The Goal Question Metric Approach - Basili, Victor R.; Caldiera,G.; Rombach,H. D (5th ACM-IEEE International Symposium on Empirical Software Engineering (ISESE’06), 2006)

Heuristic search and information visualization methods for school redistricting - desJardins, Marie; Bulka,Blazej; Carr,Ryan; Hunt,Andrew; Rathod,Priyang; Rheingans,Penny (Proceedings of the 18th conference on Innovative applications of artificial intelligence - Volume 2, 2006)
We describe an application of AI search and information visualization techniques to the problem of school redistricting, in which students are assigned to home schools within a county or school district. This is a multicriteria optimization problem in which competing objectives must be considered, such as school capacity, busing costs, and socioeconomic distribution. Because of the complexity of the decision-making problem, tools are needed to help end users generate, evaluate, and compare alternative school assignment plans. A key goal of our research is to aid users in finding multiple qualitatively different redistricting plans that represent different tradeoffs in the decision space.We present heuristic search methods that can be used to find a set of qualitatively different plans, and give empirical results of these search methods on population data from the school district of Howard County, Maryland. We show the resulting plans using novel visualization methods that we have developed for summarizing and comparing alternative plans.

How Multirobot Systems Research will Accelerate our Understanding of Social Animal Behavior - Balch, T.; Dellaert, F.; Feldman, A.; Guillory, A.; Isbell, C.L.; Zia Khan; Pratt, S.C.; Stein, A.N.; Wilde, H. (Proceedings of the IEEE, 2006)
Our understanding of social insect behavior has significantly influenced artificial intelligence (AI) and multirobot systems' research (e.g., ant algorithms and swarm robotics). In this work, however, we focus on the opposite question: "How can multirobot systems research contribute to the understanding of social animal behavior?" As we show, we are able to contribute at several levels. First, using algorithms that originated in the robotics community, we can track animals under observation to provide essential quantitative data for animal behavior research. Second, by developing and applying algorithms originating in speech recognition and computer vision, we can automatically label the behavior of animals under observation. In some cases the automatic labeling is more accurate and consistent than manual behavior identification. Our ultimate goal, however, is to automatically create, from observation, executable models of behavior. An executable model is a control program for an agent that can run in simulation (or on a robot). The representation for these executable models is drawn from research in multirobot systems programming. In this paper we present the algorithms we have developed for tracking, recognizing, and learning models of social animal behavior, details of their implementation, and quantitative experimental results using them to study social insects
Keywords: Acceleration; Animal behavior; ant movement tracking; Artificial intelligence; biology computing; Computer vision; control engineering computing; Insects; Intelligent robots; Labeling; monkey movement tracking; multi-robot systems; multirobot systems; robotics algorithms; Robotics and automation; social animal behavior; social animals; social insect behavior; Speech recognition; tracking

Identifying domain-specific defect classes using inspections and change history - Nakamura,Taiga; Hochstein, Lorin; Basili, Victor R. (Proceedings of the 2006 ACM/IEEE international symposium on Empirical software engineering, 2006)
We present an iterative, reading-based methodology for analyzing defects in source code when change history is available. Our bottom-up approach can be applied to build knowledge of recurring defects in a specific domain, even if other sources of defect data such as defect reports and change requests are unavailable, incomplete or at the wrong level of abstraction for the purposes of the defect analysis. After defining the methodology, we present the results of an empirical study where our method was applied to analyze defects in parallel programs which use the MPI (Message Passing Interface) library to express parallelism. This library is often used in the domain of high performance computing, where there is much discussion but little empirical data about the frequency and severity of defect types. Preliminary results indicate the methodology is feasible and can provide insights into the nature of real defects. We present the results, derived hypothesis, and lessons learned.
Keywords: change history; code reading; domain specific defects; Inspection

In VINI veritas: realistic and controlled network experimentation - Bavier,Andy; Feamster, Nick; Huang,Mark; Peterson,Larry; Rexford,Jennifer (SIGCOMM Comput. Commun. Rev., 2006)
This paper describes VINI, a virtual network infrastructure that allows network researchers to evaluate their protocols and services in a realistic environment that also provides a high degree of control over network conditions. VINI allows researchers to deploy and evaluate their ideas with real routing software, traffic loads, and network events. To provide researchers flexibility in designing their experiments, VINI supports simultaneous experiments with arbitrary network topologies on a shared physical infrastructure. This paper tackles the following important design question: What set of concepts and techniques facilitate flexible, realistic, and controlled experimentation (e.g., multiple topologies and the ability to tweak routing algorithms) on a fixed physical infrastructure? We first present VINI's high-level design and the challenges of virtualizing a single network. We then present PL-VINI, an implementation of VINI on PlanetLab, running the "Internet In a Slice". Our evaluation of PL-VINI shows that it provides a realistic and controlled environment for evaluating new protocols and services.
Keywords: architecture; experimentation; Internet; Routing; virtualization

Interactive sonification for blind people exploration of geo-referenced data: comparison between a keyboard-exploration and a haptic-exploration interfaces - Delogu,Franco; Belardinelli,Marta; Palmiero,Massimiliano; Pasqualotto,Emanuele; Zhao,Haixia; Plaisant, Catherine; Federici,Stefano (Cognitive Processing, 2006)

Invariant Geometric Representation of 3D Point Clouds for Registration and Matching - Biswas,S.; Aggarwal,G.; Chellapa, Rama (Image Processing, 2006 IEEE International Conference on, 2006)
Though implicit representations of surfaces have often been used for various computer graphics tasks like modeling and morphing of objects, it has rarely been used for registration and matching of 3D point clouds. Unlike in graphics, where the goal is precise reconstruction, we use isosurfaces to derive a smooth and approximate representation of the underlying point cloud which helps in generalization. Implicit surfaces are generated using a variational interpolation technique. Implicit function values on a set of concentric spheres around the 3D point cloud of object are used as features for matching. Geometric-invariance is achieved by decomposing implicit values based feature set into various spherical harmonics. The decomposition provides a compact representation of 3D point clouds while achieving rotation invariance
Keywords: 3D; cloud; computer; function; geometric; graphics; geophysical; graphics; image; Interpolation; matching; image; point; processing; image; reconstruction; image; registration; image; registration; implicit; representation; interpolation; representation; variational; signal; technique; clouds; computer; value; invariant

Issues in writing a parallel compiler starting from a serial compiler - Tzannes,A.; Barua,R.; Caragea,G.; Vishkin, Uzi (draft. Technical report, University of Maryland Institute for Advanced Compuer Studies, 2006)

KeyChains: A Decentralized Public-Key Infrastructure - Morselli,Ruggero; Bhattacharjee, Bobby; Katz, Jonathan; Marsh,Michael A (Technical Reports from UMIACS, UMIACS-TR-2006-12, 2006)
A Certification Authority (CA) can be used to certify keys and build apublic-key infrastructure (PKI) when all users trust the same CA. A decentralized PKI trades off absolute assurance on keys for independence from central control and improved scalability and robustness. The PGP ``web of trust'' model has been suggested as a decentralized certification system, and has been used with great success for secure email. Although the PGP web of trust model allows anyone to issue certificates which can be used to form certificate chains, the discovery and construction of certificate chains relies on centralized keyservers to store certificates and respond to queries. In this paper, we design and implement KeyChains, a peer-to-peer system which incorporates a novel lookup mechanism specifically tailored to the task of generating and retrieving certificate chains in completely unstructured networks. By layering our system on top of the web of trust model, we thus obtain the first PKI which is truly decentralized in all respects. Our analysis and simulations show that the resulting system is both efficient and secure.
Keywords: Technical Report

A latent dirichlet allocation model for entity resolution - Bhattacharya,I.; Getoor, Lise (6th SIAM Conference on Data Mining (SDM), Bethesda, USA, 2006)
In this paper, we address the problem of entity resolution, where given many references to un-derlying objects, the task is to predict which references correspond to the same object. We propose a probabilistic model for collective entity resolution. Our approach differs from other recently pro- posed entity resolution approaches in that it is a) unsupervised, b) generative and c) introduces a hidden ‘group’ variable to capture collections of entities which are commonly observed together. The entity resolution decisions are not considered on an independent pairwise basis, but instead decisions are made collectively. We focus on how the use of relational links among the references can be exploited. We show how we can use Gibbs Sampling to infer the collaboration groups and the entities jointly from the observed co-author relationships among entity references and how this improves entity resolution performance. We demonstrate the utility of our approach on two real-world bibliographic datasets. In addition, we present preliminary results on characterizing conditions under which collaborative infor- mation is useful.

Machine Translation: Interlingual Methods - Dorr, Bonnie J; Hovy,E.; Levin,L. (Encyclopedia of Language & Linguistics (Second Edition)Encyclopedia of Language & Linguistics (Second Edition), 2006)
An interlingua is a notation for representing the content of a text that abstracts away from the characteristics of the language itself and focuses on the meaning (semantics) alone. Interlinguas are typically used as pivot representations in machine translation, allowing the contents of a source text to be generated in many different target languages. Because of the complexities involved, few interlinguas are more than demonstration prototypes, and only one has been used in a commercial MT system. In this article, we define the components of an interlingua and the principal issues faced by designers and builders of interlinguas and interlingua MT systems, illustrating with examples from operational systems and research prototypes. We discuss current efforts to annotate texts with interlingua-based information.
Keywords: approximate interlingua; compositionality; conceptual knowledge; cross-language divergences; interlingua; interlingual speech translation; language-independent representation; lexical-conceptual structure; Machine translation; ontology; predicate-argument structure; semantic annotation; semantic frames; semantic zones; text-meaning representations; THEMATIC ROLES

Making a difference: integrating socially relevant projects into HCI teaching - Shneiderman, Ben; Bishop,Ann; Friedman,Batya; Lazar,Jonathan; Marsden,Gary; Nass,Cliff (CHI '06 extended abstracts on Human factors in computing systems, 2006)
Enriching courses on human-computer interaction with socially-relevant projects provides a compelling opportunity for students to improve their education and make socially beneficial contributions. By having clearly defined user communities outside the classroom, students have the chance to practice their interview, observation, and usability testing skills, while developing projects that continue beyond the semester. These projects often give students life-changing exposure to genuine needs and impressive results to include in their portfolio when seeking employment. Educators will present their strategies for arranging, supervising, and grading these projects. Students will describe their experience and how it influenced them.
Keywords: education; making a difference; relevance; service learning; social impact; team projects

Manufacturing of multi-material compliant mechanisms using multi-material molding - Gouker,Regina; Gupta, Satyandra K.; Bruck,Hugh; Holzschuh,Tobias (The International Journal of Advanced Manufacturing Technology, 2006)
Multi-material compliant mechanisms enable many new design possibilities. Significant progress has been made in the area of design and analysis of multi-material compliant mechanisms. What is now needed is a method to mass-produce such mechanisms economically. A feasible and practical way of producing such mechanisms is through multi-material molding. Devices based on compliant mechanisms usually consist of compliant joints. Compliant joints in turn are created by carefully engineering interfaces between a compliant and a rigid material. This paper presents an overview of multi-material molding technology and describes feasible mold designs for creating different types of compliant joints found in multi-material compliant mechanisms. It also describes guidelines essential to successfully utilizing the multi-material molding process for creating compliant mechanisms. Finally, practical applications for the use of multi-material molding to create compliant mechanisms are demonstrated.
Keywords: engineering

Mapping Multimedia Applications Onto Configurable Hardware With Parameterized Cyclo-Static Dataflow Graphs - Haim,F.; Sen,M.; Ko,Dong-Ik; Bhattacharyya, Shuvra S.; Wolf,W. (Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on, 2006)
This paper develops methods for model-based design and implementation of image processing applications. We apply our previously developed meta-modeling technique of homogeneous parameterized dataflow (HPDF) (M. Sen et al., 2005) to the framework of cyclostatic dataflow (CSDF) (G. Bilsen et al., 1996), and demonstrate this integrated modeling methodology through hardware mapping of a gesture recognition application. We also provide a comparative study between HPDF/CSDF-based representation of the gesture recognition application, and a previously developed version based on applying HPDF in conjunction with conventional synchronous dataflow (SDF) semantics (M. Sen et al., 2005)
Keywords: configurable hardware; Data communication; Gesture recognition; gesture recognition application; graph theory; hardware mapping; image processing applications; mapping multimedia applications; meta-modeling technique; model-based design; Multimedia communication; parameterized cyclo-static dataflow graphs

Matching Jobs to Resources in Distributed Desktop Grid Environments - Kim,Jik-Soo; Bhattacharjee, Bobby; Keleher, Peter J.; Sussman, Alan (Technical Reports from UMIACS, UMIACS-TR-2006-15, 2006)
Desktop grids use opportunistic sharing to exploit large collectionsof personal computers and workstations across the Internet and can achieve tremendous computing power with low cost. However, current systems are typically based on a traditional client-server architecture, which has inherent shortcomings with respect to robustness, reliability and scalability. In this paper, we propose a decentralized, robust, highly available, and scalable infrastructure to match incoming jobs to available resources. The key idea behind our proposed system is to leverage information provided by an underlying peer-to-peer system to create a hierarchical Rendezvous Node Tree, which performs the matching efficiently. Our experimental results obtained via simulation show that we can effectively match jobs with varying levels of resource constraints to available nodes and maintain good load balance in a fully decentralized heterogeneous computational environment.
Keywords: Technical Report

MCMC Data Association and Sparse Factorization Updating for Real Time Multitarget Tracking with Merged and Multiple Measurements - Zia Khan; Balch, T.; Dellaert, F. (IEEE Transactions on Pattern Analysis and Machine Intelligence, 2006)
In several multitarget tracking applications, a target may return more than one measurement per target and interacting targets may return multiple merged measurements between targets. Existing algorithms for tracking and data association, initially applied to radar tracking, do not adequately address these types of measurements. Here, we introduce a probabilistic model for interacting targets that addresses both types of measurements simultaneously. We provide an algorithm for approximate inference in this model using a Markov chain Monte Carlo (MCMC)-based auxiliary variable particle filter. We Rao-Blackwellize the Markov chain to eliminate sampling over the continuous state space of the targets. A major contribution of this work is the use of sparse least squares updating and downdating techniques, which significantly reduce the computational cost per iteration of the Markov chain. Also, when combined with a simple heuristic, they enable the algorithm to correctly focus computation on interacting targets. We include experimental results on a challenging simulation sequence. We test the accuracy of the algorithm using two sensor modalities, video, and laser range data. We also show the algorithm exhibits real time performance on a conventional PC
Keywords: algorithms; approximate inference; Artificial intelligence; auxiliary variable particle filter; Computational efficiency; continuous state space; downdating; Image Enhancement; Image Interpretation, Computer-Assisted; Inference algorithms; Information Storage and Retrieval; laser range scanner; laser range scanner.; Least squares approximation; least squares approximations; Least squares methods; linear least squares; Markov chain Monte Carlo; Markov processes; MCMC data association; merged measurements; Monte Carlo methods; Movement; multiple merged measurements; multitarget tracking; particle filter; particle filtering (numerical methods); Particle filters; Pattern Recognition, Automated; probabilistic model; QR factorization; Radar tracking; Rao-Blackwellized; real time multitarget tracking; Reproducibility of results; Sampling methods; Sensitivity and Specificity; sensor fusion; sparse factorization updating; sparse least squares; State-space methods; Subtraction Technique; target tracking; updating

Measurement-based optimal routing on overlay architectures for unicast sessions - La,R.J.; Shayman,M.A.; Bhattacharjee, Bobby (Computer Networks, 2006)
We propose a measurement-based routing algorithm to load-balance intradomain traffic along multiple paths for multi-ple unicast sources. Multiple paths are established using overlay nodes. The distributed algorithm is derived from simul- taneous perturbation stochastic approximation (SPSA) and does not assume that the gradient of an analytical cost function is known. Instead, we rely on (potentially) noisy estimates from local measurements. Using the analytical model presented in the paper, we first show the almost sure convergence of the algorithm to the optimal solution under a decreas- ing step size policy (as with a standard SPSA model). Motivated by practical concerns, we next consider the constant step size case, for which we establish weak convergence. We provide simulation results to demonstrate the advantages of our proposed algorithm under various network scenarios, and also present a comparative study with MATE (an existing opti- mal routing algorithm)

Memory management for synthesis of DSP software - Murthy,P. K; Bhattacharyya, Shuvra S. (CRC, 2006)

Memory-constrained block processing optimization for synthesis of DSP software - Ko,M. Y; Shen,C. C; Bhattacharyya, Shuvra S. (Embedded Computer Systems: Architectures, Modeling and Simulation, 2006. IC-SAMOS 2006. International Conference on, 2006)

Mesh-of-Trees and Alternative Interconnection Networks for Single Chip Parallel Processing (Extended Abstract) - Balkan,Aydin O.; Gang Qu; Vishkin, Uzi (Technical Reports from UMIACS, UMIACS-TR-2006-32, 2006)
Many applications have stimulated the recent surge of interest single-chip parallel processing. In such machines, it is crucial to implement a high-throughput low-latency interconnection network to connect the on-chip components, especially the processing units and the memory units. In this paper, we propose a new mesh of trees (MoT) implementation of the interconnection network and evaluate it relative to metrics such as wire area, register count, total switch delay, maximum throughput, latency-throughput relation and delay effects of long wires. We show that on-chip interconnection networks can facilitate higher bandwidth between processors and shared first-level cache than previously considered possible. This has significant impact for chip multiprocessing. MoT is also compared, both analytically and experimentally, to some other traditional network topologies, such as hypercube, butterfly, fat trees and butterfly fat trees. When we evaluate a 64-terminal MoT network at 65nm technology, concrete results show that MoT provides higher throughput and lower latency especially when the input traffic (or the on-chip parallelism) is high, at the cost of larger area. A recurring problem in networking and communication is that of achieving good sustained throughput in contrast to just high theoretical peak performance that does not materialize for typical work loads. Our quantitative results demonstrate a clear advantage of the proposed MoT network in the context of single-chip parallel processing.
Keywords: Technical Report

A model for computer frustration: the role of instrumental and dispositional factors on incident, session, and post-session frustration and mood - Bessière,Katie; Newhagen,John E.; Robinson,John P.; Shneiderman, Ben (Computers in Human Behavior, 2006)
Frustration is almost universally accepted as the emotional outcome of a negative computing experience. Despite the wide use of the term, however, it has not been rigorously conceptualized as a factor in the study of the human–computer interface. This project sets out to explicate frustration as a pre-emotional state generated by the user’s appraisal of the interface as an impediment to goal attainment, and looks at how user characteristics, such as self-efficacy, relate to it. This project employed episode report methodology to capture data from 144 computer users’ reports of actual frustrating events as they took place. Diaries taken as users worked at their everyday tasks yield detailed data about the problems they encountered and included information about session length and an estimate of the time lost due to the experiences. Outcomes were measured as either situational or dispositional factors. Situational factors, having to do with specific events, predicted incident frustration. However, disposition variables, especially user self-efficacy, were much stronger, predicting incident and session frustration, and post-session mood. One surprising outcome was the failure of demographic variables as predictors of frustration.
Keywords: Efficacy; Emotion; Frustration; Mood; problem solving; usability

