi,A.; Siddiquie,B.; Miezianko,R.; McCloskey,S.; Davis, Larry S.; Schwartz, W.R.; Harwood,D.; Gupta,A.; Farrell,R.; Luo,Y.; others (Proceedings of the International Conference on Computer Vision, 2009)

Scheduling to minimize staleness and stretch in real-time data warehouses - Bateni,M. H; Golab,L.; Hajiaghayi, Mohammad T.; Karloff,H. (Proceedings of the twenty-first annual symposium on Parallelism in algorithms and architectures, 2009)

Searching documentation using text, OCR, and image - Tom Yeh; Katz,Boris (Proceedings of the 32nd international ACM SIGIR conference on Research and development in information retrieval, 2009)
We describe a mixed-modality method to index and search software documentation in three ways: plain text, OCR text of embedded figures, and visual features of these figures. Using a corpus of 102 computer books with a total of 62,943 pages and 75,800 figures, we empirically demonstrate that our method achieves better precision/recall than do alternatives based on single modalities.
Keywords: Computer vision; content-based image retrieval; multimodal search

Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh - Alam,Munirul; Chowdhury,Wasimul B.; Bhuiyan,N. A.; Islam,Atiqul; Hasan,Nur A.; Nair,G. Balakrish; Watanabe,H.; Siddique,A. K.; Huq,Anwar; Sack,R. Bradley; Akhter,M. Z.; Grim,Christopher J.; et al. (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2009)
Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., “clonal cluster,” as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.

Signature schemes with bounded leakage resilience - Katz, Jonathan; Vaikuntanathan,V. (Advances in Cryptology–ASIACRYPT 2009, 2009)
A leakage-resilient cryptosystem remains secure even if arbitrary, but bounded, information about the secret key (and possibly other internal state information) is leaked to an adversary. Denote the length of the secret key by n. We show:• A full-fledged signature scheme tolerating leakage of n − n ε bits of information about the secret key (for any constant ε> 0), based on general assumptions. • A one-time signature scheme, based on the minimal assumption of one-way functions, tolerating leakage of (41−)n bits of information about the signer’s entire state. • A more efficient one-time signature scheme, that can be based on several specific assumptions, tolerating leakage of (21−)n bits of information about the signer’s entire state. The latter two constructions extend to give leakage-resilient t-time signature schemes. All the above constructions are in the standard model.

Signing a linear subspace: Signature schemes for network coding - Boneh,D.; Freeman,D.; Katz, Jonathan; Waters,B. (Public Key Cryptography–PKC 2009, 2009)
Network coding offers increased throughput and improved robustness to random faults in completely decentralized networks. In contrast to traditional routing schemes, however, network coding requires intermediate nodes to modify data packets en route; for this reason, standard signature schemes are inapplicable and it is a challenge to provide resilience to tampering by malicious nodes.We propose two signature schemes that can be used in conjunction with network coding to prevent malicious modification of data. Our schemes can be viewed as signing linear subspaces in the sense that a signature σ on a subspace V authenticates exactly those vectors in V. Our first scheme is (suitably) homomorphic and has constant public-key size and per-packet overhead. Our second scheme does not rely on random oracles and is based on weaker assumptions. We also prove a lower bound on the length of signatures for linear subspaces showing that our schemes are essentially optimal in this regard.

Smooth projective hashing and password-based authenticated key exchange from lattices - Katz, Jonathan; Vaikuntanathan,V. (Advances in Cryptology–ASIACRYPT 2009, 2009)
We describe a public-key encryption scheme based on lattices — specifically, based on the hardness of the learning with error (LWE) problem — that is secure against chosen-ciphertext attacks while admitting (a variant of) smooth projective hashing. This encryption scheme suffices to construct a protocol for password-based authenticated key exchange (PAKE) that can be proven secure based on the LWE assumption in the standard model. We thus obtain the first PAKE protocol whose security relies on a lattice-based assumption.

Streaming model based volume ray casting implementation for Cell Broadband Engine - Kim,Jusub; JaJa, Joseph F. (Scientific Programming, 2009)
Interactive high quality volume rendering is becoming increasingly more important as the amount of more complex volumetric data steadily grows. While a number of volumetric rendering techniques have been widely used, ray casting has been recognized as an effective approach for generating high quality visualization. However, for most users, the use of ray casting has been limited to datasets that are very small because of its high demands on computational power and memory bandwidth. However the recent introduction of the Cell Broadband Engine (Cell B.E.) processor, which consists of 9 heterogeneous cores designed to handle extremely demanding computations with large streams of data, provides an opportunity to put the ray casting into practical use. In this paper, we introduce an efficient parallel implementation of volume ray casting on the Cell B.E. The implementation is designed to take full advantage of the computational power and memory bandwidth of the Cell B.E. using an intricate orchestration of the ray casting computation on the available heterogeneous resources. Specifically, we introduce streaming model based schemes and techniques to efficiently implement acceleration techniques for ray casting on Cell B.E. In addition to ensuring effective SIMD utilization, our method provides two key benefits: there is no cost for empty space skipping and there is no memory bottleneck on moving volumetric data for processing. Our experimental results show that we can interactively render practical datasets on a single Cell B.E. processor.

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

A synthesis for exactly 3-edge-connected graphs - Kingsford, Carl; Marçais,G. (Arxiv preprint arXiv:0905.1053, 2009)

Task decomposition on abstract states, for planning under nondeterminism - Kuter,Ugur; Nau, Dana S.; Pistore,Marco; Traverso,Paolo (Artificial Intelligence, 2009)
Although several approaches have been developed for planning in nondeterministic domains, solving large planning problems is still quite difficult. In this work, we present a new planning algorithm, called Yoyo, for solving planning problems in fully observable nondeterministic domains. Yoyo combines an HTN-based mechanism for constraining its search and a Binary Decision Diagram (BDD) representation for reasoning about sets of states and state transitions.We provide correctness theorems for Yoyo, and an experimental comparison of it with MBP and ND-SHOP2, the two previously-best algorithms for planning in nondeterministic domains. In our experiments, Yoyo could easily deal with problem sizes that neither MBP nor ND-SHOP2 could scale up to, and could solve problems about 100 to 1000 times faster than MBP and ND-SHOP2.
Keywords: Binary decision diagrams; Hierarchical task-network (HTN) planning; Planning in nondeterministic domains

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

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.

Translating HTNs to PDDL: A small amount of domain knowledge can go a long way - Alford,R.; Kuter,U.; Nau, Dana S. (2009)
We show how to translate HTN domain descrip- tions (if they satisfy certain restrictions) into PDDL so that they can be used by classical planners. We provide correctness results for our translation al- gorithm, and show that it runs in linear time and space. We also show that even small and incom- plete amounts of HTN knowledge, when translated into PDDL using our algorithm, can greatly im- prove a classical planner’s performance. In ex- periments on several thousand randomly gener- ated problems in three different planning domains, such knowledge speeded up the well-known Fast- Forward planner by several orders of magnitude, and enabled it to solve much larger problems than it could otherwise solve.

UbiGreen: investigating a mobile tool for tracking and supporting green transportation habits - Jon Froehlich; Dillahunt,Tawanna; Klasnja,Predrag; Mankoff,Jennifer; Consolvo,Sunny; Harrison,Beverly; Landay,James A. (Proceedings of the 27th international conference on Human factors in computing systems, 2009)
Keywords: ambient displays; mobile phones; sensing; Sustainability; transportation; ubicomp

A unified approach to scheduling on unrelated parallel machines - Kumar,V. S. Anil; Marathe,Madhav V.; Parthasarathy,Srinivasan; Srinivasan, Aravind (J. ACM, 2009)
We develop a single rounding algorithm for scheduling on unrelated parallel machines; this algorithm works well with the known linear programming-, quadratic programming-, and convex programming-relaxations for scheduling to minimize completion time, makespan, and other well-studied objective functions. This algorithm leads to the following applications for the general setting of unrelated parallel machines: (i) a bicriteria algorithm for a schedule whose weighted completion-time and makespan simultaneously exhibit the current-best individual approximations for these criteria; (ii) better-than-two approximation guarantees for scheduling to minimize the Lp norm of the vector of machine-loads, for all 1 < p < ∞; and (iii) the first constant-factor multicriteria approximation algorithms that can handle the weighted completion-time and any given collection of integer Lp norms. Our algorithm has a natural interpretation as a melding of linear-algebraic and probabilistic approaches. Via this view, it yields a common generalization of rounding theorems due to Karp et al. [1987] and Shmoys & Tardos [1993], and leads to improved approximation algorithms for the problem of scheduling with resource-dependent processing times introduced by Grigoriev et al. [2007].
Keywords: Approximation algorithms; Randomized rounding; scheduling under multiple criteria

Using formal specifications to support testing - Hierons,Robert M.; Krause,Paul; Lüttgen,Gerald; Simons,Anthony J. H.; Vilkomir,Sergiy; Woodward,Martin R.; Zedan,Hussein; Bogdanov,Kirill; Bowen,Jonathan P.; Cleaveland, Rance; Derrick,John; Dick,Jeremy; et al. (ACM Computing Surveys, 2009)