Model-based mapping of image registration applications onto configurable hardware - Hemaraj,Y.; Sen,M.; Shekhar,R.; Bhattacharyya, Shuvra S. (Signals, Systems and Computers, 2006. ACSSC'06. Fortieth Asilomar Conference on, 2006)

Model-based OpenMP implementation of a 3D facial pose tracking system - Saha,S.; Chung-Ching Shen; Chia-Jui Hsu; Aggarwal,G.; Veeraraghavan,A.; Sussman, Alan; Bhattacharyya, Shuvra S. (2006 International Conference on Parallel Processing Workshops, 2006. ICPP 2006 Workshops, 2006)
Most image processing applications are characterized by computation-intensive operations, and high memory and performance requirements. Parallelized implementation on shared-memory systems offer an attractive solution to this class of applications. However, we cannot thoroughly exploit the advantages of such architectures without proper modeling and analysis of the application. In this paper, we describe our implementation of a 3D facial pose tracking system using the OpenMP platform. Our implementation is based on a design methodology that uses coarse-grain dataflow graphs to model and schedule the application. We present our modeling approach, details of the implementation that we derived based on this modeling approach, and associated performance results. The parallelized implementation achieves significant speedup, and meets or exceeds the target frame rate under various configurations
Keywords: 3D facial pose tracking system; application modeling; application program interfaces; application scheduling; coarse-grain dataflow graphs; Concurrent computing; data flow graphs; Educational institutions; face recognition; IMAGE PROCESSING; image processing applications; Inference algorithms; Message passing; OpenMP platform; parallel implementation; PARALLEL PROCESSING; parallel programming; Particle tracking; Processor scheduling; SHAPE; shared memory systems; shared-memory systems; Solid modeling; tracking

Molecular Characterization of Serine-, Alanine-, and Proline-Rich Proteins of Trypanosoma cruzi and Their Possible Role in Host Cell Infection - Baida,Renata C. P.; Santos,Marcia R. M.; Carmo,Mirian S.; Yoshida,Nobuko; Ferreira,Danielle; Ferreira,Alice Teixeira; El Sayed,Najib M.; Andersson,Bjorn; da Silveira,Jose Franco (Infect. Immun., 2006)
We previously reported the isolation of a novel protein gene family, termed SAP (serine-, alanine-, and proline-rich protein), from Trypanosoma cruzi. Aided by the availability of the completed genome sequence of T. cruzi, we have now identified 39 full-length sequences of SAP, six pseudogenes and four partial genes. SAPs share a central domain of about 55 amino acids and can be divided into four groups based on their amino (N)- and carboxy (C)-terminal sequences. Some SAPs have conserved N- and C-terminal domains encoding a signal peptide and a glycosylphosphatidylinositol anchor addition site, respectively. Analysis of the expression of SAPs in metacyclic trypomastigotes by two-dimensional electrophoresis and immunoblotting revealed that they are likely to be posttranslationally modified in vivo. We have also demonstrated that some SAPs are shed into the extracellular medium. The recombinant SAP exhibited an adhesive capacity toward mammalian cells, where binding was dose dependent and saturable, indicating a possible ligand-receptor interaction. SAP triggered the host cell Ca2+ response required for parasite internalization. A cell invasion assay performed in the presence of SAP showed inhibition of internalization of the metacyclic forms of the CL strain. Taken together, these results show that SAP is involved in the invasion of mammalian cells by metacyclic trypomastigotes, and they confirm the hypothesis that infective trypomastigotes exploit an arsenal of surface glycoproteins and shed proteins to induce signaling events required for their internalization.

Motion Based Correspondence for 3D Tracking of Multiple Dim Objects - Veeraraghavan,A.; Srinivasan, M.; Chellapa, Rama; Baird, E.; Lamont, R. (Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on, 2006)
Tracking multiple objects in a video is a demanding task that is frequently encountered in several systems such as surveillance and motion analysis. Ability to track objects in 3D requires the use of multiple cameras. While tracking multiple objects using multiples video cameras, establishing correspondence between objects in the various cameras is a nontrivial task. Specifically, when the targets are dim or are very far away from the camera, appearance cannot be used in order to establish this correspondence. Here, we propose a technique to establish correspondence across cameras using the motion features extracted from the targets, even when the relative position of the cameras is unknown. Experimental results are provided for the problem of tracking multiple bees in natural flight using two cameras. The reconstructed 3D flight paths of the bees show some interesting flight patterns
Keywords: 3D; analysis; motion; analysis; video; based; cameras; feature; correspondence; motion; dim; extraction; image; extraction; multiple; features; MOTION; objects; video; processing; signal; tracking; motion

A New Hardware Monitor Design to Measure Data Structure-Specific Cache Eviction Information - Buck, B. R; Hollingsworth, Jeffrey K (International Journal of High Performance Computing Applications, 2006)
In this paper, we propose a hardware performance monitor that provides support not only for measuring cache misses and the addresses associated with them, but also for determining what data is being evicted from the cache when a miss occurs. We describe how to use this hardware support to efficiently determine the cache behavior of application data structures at the source code level. We also present the results of a simulation-based study of this technique, in which we examined the overhead, perturbation of results, and usefulness of collecting this information.

Nuclear Envelope Dystrophies Show a Transcriptional Fingerprint Suggesting Disruption of Rb–MyoD Pathways in Muscle Regeneration - Bakay,Marina; Wang,Zuyi; Melcon,Gisela; Schiltz,Louis; Xuan,Jianhua; Zhao,Po; Sartorelli,Vittorio; Seo,Jinwook; Pegoraro,Elena; Angelini,Corrado; Shneiderman, Ben; Escolar,Diana; et al. (BrainBrain, 2006)
Mutations of lamin A/C (LMNA) cause a wide range of human disorders, including progeria, lipodystrophy, neuropathies and autosomal dominant Emery–Dreifuss muscular dystrophy (EDMD). EDMD is also caused by X-linked recessive loss-of-function mutations of emerin, another component of the inner nuclear lamina that directly interacts with LMNA. One model for disease pathogenesis of LMNA and emerin mutations is cell-specific perturbations of the mRNA transcriptome in terminally differentiated cells. To test this model, we studied 125 human muscle biopsies from 13 diagnostic groups (125 U133A, 125 U133B microarrays), including EDMD patients with LMNA and emerin mutations. A Visual and Statistical Data Analyzer (VISDA) algorithm was used to statistically model cluster hierarchy, resulting in a tree of phenotypic classifications. Validations of the diagnostic tree included permutations of U133A and U133B arrays, and use of two probe set algorithms (MAS5.0 and MBEI). This showed that the two nuclear envelope defects (EDMD LMNA, EDMD emerin) were highly related disorders and were also related to fascioscapulohumeral muscular dystrophy (FSHD). FSHD has recently been hypothesized to involve abnormal interactions of chromatin with the nuclear envelope. To identify disease-specific transcripts for EDMD, we applied a leave-one-out (LOO) cross-validation approach using LMNA patient muscle as a test data set, with reverse transcription–polymerase chain reaction (RT–PCR) validations in both LMNA and emerin patient muscle. A high proportion of top-ranked and validated transcripts were components of the same transcriptional regulatory pathway involving Rb1 and MyoD during muscle regeneration (CRI-1, CREBBP, Nap1L1, ECREBBP/p300), where each was specifically upregulated in EDMD. Using a muscle regeneration time series (27 time points) we develop a transcriptional model for downstream consequences of LMNA and emerin mutations. We propose that key interactions between the nuclear envelope and Rb and MyoD fail in EDMD at the point of myoblast exit from the cell cycle, leading to poorly coordinated phosphorylation and acetylation steps. Our data is consistent with mutations of nuclear lamina components leading to destabilization of the transcriptome in differentiated cells.
Keywords: EDMD = Emery–Dreifuss muscular dystrophy; emerin; Emery-Dreifuss muscular dystrophy; FSHD = fascioscapulohumeral muscular dystrophy; IDG = individual discriminatory genes; JDG = jointly discriminatory genes; lamin A/C; LGMD = limb-girdle muscular dystrophy; LOO = leave-one-out; RT–PCR = reverse transcription–polymerase chain reaction; VISDA = Visual and Statistical Data Analyzer; Skeletal muscle; wFC = weighted Fisher criterion

Observations about software development for high end computing - Carver, J. C; Hochstein, L. M; Kendall,R. P; Nakamura, T.; Zelkowitz, Marvin V; Basili, Victor R.; Post,D. E (CTWatch Quarterly, 2006)
In this paper, we have summarized our findings from a series of case studies conducted with ten ASC and MP Codes as a series of observations. Due to different environments in which each code is developed, some of the observations are consistent across code teams while others vary across code teams. Overall, we found high consistency among the ASC Codes and the MP Codes. Due to the different environments and foci of these projects, this result is both surprising and positive. In addition, despite the fact that a large majority of the developers on these teams have little or no formal training in software engineering, they have been able to make use of some basic software engineering principles. Further education and motivation could increase the use of these principles and further increase the quality of scientific and engineering software that has already demonstrated its value.Based on the positive results thus far, we have plans to conduct additional case studies to gather more data in support of or in contradiction to the observations presented in this paper. In future case studies, we will strive to investigate codes from additional domains, thereby allowing broader, more inclusive conclusions to be drawn.

Oceans And Health: Pathogens In The Marine Environment - Belkin,Shimshon; Rita R Colwell (Springer, 2006)
The release of non-disinfected wastewaters into the marine environment is a common worldwide practice, in under-developed as well as in highly developed countries. Consequently, the seas are constantly infused with wastewater bacteria, among them highly pathogenic ones. In view of the public health significance of this phenomenon, it is surprising how little is actually known concerning the fate of such bacteria once they enter the sea. While numerous studies have addressed the effects of various environmental parameters on colony formation, many of them actually ignore the fact that bacteria can retain viability and infectivity while losing colony-forming ability. Only in recent years have efforts also been directed at unraveling the mechanisms determining bacterial sensitivity or survival under these conditions. This, therefore, is one subject of Oceans and Health: Pathogens in the Marine Environment: the survival, infectivity, pathogenicity and viability of enteric bacteria in the sea. Chapters also detail the public health aspects of wastewater release, civil engineering and economic considerations, other sources of pathogens, and much more.
Keywords: Electronic books; Marine microbiology; Medical / Epidemiology; Medical / Microbiology; Nature / Animals / Marine Life; Pathogenic microorganisms; Science / Environmental Science; Science / Life Sciences / Biology; Science / Life Sciences / Marine Biology; Science / Life Sciences / Microbiology; Seawater/ microbiology

OMNI: An efficient overlay multicast infrastructure for real-time applications - Banerjee,Suman; Kommareddy,Christopher; Kar,Koushik; Bhattacharjee, Bobby; Khuller, Samir (Computer Networks, 2006)
We consider an overlay architecture (called OMNI) where service providers deploy a set of service nodes (called MSNs) in the network to efficiently implement media-streaming applications. These MSNs are organized into an overlay and act as application-layer multicast forwarding entities for a set of clients.We present a decentralized scheme that organizes the MSNs into an appropriate overlay structure that is particularly beneficial for real-time applications. We formulate our optimization criterion as a “degree-constrained minimum average-latency problem” which is known to be NP-Hard. A key feature of this formulation is that it gives a dynamic priority to different MSNs based on the size of its service set. Our proposed approach iteratively modifies the overlay tree using localized transformations to adapt with changing distribution of MSNs and clients, as well as network conditions. We show that a centralized greedy approach to this problem does not perform quite as well, while our distributed iterative scheme efficiently converges to near-optimal solutions.
Keywords: Application-layer multicast; Minimum latency problem; overlay multicast

Optimization of signal processing software for control system implementation - Bhattacharyya, Shuvra S.; Levine,William S. (Computer Aided Control System Design, 2006 IEEE International Conference on Control Applications, 2006 IEEE International Symposium on Intelligent Control, 2006 IEEE, 2006)
Signal processing plays a fundamental role in the design of control systems #x2014; the portion of a digitally-implemented control system between the sensor outputs and the actuator inputs is precisely a digital signal processor (DSP). Consequently, effective techniques for design and optimization of signal processing software are important in achieving efficient controller implementations. Motivated by these relationships, this paper reviews techniques for modeling signal processing functionality in a manner that exposes aspects of application structure that are useful for mapping the functionality into efficient implementations. The paper then introduces some representative techniques that operate on such models to systematically derive optimized implementations from them.

Optimization of structured programs - Zelkowitz, Marvin V; Bail,William G (Software: Practice and Experience, 2006)
The class of programs which do not contain goto statements has a structure which lends itself to optimization by an optimizer that is fast, efficient and relatively easy to program. The design of such an optimizer is described, along with some of the results obtained using this optimizer—one such result being that very little code optimization is achieved. The conjecture is made that this is true because gotoless programming languages lend themselves to more compact and concise object code at the source language level.
Keywords: compiler; Nested control structures; Optimizer; structured programming

An optimized system for expression and purification of secreted bacterial proteins - Geisbrecht,Brian V.; Bouyain,Samuel; Pop, Mihai (Protein Expression and Purification, 2006)
In this report, we describe an optimized system for the efficient overexpression, purification, and refolding of secreted bacterial proteins. Candidate secreted proteins were produced recombinantly in Escherichia coli as Tobacco Etch Virus protease-cleavable hexahistidine-c-myc eptiope fusion proteins. Without regard to their initial solubility, recombinant fusion proteins were extracted from whole cells with guanidium chloride, purified under denaturing conditions by immobilized metal affinity chromatography, and refolded by rapid dilution into a solution containing only Tris buffer and sodium chloride. Following concentration on the same resin under native conditions, each protein was eluted for further purification and/or characterization. Preliminary studies on a test set of 12 secreted proteins ranging in size from 13 to 130 kDa yielded between 10 and 50 mg of fusion protein per liter of induced culture at greater than 90% purity, as judged by Coomassie-stained SDS–PAGE. Of the nine proteins further purified, analytical gel filtration chromatography indicated that each was a monomer in solution and circular dichroism spectroscopy revealed that each had adopted a well-defined secondary structure. While there are many potential applications for this system, the results presented here suggest that it will be particularly useful for investigators employing structural approaches to understand protein function, as attested to by the crystal structures of three proteins purified using this methodology (B.V. Geisbrecht, B.Y. Hamaoka, B. Perman, A. Zemla, D.J. Leahy, J. Biol. Chem. 280 (2005) 17243–17250).
Keywords: Pathogens; Secreted proteins; Toxins; Virulence factors

Parallelism for quantum computation with qudits - O’Leary,Dianne P.; Brennen,Gavin K.; Bullock,Stephen S. (Physical Review APhys. Rev. A, 2006)
Robust quantum computation with d-level quantum systems (qudits) poses two requirements: fast, parallel quantum gates and high-fidelity two-qudit gates. We first describe how to implement parallel single-qudit operations. It is by now well known that any single-qudit unitary can be decomposed into a sequence of Givens rotations on two-dimensional subspaces of the qudit state space. Using a coupling graph to represent physically allowed couplings between pairs of qudit states, we then show that the logical depth (time) of the parallel gate sequence is equal to the height of an associated tree. The implementation of a given unitary can then optimize the tradeoff between gate time and resources used. These ideas are illustrated for qudits encoded in the ground hyperfine states of the alkali-metal atoms 87Rb and 133Cs. Second, we provide a protocol for implementing parallelized nonlocal two-qudit gates using the assistance of entangled qubit pairs. Using known protocols for qubit entanglement purification, this offers the possibility of high-fidelity two-qudit gates.

Partially overlapped channels not considered harmful - Mishra,A.; Shrivastava,V.; Banerjee,S.; Arbaugh, William A. (Proceedings of the joint international conference on Measurement and modeling of computer systems, 2006)

Participatory design with proxies: developing a desktop-PDA system to support people with aphasia - Jordan Boyd-Graber; Nikolova,Sonya S.; Moffatt,Karyn A.; Kin,Kenrick C.; Lee,Joshua Y.; Mackey,Lester W.; Tremaine,Marilyn M.; Klawe,Maria M. (Proceedings of the SIGCHI conference on Human Factors in computing systems, 2006)
In this paper, we describe the design and preliminary evaluation of a hybrid desktop-handheld system developed to support individuals with aphasia, a disorder which impairs the ability to speak, read, write, or understand language. The system allows its users to develop speech communication through images and sound on a desktop computer and download this speech to a mobile device that can then support communication outside the home. Using a desktop computer for input addresses some of this population's difficulties interacting with handheld devices, while the mobile device addresses stigma and portability issues. A modified participatory design approach was used in which proxies, that is, speech-language pathologists who work with aphasic individuals, assumed the role normally filled by users. This was done because of the difficulties in communicating with the target population and the high variability in aphasic disorders. In addition, the paper presents a case study of the proxy-use participatory design process that illustrates how different interview techniques resulted in different user feedback.
Keywords: aphasia; assistive technology; multi-modal interfaces; participatory design

Participatory, embodied, multi-agent simulation - Blikstein,Paulo; Rand, William; Wilensky,Uri (Proceedings of the fifth international joint conference on Autonomous agents and multiagent systems, 2006)
We will demonstrate the integration of a software-based multi-agent modeling platform with a participatory simulation environment and real-time control over a physical agent (robot). Both real and virtual participants will be able to act as agents in a simulation that will control a physical agent. The backbone of this demonstration is a widely used, freely available, mature modeling platform known as NetLogo.
Keywords: embedded agents; multi-agent simulation; participatory simulation; ROBOTICS; Sensors

The past, present, and future of experimental software engineering - Basili, Victor R. (Journal of the Brazilian Computer Society, 2006)
This paper gives a 40 year overview of the evolution of experimental software engineering, from the past to the future, from a personal perspective. My hypothesis is that my work followed the evolution of the field. I use my own experiences and thoughts as a barometer of how the field has changed and present some opinions about where we need to go.

Patterns of sequence conservation in presynaptic neural genes - Hadley,Dexter; Murphy,Tara; Valladares,Otto; Hannenhalli, Sridhar; Ungar,Lyle; Kim,Junhyong; Bućan,Maja (Genome Biology, 2006)
The neuronal synapse is a fundamental functional unit in the central nervous system of animals. Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved.