Visibility constraints on features of 3D objects - Basri,R.; Felzenszwalb,P. F; Girshick,R. B; Jacobs, David W.; Klivans,C. J (Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on, 2009)
To recognize three-dimensional objects it is important to model how their appearances can change due to changes in viewpoint. A key aspect of this involves understanding which object features can be simultaneously visible under different viewpoints. We address this problem in an image-based framework, in which we use a limited number of images of an object taken from unknown viewpoints to determine which subsets of features might be simultaneously visible in other views. This leads to the problem of determining whether a set of images, each containing a set of features, is consistent with a single 3D object. We assume that each feature is visible from a disk of viewpoints on the viewing sphere. In this case we show the problem is NP-hard in general, but can be solved efficiently when all views come from a circle on the viewing sphere. We also give iterative algorithms that can handle noisy data and converge to locally optimal solutions in the general case. Our techniques can also be used to recover viewpoint information from the set of features that are visible in different images. We show that these algorithms perform well both on synthetic data and images from the COIL dataset.
Keywords: 3D; algorithms; synthetic; complexity; iterative; constraints; computational; data; synthetic; dataset; NP-hard; image-based; features; COIL; framework; iterative; images; three-dimensional; methods; object; object; recognition; recognition; viewing; sphere; visibility

Visual Tag - BRETEY,STEVE; Kuhnly,Keith; Davis, Larry S. (2009)
An improved animal tag for application to an animal's ear which comprises a male portion that includes a flat segment and a projection segment, a female portion that includes a generally square or generally oval shaped flat segment and a raised segment with an aperture; wherein the projection segment of the male portion is adapted to be inserted through the animal's ear and into the aperture when pressure is applied thereto.

What's being said near "Martha"? Exploring name entities in literary text collections - Vuillemot,R.; Clement,T.; Plaisant, Catherine; Kumar,A. (Visual Analytics Science and Technology, 2009. VAST 2009. IEEE Symposium on, 2009)
A common task in literary analysis is to study characters in a novel or collection. Automatic entity extraction, text analysis and effective user interfaces facilitate character analysis. Using our interface, called POSvis, the scholar uses word clouds and self-organizing graphs to review vocabulary, to filter by part of speech, and to explore the network of characters located near characters under review. Further, visualizations show word usages within an analysis window (i.e. a book chapter), which can be compared with a reference window (i.e. the whole book). We describe the interface and report on an early case study with a humanities scholar.
Keywords: analysis; humanities; analysis; literary; analysis; user; clouds; word; collection; name; entity; entity; part-of-speech; extraction; character; filtering; linguistics; text; filtering; self-organizing; graph; text; interface; vocabulary; word; interfaces; vocabulary; POSvis; automatic; scholar; literary; text; usage; data; visualisation; information

Accountable internet protocol (aip) - Andersen,David G.; Balakrishnan,Hari; Feamster, Nick; Koponen,Teemu; Moon,Daekyeong; Shenker,Scott (SIGCOMM Comput. Commun. Rev., 2008)
This paper presents AIP (Accountable Internet Protocol), a network architecture that provides accountability as a first-order property. AIP uses a hierarchy of self-certifying addresses, in which each component is derived from the public key of the corresponding entity. We discuss how AIP enables simple solutions to source spoofing, denial-of-service, route hijacking, and route forgery. We also discuss how AIP's design meets the challenges of scaling, key management, and traffic engineering.
Keywords: accountability; address; internet architecture; scalability; Security

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.

Action recognition using ballistic dynamics - Vitaladevuni,S.N.; Kellokumpu,V.; Davis, Larry S. (Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on, 2008)
We present a Bayesian framework for action recognition through ballistic dynamics. Psycho-kinesiological studies indicate that ballistic movements form the natural units for human movement planning. The framework leads to an efficient and robust algorithm for temporally segmenting videos into atomic movements. Individual movements are annotated with person-centric morphological labels called ballistic verbs. This is tested on a dataset of interactive movements, achieving high recognition rates. The approach is also applied on a gesture recognition task, improving a previously reported recognition rate from 84% to 92%. Consideration of ballistic dynamics enhances the performance of the popular Motion History Image feature. We also illustrate the approachpsilas general utility on real-world videos. Experiments indicate that the method is robust to view, style and appearance variations.
Keywords: analysis; image; Bayesian; dynamics; gesture; feature; person-centric; framework; action; History; image; labels; psycho-kinesiological; morphological; MOTION; Movement; movements; motion; planning; interactive; processing; recognition; recognition; ballistic; recognition; image; segmentation; video; signal; studies; image; task; human

Activity sensing in the wild: a field trial of ubifit garden - Consolvo,S.; McDonald,D.W.; Toscos,T.; Chen,M.Y.; Jon Froehlich; Harrison,B.; Klasnja,P.; LaMarca,A.; LeGrand,L.; Libby,R.; others (Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems, 2008)

Aggregate message authentication codes - Katz, Jonathan; Lindell,A. (Topics in Cryptology–CT-RSA 2008, 2008)
We propose and investigate the notion of aggregate message authentication codes (MACs) which have the property that multiple MAC tags, computed by (possibly) different senders on multiple (possibly different) messages, can be aggregated into a shorter tag that can still be verified by a recipient who shares a distinct key with each sender. We suggest aggregate MACs as an appropriate tool for authenticated communication in mobile ad-hoc networks or other settings where resource-constrained devices share distinct keys with a single entity (such as a base station), and communication is an expensive resource.

Approximation Algorithms for Computing Capacity of Wireless Networks with SINR Constraints - Chafekar,D.; Kumart,V. S.A; Marathe,M. V; Parthasarathy,S.; Srinivasan, Aravind (IEEE INFOCOM 2008. The 27th Conference on Computer Communications, 2008)
A fundamental problem in wireless networks is to estimate its throughput capacity - given a set of wireless nodes, and a set of connections, what is the maximum rate at which data can be sent on these connections. Most of the research in this direction has focused on either random distributions of points, or has assumed simple graph-based models for wireless interference. In this paper, we study capacity estimation problem using the more general Signal to Interference Plus Noise Ratio (SINR) model for interference, on arbitrary wireless networks. The problem becomes much harder in this setting, because of the non-locality of the SINR model. Recent work by Moscibroda et al. (2006) has shown that the throughput in this model can differ from graph based models significantly. We develop polynomial time algorithms to provably approximate the total throughput in this setting.
Keywords: Algorithm design and analysis; approximation algorithm; Approximation algorithms; approximation theory; Computer networks; Computer science; graph theory; graph-based model; Interference constraints; polynomial time algorithm; Propagation losses; Protocols; radio networks; radiofrequency interference; signal to interference plus noise ratio; Signal to noise ratio; Throughput; wireless interference; wireless network; Wireless networks

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

Bridging game theory and cryptography: recent results and future directions - Katz, Jonathan (Proceedings of the 5th conference on Theory of cryptography, 2008)
Motivated by the desire to develop more realistic models of, and protocols for, interactions between mutually distrusting parties, there has recently been significant interest in combining the approaches and techniques of game theory with those of cryptographic protocol design. Broadly speaking, two directions are currently being pursued: Applying cryptography to game theory: Certain game-theoretic equilibria are achievable if a trusted mediator is available. The question here is: to what extent can this mediator be replaced by a distributed cryptographic protocol run by the parties themselves? Applying game-theory to cryptography: Traditional cryptographic models assume some honest parties who faithfully follow the protocol, and some arbitrarily malicious players against whom the honest players must be protected. Game-theoretic models propose instead that all players are simply self-interested (i.e., rational), and the question then is: how can we model and design meaningful protocols for such a setting? In addition to surveying known results in each of the above areas, I suggest some new definitions along with avenues for future research.

Capacity of Asynchronous Random-Access Scheduling in Wireless Networks - Chafekar,D.; Levin,D.; Kumar,V. S.A; Marathe,M. V; Parthasarathy,S.; Srinivasan, Aravind (IEEE INFOCOM 2008. The 27th Conference on Computer Communications, 2008)
We study the throughput capacity of wireless networks which employ (asynchronous) random-access scheduling as opposed to deterministic scheduling. The central question we answer is: how should we set the channel-access probability for each link in the network so that the network operates close to its optimal throughput capacity? We design simple and distributed channel-access strategies for random-access networks which are provably competitive with respect to the optimal scheduling strategy, which is deterministic, centralized, and computationally infeasible. We show that the competitiveness of our strategies are nearly the best achievable via random-access scheduling, thus establishing fundamental limits on the performance of random- access. A notable outcome of our work is that random access compares well with deterministic scheduling when link transmission durations differ by small factors, and much worse otherwise. The distinguishing aspects of our work include modeling and rigorous analysis of asynchronous communication, asymmetry in link transmission durations, and hidden terminals under arbitrary link-conflict based wireless interference models.
Keywords: asynchronous random-access scheduling; channel access probability; Computer networks; Computer science; Educational institutions; Interference; Optimal scheduling; Peer to peer computing; probability; Processor scheduling; radio link; radio links; radio networks; Routing; scheduling; Throughput; throughput capacity; wireless channels; Wireless networks

On classification, ranking, and probability estimation - Flach,P.; Matsubara,E.T.; De Raedt,L.; Dietterich,T.; Getoor, Lise; Kersting,K.; Muggleton,S. H (Internationales Begegnungs- und Forschungszentrum fur Informatik (IBFI), Schloss Dagstuhl, Germany, 2008)
Given a binary classification task, a ranker is an algorithm that can sort a set of instances from highest to lowest expectation that the instance is positive. In contrast to a classifier, a ranker does not output class predictions – although it can be turned into a classifier with help of an additional procedure to split the ranked list into two. A straightforward way to compute rankings is to train a scoring classifier to assign numerical scores to instances, for example the predicted odds that an instance is positive. However, rankings can be computed without scores, as we demonstrate in this paper. We propose a lexicographic ranker, LexRank , whose rankings are derived not from scores, but from a simple ranking of attribute values obtained from the training data. Although various metrics can be used, we show that by using the odds ratio to rank the attribute values we obtain a ranker that is conceptually close to the naive Bayes classifier, in the sense that for every instance of LexRank there exists an instance of naive Bayes that achieves the same ranking. However, the reverse is not true, which means that LexRank is more biased than naive Bayes. We systematically develop the relationships and differences between classification, ranking, and probability estimation, which leads to a novel connection between the Brier score and ROC curves. Combining LexRank with isotonic regression, which derives probability estimates from the ROC convex hull, results in the lexicographic probability estimator LexProb.