Physics-Based Detectors Applied to Long-Wave Infrared Hyperspectral Data - Broadwater,Joshua; Chellapa, Rama (CENTER FOR AUTOMATION RESEARCH, UNIVERSITY OF MARYLAND COLLEGE PARK, 2006)
Long-wave infrared (LWIR) hyperspectral image (HSI) data presents an interesting challenge for automatic target detection algorithms. LWIR HSI data is useful for both day and night operations, but weak signatures like disturbed soil can be problematic for standard matched-filter techniques. In this paper, we augment the standard matched-filter techniques with physics-based information particular to HSI data. Our results show that these physics-based detectors provide improved detection performance with quick processing times.
Keywords: *HYPERSPECTRAL IMAGERY; algorithms; AUTOMATIC; DETECTION; FAR INFRARED RADIATION; LOW STRENGTH; Matched filters; MILITARY OPERATIONS; NIGHT; OPTICS; SIGNATURES; SOILS; SPECTROMETERS; TARGET DETECTION

Postmodern internetwork architecture - Bhattacharjee, Bobby; Calvert,K.; Griffioen,J.; Spring, Neil; Sterbenz,J. P.G (ITTC-FY2006-TR-45030-01, Information and Telecommunication Center, The University of Kansas, 2006)
Network-layer innovation has proven surprisingly difficult, in part because internetworking protocols ignore com-peting economic interests and because a few protocols dominate, enabling layer violations that entrench technologies. Many shortcomings of today’s internetwork layer result from its inflexibility with respect to the policies of the stake- holders: users and service providers. The consequences of these failings are well-known: various hacks, layering violations, and overloadings are introduced to enforce policies and attempt to get the upper hand in various “tus- sles”. The result is a network that is increasingly brittle, hostile to innovation, vulnerable to attack, and insensitive to concerns about accountability and privacy. Our project aims to design, implement, and evaluate through daily use a minimalist internetwork layer and aux- iliary functionality that anticipates tussles and allows them to be played out in policy space, as opposed to in the packet-forwarding path. We call our approach postmodern internetwork architecture, because it is a reaction against many established network layer design concepts. The overall goal of the project is to make a larger portion of the network design space accessible without sacrificing the economy of scale offered by the unified Internet. We will use the postmodern architecture to explore basic architectural questions. These include: • What mechanisms should be supported by the network such that any foreseeable policy requirement can be explicitly addressed? • To what extent can routing and forwarding be isolated from each other while maintaining an efficient and usable network? • What forms of identity should be visible within the network, and what forms of accountability do different identities enable? • What mechanisms are needed to enable efficient access to cross-layer information and mechanisms such that lower layers can express their characteristics and upper layers can exert control downward? We plan to build and evaluate a complete end-to-end networking layer to help us understand feasible solutions to these questions. The Internet has fulfilled the potential of a complete generation of networking research by producing a global platform for innovation, commerce, and democracy. Unfortunately, the Internet also amply demonstrates the com- plexity and architectural ugliness that ensue when competing interests vie for benefits beyond those envisioned in the original design. This project is about redesigning the waist of the architectural hourglass to foster innovation, enhance security and accountability, and accomodate competing interests.

Programmer's Manual for XMTC Language, XMTC Compiler and XMT Simulator - Balkan,Aydin O.; Vishkin, Uzi (Technical Reports from UMIACS, UMIACS-TR-2005-45, 2006)
Explicit Multi-Threading (XMT) is a computing framework developed at the University of Maryland as part of a PRAM-on-chip vision (http://www.umiacs.umd.edu/users/vishkin/XMT). Much in the same way that performance programming of standard computers relies on C language, XMT performance programming is done using an extension of C called XMTC. This manual presents the second generation of XMTCprogramming paradigm. It is intended to be used by an application programmer, who is new to XMTC. In the first part of this technical report (UMIACS-TR 2005-45 Part 1 of 2), we define and describe key concepts, list the limitations and restrictions, and give examples. The second part (UMIACS-TR 2005-45 Part 2 of 2) is a brief tutorial, and it demonstrates the basic programming concepts of XMTC language with examples and exercises.
Keywords: Technical Report

Query planning in the presence of overlapping sources - Bleiholder,J.; Khuller, Samir; Naumann,F.; Raschid, Louiqa; Wu,Y. (Advances in Database Technology-EDBT 2006, 2006)
Navigational queries on Web-accessible life science sources pose unique query optimization challenges. The objects in these sources are interconnected to objects in other sources, forming a large and complex graph, and there is an overlap of objects in the sources. Answering a query requires the traversal of multiple alternate paths through these sources. Each path can be associated with the benefit or the cardinality of the target object set (TOS) of objects reached in the result. There is also an evaluation cost of reaching the TOS.We present dual problems in selecting the best set of paths. The first problem is to select a set of paths that satisfy a constraint on the evaluation cost while maximizing the benefit (number of distinct objects in the TOS). The dual problem is to select a set of paths that satisfies a threshold of the TOS benefit with minimal evaluation cost. The two problems can be mapped to the budgeted maximum coverage problem and the maximal set cover with a threshold. To solve these problems, we explore several solutions including greedy heuristics, a randomized search, and a traditional IP/LP formulation with bounds. We perform experiments on a real-world graph of life sciences objects from NCBI and report on the computational overhead of our solutions and their performance compared to the optimal solution.

Query planning in the presence of overlapping sources - Bleiholder,J.; Khuller, Samir; Naumann,F.; Raschid, Louiqa; Wu,Y. (Advances in Database Technology-EDBT 2006, 2006)

Query-time entity resolution - BHATTACHARVA,I.; Getoor, Lise; Licamele,L. (International conference on knowledge discovery and data mining, 2006)
The goal of entity resolution is to reconcile database references corresponding to the same real-world entities. Given the abundance of publicly available databases where entities are not resolved, we motivate the problem of quickly processing queries that require resolved entities from such 'unclean' databases. We propose a two-stage collective resolution strategy for processing queries. We then show how it can be performed on-the-fly by adaptively extracting and resolving those database references that are the most helpful for resolving the query. We validate our approach on two large real-world publication databases where we show the usefulness of collective resolution and at the same time demonstrate the need for adaptive strategies for query processing. We then show how the same queries can be answered in real time using our adaptive approach while preserving the gains of collective resolution.

Ranking search results in P2P systems - Gopalakrishnan,V.; Morselli,R.; Bhattacharjee, Bobby; Keleher,P.; Srinivasan, Aravind (Technical Report, CR-TR-4779, Department of Computer Science, University of Maryland, 2006)
P2P deployments are a natural infrastructure for buildingdistributed search networks. Proposed systems support locating and retrieving all results, but lack the information necessary to rank them. Users, however, are primarily interested in the most relevant, and not all possible results. Using random sampling, we extend a class of well- known information retrieval ranking algorithms such that they can be applied in this distributed setting. We analyze the overhead of our approach, and quantify exactly how our system scales with increasing number of documents, system size, document to node mapping (uniform versus non-uniform), and types of queries (rare versus popular terms). Our analysis and simulations show that a) these extensions are efficient, and can scale with little overhead to large systems, and b) the accuracy of the results ob- tained using distributed ranking is comparable to a cen- tralized implementation.

Ranking search results in peer-to-peer systems - Gopalakrishnan,V.; Morselli,R.; Bhattacharjee, Bobby; Keleher,P.; Srinivasan, Aravind (Technical Reports from UMIACS, 2006)
P2P deployments are a natural infrastructure for building distributed search networks. Proposed systems support locating and retrieving all results, but lack the information necessary to rank them. Users, however, are primarily interested in the most relevant, and not all possible results. Using random sampling, we extend a class of well-known information retrieval ranking algorithms such that they can be applied in this distributed setting. We analyze the overhead of our approach, and quantify exactly how our system scales with increasing number of documents, system size, document to node mapping (uniform versus non-uniform), and types of queries (rare versus popular terms). Our analysis and simulations show that a) these extensions are efficient, and can scale with little overhead to large systems, and b) the accuracy of the results obtained using distributed ranking is comparable to a centralized implementation.

Real-Time Distributed Algorithms for Visual and Battlefield Reasoning - Davis, Larry S.; Basili, Victor R.; V.S. Subrahmanian; Reggia, James A.; Aloimonos, J. (MARYLAND UNIV COLLEGE PARK OFFICE OF RESEARCH ADMINISTRATION AND ADVANCEMENT, 2006)
Information is key to the success of the next generation battlefield. There is a critical need to determine, in real-time, what the enemy is doing, and to interpret that information in the context of past related events. In this project we examined two aspects of this issue: development of a high-level task definition language for tasking a network of sensors to carry out given objectives, and interpreting recounted events so that past related scenarios could be automatically identified from a case database.

Reconfigurable image registration on FPGA platforms - Sen,M.; Hemaraj,Y.; Bhattacharyya, Shuvra S.; Shekhar,R. (Biomedical Circuits and Systems Conference, 2006. BioCAS 2006. IEEE, 2006)

Reflecting on Health: A System for Students to Monitor Diet and Exercise - Brown, Brandon; Marshini Chetty; Grimes, Andrea; Harmon, Ellie (SIGCHI EA '06, 2006)
Using an iterative design process, we designed and evaluated a system for college students to encourage the development and maintenance of healthy diet and exercise habits. The system has three components: a camera phone application to support photographic diet and exercise journaling, an automatic workout tracking application for exercise machines in the gym, and a visualization application to support users as they reflect on their diet and exercise activities.
Keywords: diet; exercise; journaling; mobile phone; Visualization

Register File Partitioning with Constraint Programming - Salmela,P.; Shen,C. C; Bhattacharyya, Shuvra S.; Takala,J. (System-on-Chip, 2006. International Symposium on, 2006)

Relational clustering for entity resolution queries - Bhattacharya,I.; Licamele,L.; Getoor, Lise (ICML 2006 Workshop on Statistical Relational Learning (SRL), 2006)
The goal of entity resolution is to recon-cile database references corresponding to the same real-world entities. Given the abun- dance of publicly available databases where entities are not resolved, we motivate the problem of quickly processing queries that require resolved entities from such ‘unclean’ databases. We first propose a cut-based rela- tional clustering formulation for collective en- tity resolution. We then show how it can be performed on-the-fly by adaptively extract- ing and resolving those database references that are the most helpful for resolving the query. We validate our approach on two large real-world publication databases, where we show the usefulness of collective resolution and at the same time demonstrate the need for adaptive strategies for query processing. We then show how the same queries can be answered in real time using our adaptive ap- proach while preserving the gains of collective resolution.

Reliable broadcast in radio networks: the bounded collision case - Koo,Chiu-Yuen; Bhandari,Vartika; Katz, Jonathan; Vaidya,Nitin H. (Proceedings of the twenty-fifth annual ACM symposium on Principles of distributed computing, 2006)
We study the problem of achieving global broadcast in a radio network where a node can multicast messages to all of its neighbors (that is, nodes within some given distance r), and up to t nodes in any single neighborhood may be corrupted. Previous work assumes that corrupted nodes can neither cause collisions nor spoof addresses of honest nodes. In this work, we eliminate these assumptions and allow each faulty node to cause a (known) bounded number of collisions and spoof the addresses of arbitrary other nodes. We show that the maximum tolerable t in this case is identical to the maximum tolerable t when collisions and address spoofing are not allowed. Thus, by causing collisions and spoofing addresses an adversary may be able to degrade the efficiency of achieving broadcast, but it cannot affect the feasibility of this task.
Keywords: broadcast; byzantine failure; Fault tolerance; radio networks

Resilient multicast using overlays - Banerjee,S.; Lee,Seungjoon; Bhattacharjee, Bobby; Srinivasan, Aravind (IEEE/ACM Transactions on Networking, 2006)
We introduce Probabilistic Resilient Multicast (PRM): a multicast data recovery scheme that improves data delivery ratios while maintaining low end-to-end latencies. PRM has both a proactive and a reactive components; in this paper we describe how PRM can be used to improve the performance of application-layer multicast protocols especially when there are high packet losses and host failures. Through detailed analysis in this paper, we show that this loss recovery technique has efficient scaling properties-the overheads at each overlay node asymptotically decrease to zero with increasing group sizes. As a detailed case study, we show how PRM can be applied to the NICE application-layer multicast protocol. We present detailed simulations of the PRM-enhanced NICE protocol for 10 000 node Internet-like topologies. Simulations show that PRM achieves a high delivery ratio (>97%) with a low latency bound (600 ms) for environments with high end-to-end network losses (1%-5%) and high topology change rates (5 changes per second) while incurring very low overheads (<5%).
Keywords: application-layer multicast protocols; Computer science; Data communication; Delay; Internet; Internet-like topologies; IP networks; loss recovery technique; Multicast; multicast data recovery scheme; Multicast protocols; Network topology; NETWORKS; overlays; Performance loss; probabilistic forwarding; probabilistic resilient multicast; Protocols; Resilience; Streaming media; telecommunication network topology; Terminology

Resource Discovery Techniques in Distributed Desktop Grid Environments - Kim,Jik-Soo; Nam,Beomseok; Keleher,Peter; Marsh,Michael; Bhattacharjee, Bobby; Sussman, Alan (Proceedings of the 7th IEEE/ACM International Conference on Grid Computing, 2006)
Desktop grids use opportunistic sharing to exploit large collections of personal computers and workstations across the Internet, achieving tremendous computing power at low cost. Traditional desktop grid systems are typically based on a client-server architecture, which has inherent shortcomings with respect to robustness, reliability and scalability. In this paper, we propose a decentralized, robust, highly available, and scalable infrastructure to match incoming jobs to available resources. Through a comparative analysis on the experimental results obtained via simulation of three different types of matchmaking algorithms under different workload scenarios, we show the trade-offs between effcient matchmaking and good load balancing in a fully decentralized, heterogeneous computational environment.

Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection - Lewinski,Mary K; Yamashita,Masahiro; Emerman,Michael; Ciuffi,Angela; Marshall,Heather; Crawford,Gregory; Collins,Francis; Shinn,Paul; Leipzig,Jeremy; Hannenhalli, Sridhar; Berry,Charles C; Ecker,Joseph R; et al. (PLoS PathogPLoS Pathog, 2006)
Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV) integrates preferentially within active transcription units, whereas murine leukemia virus (MLV) integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN) coding region into HIV (to make HIVmIN) caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN) further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag) displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I–hypersensitive sites (i.e., +/− 1 kb), and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins.

Revisiting Internet addressing: Back to the future - Vutukuru,M.; Feamster, Nick; Walfish,M.; Balakrishnan,H.; Shenker,S. (Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, 2006)
IP prefixes undermine three goals of Internet routing:accurate reflection of network-layer reachability, secure routing messages, and effective traffic control. This pa- per presents Atomic IP (AIP), a simple change to Inter- net addressing (which in fact reverts to how addressing once worked), that allows Internet routing to achieve these goals.

Ring signatures: Stronger definitions, and constructions without random oracles - Bender,A.; Katz, Jonathan; Morselli,R. (Theory of Cryptography, 2006)
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 then give separation results proving that our new notions are strictly stronger than previous ones. Next, we show two constructions of ring signature schemes in the standard model: one based on generic assumptions which satisfies our strongest definitions of security, and a second, more efficient scheme achieving weaker security guarantees and more limited functionality. These are the first constructions of ring signature schemes that do not rely on random oracles or ideal ciphers.

A scalable key management and clustering scheme for ad hoc networks - Li,Jason H.; Levy,Renato; Yu,Miao; Bhattacharjee, Bobby (Proceedings of the 1st international conference on Scalable information systems, 2006)
This paper describes a scalable key management and clustering scheme for secure group communications in ad hoc and sensor networks. The scalability problem is solved by partitioning the communicating devices into subgroups, with a leader in each subgroup, and further organizing the subgroups into hierarchies. Each level of the hierarchy is called a tier or layer. Key generation, distribution, and actual data transmissions follow the hierarchy. The Distributed, Efficient Clustering Approach (DECA) provides robust clustering to form subgroups, and analytical and simulation results demonstrate that DECA is energy-efficient and resilient against node mobility. Comparing with most other schemes, our approach is extremely scalable and efficient, provides more security guarantees, and is selective, adaptive and robust.

Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: Sixteen new members and a novel subfamily - Wu,Wenjie; Niles,Edward G.; El‐Sayed, Najib M.; Berriman,Matthew; LoVerde,Philip T. (Gene, 2006)
Nuclear receptors (NRs) are important transcriptional modulators in metazoans. Sixteen new NRs were identified in the Platyhelminth trematode, Schistosoma mansoni. Three were found to possess novel tandem DNA-binding domains that identify a new subfamily of NR. Two NRs are homologues of the thyroid hormone receptor that previously were thought to be restricted to chordates. This study brings the total number of identified NR in S. mansoni to 21. Phylogenetic and comparative genomic analyses demonstrate that S. mansoni NRs share an evolutionary lineage with that of arthropods and vertebrates. Phylogenic analysis shows that more than half of the S. mansoni nuclear receptors evolved from a second gene duplication. As the second gene duplication of NRs was thought to be specific to vertebrates, our data challenge the current theory of NR evolution.
Keywords: Nuclear receptors; Schistosoma mansoni

The Science of Hysteresis: Mathematical modeling and applications - Bertotti,Giorgio; Mayergoyz, Issak D (Academic Press, 2006)
Keywords: Business & Economics / Economics / Microeconomics; Hysteresis; Magnetism; Science / Physics / Magnetism

Seasonal Cholera Caused by Vibrio Cholerae Serogroups O1 and O139 in the Coastal Aquatic Environment of Bangladesh - Alam,Munirul; Hasan,Nur A.; Sadique,Abdus; Bhuiyan,N. A.; Ahmed,Kabir U.; Nusrin,Suraia; Nair,G. Balakrish; Siddique,A. K.; Sack,R. Bradley; Sack,David A.; Huq,Anwar; Rita R Colwell (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2006)
Since Vibrio cholerae O139 first appeared in 1992, both O1 El Tor and O139 have been recognized as the epidemic serogroups, although their geographic distribution, endemicity, and reservoir are not fully understood. To address this lack of information, a study of the epidemiology and ecology of V. cholerae O1 and O139 was carried out in two coastal areas, Bakerganj and Mathbaria, Bangladesh, where cholera occurs seasonally. The results of a biweekly clinical study (January 2004 to May 2005), employing culture methods, and of an ecological study (monthly in Bakerganj and biweekly in Mathbaria from March 2004 to May 2005), employing direct and enrichment culture, colony blot hybridization, and direct fluorescent-antibody methods, showed that cholera is endemic in both Bakerganj and Mathbaria and that V. cholerae O1, O139, and non-O1/non-O139 are autochthonous to the aquatic environment. Although V. cholerae O1 and O139 were isolated from both areas, most noteworthy was the isolation of V. cholerae O139 in March, July, and September 2004 in Mathbaria, where seasonal cholera was clinically linked only to V. cholerae O1. In Mathbaria, V. cholerae O139 emerged as the sole cause of a significant outbreak of cholera in March 2005. V. cholerae O1 reemerged clinically in April 2005 and established dominance over V. cholerae O139, continuing to cause cholera in Mathbaria. In conclusion, the epidemic potential and coastal aquatic reservoir for V. cholerae O139 have been demonstrated. Based on the results of this study, the coastal ecosystem of the Bay of Bengal is concluded to be a significant reservoir for the epidemic serogroups of V. cholerae.

Selection of Target Sites for Mobile DNA Integration in the Human Genome - Berry,Charles; Hannenhalli, Sridhar; Leipzig,Jeremy; Bushman,Frederic D. (PLoS Comput BiolPLoS Comput Biol, 2006)
DNA sequences from retroviruses, retrotransposons, DNA transposons, and parvoviruses can all become integrated into the human genome. Accumulation of such sequences accounts for at least 40% of our genome today. These integrating elements are also of interest as gene-delivery vectors for human gene therapy. Here we present a comprehensive bioinformatic analysis of integration targeting by HIV, MLV, ASLV, SFV, L1, SB, and AAV. We used a mathematical method which allowed annotation of each base pair in the human genome for its likelihood of hosting an integration event by each type of element, taking advantage of more than 200 types of genomic annotation. This bioinformatic resource documents a wealth of new associations between genomic features and integration targeting. The study also revealed that the length of genomic intervals analyzed strongly affected the conclusions drawn—thus, answering the question “What genomic features affect integration?” requires carefully specifying the length scale of interest.

Shared family calendars: Promoting symmetry and accessibility - Plaisant, Catherine; Clamage,Aaron; Hutchinson,Hilary Browne; Bederson, Benjamin B.; Druin, Allison (ACM Trans. Comput.-Hum. Interact., 2006)
We describe the design and use of a system facilitating the sharing of calendar information between remotely located, multi-generational family members. Most previous work in this area involves software enabling younger family members to monitor their parents. We have found, however, that older adults are equally if not more interested in the activities of younger family members. The major obstacle preventing them from participating in information sharing is the technology itself. Therefore, we developed a multi-layered interface approach that offers simple interaction to older users. In our system, users can choose to enter information into a computerized calendar or write it by hand on digital paper calendars. All of the information is automatically shared among everyone in the distributed family. By making the interface more accessible to older users, we promote symmetrical sharing of information among both older and younger family members. We present our participatory design process, describe the user interface, and report on an exploratory field study in three households of an extended family.
Keywords: calendar; digital paper; elderly; family technology; Home; layered interface; privacy; universal usability

A Statistical Analysis of Attack Data to Separate Attacks - Michel Cukier; Berthier,R.; Panjwani,S.; Tan,S. (2006)
This paper analyzes malicious activity collected from a test-bed, consisting of two target computers dedicated solely to the purpose of being attacked, over a 109 day time period. We separated port scans, ICMP scans, and vulnerability scans from the malicious activity. In the remaining attack data, over 78% (i.e., 3,677 attacks) targeted port 445, which was then statistically analyzed. The goal was to find the characteristics that most efficiently separate the attacks. First, we separated the attacks by analyzing their messages. Then we separated the attacks by clustering characteristics using the K-Means algorithm. The comparison between the analysis of the messages and the outcome of the K-Means algorithm showed that 1) the mean of the distributions of packets, bytes and message lengths over time are poor characteristics to separate attacks and 2) the number of bytes, the mean of the distribution of bytes and message lengths as a function of the number packets are the best characteristics for separating attacks
Keywords: attack data statistical analysis; attack separation; computer crime; Data analysis; data mining; ICMP scans; K-Means algorithm; pattern clustering; port scans; statistical analysis; vulnerability scans

A Step Towards Automated Design of Side Actions in Injection Molding of Complex Parts - Banerjee,Ashis; Gupta, Satyandra K. (Geometric Modeling and Processing - GMP 2006, 2006)
Side actions contribute to mold cost by resulting in an additional manufacturing and assembly cost as well as by increasing the molding cycle time. Therefore, generating shapes of side actions requires solving a complex geometric optimization problem. Different objective functions may be needed depending upon different molding scenarios (e.g., prototyping versus large production runs). Manually designing side actions is a challenging task and requires considerable expertise. Automated design of side actions will significantly reduce mold design lead times. This paper describes algorithms for generating shapes of side actions to minimize a customizable molding cost function.
Keywords: Computer science

System synthesis for optically-connected, multiprocessors on-chip - Bambha,N. K; Bhattacharyya, Shuvra S.; STUDIES,MARYLAND UNIV COLLEGE PARK INST FOR ADVANCED COMPUTER (Citeseer, 2006)

Target size study for one-handed thumb use on small touchscreen devices - Parhi,P.; Karlson,A.K.; Bederson, Benjamin B. (Proceedings of the 8th conference on Human-computer interaction with mobile devices and services, 2006)

Toward an enriched (and revitalized) sense of help: Summary of an ASIS&T 2005 panel session - Haas,Stephanie W; Denn,Sheila; Locke,David; Shneiderman, Ben; Brown,Laurie (Bulletin of the American Society for Information Science and Technology, 2006)

TreePlus: Interactive Exploration of Networks with Enhanced Tree Layouts - Lee,B.; Parr,C.S.; Plaisant, Catherine; Bederson, Benjamin B.; Veksler,V.D.; Gray,W.D.; Kotfila,C. (Visualization and Computer Graphics, IEEE Transactions on, 2006)
Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food Webs, ontologies and social networks difficult to understand and interact with. We propose a new interactive visual analytics component called TreePlus that is based on a tree-style layout. TreePlus reveals the missing graph structure with visualization and interaction while maintaining good readability. To support exploration of the local structure of the graph and gathering of information from the extensive reading of labels, we use a guiding metaphor of "plant a seed and watch it grow." It allows users to start with a node and expand the graph as needed, which complements the classic overview techniques that can be effective at (but often limited to) revealing clusters. We describe our design goals, describe the interface and report on a controlled user study with 28 participants comparing TreePlus with a traditional graph interface for six tasks. In general, the advantage of TreePlus over the traditional interface increased as the density of the displayed data increased. Participants also reported higher levels of confidence in their answers with TreePlus and most of them preferred TreePlus
Keywords: Automated; Software; User-Computer Interface; Biological; Pattern Recognition; data visualization; graph structure; graphical user interface; interactive visual analytics; occlusion; tree-style layout; data visualisation; graphical user interfaces; hidden feature removal; interactive systems; trees (mathematics); Algorithms; Computer Graphics; C

The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion - Bringaud,F.; Bartholomeu,D. C; Blandin,G.; Delcher,A.; Baltz,T.; El‐Sayed, Najib M.; Ghedin,E. (Molecular biology and evolution, 2006)

Using PlanetLab for network research - Spring, Neil; Peterson,Larry; Bavier,Andy; Pait,Vivek (ACM SIGOPS Operating Systems Review, 2006)

Video Mensuration Using a Stationary Camera - Guo,Feng; Chellapa, Rama (Computer Vision – ECCV 2006Computer Vision – ECCV 2006, 2006)
This paper presents a method for video mensuration using a single stationary camera. The problem we address is simple, i.e., the mensuration of any arbitrary line segment on the reference plane using multiple frames with minimal calibration. Unlike previous solutions that are based on planar rectification, our approach is based on fitting the image of multiple concentric circles on the plane. Further, the proposed method aims to minimize the error in mensuration. Hence we can calculate the mensuration of the line segments not lying on the reference plane. Using an algorithm for detecting and tracking wheels of an automobile, we have implemented a fully automatic system for wheel base mensuration. The mensuration results are accurate enough that they can be used to determine the vehicle classes. Furthermore, we measure the line segment between any two points on the vehicle and plot them in top and side views.

View-invariant estimation of height and stride for gait recognition - BenAbdelkader,C.; Cutler, R.; Davis, Larry S. (Biometric Authentication, 2006)
We present a parametric method to automatically identify people in monocular low-resolution video by estimating the height and stride parameters of their walking gait. Stride parameters (stride length and cadence) are functions of body height, weight, and gender. Previous work has demonstrated effective use of these biometrics for identification and verification of people. In this paper, we show that performance is significantly improved by using height as an additional discriminant feature. Height is estimated by robustly segmenting the person from the background and fitting their apparent height to a time-dependent model. This method is correspondence-free and works with low-resolution images of people. It is also view-invariant, albeit performance is optimal in near fronto-parallel configurations. Identification accuracy is estimated at 47% for fronto-parallel sequences of 41 people, and 65% for non-fronto-parallel sequences of 17 people, compared with 18% and 51%, respectively, when only stride and cadence are used.

Visualization Support for Fusing Relational, Spatio-Temporal Data: Building Career Histories - Blythe,Jim; Patwardhan,Mithila; Oates,Tim; desJardins, Marie; Rheingans,Penny (Information Fusion, 2006 9th International Conference on, 2006)
Many real-world domains resist analysis because they are best characterized by a variety of data types, including relational, spatial, and temporal components. Examples of such domains include disease outbreaks, criminal networks, and the World-Wide Web. We present two types of visualizations based on physical metaphors that facilitate fusion, analysis, and deep understanding of relational, spatio-temporal data. The first visualization is based on the metaphor of fluid flow through elastic pipes, and the second on wave propagation. We discuss both types of visualizations in the context of fusing information about the activities of scientists over time with the goal of constructing career histories

Visualizing Graphs as Trees: Plant a Seed and Watch it Grow - Lee,Bongshin; Parr,Cynthia; Plaisant, Catherine; Bederson, Benjamin B. (Graph DrawingGraph Drawing, 2006)
TreePlus is a graph browsing technique based on a tree-style layout. It shows the missing graph structure using interaction techniques and enables users to start with a specific node and incrementally explore the local structure of graphs. We believe that it supports particularly well tasks that require rapid reading of labels.

VoIP deregulation in South Africa: Implications for underserviced areas - Marshini Chetty; Blake, Edwin; McPhie, Ewan (Telecommunications Policy, 2006)
Several statutory restrictions have recently been lifted on the use of Voice over Internet Protocol (VoIP) in South Africa. Previously, VoIP could only be utilised by the incumbent telecommunications operator, Telkom, the Second National Operator (SNO) and under serviced area licensees (USALs). This means new opportunities and cost savings for both network service providers and consumers. However, in rural and remote regions, further liberalisation is required so that service providers can take advantage of wireless technologies to provide connectivity in these areas. This paper discusses the legislative environment in South Africa and around the world with respect to VoIP and Wireless Fidelity (WiFi). In addition, examples are provided of how these technologies have been combined to provide last mile solutions around the world and particularly in South Africa. The paper concludes that further liberalisation in the telecommunications environment in South Africa is required if the goal of providing affordable access in rural areas is to be attained. Specifically, it is recommended that wireless technologies be deregulated since the combination of VoIP and WiFi may benefit rural areas. Also, the paper finds that USALs may not be the right model for underserviced areas in South Africa. Lastly, it is apparent that applications drive development and dictate which technologies are relevant for rural areas.
Keywords: South Africa; VoIP; WiFi

Wavelet-Based Super-Resolution Reconstruction: Theory and Algorithm - Hui Ji; Fermüller, Cornelia (Computer Vision – ECCV 2006Computer Vision – ECCV 2006, 2006)
We present a theoretical analysis and a new algorithm for the problem of super-resolution imaging: the reconstruction of HR (high-resolution) images from a sequence of LR (low-resolution) images. Super-resolution imaging entails solutions to two problems. One is the alignment of image frames. The other is the reconstruction of a HR image from multiple aligned LR images. Our analysis of the latter problem reveals insights into the theoretical limits of super-resolution reconstruction. We find that at best we can reconstruct a HR image blurred by a specific low-pass filter. Based on the analysis we present a new wavelet-based iterative reconstruction algorithm which is very robust to noise. Furthermore, it has a computationally efficient built-in denoising scheme with a nearly optimal risk bound. Roughly speaking, our method could be described as a better-conditioned iterative back-projection scheme with a fast and optimal regularization criteria in each iteration step. Experiments with both simulated and real data demonstrate that our approach has significantly better performance than existing super-resolution methods. It has the ability to remove even large amounts of mixed noise without creating smoothing artifacts.

What Is the Range of Surface Reconstructions from a Gradient Field? - Agrawal,Amit; Raskar,Ramesh; Chellapa, Rama (Computer Vision – ECCV 2006Computer Vision – ECCV 2006, 2006)
We propose a generalized equation to represent a continuum of surface reconstruction solutions of a given non-integrable gradient field. We show that common approaches such as Poisson solver and Frankot-Chellappa algorithm are special cases of this generalized equation. For a N × N pixel grid, the subspace of all integrable gradient fields is of dimension N 2 – 1. Our framework can be applied to derive a range of meaningful surface reconstructions from this high dimensional space. The key observation is that the range of solutions is related to the degree of anisotropy in applying weights to the gradients in the integration process. While common approaches use isotropic weights, we show that by using a progression of spatially varying anisotropic weights, we can achieve significant improvement in reconstructions. We propose (a) α-surfaces using binary weights, where the parameter α allows trade off between smoothness and robustness, (b) M-estimators and edge preserving regularization using continuous weights and (c) Diffusion using affine transformation of gradients. We provide results on photometric stereo, compare with previous approaches and show that anisotropic treatment discounts noise while recovering salient features in reconstructions.

Widgets, Planets, and Demons: the Case for the Integration of Human, Embedded, and Virtual Agents via Mediation - Rand, William; Blikstein,P.; Wilensky,U. (Proceedings of Swarmfest, 2006)

3D Facial Pose Tracking in Uncalibrated Videos - Aggarwal,Gaurav; Veeraraghavan,Ashok; Chellapa, Rama (Pattern Recognition and Machine IntelligencePattern Recognition and Machine Intelligence, 2005)
This paper presents a method to recover the 3D configuration of a face in each frame of a video. The 3D configuration consists of the 3 translational parameters and the 3 orientation parameters which correspond to the yaw, pitch and roll of the face, which is important for applications like face modeling, recognition, expression analysis, etc. The approach combines the structural advantages of geometric modeling with the statistical advantages of a particle-filter based inference. The face is modeled as the curved surface of a cylinder which is free to translate and rotate arbitrarily. The geometric modeling takes care of pose and self-occlusion while the statistical modeling handles moderate occlusion and illumination variations. Experimental results on multiple datasets are provided to show the efficacy of the approach. The insensitivity of our approach to calibration parameters (focal length) is also shown.

Algorithm 844: Computing sparse reduced-rank approximations to sparse matrices - Berry,M. W; Pulatova,S. A; Stewart, G.W. (ACM Transactions on Mathematical Software-TOMS, 2005)

An architectural level design methodology for embedded face detection - Kianzad,V.; Saha,S.; Schlessman,J.; Aggarwal,G.; Bhattacharyya, Shuvra S.; Wolf,W.; Chellapa, Rama (Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis, 2005)
Face detection and recognition research has attracted great attention in recent years. Automatic face detection has great potential in a large array of application areas, including banking and security system access control, video surveillance, and multimedia information retrieval. In this paper, we discuss an architectural level design methodology for implementation of an embedded face detection system on a reconfigurable system on chip. We present models for performance estimation and validate these models with experimental values obtained from implementing our system on an FPGA platform. This modeling approach is shown to be efficient, accurate, and intuitive for designers to work with. Using this approach, we present several design options that trade-off various architectural features.
Keywords: design space exploration; Face detection; platforms; reconfigurable; system-level models

Asymptotically Optimal Quantum Circuits for d-Level Systems - Bullock,Stephen S.; O’Leary,Dianne P.; Brennen,Gavin K. (Physical Review LettersPhys. Rev. Lett., 2005)
Scalability of a quantum computation requires that the information be processed on multiple subsystems. However, it is unclear how the complexity of a quantum algorithm, quantified by the number of entangling gates, depends on the subsystem size. We examine the quantum circuit complexity for exactly universal computation on many d-level systems (qudits). Both a lower bound and a constructive upper bound on the number of two-qudit gates result, proving a sharp asymptotic of Θ(d2n) gates. This closes the complexity question for all d-level systems (d finite). The optimal asymptotic applies to systems with locality constraints, e.g., nearest neighbor interactions.

Average relative radiance transform for subpixel detection - Broadwater, J.; Meth, R.; Chellapa, Rama (Geoscience and Remote Sensing Symposium, 2005. IGARSS '05. Proceedings. 2005 IEEE International, 2005)

Building a Coherent Data Pipeline in Microarray Data Analyses: Optimization of Signal/Noise Ratios Using an Interactive Visualization Tool and a Novel Noise Filtering Method (2003) - Seo,Jinwook; Bakay,Marina; Chen,Yi-Wen; Hilmer,Sara; Shneiderman, Ben; Hoffman,Eric P (Institute for Systems Research Technical Reports, 2005)
Motivation: Sources of uncontrolled noise strongly influence data analysis in microarray studies, yet signal/noise ratios are rarely considered in microarray data analyses. We hypothesized that different research projects would have different sources and levels of confounding noise, and built an interactive visual analysis tool to test and define parameters in Affymetrix analyses that optimize the ratio of signal (desired biological variable) versus noise (confounding uncontrolled variables). Results: Five probe set algorithms were studied with and without statistical weighting of probe sets using Microarray Suite (MAS) 5.0 probe set detection p values. The signal/noise optimization method was tested in two large novel microarray datasets with different levels of confounding noise; a 105 sample U133A human muscle biopsy data set (11 groups) (extensive noise), and a 40 sample U74A inbred mouse lung data set (8 groups) (little noise). Success was measured using F-measure value of success of unsupervised clustering into appropriate biological groups (signal). We show that both probe set signal algorithm and probe set detection p-value weighting have a strong effect on signal/noise ratios, and that the different methods performed quite differently in the two data sets. Among the signal algorithms tested, dChip difference model with p-value weighting was the most consistent at maximizing the effect of the target biological variables on data interpretation of the two data sets. Availability: The Hierarchical Clustering Explorer 2.0 is [url=http://www.cs.umd.edu/hcil/hce/]available[/url] online and the improved version of the Hierarchical Clustering Explorer 2.0 with p-value weighting and Fmeasure is available upon request to the first author. Murine arrays (40 samples) are publicly available at the [url=http://microarray.cnmcresearch.org/pgadatatable.asp]PEPR resource.[/url] (Chen et al., 2004).
Keywords: Technical Report

Capital and benefit in social networks - Licamele,Louis; Bilgic,Mustafa; Getoor, Lise; Roussopoulos, Nick (Proceedings of the 3rd international workshop on Link discovery, 2005)
Recently there has been a surge of interest in social networks. Email traffic, disease transmission, and criminal activity can all be modeled as social networks. In this paper, we introduce a particular form of social network which we call a friendship-event network. A friendship-event network describes two inter-related networks. One is a friendship network among a set of actors. The other is an event network that describes events, event organizers and event participants. Within these types of networks, we formulate the notion of capital based on the actor-organizer friendship relationship and the notion of benefit, based on event participation. We ground these definitions in a real-world example of academic collaboration networks, where the actors are researchers, the friendships are collaborations, the events are conferences, the organizers are program committee members and the participants are conference authors. We incorporate a temporal component by considering the notion of an event series. We explore the use of these measures on a data set describing three computer science conferences over the past ten years.