Combining Domain-Independent Planning and HTN Planning: The Duet Planner - Gerevini,Alfonso; Kuter,Ugur; Nau, Dana S.; Saetti,Alessandro; Waisbrot,Nathaniel (IOS Press, 2008)
Despite the recent advances in planning for classical domains, the question of how to use domain knowledge in planning is yet to be completely and clearly answered. Some of the existing planners use domain-independent search heuristics, and some others depend on intensively-engineered domain-specific knowledge to guide the planning process. In this paper, we describe an approach to combine ideas from both of the above schools of thought. We present Duet, our planning system that incorporates the ability of using hierarchical domain knowledge in the form of Hierarchical Task Networks (HTNs) as in SHOP2 [14] and using domain-independent local search techniques as in LPG [8]. In our experiments, Duet was able to solve much larger problems than LPG could solve, with only minimal domain knowledge encoded in HTNs (much less domain knowledge than SHOP2 needed to solve those problems by itself).

On the Comparison of Network Attack Datasets: An Empirical Analysis - Berthier,R.; Korman,D.; Michel Cukier; Hiltunen,M.; Vesonder,G.; Sheleheda,D. (2008)
Network malicious activity can be collected and reported by various sources using different attack detection solutions. The granularity of these solutions provides either very detailed information (intrusion detection systems, honeypots) or high-level trends (CAIDA, SANS). The problem for network security operators is often to select the sources of information to better protect their network. How much information from these sources is redundant and how much is unique? The goal of this paper is to show empirically that while some global attack events can be correlated across various sensors, the majority of incoming malicious activity has local specificities. This study presents a comparative analysis of four different attack datasets offering three different levels of granularity: 1) two high interaction honeynets deployed at two different locations (i.e., a corporate and an academic environment); 2) ATLAS which is a distributed network telescope from Arbor; and 3) Internet Protecttrade which is a global alerting service from AT amp;T.
Keywords: ATLAS; distributed network telescope; Internet; intrusion detection systems; network attack datasets; network malicious activity; network security operators; security of data

The Complete Genome Sequence of Thermococcus Onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism - Lee,Hyun Sook; Kang,Sung Gyun; Bae,Seung Seob; Lim,Jae Kyu; Cho,Yona; Kim,Yun Jae; Jeon,Jeong Ho; Cha,Sun-Shin; Kwon,Kae Kyoung; Kim,Hyung-Tae; Park,Cheol-Joo; Lee,Hee-Wook; et al. (Journal of BacteriologyJ. Bacteriol., 2008)
Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO2, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus.

Context and observation driven latent variable model for human pose estimation - Gupta,A.; Chen,T.; Chen,F.; Kimber,D.; Davis, Larry S. (Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on, 2008)
Current approaches to pose estimation and tracking can be classified into two categories: generative and discriminative. While generative approaches can accurately determine human pose from image observations, they are computationally expensive due to search in the high dimensional human pose space. On the other hand, discriminative approaches do not generalize well, but are computationally efficient. We present a hybrid model that combines the strengths of the two in an integrated learning and inference framework. We extend the Gaussian process latent variable model (GPLVM) to include an embedding from observation space (the space of image features) to the latent space. GPLVM is a generative model, but the inclusion of this mapping provides a discriminative component, making the model observation driven. Observation Driven GPLVM (OD-GPLVM) not only provides a faster inference approach, but also more accurate estimates (compared to GPLVM) in cases where dynamics are not sufficient for the initialization of search in the latent space. We also extend OD-GPLVM to learn and estimate poses from parameterized actions/gestures. Parameterized gestures are actions which exhibit large systematic variation in joint angle space for different instances due to difference in contextual variables. For example, the joint angles in a forehand tennis shot are function of the height of the ball (Figure 2). We learn these systematic variations as a function of the contextual variables. We then present an approach to use information from scene/objects to provide context for human pose estimation for such parameterized actions.
Keywords: estimation; estimation; image; Gaussian; gestures; pose; latent; learning; parameterized; model; human; observations; integrated; pose; process; processes; gesture; processing; pose; recognition; image; tracking; Gaussian; variable

Digital Signatures - Yung,M.; Katz, Jonathan (Springer Verlag, 2008)

Directing javascript with arrows (functional pearl) - Khoo,Y.P.; Hicks, Michael W.; Foster, Jeffrey S.; Sazawal,V. (Technical Reports of the Computer Science Department, 2008)
JavaScript, being a single-threaded language, makes extensive use of event-driven programming to enable responsive web applications. However, standard approaches to sequencing events are messy, and often lead to code that is difficult to understand and maintain. We have found that arrows, a generalization of monads, are an elegant solution to this problem. Arrows allow us to easily write asynchronous programs in small, modular units of code, and flexibly compose them in many different ways, while nicely abstracting the details of asynchronous program composition. In particular, we show how to use arrows to construct a variety of state machines, such as autoscrollers and drag-and-drop handlers.

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 and Resilient Backbones for Multihop Wireless Networks - Lee,Seungjoon; Bhattacharjee, Bobby; Srinivasan, Aravind; Khuller, Samir (Mobile Computing, IEEE Transactions on, 2008)
We consider the problem of finding "backbones" in multihop wireless networks. The backbone provides end-to-end connectivity, allowing nonbackbone nodes to save energy since they do not have to route nonlocal data or participate in the routing protocol. Ideally, such a backbone would be small, consist primarily of high capacity nodes, and remain connected even when nodes are mobile or fail. Unfortunately, it is often infeasible to construct a backbone that has all of these properties; e.g., a small optimal backbone is often too sparse to handle node failures or high mobility. We present a parameterized backbone construction algorithm that permits explicit trade-offs between backbone size, resilience to node movement and failure, energy consumption, and path lengths. We prove that our scheme can construct essentially best possible backbones (with respect to energy consumption and backbone size) when the network is relatively static. We generalize our scheme to build more robust structures better suited to networks with higher mobility. We present a distributed protocol based upon our algorithm and show that this protocol builds and maintains a connected backbone in dynamic networks. Finally, we present detailed packet-level simulation results to evaluate and compare our scheme with existing energy-saving techniques. Our results show that, depending on the network environment, our scheme increases network lifetimes by 20 percent to 220 percent without adversely affecting delivery ratio or end-to-end latency.
Keywords: algorithm; protocols; wireless; backbone; channels; CONSTRUCTION; distributed; networks; parameterized; protocol; multihop; wireless

Embedded menus: selecting items in context - Koved,L.; Shneiderman, Ben (Sparks of innovation in human-computer interaction, 2008)

Energy Efficient Monitoring in Sensor Networks - Deshpande, Amol; Khuller, Samir; Malekian,Azarakhsh; Toossi,Mohammed (LATIN 2008: Theoretical InformaticsLATIN 2008: Theoretical Informatics, 2008)
In this paper we study a set of problems related to efficient energy management for monitoring applications in wireless sensor networks. We study several generalizations of a basic problem called Set k -Cover, which can be described as follows: we are given a set of sensors, and a set of regions to be monitored. Each region can be monitored by a subset of the sensors. To increase the lifetime of the sensor network, we would like to partition the sensors into k sets (or time-slots) and activate each partition in a different time-slot. The goal is to find the partitioning that maximizes the coverage of the regions. This problem is known to be NP -hard. We first develop improved approximation algorithms for this problem based on its similarities to the max k -cut problem. We then consider a variation, called Set ( k , α )-cover, where each sensor is allowed to be active in α different time-slots. We develop a randomized routing algorithm for this problem. We then consider extensions where each sensor can monitor only a bounded number of regions in any time-slot. We develop the first approximation algorithms for this problem. An experimental evaluation of the algorithms we propose can be found in the full version of the paper.

Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming with an Application to Phylogenetic Analysis of Gene Expression - Corrada Bravo, Hector; Eng,K. H; Keles,S.; Wahba,G.; Wright,S. (Department of Statistics, University of Wisconsin, 2008)
We present a novel method for estimating tree-structured covariance matrices directly fromobserved continuous data. A representation of these classes of matrices as linear combinations of rank-one matrices indicating object partitions is used to formulate estimation as instances of well-studied numerical optimization problems. In particular, we present estimation based on projection where the covariance estimate is the nearest tree-structured covariance matrix to an observed sample covariance matrix. The problem is posed as a linear or quadratic mixed-integer program (MIP) where a setting of the integer variables in the MIP specifies a set of tree topologies of the structured covariance matrix. We solve these problems to optimality using efficient and robust existing MIP solvers. We also show that the least squares distance method of Fitch and Margoliash (1967) can be formulated as a quadratic MIP and thus solved exactly using existing, robust branch-and-bound MIP solvers. Our motivation for this method is the discovery of phylogenetic structure directly from gene expression data. Recent studies have adapted traditional phylogenetic comparative anal- ysis methods to expression data. Typically, these methods first estimate a phylogenetic tree from genomic sequence data and subsequently analyze expression data. A covariance matrix constructed from the sequence-derived tree is used to correct for the lack of independence in phy- logenetically related taxa. However, recent results have shown that the hierarchical structure of sequence-derived tree estimates are highly sensitive to the genomic region chosen to build them. To circumvent this difficulty, we propose a stable method for deriving tree-structured covariance matrices directly from gene expression as an exploratory step that can guide investigators in their modelling choices for these types of comparative analysis. We present a case study in phylogenetic analysis of expression in yeast gene families. Our method is able to corroborate the presence of phylogenetic structure in the response of expression in a subset of the gene families under particular experimental conditions. Additionally, when used in conjunction with transcription factor occupancy data, our methods show that alternative modelling choices should be considered when creating sequence-derived trees for this comparative analysis.

Evaluating Exploratory Search Systems - Kules,B.; Shneiderman, Ben (Information processing & management, 2008)

Exploiting Prior Knowledge in Intelligent Assistants: Combining Relational Models with Hierarchies - Natarajan,S.; Tadepalli,P.; Fern,A.; De Raedt,L.; Dietterich,T.; Getoor, Lise; Kersting,K.; Muggleton,S. H (Probabilistic, Logical and Relational Learning - A Further Synthesis, 2008)
Statitsical relational models have been successfully used to model static probabilistic relationships between the entities of the domain. In this talk, we illustrate their use in a dynamic decison-theoretic setting where the task is to assist a user by inferring his intentional structure and taking appropriate assistive actions. We show that the statistical relational models can be used to succintly express the system's prior knowledge about the user's goal-subgoal structure and tune it with experience. As the system is better able to predict the user's goals, it improves the effectiveness of its assistance. We show through experiments that both the hierarchical structure of the goals and the parameter sharing facilitated by relational models significantly improve the learning speed.

Extending sense-making models with ideas from cognition and learning theories - Zhang,P.; Soergel,D.; Klavans,J. L; Oard, Douglas (Proceedings of the American Society for Information Science and Technology, 2008)

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 flux service networks: Dynamics and roles in hosting online scams - Konte,M.; Feamster, Nick; Jung,J. (School of Computer Science, Georgia Tech, 2008)
This paper studies the dynamics of fast flux service networks and their role in online scam hosting infrastructures. By monitoring changes in DNS records of over 350 distinct fast flux domains collected from URLs in 115,000 spam emails at a large spam sinkhole, we measure the rate of change of DNS records, accumulation of new distinct IPs in the hosting infrastructure, and location of change both for individual domains and across 21 different scam campaigns. We find that fast flux networks redirect clients at much different rates—and at different locations in the DNS hierarchy—than conventional load-balanced Web sites. We also find that the IP addresses in the fast flux infrastructure itself change rapidly, and that this infrastructure is shared extensively across scam campaigns, and some of these IP addresses are also used to send spam. Finally, we compared IP addresses in fast-flux infrastructure and flux domains with various blacklists (i.e., SBL, XBL/PBL, and URIBL) and found that nearly one-third of scam sites were not listed in the URL blacklist at the time they were hosting scams. We also observed many hosting sites and nameservers that were listed in both the SBL and XBL both before and after we observed fast-flux activity; these observations lend insight into both the responsiveness of existing blacklists and the life cycles of fast-flux nodes.

A Fault Model for Upgrades in Distributed Systems (CMU-PDL-08-115) - Tudor Dumitras; Kavulya, Soila; Narasimhan, Priya (Parallel Data Laboratory, 2008)

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.

Flowers or a robot army?: encouraging awareness & activity with personal, mobile displays - Consolvo,Sunny; Klasnja,Predrag; McDonald,David W.; Avrahami,Daniel; Jon Froehlich; LeGrand,Louis; Libby,Ryan; Mosher,Keith; Landay,James A. (Proceedings of the 10th international conference on Ubiquitous computing, 2008)
Personal, mobile displays, such as those on mobile phones, are ubiquitous, yet for the most part, underutilized. We present results from a field experiment that investigated the effectiveness of these displays as a means for improving awareness of daily life (in our case, self-monitoring of physical activity). Twenty-eight participants in three experimental conditions used our UbiFit system for a period of three months in their day-to-day lives over the winter holiday season. Our results show, for example, that participants who had an awareness display were able to maintain their physical activity level (even during the holidays), while the level of physical activity for participants who did not have an awareness display dropped significantly. We discuss our results and their general implications for the use of everyday mobile devices as awareness displays.
Keywords: ambient display; awareness; calm technology; field experiment; fitness; glanceable display; mobile phone; personal mobile display; persuasive technology; physical activity

Growth of the flickr social network - Mislove,Alan; Koppula,Hema Swetha; Gummadi,Krishna P.; Druschel,Peter; Bhattacharjee, Bobby (Proceedings of the first workshop on Online social networks, 2008)
Online social networking sites like MySpace, Orkut, and Flickr are among the most popular sites on the Web and continue to experience dramatic growth in their user population. The popularity of these sites offers a unique opportunity to study the dynamics of social networks at scale. Having a proper understanding of how online social networks grow can provide insights into the network structure, allow predictions of future growth, and enable simulation of systems on networks of arbitrary size. However, to date, most empirical studies have focused on static network snapshots rather than growth dynamics. In this paper, we collect and examine detailed growth data from the Flickr online social network, focusing on the ways in which new links are formed. Our study makes two contributions. First, we collect detailed data covering three months of growth, encompassing 950,143 new users and over 9.7 million new links, and we make this data available to the research community. Second, we use a first-principles approach to investigate the link formation process. In short, we find that links tend to be created by users who already have many links, that users tend to respond to incoming links by creating links back to the source, and that users link to other users who are already close in the network.
Keywords: growth; measurement; social networks

Handling expected polynomial-time strategies in simulation-based security proofs - Katz, Jonathan; Lindell,Y. (Journal of Cryptology, 2008)
The standard class of adversaries considered in cryptography is that of strict polynomial-time probabilistic machines. However, expected polynomial-time machines are often also considered. For example, there are many zero-knowledge protocols for which the only known simulation techniques run in expected (and not strict) polynomial time. In addition, it has been shown that expected polynomial-time simulation is essential for achieving constant-round black-box zero-knowledge protocols. This reliance on expected polynomial-time simulation introduces a number of conceptual and technical difficulties. In this paper, we develop techniques for dealing with expected polynomial-time adversaries in simulation-based security proofs.

Hci for community and international development - Thomas, John; Dearden, Andy; Dray, Susan; Light, Ann; Best, Michael; Arkin, Nuray; Maunder, Andrew; Kam, Mathew; Marshini Chetty; Sambasivan, Nithya; Buckhalter, Celeste; Krishnan, Gaurishankar (SIGCHI EA '08, 2008)
This workshop explores the challenges in applying, extending and inventing appropriate methods and contributions of Human Computer Interaction (HCI) to International economic and community Development. We address interaction design for parts of the world that are often marginalized by the Global North as well as people in the Global North who are themselves similarly marginalized by poverty or other barriers. We hope to extend the boundaries of the field of Human Computer Interaction by spurring a discussion on how existing methods and practices can be adapted and modified, and how new practices can be developed, to deal with the unique challenges posed by these contexts.
Keywords: community design; ict4d; information and communication technology; international development; participatory design; ucd4id; User centered design

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.

How to encrypt with a malicious random number generator - Kamara,S.; Katz, Jonathan (Fast Software Encryption, 2008)
Chosen-plaintext attacks on private-key encryption schemes are currently modeled by giving an adversary access to an oracle that encrypts a given message m using random coins that are generated uniformly at random and independently of anything else. This leaves open the possibility of attacks in case the random coins are poorly generated (e.g., using a faulty random number generator), or are under partial adversarial control (e.g., when encryption is done by lightweight devices that may be captured and tampered with).We introduce new notions of security modeling such attacks, propose two concrete schemes meeting our definitions, and show generic transformations for achieving security in this context.

Implicit Flows: Can’t Live with ‘Em, Can’t Live without ‘Em - King,Dave; Hicks,Boniface; Hicks, Michael W.; Jaeger,Trent (Information Systems SecurityInformation Systems Security, 2008)
Verifying that programs trusted to enforce security actually do so is a practical concern for programmers and administrators. However, there is a disconnect between the kinds of tools that have been successfully applied to real software systems (such as taint mode in Perl and Ruby), and information-flow compilers that enforce a variant of the stronger security property of noninterference. Tools that have been successfully used to find security violations have focused on explicit flows of information, where high-security information is directly leaked to output. Analysis tools that enforce noninterference also prevent implicit flows of information, where high-security information can be inferred from a program’s flow of control. However, these tools have seen little use in practice, despite the stronger guarantees that they provide. To better understand why, this paper experimentally investigates the explicit and implicit flows identified by the standard algorithm for establishing noninterference. When applied to implementations of authentication and cryptographic functions, the standard algorithm discovers many real implicit flows of information, but also reports an extremely high number of false alarms, most of which are due to conservative handling of unchecked exceptions (e.g., null pointer exceptions). After a careful analysis of all sources of true and false alarms, due to both implicit and explicit flows, the paper concludes with some ideas to improve the false alarm rate, toward making stronger security analysis more practical.