CASPER: an integrated energy-driven approach for task graph scheduling on distributed embedded systems - Kianzad,V.; Bhattacharyya, Shuvra S.; Gang Qu (Application-Specific Systems, Architecture Processors, 2005. ASAP 2005. 16th IEEE International Conference on, 2005)
For multiprocessor embedded systems, the dynamic voltage scaling (DVS) technique can be applied to scheduled applications for energy reduction. DVS utilizes slack in the schedule to slow down processes and save energy. Therefore, it is generally believed that the maximal energy saving is achieved on a schedule with the minimum makespan (maximal slack). Most current approaches treat task assignment, scheduling, and DVS separately. In this paper, we present a framework called CASPER (combined assignment, scheduling, and power-management) that challenges this common belief by integrating task scheduling and DVS under a single iterative optimization loop via genetic algorithm. We have conducted extensive experiments to validate the energy efficiency of CASPER. For homogeneous multiprocessor systems (in which all processors are of the same type), we consider a recently proposed slack distribution algorithm (PDP-SPM) by S. Hua and G. Qu (2005): applying PDP-SPM on the schedule with the minimal makespan gives an average of 53.8% energy saving; CASPER finds schedules with slightly larger makespan but a 57.3% energy saving, a 7.8% improvement. For heterogeneous systems, we consider the power variation DVS (PV-DVS) algorithm by Schmitz et al. (2004), CASPER improves its energy efficiency by 8.2%. Finally, our results also show that the proposed single loop CASPER framework saves 23.3% more energy over GMA+EE-GLSA by Schmitz et al. (2002), the only other known integrated approach with a nested loop that combines scheduling and power management in the inner loop but leaves assignment in the outer loop.
Keywords: CASPER; combined-assignment-scheduling-and-power-management; computational complexity; distributed system; dynamic voltage scaling; embedded systems; energy reduction; genetic algorithm; Genetic algorithms; graph theory; homogeneous multiprocessor system; maximal energy saving; Multiprocessing systems; multiprocessor embedded system; optimization loop; power management; power variation; Processor scheduling; slack distribution algorithm; task assignment; task graph scheduling

Combining self-reported and automatic data to improve programming effort measurement - Hochstein, Lorin; Basili, Victor R.; Zelkowitz, Marvin V; Hollingsworth, Jeffrey K; Carver, Jeff (Proceedings of the 10th European software engineering conference held jointly with 13th ACM SIGSOFT international symposium on Foundations of software engineering, 2005)
Measuring effort accurately and consistently across subjects in a programming experiment can be a surprisingly difficult task. In particular, measures based on self-reported data may differ significantly from measures based on data which is recorded automatically from a subject's computing environment. Since self-reports can be unreliable, and not all activities can be captured automatically, a complete measure of programming effort should incorporate both classes of data. In this paper, we show how self-reported and automatic effort can be combined to perform validation and to measure total programming effort.
Keywords: effort; experimentation; human factors; manual approaches; measurement; process metrics; verification

Comparative Genomics of Trypanosomatid Parasitic Protozoa - El‐Sayed, Najib M.; Myler,Peter J.; Blandin,Gaëlle; Berriman,Matthew; Crabtree,Jonathan; Aggarwal,Gautam; Caler,Elisabet; Renauld,Hubert; Worthey,Elizabeth A.; Hertz-Fowler,Christiane; Ghedin,Elodie; Peacock,Christopher; et al. (Science, 2005)
A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that—along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions—have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.

Computer vision on FPGAs: Design methodology and its application to gesture recognition - Sen,M.; Corretjer,I.; Haim,F.; Saha,S.; Bhattacharyya, Shuvra S.; Schlessman,J.; Wolf,W. (Computer Vision and Pattern Recognition-Workshops, 2005. CVPR Workshops. IEEE Computer Society Conference on, 2005)

Content Index to Volume 18 - Kuniavsky,M.; Vaughan,M.; Bederson, Benjamin B.; Shneiderman, Ben; Rau,P.L.P.; from Menus,T.; Lane,D.M.; Napier,H.A.; Peres,S.C.; Sándor,A. (INTERNATIONAL JOURNAL OF HUMAN–COMPUTER INTERACTION, 2005)

Correctness properties for Internet routing - Feamster, Nick; Balakrishnan,H. (Allerton Conference on Communication, Control, and Computing, 2005)
This paper motivates and presents a correctness specifi-cation for Internet routing. This specification is based on three properties—route validity, path visibility, and safety. This specification may be of use to people de- veloping tools to check routing configurations, to people designing solutions to specific problems in the current sys- tem, and to designers of new protocols and routing archi- tectures, all of whom can benefit from knowing what it means for Internet routing to be “correct”.

Criteria for exact qudit universality - Brennen,Gavin K.; O’Leary,Dianne P.; Bullock,Stephen S. (Physical Review APhys. Rev. A, 2005)
We describe criteria for implementation of quantum computation in qudits. A qudit is a d-dimensional system whose Hilbert space is spanned by states ∣0⟩, ∣1⟩, …, ∣d−1⟩. An important earlier work [ A. Muthukrishnan and C.R. Stroud, Jr. Phys. Rev. A 62 052309 (2000)] describes how to exactly simulate an arbitrary unitary on multiple qudits using a 2d−1 parameter family of single qudit and two qudit gates. That technique is based on the spectral decomposition of unitaries. Here we generalize this argument to show that exact universality follows given a discrete set of single qudit Hamiltonians and one two-qudit Hamiltonian. The technique is related to the QR-matrix decomposition of numerical linear algebra. We consider a generic physical system in which the single qudit Hamiltonians are a small collection of Hjkx=ℏΩ(∣k⟩⟨j∣+∣j⟩⟨k∣) and Hjky=ℏΩ(i∣k⟩⟨j∣−i∣j⟩⟨k∣). A coupling graph results taking nodes 0, …, d−1 and edges j↔k iff Hjkx,y are allowed Hamiltonians. One qudit exact universality follows iff this graph is connected, and complete universality results if the two-qudit Hamiltonian H=ℏΩ∣d−1,d−1⟩⟨d−1,d−1∣ is also allowed. We discuss implementation in the eight dimensional ground electronic states of 87Rb and construct an optimal gate sequence using Raman laser pulses.

Data Redistribution and Remote Method Invocation in Parallel Component Architectures - Bertrand,Felipe; Bramley,Randall; Sussman, Alan; Bernholdt,David E.; Kohl,James A.; Larson,Jay W.; Damevski,Kostadin B. (Parallel and Distributed Processing Symposium, International, 2005)
With the increasing availability of high-performance massively parallel computer systems, the prevalence of sophisticated scientific simulation has grown rapidly. The complexity of the scientific models being simulated has also evolved, leading to a variety of coupled multi-physics simulation codes. Such cooperating parallel programs require fundamentally new interaction capabilities, to efficiently exchange parallel data structures and collectively invoke methods across programs. So-called "M?N" research, as part of the Common Component Architecture (CCA) effort, addresses these special and challenging needs, to provide generalized interfaces and tools that support flexible parallel data redistribution and parallel remote method invocation. Using this technology, distinct simulation codes with disparate distributed data decompositions can work together to achieve greater scientific discoveries.

Detecting BGP configuration faults with static analysis - Feamster, Nick; Balakrishnan,Hari (Proceedings of the 2nd conference on Symposium on Networked Systems Design & Implementation - Volume 2, 2005)
The Internet is composed of many independent autonomous systems (ASes) that exchange reachability information to destinations using the Border Gateway Protocol (BGP). Network operators in each AS configure BGP routers to control the routes that are learned, selected, and announced to other routers. Faults in BGP configuration can cause forwarding loops, packet loss, and unintended paths between hosts, each of which constitutes a failure of the Internet routing infrastructure. This paper describes the design and implementation of rcc, the router configuration checker, a tool that finds faults in BGP configurations using static analysis. rcc detects faults by checking constraints that are based on a high-level correctness specification. rcc detects two broad classes of faults: route validity faults, where routers may learn routes that do not correspond to usable paths, and path visibility faults, where routers may fail to learn routes for paths that exist in the network. rcc enables network operators to test and debug configurations before deploying them in an operational network, improving on the status quo where most faults are detected only during operation. rcc has been downloaded by more than sixty-five network operators to date, some of whom have shared their configurations with us. We analyze network-wide configurations from 17 different ASes to detect a wide variety of faults and use these findings to motivate improvements to the Internet routing infrastructure.

Determining Causes and Severity of End-User Frustration (2002) - Ceaparu,Irina; Lazar,Jonathan; Bessiere,Katie; Robinson,John; Shneiderman, Ben (Institute for Systems Research Technical Reports, 2005)
While computers are beneficial to individuals and society, frequently, users encounter frustrating experiences when using computers. This study attempts to measure, through 111 participants, the frequency, cause, and the level of severity of frustrating experiences. The data showed that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47-53% of time spent on a computer depending on the location and study method. After discarding extreme cases the time lost was still above 38%. These disturbing results should be a basis for future study.
Keywords: Technical Report

Differentiated traffic engineering for QoS provisioning - Tabatabaee,V.; Bhattacharjee, Bobby; La,R.J.; Shayman,M.A. (INFOCOM 2005. 24th Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings IEEE, 2005)
We introduce a new approach for QoS provisioning in packet networks based on the notion of differentiated traffic engineering (DTE). We consider a single AS network capable of source based multi-path routing. We do not require sophisticated queuing or per-class scheduling at individual routers; instead, if a link is used to forward QoS sensitive packets, we maintain its utilization below a threshold. As a consequence, DTE eliminates the need for per-flow (IntServ) or per-class (DiffServ) packet processing tasks such as traffic classification, queueing, shaping, policing and scheduling in the core and hence poses a lower burden on the network management unit. Conversely, DTE utilizes network bandwidth much more efficiently than simple over-provisioning. In this paper, we propose a complete architecture and an algorithmic structure for DTE. We show that our scheme can be formulated as a non-convex optimization problem, and we present an optimal solution framework based on simulated annealing. We present a simulation-based performance evaluation of DTE, and compare our scheme to existing (gradient projection) methods.
Keywords: based; Computer; differentiated; DiffServ; DTE; engineering; evaluation; link; links; management; multipath; network; networks; nonconvex; of; optimisation; OPTIMIZATION; packet; performance; problem; provisioning; QoS; QUALITY; routing; service; simulation-based; source; Telecommunication; traffic; traffic

DSP address optimization using evolutionary algorithms - Leventhal,S.; Yuan,L.; Bambha,N. K; Bhattacharyya, Shuvra S.; Qu,G. (Proceedings of the 2005 workshop on Software and compilers for embedded systems, 2005)

Dynamic configuration of dataflow graph topology for DSP system design - Ko,D. I; Bhattacharyya, Shuvra S. (Proc. of the Int. Conf. on Acoustics, Speech, and Signal Processing, 2005)

Dynamic Querying for Pattern Identification in Microarray and Genomic Data (2003) - Hochheiser,Harry; Baehrecke,Eric H; Mount, Stephen M.; Shneiderman, Ben (Institute for Systems Research Technical Reports, 2005)
Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool TimeSearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. TimeSearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. TimeSearcher can be used to search these data sets for candidate splicing signals.
Keywords: Technical Report

Efficient geographic routing in multihop wireless networks - Lee,Seungjoon; Bhattacharjee, Bobby; Banerjee,Suman (Proceedings of the 6th ACM international symposium on Mobile ad hoc networking and computing, 2005)
We propose a new link metric called normalized advance (NADV) for geographic routing in multihop wireless networks. NADV selects neighbors with the optimal trade-off between proximity and link cost. Coupled with the local next hop decision in geographic routing, NADV enables an adaptive and efficient cost-aware routing strategy. Depending on the objective or message priority, applications can use the NADV framework to minimize various types of link cost.We present efficient methods for link cost estimation and perform detailed simulations in diverse scenarios. Our results show that NADV outperforms current schemes in many aspects: for example, in high noise environments with frequent packet losses, the use of NADV leads to 81% higher delivery ratio. When compared to centralized routing under certain settings, geographic routing using NADV finds paths whose cost is close to the optimum.
Keywords: Geographic routing; Link cost estimation; Routing metric; Wireless multihop networks

Efficient lookup on unstructured topologies - Morselli,Ruggero; Bhattacharjee, Bobby; Srinivasan, Aravind; Marsh,Michael A (Proceedings of the twenty-fourth annual ACM symposium on Principles of distributed computing, 2005)
We present LMS, a protocol for efficient lookup on unstructured networks. Our protocol uses a virtual namespace without imposing specific topologies. It is more efficient than existing lookup protocols for unstructured networks, and thus is an attractive alternative for applications in which the topology cannot be structured as a Distributed Hash Table (DHT).We present analytic bounds for the worst-case performance of our protocol. Through detailed simulations (with up to 100,000 nodes), we show that the actual performance on realistic topologies is significantly better. We also show in both simulations and a complete implementation (which includes over five hundred nodes) that our protocol is inherently robust against multiple node failures and can adapt its replication strategy to optimize searches according to a specific heuristic. Moreover, the simulation demonstrates the resilience of LMS to high node turnover rates, and that it can easily adapt to orders of magnitude changes in network size. The overhead incurred by LMS is small, and its performance approaches that of DHTs on networks of similar size.
Keywords: distributed algorithms; lookup protocols; peer-to-peer networks; random walks

Efficient strategies for channel management in wireless lans - Mishra,A.; Brik,V.; Banerjee,S.; Srinivasan, Aravind; Arbaugh, William A. (UMD, CS Tech. Rep. CS-TR, 2005)
We define efficient algorithms for channel management (channelassignment and load balancing among APs) in 802.11-based WLANs that lead to better usage of the wireless spectrum. These algorithms (called CFAssign) are based on a “conflict-free set coloring” for- mulation that jointly perform load balancing along with channel assignment. Such a formulation has a number of advantages. First, it explicitly captures interference effects at clients. Next, it intrinsi- cally exposes opportunities for better channel re-use. Finally, algo- rithms based on this formulation do not depend on specific physical RF models and hence can be applied efficiently to a wide-range of in-building as well as outdoor scenarios. We have performed extensive packet-level simulations and mea- surements on a deployed wireless testbed of 70 APs to validate the performance of our proposed algorithms. We show that in ad- dition to single network scenarios, CFAssign algorithms are well suited for channel assignment in scenarios where multiple wireless networks share the same physical space and contend for the same frequency spectrum. Our results over a wide range of scenarios indicate that CFAssign reduces the interference at clients by about 50-70% in comparison to current best-known techniques.

An empirical study of "bogon" route advertisements - Feamster, Nick; Jung,Jaeyeon; Balakrishnan,Hari (SIGCOMM Comput. Commun. Rev., 2005)
An important factor in the robustness of the interdomain routing system is whether the routers in autonomous systems (ASes) filter routes for "bogon" address space---i.e., private address space and address space that has not been allocated by the Internet Assigned Numbers Authority (IANA). This paper presents an empirical study of bogon route announcements, as observed at eight vantage points on the Internet. On average, we observe several bogon routes leaked every few days; a small number of ASes also temporarily leak hundreds of bogon routes. About 40% of these bogon routes are not withdrawn for at least a day. We observed 110 different ASes originating routes for bogon prefixes and a few ASes that were responsible for advertising a disproportionate number of these routes. We also find that some ASes that do filter unallocated prefixes continue to filter them for as long as five months after they have been allocated, mistakenly filtering valid routes. Both of these types of delinquencies have serious implications: the failure to filter valid prefixes can could make nefarious activities such as denial of service attacks difficult to trace; failure to update filters when new prefixes are allocated prevents legitimate routes from being globally visible.
Keywords: anomalies; BGP; bogon prefixes

Entity resolution in graph data - Bhattacharya,I.; Getoor, Lise (Technical report, University of Maryland, College Park, 2005)
The goal of entity resolution is to reconcile data references corresponding to the same realworld entity. Here we introduce the problem of entity resolution in graphs, where the nodes are the references in the data and the hyper-edges represent the relations that are observed to hold between the references. The goal then is to reconstruct a 'cleaned' entity graph that captures the relations among the true underlying entities from the reference graph. This is an important first step in any graph mining process; mining an unresolved graph will be inefficient and result in inaccurate conclusions. We also motivate collective entity resolution in graphs where references sharing hyper-edges are resolved jointly, as opposed to independent pair-wise resolution of the references. We illustrate the problem of graph-based entity resolution in bibliographic datasets. We discuss several interesting issues such as mul- tiple entity types, local and global resolution and different kinds of graph-based evidence. We formulate the graph-based entity resolution problem as an unsupervised clustering task, where each cluster represents references that map to the same entity, and the similarity measure between two clusters incorporates the similarity of the references attributes and, more interestingly, the similarity between their relations. We explore two different measures of relational similarity. One approach, which we call 'edge detail similarity', explicitly com- pares the individual edges that each cluster participates in, but is expensive to compute. A less computationally intensive alternative is measuring 'neighborhood similarity', which only compares the multi-set of neighboring clusters for each cluster. We perform an extensive empirical evaluation of the two relational similarity measures for author resolution using co- author relations in two real bibliographic datasets. We show that both similarity measures improve performance over unsupervised algorithms that consider only reference attributes. We also describe an efficient implementation and show that these algorithms scale gracefully with increasing size of the data.

Envisioning help resources for the future information ecology: Toward an enriched sense of help - Haas,Stephanie W; Brown,Laurie; Denn,Sheila; Locke,David; Shneiderman, Ben (Proceedings of the American Society for Information Science and Technology, 2005)

An evolutionary testbed for software technology evaluation - Lindvall,M.; Rus,I.; Shull, F.; Zelkowitz, Marvin V; Donzelli,P.; Memon, Atif M.; Basili, Victor R.; Costa,P.; Tvedt,R.; Hochstein, L. (Innovations in Systems and Software Engineering, 2005)
Empirical evidence and technology evaluation are needed to close the gap between the state of the art and the state of the practice in software engineering. However, there are difficulties associated with evaluating technologies based on empirical evidence: insufficient specification of context variables, cost of experimentation, and risks associated with trying out new technologies. In this paper, we propose the idea of an evolutionary testbed for addressing these problems. We demonstrate the utility of the testbed in empirical studies involving two different research technologies applied to the testbed, as well as the results of these studies. The work is part of NASArsquos High Dependability Computing Project (HDCP), in which we are evaluating a wide range of new technologies for improving the dependability of NASA mission-critical systems.

Evolving and packaging reading technologies - Basili, Victor R. (Foundations of Empirical Software Engineering: The Legacy of Victor R. BasiliFoundations of Empirical Software Engineering: The Legacy of Victor R. Basili, 2005)

EvoSTOC Contributions - Merkle,D.; Middendorf,M.; Scheidler,A.; Avigad,G.; Moshaiov,A.; Brauner,N.; Parsopoulos,K.E.; Vrahatis,M.N.; Rand, William; Riolo,R (Applications of evolutionary computing: EvoWorkshops 2005, EvoBIO, EvoCOMNET, EvoHOT, EvoIASP, EvoMUSART, and EvoSTOC, 2005)

Exploiting partially overlapping channels in wireless networks: Turning a peril into an advantage - Mishra,A.; Rozner,E.; Banerjee,S.; Arbaugh, William A. (Proceedings of the 5th ACM SIGCOMM conference on Internet Measurement, 2005)

Fusing Depth and Video Using Rao-Blackwellized Particle Filter - Agrawal,Amit; Chellapa, Rama (Pattern Recognition and Machine IntelligencePattern Recognition and Machine Intelligence, 2005)
We address the problem of fusing sparse and noisy depth data obtained from a range finder with features obtained from intensity images to estimate ego-motion and refine 3D structure of a scene using a Rao-Blackwellized particle filter. For scenes with low depth variability, the algorithm shows an alternate way of performing Structure from Motion (SfM) starting with a flat depth map. Instead of using 3D depths, we formulate the problem using 2D image domain parallax and show that conditioned on non-linear motion parameters, the parallax magnitude with respect to the projection of the vanishing point forms a linear subsystem independent of camera motion and their distributions can be analytically integrated. Thus, the structure is obtained by estimating parallax with respect to the given depths using a Kalman filter and only the ego-motion is estimated using a particle filter. Hence, the required number of particles becomes independent of the number of feature points which is an improvement over previous algorithms. Experimental results on both synthetic and real data show the effectiveness of our approach.