Improving the round complexity of vss in point-to-point networks - Katz, Jonathan; Koo,C. Y; Kumaresan,R. (Automata, Languages and Programming, 2008)
We revisit the following question: what is the optimal round complexity of verifiable secret sharing (VSS)? We focus here on the case of perfectly-secure VSS where the number of corrupted parties t satisfies t < n/3, with n being the total number of parties. Work of Gennaro et al. (STOC 2001) and Fitzi et al. (TCC 2006) shows that, assuming a broadcast channel, 3 rounds are necessary and sufficient for efficient VSS. The efficient 3-round protocol of Fitzi et al., however, treats the broadcast channel as being available “for free” and does not attempt to minimize its usage. This approach leads to relatively poor round complexity when protocols are compiled for a point-to-point network.We show here a VSS protocol that is simultaneously optimal in terms of both the number of rounds and the number of invocations of broadcast. Our protocol also has a certain “2-level sharing” property that makes it useful for constructing protocols for general secure computation.

Integrating categorical resource types into a P2P desktop grid system - Kim,Jik-Soo; Nam,Beomseok; Marsh,M.; Keleher,P.; Bhattacharjee, Bobby; Sussman, Alan (Grid Computing, 2008 9th IEEE/ACM International Conference on, 2008)
We describe and evaluate a set of protocols that implement a distributed, decentralized desktop grid. Incoming jobs are matched with system nodes through proximity in an N-dimensional resource space. This work improves on prior work by (1) efficiently accommodating node and job characterizations that include both continuous and categorical resource types, and (2) scaling gracefully to large system sizes even with highly non-uniform distributions of job and node types. We use extensive simulation results to show that the resulting system handles both continuous and categorical constraints efficiently, and that the new scalability techniques are effective.
Keywords: computing; peer-to-peer; computing; protocols; computing; protocols; scalability; desktop; Grid; grid; distributed; grid; peer-to-peer; N-dimensional; resource; space; P2P; system; categorical; technique; grid; types; decentralized

Interactive Entity Resolution in Relational Data: A Visual Analytic Tool and Its Evaluation - Kang,Hyunmo; Getoor, Lise; Shneiderman, Ben; Bilgic,M.; Licamele,L. (IEEE Transactions on Visualization and Computer Graphics, 2008)
Databases often contain uncertain and imprecise references to real-world entities. Entity resolution, the process of reconciling multiple references to underlying real-world entities, is an important data cleaning process required before accurate visualization or analysis of the data is possible. In many cases, in addition to noisy data describing entities, there is data describing the relationships among the entities. This relational data is important during the entity resolution process; it is useful both for the algorithms which determine likely database references to be resolved and for visual analytic tools which support the entity resolution process. In this paper, we introduce a novel user interface, D-Dupe, for interactive entity resolution in relational data. D-Dupe effectively combines relational entity resolution algorithms with a novel network visualization that enables users to make use of an entity's relational context for making resolution decisions. Since resolution decisions often are interdependent, D-Dupe facilitates understanding this complex process through animations which highlight combined inferences and a history mechanism which allows users to inspect chains of resolution decisions. An empirical study with 12 users confirmed the benefits of the relational context visualization on the performance of entity resolution tasks in relational data in terms of time as well as users' confidence and satisfaction.
Keywords: algorithms; Computer Graphics; D-Dupe; data visualisation; database management systems; Databases, Factual; graphical user interface; Graphical user interfaces; human-centered computing; Image Interpretation, Computer-Assisted; Information Storage and Retrieval; Information Visualization; interactive entity resolution; relational context visualization; Relational databases; relational entity resolution algorithm; User interfaces; user-centered design; User-Computer Interface; visual analytic tool

Introduction to Modern Cryptography - Katz, Jonathan; Lindell,Yehuda (CRC Press, 2008)
Cryptography plays a key role in ensuring the privacy and integrity of data and the security of computer networks. Introduction to Modern Cryptography provides a rigorous yet accessible treatment of modern cryptography, with a focus on formal definitions, precise assumptions, and rigorous proofs. The authors introduce the core principles of modern cryptography, including the modern, computational approach to security that overcomes the limitations of perfect secrecy. An extensive treatment of private-key encryption and message authentication follows. The authors also illustrate design principles for block ciphers, such as the Data Encryption Standard (DES) and the Advanced Encryption Standard (AES), and present provably secure constructions of block ciphers from lower-level primitives. The second half of the book focuses on public-key cryptography, beginning with a self-contained introduction to the number theory needed to understand the RSA, Diffie-Hellman, El Gamal, and other cryptosystems. After exploring public-key encryption and digital signatures, the book concludes with a discussion of the random oracle model and its applications. Serving as a textbook, a reference, or for self-study, Introduction to Modern Cryptography presents the necessary tools to fully understand this fascinating subject.
Keywords: Computer networks; computer security; Computers / Operating Systems / General; Computers / Security / General; cryptography; Language Arts & Disciplines / Communication Studies; Mathematics / Combinatorics

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

Memory-constrained block processing for dsp software optimization - Ko,M. Y; Shen,C. C; Bhattacharyya, Shuvra S. (Journal of Signal Processing Systems, 2008)

A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13 - Kohlsdorf,T; Cummings, Michael P.; Lynch,VJ; Stopper,GF; Takahashi,K; Wagner,GP (J Mol Evol, 2008)
The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with the release of functional constraints caused by limb loss. Fragments of the Hoxa-13 exon 1 were sequenced from 13 species and analyzed, with additional published sequences of the same region, using relative rates and likelihood-ratio tests. Five amino acid sites in exon 1 of Hoxa-13 were detected as evolving under positive selection in the stem lineage of snakes. To further investigate whether there is an association between limb loss and sequence variation in Hoxa-13, we used the random forest method on an alignment that included shark, basal fish lineages, and "eu-tetrapods" such as mammals, turtle, alligator, and birds. The random forest method approaches the problem as one of classification, where we seek to predict the presence or absence of autopodium based on amino acid variation in Hoxa-13 sequences. Different alignments tested were associated with similar error rates (18.42%). The random forest method suggested that phenotypic states (autopodium present and absent) can often be correctly predicted based on Hoxa-13 sequences. Basal, nontetrapod gnat-hostomes that never had an autopodium were consistently classified as limbless together with the snakes, while eu-tetrapods without any history of limb loss in their phylogeny were also consistently classified as having a limb. Misclassifications affected mostly lizards, which, as a group, have a history of limb loss and limb re-evolution, and the urodele and caecilian in our sample. We conclude that a molecular footprint can be detected in Hoxa-13 that is associated with the lack of an autopodium; groups with classification ambiguity (lizards) are characterized by a history of repeated limb loss and possible limb re-evolution.

Name translation in statistical machine translation: Learning when to transliterate - Hermjakob,U.; Knight,K.; Daumé, Hal (Proceedings of ACL-08: HLT, 2008)

New records of phytoplankton for Bangladesh. 2. Cryptophyceae and Synurophyceae - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Botany, 2008)
This study presents two species of Rhodomonas, four species of Chroomonas, six species of Cryptomonas and Cryptochrysis minor, Cyanomonas coeruleus, Chrysodidymus synuroideus and Mallomonas akrokomos. These species have been reported from some ponds of Mathbaria in Pirojpur and Bakerganj of Barisal district in Bangladesh.

New records of phytoplankton for Bangladesh. 5. Euglena, Euglenocapsa - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Plant Taxonomy, 2008)
This study presents 20 taxa of the genus Euglena and one species of the rare euglenoid genus Euglenocapsa. All these taxa are reported for the first time from some pond ecosystems of Mathbaria in Pirojpur and Bakerganj of Barisal districts of Bangladesh.

New records of phytoplankton for Bangladesh. 7. Phacus spp. - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Botany, 2008)
Thirteen species of Phacus hitherto not reported from Bangladesh have been described and illustrated. Freshwater ponds at southern districts of Pirojpur and Barisal revealed these presence of the species.

New records of phytoplankton for Bangladesh. 8. Trachelomonas Ehr. (Euglenophyceae) - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Botany, 2008)
Investigation of pelagic plankton communities from some freshwater ponds of Pirojpur and Barisal districts revealed the presence of 17 species under the genus Trachelomonas Ehr. for the first time in Bangladesh.