Generating testable hypotheses from tacit knowledge for high productivity computing - Asgari, Sima; Hochstein, Lorin; Basili, Victor R.; Zelkowitz, Marvin V; Hollingsworth, Jeffrey K; Carver, Jeff; Shull, Forrest (Proceedings of the second international workshop on Software engineering for high performance computing system applications, 2005)
In this research, we are developing our understanding of how the high performance computing community develops effective parallel implementations of programs by collecting the folklore within the community. We use this folklore as the basis for a series of experiments, which we expect, will validate or negate these assumptions.
Keywords: folklore elicitation; high productivity development time experimental studies; hypothesis generation; tacit knowledge solicitation; testable hypotheses

The genetic map and comparative analysis with the physical map of Trypanosoma brucei - MacLeod,A.; Tweedie,A.; McLellan,S.; Taylor,S.; Hall,N.; Berriman,M.; El‐Sayed, Najib M.; Hope,M.; Turner,C. M.R; Tait,A. (Nucleic acids research, 2005)

The genome of the African trypanosome Trypanosoma brucei - Berriman,M.; Ghedin,E.; Hertz-Fowler,C.; Blandin,G.; Renauld,H.; Bartholomeu,D. C; Lennard,N. J; Caler,E.; Hamlin,N. E; Haas,B.; others (Science, 2005)

The genome of the protist parasite Entamoeba histolytica - Loftus,B.; Anderson,I.; Davies,R.; Alsmark,U. C.M; Samuelson,J.; Amedeo,P.; Roncaglia,P.; Berriman,M.; Hirt,R. P; Mann,B. J; others (Nature, 2005)

The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease - El‐Sayed, Najib M.; Myler,Peter J.; Bartholomeu,Daniella C.; Nilsson,Daniel; Aggarwal,Gautam; Tran,Anh-Nhi; Ghedin,Elodie; Worthey,Elizabeth A.; Delcher,Arthur L.; Blandin,Gaëlle; Westenberger,Scott J.; Caler,Elisabet; et al. (Science, 2005)
Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease - El-Sayed, N.M.; Myler,P. J; Bartholomeu,D. C; Nilsson,D.; Aggarwal,G.; Tran,A. N; Ghedin,E.; Worthey,E. A; Delcher,A. L; Blandin,G.; others (Science, 2005)

The Genome Sequence of Trypanosoma Cruzi, Etiologic Agent of Chagas Disease - El‐Sayed, Najib M.; Myler,Peter J.; Bartholomeu,Daniella C.; Nilsson,Daniel; Aggarwal,Gautam; Tran,Anh-Nhi; Ghedin,Elodie; Worthey,Elizabeth A.; Delcher,Arthur L.; Blandin,Gaëlle; Westenberger,Scott J.; Caler,Elisabet; et al. (ScienceScience, 2005)
Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.

Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription - Lewinski,M. K; Bisgrove,D.; Shinn,P.; Chen,H.; Hoffmann,C.; Hannenhalli, Sridhar; Verdin,E.; Berry,C. C; Ecker,J. R; Bushman,F. D (Journal of VirologyJ. Virol., 2005)
We have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients.

Genome-wide analysis of retroviral DNA integration - Bushman,Frederic; Lewinski,Mary; Ciuffi,Angela; Barr,Stephen; Leipzig,Jeremy; Hannenhalli, Sridhar; Hoffmann,Christian (Nat Rev MicroNat Rev Micro, 2005)

Geographic locality of IP prefixes - Freedman,Michael J.; Vutukuru,Mythili; Feamster, Nick; Balakrishnan,Hari (Proceedings of the 5th ACM SIGCOMM conference on Internet Measurement, 2005)
Information about the geographic locality of IP prefixes can be useful for understanding the issues related to IP address allocation, aggregation, and BGP routing table growth. In this paper, we use traceroute data and geographic mappings of IP addresses to study the geographic properties of IP prefixes and their implications on Internet routing. We find that (1) IP prefixes may be too coarse-grained for expressing routing policies, (2) address allocation policies and the granularity of routing contribute significantly to routing table size, and (3) not considering the geographic diversity of contiguous prefixes may result in overestimating the opportunities for aggregation in the BGP routing table.

Help! I'm Lost: User Frustration in Web Navigation (2003) - Lazar,Jonathan; Bessiere,Katie; Ceaparu,Irina; Robinson,John; Shneiderman, Ben (Institute for Systems Research Technical Reports, 2005)
Computers can be valuable tools, and networked resources via the Internet can be beneficial to many different populations and communities. Unfortunately, when people are unable to reach their task goals due to frustrating experiences, this can hinder the effectiveness of technology. This research summary provides information about the user frustration research that has been performed at the University of Maryland and Towson University. Causes of user frustration are discussed in this research summary, along with the surprising finding that nearly one-third to one-half of the time spent in front of the computer is wasted due to frustrating experiences. Furthermore, when interfaces are planned to be deceptive and confusing, this
Keywords: Technical Report

How do I find blue books about dogs? The errors and frustrations of young digital library users - Hutchinson,H.; Druin, Allison; Bederson, Benjamin B.; Reuter,K.; Rose,A.; Weeks,A. C (Proceedings of HCII 2005, 2005)

Identifying and segmenting human-motion for mobile robot navigation using alignment errors - Abd-Almageed, Wael; Burns,B. J; Davis, Larry S. (12th International Conference on Advanced Robotics, 2005. ICAR '05. Proceedings, 2005)
This paper presents a new human-motion identification and segmentation algorithm, for mobile robot platforms. The algorithm is based on computing the alignment error between pairs of object images acquired from a moving platform. Pairs of images generating relatively small alignment errors are used to estimate the fundamental frequency of the object's motion. A decision criterion is then used to test the significance of the estimated frequency and to classify the object's motion. To verify the validity of the proposed approach, experimental results are shown on different classes of objects
Keywords: Computer errors; Educational institutions; Frequency estimation; human-motion identification; human-motion segmentation; HUMANS; Image motion analysis; Image segmentation; mobile robot navigation; Mobile robots; Motion estimation; Navigation; Object detection; robot vision; SHAPE

Image Sequence Stabilization, Mosaicking, and Superresolution - Chellapa, Rama; Srinivasan, S.; Aggarwal,G.; Veeraraghavan,A. (Handbook of Image and Video Processing (Second Edition)Handbook of Image and Video Processing (Second Edition), 2005)
A sequence of temporal images gathered from a single sensor adds a whole new dimension to two-dimensional (2D) image data. Availability of an image sequence permits the measurement of quantities such as subpixel intensities, camera motion and depth, and detection and tracking of moving objects. In turn, the processing of image sequences necessitates the development of sophisticated techniques to extract this information. With the recent availability of powerful yet inexpensive computers, data storage systems, and image acquisition devices, image sequence analysis has transitioned from an esoteric research domain to a practical area with significant commercial interest.

Implications of autonomy for the expressiveness of policy routing - Feamster, Nick; Johari,Ramesh; Balakrishnan,Hari (Proceedings of the 2005 conference on Applications, technologies, architectures, and protocols for computer communications, 2005)
Thousands of competing autonomous systems must cooperate with each other to provide global Internet connectivity. Each autonomous system (AS) encodes various economic, business, and performance decisions in its routing policy. The current interdomain routing system enables each AS to express policy using rankings that determine how each router inthe AS chooses among different routes to a destination, and filters that determine which routes are hidden from each neighboring AS. Because the Internet is composed of many independent, competing networks, the interdomain routing system should provide autonomy, allowing network operators to set their rankings independently, and to have no constraints on allowed filters. This paper studies routing protocol stability under these conditions. We first demonstrate that certain rankings that are commonly used in practice may not ensure routing stability. We then prove that, when providers can set rankings and filters autonomously, guaranteeing that the routing system will converge to a stable path assignment essentially requires ASes to rank routes based on AS-path lengths. We discuss the implications of these results for the future of interdomain routing.
Keywords: autonomy; BGP; Internet; policy; protocol; Routing; Safety; stability

Improved efficiency for CCA-secure cryptosystems built using identity-based encryption - Boneh,D.; Katz, Jonathan (Topics in Cryptology–CT-RSA 2005, 2005)
Recently, Canetti, Halevi, and Katz showed a general method for constructing CCA-secure encryption schemes from identity-based encryption schemes in the standard model. We improve the efficiency of their construction, and show two specific instantiations of our resulting scheme which offer the most efficient encryption (and, in one case, key generation) of any CCA-secure encryption scheme to date.

Interactive Color Mosaic and Dendogram Displays for Signal/Noise Optimization in Microarray Data Analysis (2003) - Seo,Jinwook; Bakay,Marina; Zhao,Po; Chen,Yi-Wen; Clarkson,Priscilla; Shneiderman, Ben; Hoffman,Eric P (Institute for Systems Research Technical Reports, 2005)
Data analysis and visualization is strongly influenced by noise and noise filters. There are multiple sources of oisein microarray data analysis, but signal/noise ratios are rarely optimized, or even considered. Here, we report a noise analysis of a novel 13 million oligonucleotide dataset - 25 human U133A (~500,000 features) profiles of patient muscle biposies. We use our recently described interactive visualization tool, the Hierarchical Clustering Explorer (HCE) to systemically address the effect of different noise filters on resolution of arrays into orrectbiological groups (unsupervised clustering into three patient groups of known diagnosis). We varied probe set interpretation methods (MAS 5.0, RMA), resent callfilters, and clustering linkage methods, and investigated the results in HCE. HCE interactive features enabled us to quickly see the impact of these three variables. Dendrogram displays showed the clustering results systematically, and color mosaic displays provided a visual support for the results. We show that each of these three variables has a strong effect on unsupervised clustering. For this dataset, the strength of the biological variable was maximized, and noise minimized, using MAS 5.0, 10% present call filter, and Average Group Linkage. We propose a general method of using interactive tools to identify the optimal signal/noise balance or the optimal combination of these three variables to maximize the effect of the desired biological variable on data interpretation.
Keywords: Technical Report

Interactive pattern search in time series - Buono,Paolo; Aris,Aleks; Plaisant, Catherine; Khella,Amir; Shneiderman, Ben (Proceedings of SPIE, 2005)
The need for pattern discovery in long time series data led researchers to develop algorithms for similarity search. Most of the literature about time series focuses on algorithms that index time series and bring the data into the main storage, thus providing fast information retrieval on large time series. This paper reviews the state of the art in visualizing time series, and focuses on techniques that enable users to visually and interactively query time series. Then, it presents TimeSearcher 2, a tool that enables users to explore multidimensional data using synchronized tables and graphs with overview+detail, filter the time series data to reduce the scope of the search, select an existing pattern to find similar occurrences, and interactively adjust similarity parameters to narrow the result set. This tool is an extension of previous work, TimeSearcher 1, which uses graphical timeboxes to interactively query time series data.

Interactive Pattern Search in Time Series (2004) - Buono,Paolo; Aris,Aleks; Plaisant, Catherine; Khella,Amir; Shneiderman, Ben (Institute for Systems Research Technical Reports, 2005)
The need for pattern discovery in long time series data led researchers to develop algorithms for similarity search. Most of the literature about time series focuses on algorithms that index time series and bring the data into the main storage, thus providing fast information retrieval on large time series. This paper reviews the state of the art in visualizing time series, and focuses on techniques that enable users to interactively query time series. Then it presents TimeSearcher 2, a tool that enables users to explore multidimensional data using coordinated tables and graphs with overview+detail, filter the time series data to reduce the scope of the search, select an existing pattern to find similar occurrences, and interactively adjust similarity parameters to narrow the result set. This tool is an extension of previous work, TimeSearcher 1, which uses graphical timeboxes to interactively query time series data.
Keywords: Technical Report

The International Children’s Digital Library: A Case Study in Designing for a MultiLingual - Hutchinson,H.B.; Rose,A.; Bederson, Benjamin B.; Weeks,A. C; Druin, Allison (Multi-Cultural, Multi-Generational Audience. Information Technology and Libraries, 2005)

Iterative enhancement: a practical technique for software development - Basili, Victor R.; Turner,A. J (Foundations of Empirical Software Engineering: The Legacy of Victor R. BasiliFoundations of Empirical Software Engineering: The Legacy of Victor R. Basili, 2005)

Joint application mapping/interconnect synthesis techniques for embedded chip-scale multiprocessors - Bambha,N. K; Bhattacharyya, Shuvra S. (Parallel and Distributed Systems, IEEE Transactions on, 2005)

Lambertian reflectance and linear subspaces - Jacobs, David W.; Basri,Ronen (2005)
A method for choosing an image from a plurality of three-dimensional models which is most similar to an input image is provided. The method includes the steps of: (a) providing a database of the plurality of three-dimensional models; (b) providing an input image; (c) positioning each three-dimensional model relative to the input image; (d) for each three-dimensional model, determining a rendered image that is most similar to the input image by: (d)(i) computing a linear subspace that describes an approximation to the set of all possible rendered images that each three-dimensional model can produce under all possible lighting conditions where each point in the linear subspace represents a possible image; and one of (d)(ii) finding the point on the linear subspace that is closest to the input image or finding a rendered image in a subset of the linear subspace obtained by projecting the set of images that are generated by positive lights onto the linear subspace; (e) computing a...

A learning automata based power management for ad-hoc networks - El-Osery,A. I; Baird,D.; Abd-Almageed, Wael (2005 IEEE International Conference on Systems, Man and Cybernetics, 2005)
Power management is a very important aspect of ad-hoc networks. It directly impacts the network throughput among other network metrics. On the other hand, transmission power management may result in disconnected networks and increased level of collisions. In this paper, we introduce a transmission power control based on stochastic learning automata (SLA) to modify the transmission power. Based on the level of successful transmissions and the level of packet retransmissions, the SLA will modify the transmission power level either by increasing it or decreasing it. The probabilistic nature of SLA makes it a useful choice for ad-hoc networks. Using the network simulator NS, we show that using SLA for transmission power will result in an increased system bandwidth and a decrease in the collision levels.
Keywords: ad hoc networks; ad-hoc networks; Computer network management; Computer networks; Energy management; Engineering management; learning automata; network metrics; network simulator; packet retransmissions; power control; power system management; power transmission control; stochastic learning automata; stochastic learning automta; Stochastic processes; system bandwidth; Technology management; Throughput; transmission power control; transmission power level; transmission power management

Maintaining concentration to achieve task completion - Shneiderman, Ben; Bederson, Benjamin B. (Proceedings of the 2005 conference on Designing for User eXperience, 2005)

Maintaining concentration to achieve task completion - Shneiderman, Ben; Bederson, Benjamin B. (Proceedings of the 2005 conference on Designing for User eXperience, 2005)
When faced with a challenging goal, knowledge workers need to concentrate on their tasks so that they move forward toward completion. Since frustrations, distractions, and interruptions can interfere with their smooth progress, design strategies should enable users to maintain concentration. This paper promotes awareness of this issue, reviews related work, and suggests three initial strategies: Reduce short-term and working memory load, provide information abundant interfaces, and increase automaticity.
Keywords: avoid interruption; calm; flow; focus; goal attainment; interface design; maintain concentration; situation awareness; task completion

MCMC-based particle filtering for tracking a variable number of interacting targets - Zia Khan; Balch, T.; Dellaert, F. (IEEE Transactions on Pattern Analysis and Machine Intelligence, 2005)
We describe a particle filter that effectively deals with interacting targets, targets that are influenced by the proximity and/or behavior of other targets. The particle filter includes a Markov random field (MRF) motion prior that helps maintain the identity of targets throughout an interaction, significantly reducing tracker failures. We show that this MRF prior can be easily implemented by including an additional interaction factor in the importance weights of the particle filter. However, the computational requirements of the resulting multitarget filter render it unusable for large numbers of targets. Consequently, we replace the traditional importance sampling step in the particle filter with a novel Markov chain Monte Carlo (MCMC) sampling step to obtain a more efficient MCMC-based multitarget filter. We also show how to extend this MCMC-based filter to address a variable number of interacting targets. Finally, we present both qualitative and quantitative experimental results, demonstrating that the resulting particle filters deal efficiently and effectively with complicated target interactions.
Keywords: algorithms; Animals; Artificial intelligence; Computer simulation; Computer vision; Filtering; filtering theory; HUMANS; Image Enhancement; Image Interpretation, Computer-Assisted; Index Terms- Particle filters; Information Storage and Retrieval; Insects; interacting targets; Markov chain Monte Carlo sampling step; Markov chain Monte Carlo.; Markov chains; Markov processes; Markov random field motion; Markov random fields; Models, Biological; Models, Statistical; Monte Carlo Method; Monte Carlo methods; MOTION; Movement; multitarget filter; multitarget tracking; particle filtering; Particle filters; Particle tracking; Pattern Recognition, Automated; Sampling methods; Subtraction Technique; target tracking; Video Recording

Measurement-based multipath multicast - Guven,T.; La,R.J.; Shayman,M.A.; Bhattacharjee, Bobby (INFOCOM 2005. 24th Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings IEEE, 2005)
We propose a measurement-based routing algorithm to load balance intradomain traffic along multiple paths for multiple multicast sources. Multiple paths are established using application-layer overlaying. The proposed algorithm is able to converge under different network models, where each model reflects a different set of assumptions about the multicasting capabilities of the network. The algorithm is derived from simultaneous perturbation stochastic approximation and relies only on noisy estimates from measurements. Simulation results are presented to demonstrate the additional benefits obtained by incrementally increasing the multicasting capabilities.
Keywords: algorithm; allocation; application-layer; approximation; approximation; balance; communication; Convergence; convergence; intradomain; load; measurement-based; methods; Multicast; multipath; network; numerical; of; overlaying; perturbation; processes; resource; Routing; routing; source; Stochastic; techniques; Telecommunication; theory; traffic

Measuring productivity on high performance computers - Zelkowitz, Marvin V; Basili, Victor R.; Asgari, S.; Hochstein, L.; Hollingsworth, Jeffrey K; Nakamura, T. (11th IEEE International Symposium on Software Metric, 2005)
In the high performance computing domain, the speed ofexecution of a program has typically been the primary performance metric. But productivity is also of concern to high performance computing developers. In this paper we will discuss the problems of defining and measuring productivity for these machines and we develop a model of productivity that includes both a performance component and a component that measures the development time of the program. We ran several experiments using students in high performance courses at several universities, and we report on those results with respect to our model of productivity.

A metric space for productivity measurement in software development - Numrich,Robert W.; Hochstein, Lorin; Basili, Victor R. (Proceedings of the second international workshop on Software engineering for high performance computing system applications, 2005)
We define a metric space to measure the contributions of individual programmers to a software development project. It allows us to measure the distance between the contributions of two different programmers as well as the absolute contribution of each individual programmer. Our metric is based on an action function that provides a picture of how one programmer's approach differs from another at each instance of time during the project. We apply our metric to data we collected from students taking a course in parallel programming. We display the pictures for two students who showed approximately equal contributions but who followed very different paths through the course.

Metrics of software architecture changes based on structural distance - Nakamura, T.; Basili, Victor R. (IEEE METRICS, 2005)
Software architecture is an important form of abstrac-tion, representing the overall system structure and the re- lationship among components. When software is modified from one version to another, its architecture may change. Software modification involving architectural change is of- ten difficult when the change goes beyond the original ar- chitectural design, involving changes to the connectivity of multiple components. Existing research has looked at ar- chitectural change at the level of architecture metrics such as size, complexity, coupling and cohesion, which abstract a particular version of the software in isolation. In this pa- per, we argue that this level of abstraction is often too high to characterize some interesting aspects of the architectural change process, and propose an approach that takes into account the change in connectivity from version to version of individual components. In this approach, two endpoints of a major change are taken as reference points, and inter- mediate connectivity changes are examined relative to the endpoints. We define a distance measure between software structures using a graph kernel function, which is quite powerful as it is applicable to any software structure repre- sentable as a graph. Using this distance measure, we define a metric which models the architecture change as a transi- tion between two endpoints. In addition to theoretical anal- ysis of the approach, we present empirical results obtained by applying the approach to open-source software projects to evaluate its validity and usefulness.

Misbehaving TCP receivers can cause internet-wide congestion collapse - Sherwood,Rob; Bhattacharjee, Bobby; Braud,Ryan (Proceedings of the 12th ACM conference on Computer and communications security, 2005)
An optimistic acknowledgment (opt-ack) is an acknowledgment sent by a misbehaving client for a data segment that it has not received. Whereas previous work has focused on opt-ack as a means to greedily improve end-to-end performance, we study opt-ack exclusively as a denial of service attack. Specifically, an attacker sends optimistic acknowledgments to many victims in parallel, thereby amplifying its effective bandwidth by a factor of 30 million (worst case). Thus, even a relatively modest attacker can totally saturate the paths from many victims back to the attacker. Worse, a distributed network of compromised machines ("zombies") attacking in parallel can exploit over-provisioning in the Internet to bring about wide-spread, sustained congestion collapse.We implement this attack both in simulation and in a wide-area network, and show it severity both in terms of number of packets and total traffic generated. We engineer and implement a novel solution that does not require client or network modifications allowing for practical deployment. Additionally, we demonstrate the solution's efficiency on a real network.
Keywords: Congestion control; distributed denial of service

Modeling image processing systems with homogeneous parameterized dataflow graphs - Sen,Mainak; Bhattacharyya, Shuvra S.; Lv,Tiehan; Wolf,W. (Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP '05). IEEE International Conference on, 2005)
We describe a new dataflow model called homogeneous parameterized dataflow (HPDF). This form of dynamic dataflow graph takes advantage of the fact that in a large number of image processing applications, data production and consumption rates, though dynamic, are equal across graph edges for any particular iteration, which leads to a homogeneous rate of actor execution, even though data production and consumption values are dynamic and vary across graph edges. We discuss existing dataflow models and formulate in detail the HPDF model. We develop examples of applications that are described naturally in terms of HPDF semantics and present experimental results that demonstrate the efficacy of the HPDF approach.
Keywords: data consumption; data flow graphs; data production; dynamic dataflow graph; graph edges; homogeneous parameterized dataflow graphs; IMAGE PROCESSING; image processing system modeling; iteration; iterative methods

Modeling of block-based DSP systems - Ko,D. I; Bhattacharyya, Shuvra S. (The Journal of VLSI Signal Processing, 2005)

Moving Object Detection and Compression in IR Sequences - Vaswani,Namrata; Agrawal,Amit; Qinfen Zheng; Chellapa, Rama (Computer Vision Beyond the Visible SpectrumComputer Vision Beyond the Visible Spectrum, 2005)
We consider the problem of remote surveillance using infrared (IR) sensors. The aim is to use IR image sequences to detect moving objects (humans or vehicles), and to transmit a few “best-view images” of every new object that is detected. Since the available bandwidth is usually low, if the object chip is big, it needs to be compressed before being transmitted. Due to low computational power of computing devices attached to the sensor, the algorithms should be computationally simple. We present two approaches for object detection — one which specifically solves the more difficult long-range object detection problem, and the other for objects at short range. For objects at short range, we also present techniques for selecting a single best-view object chip and computationally simple techniques for compressing it to very low bit rates due to the channel bandwidth constraint. A fast image chip compression scheme implemented in the wavelet domain by combining a non-iterative zerotree coding method with 2D-DPCM for both low-and high-frequency subbands is presented. Comparisons with some existing schemes are also included. The object detection and compression algorithms have been implemented in C/C++ and their performance has been evaluated using the Hitachi’s SH4 platform with software simulation.

Multitarget tracking with split and merged measurements - Zia Khan; Balch, T.; Dellaert, F. (IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2005. CVPR 2005, 2005)
In many multitarget tracking applications in computer vision, a detection algorithm provides locations of potential targets. Subsequently, the measurements are associated with previously estimated target trajectories in a data association step. The output of the detector is often imperfect and the detection data may include multiple, split measurements from a single target or a single merged measurement from several targets. To address this problem, we introduce a multiple hypothesis tracker for interacting targets that generate split and merged measurements. The tracker is based on an efficient Markov chain Monte Carlo (MCMC) based auxiliary variable particle filter. The particle filter is Rao-Blackwellized such that the continuous target state parameters are estimated analytically, and an MCMC sampler generates samples from the large discrete space of data associations. In addition, we include experimental results in a scenario where we track several interacting targets that generate these split and merged measurements.
Keywords: Application software; Computer vision; Detection algorithms; Detectors; filtering theory; Markov chain Monte Carlo based auxiliary variable particle filter; Markov processes; merged measurements; Monte Carlo methods; multiple hypothesis tracker; multitarget tracking; parameter estimation; Particle filters; Particle tracking; Rao-Blackwellized filter; split measurements; target tracking; Trajectory

Mutatis mutandis: safe and predictable dynamic software updating - Stoyle,Gareth; Hicks, Michael W.; Bierman,Gavin; Sewell,Peter; Neamtiu,Iulian (Proceedings of the 32nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages, 2005)
Dynamic software updates can be used to fix bugs or add features to a running program without downtime. Essential for some applications and convenient for others, low-level dynamic updating has been used for many years. Perhaps surprisingly, there is little high-level understanding or language support to help programmers write dynamic updates effectively.To bridge this gap, we present Proteus, a core calculus for dynamic software updating in C-like languages that is flexible, safe, and predictable. Proteus supports dynamic updates to functions (even active ones), to named types and to data, allowing on-line evolution to match source-code evolution as we have observed it in practice. We ensure updates are type-safe by checking for a property we call "con-freeness" for updated types t at the point of update. This means that non-updated code will not use t concretely beyond that point (concrete usages are via explicit coercions) and thus t's representation can safely change. We show how con-freeness can be enforced dynamically for a particular program state. We additionally define a novel and efficient static updateability analysis to establish con-freeness statically, and can thus automatically infer program points at which all future (well-formed) updates will be type-safe. We have implemented our analysis for C and tested it on several well-known programs.
Keywords: capability; dynamic software updating; proteus; Type inference; updateability analysis

New experimental data of STBLI at DNS/LES accessible Reynolds numbers - Bookey,P.; Wyckham,C.; Smits,A. J.; Martin, M.P (AIAA paper, 2005)

Ordered and Quantum Treemaps: Making Effective Use of 2D Space to Display Hierarchies (2001) - Bederson, Benjamin B.; Shneiderman, Ben; Wattenberg,Martin (Institute for Systems Research Technical Reports, 2005)
Treemaps, a space- filling method of visualizing large hierarchical data sets, are receiving increasing attention. Several algorithms have been proposed to create more useful displays by controlling the aspect ratios of the rectangles that make up a treemap. While these algorithms do improve visibility of small items in a single layout, they introduce instability over time in the display of dynamically changing data, fail to preserve order of the underlying data, and create layouts that are difficult to visually search. In addition, continuous treemap algorithms are not suitable for displaying quantum-sized objects within them, such as images. This paper introduces several new treemap algorithms, which address these shortcomings. In addition, we show a new application of these treemaps, using them to present groups of images. The ordered treemap algorithms ensure that items near each other in the given order will be near each other in the treemap layout. Using experimental evidence from Monte Carlo trials, we show that compared to other layout algorithms ordered treemaps are more stable while maintaining relatively favorable aspect ratios of the constituent rectangles. A second test set uses stock market data. The quantum treemap algorithms modify the layout of the continuous treemap algorithms to generate rectangles that are integral multiples of an input object size. The quantum treemap algorithm has been applied to PhotoMesa, an application that supports browsing of large numbers of images.
Keywords: Technical Report

An outdoor 3-D visual tracking system for the study of spatial navigation and memory in rhesus monkeys - Zia Khan; Herman, Rebecca A.; Wallen, Kim; Balch, Tucker (Behavior Research Methods, 2005)
Previous studies of the navigational abilities of nonhuman primates have largely been limited to what could be described by a human observer with a pen and paper. Consequently, we have developed a system that uses a pair of cameras to automatically obtain the three-dimensional trajectory of rhesus monkeys performing an outdoor spatial navigation and memory task. The system provides trajectories, path length, speed, and other variables that would be impossible for an unaided observer to note. From trajectory data, we computed and validated a path-length measurement. We use this measurement to compare the navigation abilities of several animals. In addition, we provide quantitative data on the accuracy of a method for automatic behavior detection. Currently, the system is being used to examine the sex differences in spatial navigation of rhesus monkeys. We expect that measures derived from the trajectory data will reveal strategies used by animals to solve spatial problems.
Keywords: cognitive psychology

Path dependence and the validation of agent‐based spatial models of land use - Brown,Daniel G.; Page,Scott; Riolo,Rick; Zellner,Moira; Rand, William (International Journal of Geographical Information Science, 2005)
In this paper, we identify two distinct notions of accuracy of land?use models and highlight a tension between them. A model can have predictive accuracy: its predicted land?use pattern can be highly correlated with the actual land?use pattern. A model can also have process accuracy: the process by which locations or land?use patterns are determined can be consistent with real world processes. To balance these two potentially conflicting motivations, we introduce the concept of the invariant region, i.e., the area where land?use type is almost certain, and thus path independent; and the variant region, i.e., the area where land use depends on a particular series of events, and is thus path dependent. We demonstrate our methods using an agent?based land?use model and using multi?temporal land?use data collected for Washtenaw County, Michigan, USA. The results indicate that, using the methods we describe, researchers can improve their ability to communicate how well their model performs, the situations or instances in which it does not perform well, and the cases in which it is relatively unlikely to predict well because of either path dependence or stochastic uncertainty.

Pattern Recognition in Video - Chellapa, Rama; Veeraraghavan,Ashok; Aggarwal,Gaurav (Pattern Recognition and Machine IntelligencePattern Recognition and Machine Intelligence, 2005)
Images constitute data that live in a very high dimensional space, typically of the order of hundred thousand dimensions. Drawing inferences from correlated data of such high dimensions often becomes intractable. Therefore traditionally several of these problems like face recognition, object recognition, scene understanding etc. have been approached using techniques in pattern recognition. Such methods in conjunction with methods for dimensionality reduction have been highly popular and successful in tackling several image processing tasks. Of late, the advent of cheap, high quality video cameras has generated new interests in extending still image-based recognition methodologies to video sequences. The added temporal dimension in these videos makes problems like face and gait-based human recognition, event detection, activity recognition addressable. Our research has focussed on solving several of these problems through a pattern recognition approach. Of course, in video streams patterns refer to both patterns in the spatial structure of image intensities around interest points and temporal patterns that arise either due to camera motion or object motion. In this paper, we discuss the applications of pattern recognition in video to problems like face and gait-based human recognition, behavior classification, activity recognition and activity based person identification.

Porting DSP applications across design tools using the dataflow interchange format - Hsu,C.-J.; Bhattacharyya, Shuvra S. (Rapid System Prototyping, 2005. (RSP 2005). The 16th IEEE International Workshop on, 2005)
Modeling DSP applications through coarse-grain dataflow graphs is popular in the DSP design community, and a growing set of rapid prototyping tools support such dataflow semantics. Since different tools may be suitable for different phases or generations of a design, it is often desirable to migrate a dataflow-based application model from one prototyping tool to another. Two critical problems in transferring dataflow-based designs across different prototyping tools are the lack of a vendor-independent language for DSP-oriented dataflow graphs, and the lack of an efficient porting methodology. In our previous work, the dataflow interchange format (DIF) (C. Hsu et al., 2004) has been developed as a standard language to specify mixed-grain dataflow models for DSP systems. This paper presents the augmentation of the DIF infrastructure with a systematic porting approach that integrates DIF tightly with the specific exporting and importing mechanisms that interface DIF to specific DSP design tools. In conjunction with this porting mechanism, this paper also introduces a novel language, called the actor interchange format (AIF), for transferring relevant information pertaining to DSP library components across different tools. Through a case study of a synthetic aperture radar application, we demonstrate the high degree of automation offered by our DIF-based porting approach.
Keywords: actor interchange format; coarse-grain dataflow graph; data flow analysis; data flow graphs; dataflow interchange format; dataflow model; dataflow semantic; DSP application; DSP design tool; DSP library component; electronic data interchange; formal specification; rapid prototyping tool; Signal processing; software prototyping; Specification languages; vendor-independent language

QR Factorizations Using a Restricted Set of Rotations - O'Leary, Dianne P.; Bullock,Stephen S. (Electronic Transactions on Numerical Analysis, 2005)

Relational clustering for multi-type entity resolution - Bhattacharya,Indrajit; Getoor, Lise (Proceedings of the 4th international workshop on Multi-relational mining, 2005)
In many applications, there are a variety of ways of referring to the same underlying entity. Given a collection of references to entities, we would like to determine the set of true underlying entities and map the references to these entities. The references may be to entities of different types and more than one type of entity may need to be resolved at the same time. We propose similarity measures for clustering references taking into account the different relations that are observed among the typed references. We pose typed entity resolution in relational data as a clustering problem and present experimental results on real data showing improvements over attribute-based models when relations are leveraged.

Secure remote authentication using biometric data - Boyen,X.; Dodis,Y.; Katz, Jonathan; Ostrovsky,R.; Smith,A. (Advances in Cryptology–EUROCRYPT 2005, 2005)
Biometric data offer a potential source of high-entropy, secret information that can be used in cryptographic protocols provided two issues are addressed: (1) biometric data are not uniformly distributed; and (2) they are not exactly reproducible. Recent work, most notably that of Dodis, Reyzin, and Smith, has shown how these obstacles may be overcome by allowing some auxiliary public information to be reliably sent from a server to the human user. Subsequent work of Boyen has shown how to extend these techniques, in the random oracle model, to enable unidirectional authentication from the user to the server without the assumption of a reliable communication channel.We show two efficient techniques enabling the use of biometric data to achieve mutual authentication or authenticated key exchange over a completely insecure (i.e., adversarially controlled) channel. In addition to achieving stronger security guarantees than the work of Boyen, we improve upon his solution in a number of other respects: we tolerate a broader class of errors and, in one case, improve upon the parameters of his solution and give a proof of security in the standard model.

Social and Psychological Influences on Computer User Frustration (Newhagen book chapter, 2002) - Bessiere,Katie; Ceaparu,Irina; Lazar,Jonathan; Robinson,John; Shneiderman, Ben (Institute for Systems Research Technical Reports, 2005)
As computer usage has proliferated, so has user frustration. Even devoted and knowledgeable users encounter annoying delays, incomprehensible messages, incompatible files, and indecipherable menus. The frustration generated by these problems can be personally disturbing and socially disruptive. Psychological and social perspectives on frustration may clarify the relationships among variables such as personality types, cultural factors, goal attainment, workplace anger, and computer anxiety. These perspectives may also help designers, managers, and users understand the range of responses to frustration, which could lead to effective interventions such as redesign of software, improved training, better online help, user discipline, and even resetting of national research priorities.
Keywords: Technical Report

Software defect reduction top 10 list - Boehm,B.; Basili, Victor R. (Foundations of empirical software engineering: the legacy of Victor R. Basili, 2005)

Software synthesis from the dataflow interchange format - Hsu,C. J; Ko,M. Y; Bhattacharyya, Shuvra S. (Proceedings of the 2005 workshop on Software and compilers for embedded systems, 2005)

Spatial process and data models: Toward integration of agent-based models and GIS - Brown,D.G.; Riolo,R; Robinson,D.T.; North,M.; Rand, William (Journal of Geographical Systems, 2005)
The use of object-orientation for both spatial data and spatial process models facilitates their integration, which can allow exploration and explanation of spatial-temporal phenomena. In order to better understand how tight coupling might proceed and to evaluate the possible functional and efficiency gains from such a tight coupling, we identify four key relationships affecting how geographic data (fields and objects) and agent-based process models can interact: identity, causal, temporal and topological. We discuss approaches to implementing tight integration, focusing on a middleware approach that links existing GIS and ABM development platforms, and illustrate the need and approaches with example agent-based models.

Stable Policy Routing with Provider Independence - Feamster, Nick; Johari,Ramesh; Balakrishnan,Hari (Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, 2005)
Thousands of competing autonomous systems (ASes) mustcooperate with each other to provide global Internet connectivity.These ASes encode various economic, business,and performance decisions in their routing policies. The currentinterdomain routing system enables ASes to express policyusing rankings that determine how each router in an ASorders the different routes to a destination, and filters thatdetermine which routes are hidden from each neighboringAS. Since the Internet is composed of many independent,competing networks, the interdomain routing system shouldallow providers to set their rankings independently, and tohave no constraints on allowed filters. This paper studiesrouting protocol stability under these constraints. We firstdemonstrate that certain rankings that are commonly usedin practice may not ensure routing stability. We then provethat, with ranking independence and unrestricted filtering,guaranteeing that the routing system will converge to a stablepath assignment essentially requires ASes to rank routesbased on AS-path lengths. Finally, we discuss the implicationsof these results for the future of interdomain routing.