One-handed touchscreen input for legacy applications - Karlson,A.K.; Bederson, Benjamin B. (Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems, 2008)

Online Filtering, Smoothing and Probabilistic Modeling of Streaming data - Kanagal,B.; Deshpande, Amol (IEEE 24th International Conference on Data Engineering, 2008. ICDE 2008, 2008)
In this paper, we address the problem of extending a relational database system to facilitate efficient real-time application of dynamic probabilistic models to streaming data. We use the recently proposed abstraction of model-based views for this purpose, by allowing users to declaratively specify the model to be applied, and by presenting the output of the models to the user as a probabilistic database view. We support declarative querying over such views using an extended version of SQL that allows for querying probabilistic data. Underneath we use particle filters, a class of sequential Monte Carlo algorithms, to represent the present and historical states of the model as sets of weighted samples (particles) that are kept up-to-date as new data arrives. We develop novel techniques to convert the queries on the model-based view directly into queries over particle tables, enabling highly efficient query processing. Finally, we present experimental evaluation of our prototype implementation over several synthetic and real datasets, that demonstrates the feasibility of online modeling of streaming data using our system and establishes the advantages of tight integration between dynamic probabilistic models and databases.
Keywords: Data analysis; data streaming; declarative query; dynamic probabilistic model; Filtering; Global Positioning System; hidden Markov models; Monitoring; Monte Carlo methods; Noise generators; Noise measurement; online filtering; particle filter; particle filtering (numerical methods); probabilistic database view; probability; Real time systems; real-time application; relational database system; Relational databases; sequential Monte Carlo algorithm; Smoothing methods; SQL

An Optimal Incremental Algorithm for Minimizing Lateness with Rejection - Khuller, Samir; Mestre,J. (Algorithms-ESA 2008, 2008)
This paper re-examines the classical problem of minimizing maximum lateness which is defined as follows: given a collection of n jobs with processing times and due dates, in what order should they be processed on a single machine to minimize maximum lateness? The lateness of a job is defined as its completion time minus its due date. This problem can be solved easily by ordering the jobs in non-decreasing due date order. We now consider the following question: which subset of k jobs should we reject to reduce the maximum lateness by the largest amount? While this problem can be solved optimally in polynomial time, we show the following surprising result: there is a fixed permutation of the jobs, such that for all k, if we reject the first k jobs from this permutation, we derive an optimal solution for the problem in which we are allowed to reject k jobs. This allows for an incremental solution in which we can keep incrementally rejecting jobs if we need a solution with lower maximum lateness value. Moreover, we also develop an optimal O(n logn) time algorithm to find this permutation.

Path projection for user-centered static analysis tools - Khoo,Yit Phang; Foster, Jeffrey S.; Hicks, Michael W.; Sazawal,Vibha (Proceedings of the 8th ACM SIGPLAN-SIGSOFT workshop on Program analysis for software tools and engineering, 2008)
The research and industrial communities have made great strides in developing sophisticated defect detection tools based on static analysis. To date most of the work in this area has focused on developing novel static analysis algorithms, but has neglected study of other aspects of static analysis tools, particularly user interfaces. In this work, we present a novel user interface toolkit called Path Projection that helps users visualize, navigate, and understand program paths, a common component of many tools' error reports. We performed a controlled user study to measure the benefit of Path Projection in triaging error reports from Locksmith, a data race detection tool for C. We found that Path Projection improved participants' time to complete this task without affecting accuracy, while participants felt Path Projection was useful and strongly preferred it to a more standard viewer.

Persuading Visual Attention through Geometry - Kim,Youngmin; Varshney, Amitabh (Visualization and Computer Graphics, IEEE Transactions on, 2008)
Artists, illustrators, photographers, and cinematographers have long used the principles of contrast and composition to guide visual attention. In this paper, we introduce geometry modification as a tool to persuasively direct visual attention. We build upon recent advances in mesh saliency to develop techniques to alter geometry to elicit greater visual attention. Eye-tracking-based user studies show that our approach successfully guides user attention in a statistically significant manner. Our approach operates directly on geometry and, therefore, produces view-independent results that can be used with existing view-dependent techniques of visual persuasion.
Keywords: attention; visual; generation; Attention; Awareness; Computer; Geometry; Graphics; Cues; Humans; Photic; Interface; Visual; modification; mesh; perception; persuasion; art; mesh; saliency; visual; Stimulation; User-Computer

Predicate encryption supporting disjunctions, polynomial equations, and inner products - Katz, Jonathan; Sahai,Amit; Waters,Brent (Proceedings of the theory and applications of cryptographic techniques 27th annual international conference on Advances in cryptology, 2008)
Predicate encryption is a new paradigm generalizing, among other things, identity-based encryption. In a predicate encryption scheme, secret keys correspond to predicates and ciphertexts are associated with attributes; the secret key SKf corresponding to a predicate f can be used to decrypt a ciphertext associated with attribute I if and only if f(I) = 1. Constructions of such schemes are currently known for relatively few classes of predicates. We construct such a scheme for predicates corresponding to the evaluation of inner products over ZN (for some large integer N). This, in turn, enables constructions in which predicates correspond to the evaluation of disjunctions, polynomials, CNF/DNF formulae, or threshold predicates (among others). Besides serving as a significant step forward in the theory of predicate encryption, our results lead to a number of applications that are interesting in their own right.

Resource allocation for tracking multiple targets using particle filters - Kembhavi,A.; Schwartz, W.R.; Davis, Larry S.; others (The Eighth International Workshop on Visual Surveillance, 2008)
Particle filters have been very widely used to track targets in video sequences. However, they suffer from an exponential rise in the number of particles needed to jointly track multiple targets. On the other hand, using multiple independent filters to track in crowded scenes often leads to erroneous results. We present a new particle filtering framework which uses an intelligent resource allocation scheme allowing us to track a large number of targets using a small set of particles. First, targets with overlapping posterior distributions and similar appearance models are clustered into interaction groups and tracked jointly, but independent of other targets in the scene. Second, different number of particles are allocated to different groups based on the following observations. Groups with higher associations (quantifying spatial proximity and pairwise appearance similarity) are given more particles. Groups with larger number of targets are given a larger number of particles. Finally, groups with ineffective proposal distributions are assigned more particles. Our experiments demonstrate the effectiveness of this framework over the commonly used joint particle filter with Markov Chain Monte Carlo (MCMC) sampling.

A review of overview+ detail, zooming, and focus+ context interfaces - Cockburn,A.; Karlson,A.; Bederson, Benjamin B. (ACM Computing Surveys (CSUR), 2008)

Route prediction from trip observations - Jon Froehlich; Krumm,J. (SAE SP, 2008)

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.

SNARE: Spatio-temporal Network-level Automatic Reputation Engine - Feamster, Nick; Gray,A.G.; Krasser,S.; Syed,N.A. (Georgia Institute of Technology, 2008)
Current spam filtering techniques classify email based oncontent and IP reputation blacklists or whitelists. Unfortu- nately, spammers can alter spam content to evade content- based filters, and spammers continually change the IP ad- dresses from which they send spam. Previous work has sug- gested that filters based on network-level behavior might be more efficient and robust, by making decisions based on how messages are sent, as opposed to what is being sent or who is sending them. This paper presents a technique to identify spammers based on features that exploit the network-level spatio- temporal behavior of email senders to differentiate the spam- ming IPs from legitimate senders. Our behavioral classifier has two benefits: (1) it is early (i.e., it can automatically detect spam without seeing a large amount of email from a sending IP address—sometimes even upon seeing only a single packet); (2) it is evasion-resistant (i.e., it is based on spatial and temporal features that are difficult for a sender to change). We build classifiers based on these features us- ing two different machine learning methods, support vec- tor machine and decision trees, and we study the efficacy of these classifiers using labeled data from a deployed com- mercial spam-filtering system. Surprisingly, using only fea- tures from a single IP packet header (i.e., without looking at packet contents), our classifier can identify spammers with about 93% accuracy and a reasonably low false-positive rate (about 7%). After looking at a single message spammer identification accuracy improves to more than 94% with a false rate of just over 5%. These suggest an effective sender reputation mechanism.

Streaming algorithms for k-center clustering with outliers and with anonymity - Matthew McCutchen,R.; Khuller, Samir (Approximation, Randomization and Combinatorial Optimization. Algorithms and Techniques, 2008)
Clustering is a common problem in the analysis of large data sets. Streaming algorithms, which make a single pass over the data set using small working memory and produce a clustering comparable in cost to the optimal offline solution, are especially useful. We develop the first streaming algorithms achieving a constant-factor approximation to the cluster radius for two variations of the k-center clustering problem. We give a streaming (4 + ε)-approximation algorithm using O(ε − 1 kz) memory for the problem with outliers, in which the clustering is allowed to drop up to z of the input points; previous work used a random sampling approach which yields only a bicriteria approximation. We also give a streaming (6 + ε)-approximation algorithm using O(ε − 1 ln (ε − 1) k + k 2) memory for a variation motivated by anonymity considerations in which each cluster must contain at least a certain number of input points.

Structural Sampling for Statistical Software Testing - Baskiotis,N.; Sebag,M.; De Raedt,L.; Dietterich,T.; Getoor, Lise; Kersting,K.; Muggleton,S. H (Probabilistic, Logical and Relational Learning-A Further Synthesis, 2008)
Structural Statistical Software Testing exploits the control flow graph of the program being tested to construct test cases. While test cases can easily be extracted from {em feasible paths} in the control flow graph, that is, paths which are actually exerted for some values of the program input, the feasible path region is a tiny fraction of the graph paths (less than $10^{-5}]$ for medium size programs). The S4T algorithm presented in this paper aims to address this limitation; as an Active Relational Learning Algorithm, it uses the few feasible paths initially available to sample new feasible paths. The difficulty comes from the non-Markovian nature of the feasible path concept, due to the long-range dependencies between the nodes in the control flow graph. Experimental validation on real-world and artificial problems demonstrates significant improvements compared to the state of the art.

A Survey of the Virtual Environments-based Assembly Training Applications - Gupta,S.K.; Anand,D. K.; Brough,J. E.; Kavetsky,R. A.; Schwartz,M.; Thakur,A. (2008)
The advent of virtual environments is presenting new ways of trainingtomorrow’s workforce. Virtual environments offer numerous benefits in training applications. First, virtual environments allow extensive user interactions in a very convenient and natural manner. This interaction is greatly beneficial for increasing the user’s retention of spatial information compared to text-based or video-based instructions that are non-interactive in nature. Second, virtual environments provide users with a 3D immersive experience. This feature helps users gain a better understanding of spatial relationships compared to 2D displays. Third, virtual environments support multi-media instructions. One can watch standard videos, view 3D animations, view text instructions, listen to audio instructions, and interact with 3D objects in the scene. This paper describes representative research and associated systems that use of virtual environments in assembly training applications.

Synthesis of strategies from interaction traces - Au,Tsz-Chiu; Kraus,Sarit; Nau, Dana S. (International Foundation for Autonomous Agents and Multiagent Systems, 2008)
We describe how to take a set of interaction traces produced by different pairs of players in a two-player repeated game, and combine them into a composite strategy. We provide an algorithm that, in polynomial time, can generate the best such composite strategy. We describe how to incorporate the composite strategy into an existing agent, as an enhancement of the agent's original strategy. We provide experimental results using interaction traces from 126 agents (most of them written by students as class projects) for the Iterated Prisoner's Dilemma, Iterated Chicken Game, and Iterated Battle of the Sexes. We compared each agent with the enhanced version of that agent produced by our algorithm. The enhancements improved the agents' scores by about 5% in the IPD, 11% in the ICG, and 26% in the IBS, and improved their rank by about 12% in the IPD, 38% in the ICG, and 33% in the IBS.
Keywords: agents; interaction; learning; multi-agent systems; prisoner's dilemma; repeated games

Tracking Down Under: Following the Satin Bowerbird - Kembhavi,A.; Farrell,R.; Luo,Yuancheng; Jacobs, David W.; Duraiswami, Ramani; Davis, Larry S. (Applications of Computer Vision, 2008. WACV 2008. IEEE Workshop on, 2008)
Socio biologists collect huge volumes of video to study animal behavior (our collaborators work with 30,000 hours of video). The scale of these datasets demands the development of automated video analysis tools. Detecting and tracking animals is a critical first step in this process. However, off-the-shelf methods prove incapable of handling videos characterized by poor quality, drastic illumination changes, non-stationary scenery and foreground objects that become motionless for long stretches of time. We improve on existing approaches by taking advantage of specific aspects of this problem: by using information from the entire video we are able to find animals that become motionless for long intervals of time; we make robust decisions based on regional features; for different parts of the image, we tailor the selection of model features, choosing the features most helpful in differentiating the target animal from the background in that part of the image. We evaluate our method, achieving almost 83% tracking accuracy on a more than 200,000 frame dataset of Satin Bowerbird courtship videos.
Keywords: analysis; behavior; animal; Bowerbird; animal; computing; feature; detection; animal; extraction; tracking; video; processing; zoology; Satin; sciences; selection; behavioural; signal; tool; feature; tracking; automated; video

Trade-offs in matching jobs and balancing load for distributed desktop grids - Kim,Jik-Soo; Nam,Beomseok; Keleher,Peter; Marsh,Michael; Bhattacharjee, Bobby; Sussman, Alan (Future Generation Computer Systems, 2008)
Desktop grids can achieve tremendous computing power at low cost through opportunistic sharing of resources. However, traditional client–server Grid architectures do not deal with all types of failures, and do not always cope well with very dynamic environments. This paper describes the design of a desktop grid implemented over a modified Peer-to-Peer (P2P) architecture. The underlying P2P system is decentralized and inherently adaptable, giving the Grid robustness, scalability, and the ability to cope with dynamic environments, while still efficiently mapping application instances to available resources throughout the system.We use simulation to compare three different types of matching algorithms under differing workloads. Overall, the P2P approach produces significantly lower wait times than prior approaches, while adapting efficiently to the dynamic environment.
Keywords: Desktop grid; load balancing; Matchmaking; peer-to-peer computing; Resource discovery

Trusting spam reporters: A reporter-based reputation system for email filtering - Zheleva,Elena; Kolcz,Aleksander; Getoor, Lise (ACM Transactions on Information Systems (TOIS), 2008)
Spam is a growing problem; it interferes with valid email and burdens both email users and service providers. In this work, we propose a reactive spam-filtering system based on reporter reputation for use in conjunction with existing spam-filtering techniques. The system has a trust-maintenance component for users, based on their spam-reporting behavior. The challenge that we consider is that of maintaining a reliable system, not vulnerable to malicious users, that will provide early spam-campaign detection to reduce the costs incurred by users and systems. We report on the utility of a reputation system for spam filtering that makes use of the feedback of trustworthy users. We evaluate our proposed framework, using actual complaint feedback from a large population of users, and validate its spam-filtering performance on a collection of real email traffic over several weeks. To test the broader implication of the system, we create a model of the behavior of malicious reporters, and we simulate the system under various assumptions using a synthetic dataset.
Keywords: reputation systems; Spam filtering; trust

Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques - Nagarajan,N.; Kingsford, Carl (IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM '08, 2008)
The evolutionary histories of viral genomes have received significant recent attention due to their importance in understanding virulence and the corresponding ramifications to public health. We present a novel framework to detect reassortment events in influenza based on the comparison of two distributions of phylogenetic trees, rather than a pair of, possibly unreliable, consensus trees. We show how to detect all high-probability inconsistencies between two distributions of trees by enumerating maximal bicliques within a defined incompatibility graph. In the process, we give the first quadratic delay algorithm for enumerating maximal bicliques within general bipartite graphs. We demonstrate the utility of our approach by applying it to several sets of influenza genomes (both human- and avian-hosted) and successfully identify all known reassortment events and a few novel candidate reassortments. In addition, on simulated datasets, our approach correctly finds implanted reassortments and rarely detects reassortments where none were introduced.
Keywords: avian hosted influenza genome; Bioinformatics; Capacitive sensors; Delay; diseases; Event detection; general bipartite graphs; genomic reassortments; Genomics; graph theory; high probability inconsistencies; History; human hosted influenza genome; incompatibility graph; Influenza; influenza strain; maximal biclique; maximal biclique enumeration; microorganisms; phylogenetic trees; Phylogeny; Public healthcare; quadratic delay algorithm; reassortment; reassortment event detection; Tree graphs; viral genome evolutionary history; virulence

Universally composable multi-party computation with an unreliable common reference string - Goyal,V.; Katz, Jonathan (Theory of Cryptography, 2008)
Universally composable (UC) multi-party computation has been studied in two settings. When a majority of parties are honest, UC multi-party computation is possible without any assumptions. Without a majority of honest parties, UC multi-party computation is impossible in the plain model, but feasibility results have been obtained in various augmented models. The most popular such model posits a common reference string (CRS) available to parties executing the protocol.In either of the above settings, some assumption regarding the protocol execution is made: i.e., that many parties are honest in the first case, or that a legitimately-chosen string is available in the second. If this assumption is incorrect then all security is lost. A natural question is whether it is possible to design protocols secure if either one of these assumptions holds, i.e., a protocol which is secure if either at most s players are dishonest or if up to t > s players are dishonest but the CRS is chosen in the prescribed manner. We show that such protocols exist if and only if s + t < n. This work was done in part while the authors were visiting IPAM.

Users can change their web search tactics: Design guidelines for categorized overviews - Kules,Bill; Shneiderman, Ben (Information Processing & Management, 2008)
Categorized overviews of web search results are a promising way to support user exploration, understanding, and discovery. These search interfaces combine a metadata-based overview with the list of search results to enable a rich form of interaction. A study of 24 sophisticated users carrying out complex tasks suggests how searchers may adapt their search tactics when using categorized overviews. This mixed methods study evaluated categorized overviews of web search results organized into thematic, geographic, and government categories. Participants conducted four exploratory searches during a 2-hour session to generate ideas for newspaper articles about specified topics such as “human smuggling.” Results showed that subjects explored deeper while feeling more organized, and that the categorized overview helped subjects better assess their results, although no significant differences were detected in the quality of the article ideas. A qualitative analysis of searcher comments identified seven tactics that participants reported adopting when using categorized overviews. This paper concludes by proposing a set of guidelines for the design of exploratory search interfaces. An understanding of the impact of categorized overviews on search tactics will be useful to web search researchers, search interface designers, information architects and web developers.
Keywords: categorization; Categorized overviews; Categorized search results; Exploratory search; Human-computer interaction; information seeking; Search result visualization; Search user interfaces; Web search

Using wearable sensors and real time inference to understand human recall of routine activities - Klasnja,Predrag; Harrison,Beverly L.; LeGrand,Louis; LaMarca,Anthony; Jon Froehlich; Hudson,Scott E. (Proceedings of the 10th international conference on Ubiquitous computing, 2008)
Keywords: empirical evaluation; ESM; experience sampling method; recall accuracy; self-reports; survey frequency; user study

Variational Bayes via Propositionalization - Sato,T.; Kameya,Y.; Kurihara,K.; De Raedt,L.; Dietterich,T.; Getoor, Lise; Kersting,K.; Muggleton,S. H (Probabilistic, Logical and Relational Learning-A Further Synthesis, 2008)

What are decision trees? - Kingsford, Carl; Salzberg,S. L (Nature biotechnology, 2008)

Which languages have 4-round zero-knowledge proofs? - Katz, Jonathan (Theory of Cryptography, 2008)
We show that if a language L has a 4-round, black-box, computational zero-knowledge proof system with negligible soundness error, then . Assuming the polynomial hierarchy does not collapse, this means in particular that NP-complete languages do not have 4-round zero-knowledge proofs (at least with respect to black-box simulation).

Who killed the directed model? - Domke, Justin; Karapurkar, Alap; Aloimonos, J. (Computer Vision and Pattern Recognition, IEEE Computer Society Conference on, 2008)
Prior distributions are useful for robust low-level vision, and undirected models (e.g. Markov Random Fields) have become a central tool for this purpose. Though sometimes these priors can be specified by hand, this becomes difficult in large models, which has motivated learning these models from data. However, maximum likelihood learning of undirected models is extremely difficult- essentially all known methods require approximations and/or high computational cost. Conversely, directed models are essentially trivial to learn from data, but have not received much attention for low-level vision. We compare the two formalisms of directed and undirected models, and conclude that there is no a priori reason to believe one better represents low-level vision quantities. We formulate two simple directed priors, for natural images and stereo disparity, to empirically test if the undirected formalism is superior. We find in both cases that a simple directed model can achieve results similar to the best learnt undirected models with significant speedups in training time, suggesting that directed models are an attractive choice for tractable learning.

On achieving the "best of both worlds" in secure multiparty computation - Katz, Jonathan (Proceedings of the thirty-ninth annual ACM symposium on Theory of computing, 2007)
Two settings are typically considered for secure multipartycomputation, depending on whether or not a majority of the partiesare assumed to be honest. Protocols designed under this assumptionprovide "full security" (and, in particular, guarantee outputdelivery and fairness) when this assumption is correct; however, if half or more of the parties are dishonest then security iscompletely compromised. On the other hand, protocols toleratingarbitrarily-many faults do not provide fairness or guaranteed output delivery even if only a single party is dishonest. It isnatural to wonder whether it is possible to achieve the "best ofboth worlds" : namely, a single protocol that simultaneouslyachieves the best possible security in both the above settings. Ishai, et al. (Crypto 2006) recently addressed this question, andruled out constant-round protocols of this type. As our main result, we completely settle the question by ruling outprotocols using any (expected) polynomial number of rounds. Given this stark negative result, we then ask what can be achieved if we are willing to assume simultaneous message transmission (or, equivalently, a non-rushing adversary). In this setting, we show that impossibility still holdsfor logarithmic-round protocols. We also show, for any polynomialp, a protocol (whose round complexity depends on p) that can be simulated to within closeness O(1/p).
Keywords: COMPUTATION; secure

Active semantic caching to optimize multidimensional data analysis in parallel and distributed environments - Andrade,Henrique; Kurc,Tahsin; Sussman, Alan; Saltz,Joel (Parallel Computing, 2007)
In this paper, we present a multi-query optimization framework based on the concept of active semantic caching. The framework permits the identification and transparent reuse of data and computation in the presence of multiple queries (or query batches) that specify user-defined operators and aggregations originating from scientific data-analysis applications. We show how query scheduling techniques, coupled with intelligent cache replacement policies, can further improve the performance of query processing by leveraging the active semantic caching operators. We also propose a methodology for functionally decomposing complex queries in terms of primitives so that multiple reuse sites are exposed to the query optimizer, to increase the amount of reuse. The optimization framework and the database system implemented with it are designed to be efficient irrespective of the underlying parallel and/or distributed machine configuration. We present experimental results highlighting the performance improvements obtained by our methods using real scientific data-analysis applications on multiple parallel and distributed processing configurations (e.g., single symmetric multiprocessor (SMP) machine, cluster of SMP nodes, and a Grid computing configuration).
Keywords: Active semantic caching; Parallel databases; Query optimization; Scientific data analysis

Applied cryptography and network security: 5th international conference, ACNS 2007, Zhuhai, China, June 5-8, 2007: proceedings - Katz, Jonathan; Yung,M. (Springer-Verlag New York Inc, 2007)

Barrier pointing: using physical edges to assist target acquisition on mobile device touch screens - Jon Froehlich; Wobbrock,J.O.; Kane,S.K. (Proceedings of the 9th international ACM SIGACCESS conference on Computers and accessibility, October, 2007)

Beyond single-appearance schedules: Efficient DSP software synthesis using nested procedure calls - Ko,M. Y; Murthy,P. K; Bhattacharyya, Shuvra S. (ACM Transactions on Embedded Computing Systems (TECS), 2007)

Capture, annotate, browse, find, share: novel interfaces for personal photo management - Kang,H.; Bederson, Benjamin B.; Suh,B. (International Journal of Human-] Computer Interaction, 2007)

Chit-based access control - Keleher,P. J; Spring, Neil; Bhattacharjee, Bobby (Technical Report CS-TR-4878, University of Maryland at College Park, 2007)

Chosen-ciphertext security from identity-based encryption - Boneh,D.; Canetti,R.; Halevi,S.; Katz, Jonathan (SIAM Journal on Computing, 2007)
We propose simple and efficient CCA-secure public-key encryption schemes (i.e., schemessecure against adaptive chosen-ciphertext attacks) based on any identity-based encryption (IBE) scheme. Our constructions have ramifications of both theoretical and practical interest. First, our schemes give a new paradigm for achieving CCA-security; this paradigm avoids “proofs of well-formedness” that have been shown to underlie previous constructions. Second, instantiating our construction using known IBE constructions we obtain CCA-secure encryption schemes whose performance is competitive with the most efficient CCA-secure schemes to date. Our techniques extend naturally to give an efficient method for securing IBE schemes (even hierarchical ones) against adaptive chosen-ciphertext attacks. Coupled with previous work, this gives the first efficient constructions of CCA-secure IBE schemes.

Colluding Fingerprinted Video using the Gradient Attack - He,Shan; Kirovski,D.; M. Wu (Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on, 2007)
Digital fingerprinting is an emerging tool to protect multimedia content from unauthorized distribution by embedding a unique fingerprint into each user's copy. Although several fingerprinting schemes have been proposed in related work, disproportional effort has been targeted towards identifying effective collusion attacks on fingerprinting schemes. Recent introduction of the gradient attack has refined the definition of an optimal attack and demonstrated strong effect on direct-sequence, uniformly distributed, and Gaussian spread spectrum fingerprints when applied to synthetic signals. In this paper, we apply the gradient attack on an existing well-engineered video fingerprinting scheme, refine the attack procedure, and demonstrate that the gradient attack is effective on Laplace fingerprints. Finally, we explore an improvement on fingerprint design to thwart the gradient attack. Results suggest that Laplace fingerprint should be avoided. However, we show that a signal mixed of Laplace and Gaussian fingerprints may serve as a design strategy to disable the gradient attack and force pirates into averaging as a form of adversary collusion.
Keywords: attack; multimedia; attacks; digital; content; data; video; distribution; fingerprint; effort; gradient; fingerprinted; fingerprinting; disproportional; fingerprints; colluding; fingerprints; Laplace; Gaussian; identification; multimedia; of; processing; protection; unauthorized; signal; spectrum; spread; systems; security; video; collusion

Compact, low power wireless sensor network system for line crossing recognition - Shen,C. C; Kupershtok,R.; Yang,B.; Vanin,F. M; Shao,X.; Sheth,D.; Goldsman,N.; Balzano,Q.; Bhattacharyya, Shuvra S. (Circuits and Systems, 2007. ISCAS 2007. IEEE International Symposium on, 2007)

Component-based Data Layout for Efficient Slicing of Very Large Multidimensional Volumetric Data - Kim,Jusub; JaJa, Joseph F. (Scientific and Statistical Database Management, 2007. SSBDM '07. 19th International Conference on, 2007)
In this paper, we introduce a new efficient data layout scheme to efficiently handle out-of-core axis-aligned slicing queries of very large multidimensional volumetric data. Slicing is a very useful dimension reduction tool that removes or reduces occlusion problems in visualizing 3D/4D volumetric data sets and that enables fast visual exploration of such data sets. We show that the data layouts based on typical space-filling curves are not optimal for the out-of-core slicing queries and present a novel component-based data layout scheme for a specialized problem domain, in which it is only required to provide fast slicing at every k-th value, for any k gt; 1. Our component-based data layout scheme provides much faster processing time for any axis-aligned slicing direction at every k-th value, k gt; 1, requiring less cache memory size and without any replication of data. In addition, the data layout can be generalized to any high dimension.
Keywords: axis-aligned; cache; curves; very; data; data; data; databases; handling; query; large; layout; data; memory; multidimensional; processing; very; queries; space-filling; size; component-based; slicing; slicing; out-of-core; volumetric