Stub Domain DDoS Detection - Kommareddy,C.; Levin,D.; Bhattacharjee, Bobby; La,R.J.; Shayman,M. (Technical Report of the Department of Computer Science, University of Maryland, College Park, 2005)

Time reversal and n-qubit canonical decompositions - Bullock,Stephen S.; Brennen,Gavin K.; O’Leary,Dianne P. (Journal of Mathematical Physics, 2005)
On pure states of n quantum bits, the concurrence entanglement monotone returns the norm of the inner product of a pure state with its spin-flip. The monotone vanishes for n odd, but for n even there is an explicit formula for its value on mixed states, i.e., a closed-form expression computes the minimum over all ensemble decompositions of a given density. For n even a matrix decomposition ν = k1ak2 of the unitary group is explicitly computable and allows for study of the monotone’s dynamics. The side factors k1 and k2 of this concurrence canonical decomposition (CCD) are concurrence symmetries, so the dynamics reduce to consideration of the a factor. This unitary a phases a basis of entangled states, and the concurrence dynamics of u are determined by these relative phases. In this work, we provide an explicit numerical algorithm computing ν = k1ak2 for n odd. Further, in the odd case we lift the monotone to a two-argument function. The concurrence capacity of ν according to the double argument lift may be nontrivial for n odd and reduces to the usual concurrence capacity in the literature for n even. The generalization may also be studied using the CCD, leading again to maximal capacity for most unitaries. The capacity of ν⊗I2 is at least that of ν, so odd-qubit capacities have implications for even-qubit entanglement. The generalizations require considering the spin-flip as a time reversal symmetry operator in Wigner’s axiomatization, and the original Lie algebra homomorphism defining the CCD may be restated entirely in terms of this time reversal. The polar decomposition related to the CCD then writes any unitary evolution as the product of a time-symmetric and time-antisymmetric evolution with respect to the spin-flip. En route we observe a Kramers’ nondegeneracy: the existence of a nondegenerate eigenstate of any time reversal symmetric n-qubit Hamiltonian demands (i) n even and (ii) maximal concurrence of said eigenstate. We provide examples of how to apply this work to study the kinematics and dynamics of entanglement in spin chain Hamiltonians.

Toward a graphical ABM toolkit with GIS integration - Rand, William; Brown,D; Riolo,R; Robinson,D (Proceedings of Agent2005, 2005)
Agent-based modeling (ABM) has proved useful in a number of fields. Many of theearly successes of ABM were due to its ability to represent the processes of a phenomenon. However, less emphasis has been placed in ABM on developing its ability to replicate spatial patterns of phenomena. In order to do that, more powerful spatial modeling techniques, like those within geographical information systems (GIS), are necessary. The integration of these two tool sets into a cohesive package would allow for elegant modeling of both process and pattern. One problem with an integrated toolkit is that most GIS users are not programmers, but most GIS users are familiar with the use of detailed graphical user interfaces (GUIs) in order to create complex visualizations of data. Thus providing a detailed GUI to access an integrated ABM-GIS toolkit would vastly expand the number of users for such a toolkit. This paper is a first step toward that goal. We first outline several design principles for an ABM-GIS toolkit and then describe a survey of extant toolkits (RepastPy, NetLogo, and MobiDyc) that were selected based on the design principles. The toolkits were surveyed to see how well they fulfill some of the design principles. This survey is not meant to be a comparative review of these toolkits but rather it was conducted to determine what useful design principles can be gathered from them that might inform a new “ideal” ABM-GIS toolkit. Finally, the paper concludes with some design recommendations for such a toolkit.

Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non‐lethal cold shock - Boonyaratanakornkit,Boonchai B; Simpson,Anjana J.; Whitehead,Timothy A; Fraser,Claire M.; El‐Sayed, Najib M.; Clark,Douglas S (Environmental Microbiology, 2005)
Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85°C to 65°C and 95°C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95°C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an α subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65°C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18 kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.

Turning information visualization innovations into commercial products: lessons to guide the next success - Shneiderman, Ben; Rao,R.; Andrews,K.; Ahlberg,C.; Brodbeck,D.; Jewitt,T.; Mackinlay,J. (IEEE Symposium on Information Visualization, 2005. INFOVIS 2005, 2005)
As information visualization matures as an academic research field, commercial spinoffs are proliferating, but success stories are harder to find. This is the normal process of emergence for new technologies, but the panel organizers believe that there are certain strategies that facilitate success. To teach these lessons, we have invited several key figures who are seeking to commercialize information visualization tools. The panelists make short presentations, engage in a moderated discussion, and respond to audience questions.
Keywords: Books; commercial development; commercial product; Computer interfaces; Computer science; data visualisation; Data visualization; Educational institutions; exploratory data analysis; information visualization innovation; information visualization tool; innovation management; Laboratories; Management training; new technology emergence; Technological innovation; technology transfer; Turning; User interfaces

UMD Experiments with FRGC Data - Aggarwal,G.; Biswas,S.; Chellapa, Rama (Computer Vision and Pattern Recognition - Workshops, 2005. CVPR Workshops. IEEE Computer Society Conference on, 2005)
Although significant work has been done in the field of face recognition, the performance of state-of-the art face recognition algorithms is not good enough to be effective in operational systems. Though most algorithms work well for controlled images, they are quite susceptible to changes in illumination and pose. Face Recognition Grand Challenge (FRGC) is an effort to examine such issues to suitably guide future research in the area. This paper describes the efforts made at UMD in this direction. We present our results on several experiments suggested in FRGC. We believe that though pattern classification techniques play an extremely significant role in automatic face recognition under controlled conditions, physical modeling is required to generalize across varying situations. Accordingly, we describe a generative approach to recognize faces across varying illumination. Unlike most current methods, our method does not ignore shadows. Instead we use them to our benefit by modeling attached shadows in our formulation.

Unsupervised learning applied to progressive compression of time-dependent geometry - Baby,Thomas; Kim,Youngmin; Varshney, Amitabh (Computers & Graphics, 2005)
We propose a new approach to progressively compress time-dependent geometry. Our approach exploits correlations in motion vectors to achieve better compression. We use unsupervised learning techniques to detect good clusters of motion vectors. For each detected cluster, we build a hierarchy of motion vectors using pairwise agglomerative clustering, and succinctly encode the hierarchy using entropy encoding. We demonstrate our approach on a client–server system that we have built for downloading time-dependent geometry.
Keywords: Clustering algorithms; Distributed/network graphics; pattern recognition

User Frustration with Technology in the Workplace (2004) - Lazar,Jonathan; Jones,Adam; Bessiere,Katie; Ceaparu,Irina; Shneiderman, Ben (Institute for Systems Research Technical Reports, 2005)
When hard to use computers cause users to become frustrated, it can affect workplace productivity, user mood, and interactions with other co-workers. Previous research has examined the frustration that graduate students and their families face in using computers. To learn more about the causes and effects of user frustration with computers in the workplace, we collected modified time diaries from 50 workplace users, who spent an average of 5.1 hours on the computer. In this experiment, users reported wasting on average, 42-43% of their time on the computer due to frustrating experiences. The causes of the frustrating experiences, the time lost due to the frustrating experiences, and the effects of the frustrating experiences on the mood of the users are discussed in this paper. Implications for designers, managers, users, information technology staff, and policymakers are discussed.
Keywords: Technical Report

Using measurement to build core competencies in software - Basili, Victor R. (Seminar sponsored by Data and Analysis Center for Software, 2005)

Web Service Composition with Volatile Information - Au,Tsz-Chiu; Kuter,Ugur; Nau, Dana S. (The Semantic Web – ISWC 2005, 2005)
In many Web service composition problems, information may be needed from Web services during the composition process. Existing research on Web service composition (WSC) procedures has generally assumed that this information will not change. We describe two ways to take such WSC procedures and systematically modify them to deal with volatile information. The black-box approach requires no knowledge of the WSC procedure’s internals: it places a wrapper around the WSC procedure to deal with volatile information. The gray-box approach requires partial information of those internals, in order to insert coding to perform certain bookkeeping operations. We show theoretically that both approaches work correctly. We present experimental results showing that the WSC procedures produced by the gray-box approach can run much faster than the ones produced by the black-box approach.
Keywords: Computer science

Weighted coloring based channel assignment for WLANs - Mishra,A.; Banerjee,S.; Arbaugh, William A. (ACM SIGMOBILE Mobile Computing and Communications Review, 2005)

What Are the Ants Doing? Vision-Based Tracking and Reconstruction of Control Programs - Egerstedt, M.; Balch, T.; Dellaert, F.; Delmotte, F.; Zia Khan (Proceedings of the 2005 IEEE International Conference on Robotics and Automation, 2005. ICRA 2005, 2005)
In this paper, we study the problem of going from a real-world, multi-agent system to the generation of control programs in an automatic fashion. In particular, a computer vision system is presented, capable of simultaneously tracking multiple agents, such as social insects. Moreover, the data obtained from this system is fed into a mode-reconstruction module that generates low-complexity control programs, i.e. strings of symbolic descriptions of control-interrupt pairs, consistent with the empirical data. The result is a mechanism for going from the real system to an executable implementation that can be used for controlling multiple mobile robots.
Keywords: Animals; Automatic generation control; Biological information theory; Computer vision; Control systems; Mobile robots; Probability distribution; Robot control; target tracking; Trajectory

Adaptive replication in peer-to-peer systems - Gopalakrishnan,V.; Silaghi,B.; Bhattacharjee, Bobby; Keleher,P. (Distributed Computing Systems, 2004. Proceedings. 24th International Conference on, 2004)
Peer-to-peer systems can be used to form a low-latency decentralized data delivery system. Structured peer-to-peer systems provide both low latency and excellent load balance with uniform query and data distributions. Under the more common skewed access distributions, however, individual nodes are easily overloaded, resulting in poor global performance and lost messages. This paper describes a lightweight, adaptive, and system-neutral replication protocol, called LAR, that maintains low access latencies and good load balance even under highly skewed demand. We apply LAR to Chord and show that it has lower overhead and better performance than existing replication strategies.
Keywords: adaptive; allocation; data; databases; decentralized; delivery; distributed; LAR; low-latency; peer-to-peer; processing; protocol; replicated; replication; resource; strategies; structured; system-neutral; system; systems

Advances in schistosome genomics - El‐Sayed, Najib M.; Bartholomeu,Daniella; Ivens,Alasdair; Johnston,David A.; LoVerde,Philip T. (Trends in Parasitology, 2004)
In Spring 2004, the first draft of the 270 Mb genome of Schistosoma mansoni will be released. This sequence is based on the assembly and annotation of a >7.5-fold coverage, shotgun sequencing project. The key stages involved in the international collaborative efforts that have led to the generation of these sequencing data for the parasite S. mansoni are discussed here.

Agent-based and analytical modeling to evaluate the effectiveness of greenbelts - Brown,Daniel G.; Page,Scott E.; Riolo,Rick; Rand, William (Environmental Modelling & Software, 2004)
We present several models of residential development at the rural–urban fringe to evaluate the effectiveness of a greenbelt located beside a developed area, for delaying development outside the greenbelt. First, we develop a mathematical model, under two assumptions about the distributions of service centers, that represents the trade-off between greenbelt placement and width, their effects on the rate of development beyond the greenbelt, and how these interact with spatial patterns of aesthetic quality and the locations of services. Next, we present three agent-based models (ABMs) that include agents with the potential for heterogeneous preferences and a landscape with the potential for heterogeneous attributes. Results from experiments run with a one-dimensional ABM agree with the starkest of the results from the mathematical model, strengthening the support for both models. Further, we present two different two-dimensional ABMs and conduct a series of experiments to supplement our mathematical analysis. These include examining the effects of heterogeneous agent preferences, multiple landscape patterns, incomplete or imperfect information available to agents, and a positive aesthetic quality impact of the greenbelt on neighboring locations. These results suggest how width and location of the greenbelt could help determine the effectiveness of greenbelts for slowing sprawl, but that these relationships are sensitive to the patterns of landscape aesthetic quality and assumptions about service center locations.
Keywords: Agent-based modeling; Land-use change; Landscape ecology; Urban sprawl

Analysis of dataflow programs with interval-limited data-rates - Teich,J.; Bhattacharyya, Shuvra S. (Computer Systems: Architectures, Modeling, and Simulation, 2004)

An Appearance-based Approach for Consistent Labeling of Humans and Objects in Video - Balcells-Capellades,M.; DeMenthon,D.; David Doermann (Pattern Analysis and Applications, 2004)
We present an approach for consistently labeling people and for detecting human-object interactions using mono-camera surveillance video. The approach is based on a robust appearance based correlogram model which is combined with histogram information to model color distributions of people and objects in the scene. The models are dynamically built from non-stationary objects which are the outputs of background subtraction, and are used to identify objects on a frame-by-frame basis. We are able to detect when people merge into groups and to segment them even during partial occlusion. We can also detect when a person deposits or removes an object. The models persist when a person or object leaves the scene and are used to identify them when they reappear. Experiments show that the models are able to accommodate perspective foreshortening that occurs with overhead camera angles, as well as partial occlusion. The results show that this is an effective approach able to provide important information to algorithms performing higher-level analysis such as activity recognition, where human-object interactions play an important role.

Arbitrate-and-move primitives for high throughput on-chip interconnection networks - Balkan,A.O.; Gang Qu; Vishkin, Uzi (Circuits and Systems, 2004. ISCAS '04. Proceedings of the 2004 International Symposium on, 2004)
An n-leaf pipelined balanced binary tree is used for arbitration of order and movement of data from n input ports to one output port. A novel arbitrate-and-move primitive circuit for every node of the tree, which is based on a concept of reduced synchrony that benefits from attractive features of both asynchronous and synchronous designs, is presented. The design objective of the pipelined binary tree is to provide a key building block in a high-throughput mesh-of-trees interconnection network for Explicit Multi Threading (XMT) architecture, a recently introduced parallel computation framework. The proposed reduced synchrony circuit was compared with asynchronous and synchronous designs of arbitrate-and-move primitives. Simulations with 0.18 mu;m technology show that compared to an asynchronous design, the proposed reduced synchrony implementation achieves a higher throughput, up to 2 Giga-Requests per second on an 8-leaf binary tree. Our circuit also consumes less power than the synchronous design, and requires less silicon area than both the synchronous and asynchronous designs.
Keywords: 8; arbiter; arbitrate-and-move; architecture; asynchronous; balanced; binary; circuit; circuit; circuits; consumption; data; explicit; interconnection; interconnections; leaf; mesh-of-trees; multi-threading; Multithreading; n-leaf; network; pipeline; pipelined; power; primitive; processing; reduced; simulation; structures; synchronous; synchrony; system-on-chip; tree; tree

The Argus eye: a new imaging system designed to facilitate robotic tasks of motion - Baker, P.; Ogale, A. S; Fermüller, Cornelia (IEEE Robotics & Automation Magazine, 2004)
This article describes an imaging system that has been designed to facilitate robotic tasks of motion. The system consists of a number of cameras in a network, arranged so that they sample different parts of the visual sphere. This geometric configuration has provable advantages compared to small field of view cameras for the estimation of the system's own motion and, consequently, the estimation of shape models from the individual cameras. The reason is, inherent ambiguities of confusion between translation and rotation disappear. Pairs of cameras may also be arranged in multiple stereo configurations, which provide additional advantages for segmentation. Algorithms for the calibration of the system and the three-dimensional (3-D) motion estimation are provided.
Keywords: Argus eye; Calibration; CAMERAS; computational geometry; Design automation; Eyes; image formation; imaging system; Information geometry; Layout; Motion estimation; multiple stereo configurations; panoramic robots; robot vision; Robot vision systems; robotic motion tasks; Robotics and automation; SHAPE; shape model estimation; system calibration

The Argus eye, a new tool for robotics - Baker, P.; Ogale, A. S; Fermüller, Cornelia; Aloimonos, J. (IEEE Robotics and Automation Magazine, 2004)

Automatic recognition of spontaneous speech for access to multilingual oral history archives - Byrne,W.; David Doermann; Franz,M.; Gustman,S.; Hajic,J.; Oard, Douglas; Picheny,M.; Psutka,J.; Ramabhadran,B. (IEEE Transactions on Speech and Audio Processing, Special Issue on Spontaneous Speech Processing, 2004)
The MALACH project has the goal of developing the technologies needed to facilitate access to large collections of spontaneous speech. Its aim is to dramatically improve the state of the art in key Automatic Speech Recognition (ASR), Natural Language Processing (NLP) technologies for use in large-scale retrieval systems. The project leverages a unique collection of oral history interviews with survivors of the Holocaust that has been assembled and extensively annotated by the Survivors of the Shoah Visual History Foundation. This paper describes the collection, 116,000 hours of interviews in 32 languages, and the way in which system requirements have been discerned through user studies. It discusses ASR methods for very difficult speech (heavily accented, emotional, and elderly spontaneous speech), including transcription to create training data and methods for language modeling and speaker adaptation. Results are presented for for English and Czech. NLP results are presented for named entity tagging, topic segmentation, and supervised topic classification, and the architecture of an integrated search system that uses these results is described.

Buffer merging—a powerful technique for reducing memory requirements of synchronous dataflow specifications - Murthy,P. K; Bhattacharyya, Shuvra S. (ACM Transactions on Design Automation of Electronic Systems (TODAES), 2004)

Building KidPad: an application for children's collaborative storytelling - Hourcade,J. P; Bederson, Benjamin B.; Druin, Allison (Software: Practice and Experience, 2004)

The case for a multi-hop wireless local area network - Lee,Seungjoon; Banerjee,S.; Bhattacharjee, Bobby (INFOCOM 2004. Twenty-third AnnualJoint Conference of the IEEE Computer and Communications Societies, 2004)
We propose a multi-hop wireless LAN architecture and demonstrate its benefits to wireless clients. For this architecture, we define implementation paths that allow interoperation with existing wireless LANs which can lead to an incremental deployment of this system. We quantify the performance benefits of the proposed schemes through measurements in realistic wireless LAN environments. We also examine the performance of such multi-hop wireless LANs through detailed simulation studies. Our results show that these multi-hop extensions can significantly improve the wireless access experience (in terms of data throughput, latency, etc.) for clients who enable such mechanisms. More interestingly, when multi-hop extensions are enabled by some of the clients, it also positively impacts the performance at other clients that are completely unaware of these extensions.
Keywords: access; access; area; benefits; client-server; clients; interoperation; LAN; local; multihop; network; networks; performance; radio; systems; wireless

The case for separating routing from routers - Feamster, Nick; Balakrishnan,Hari; Rexford,Jennifer; Shaikh,Aman; van der Merwe,Jacobus (Proceedings of the ACM SIGCOMM workshop on Future directions in network architecture, 2004)
Over the past decade, the complexity of the Internet's routing infrastructure has increased dramatically. This complexity and the problems it causes stem not just from various new demands made of the routing infrastructure, but also from fundamental limitations in the ability of today's distributed infrastructure to scalably cope with new requirements.The limitations in today's routing system arise in large part from the fully distributed path-selection computation that the IP routers in an autonomous system (AS) must perform. To overcome this weakness, interdomain routing should be separated from today's IP routers, which should simply forward packets (for the most part). Instead, a separate Routing Control Platform (RCP) should select routes on behalf of the IP routers in each AS and exchange reachability information with other domains.Our position is that an approach like RCP is a good way of coping with complexity while being responsive to new demands and can lead to a routing system that is substantially easier to manage than today. We present a design overview of RCP based on three architectural principles path computation based on a consistent view of network state, controlled interactions between routing protocol layers, and expressive specification of routing policies and discuss the architectural strengths and weaknesses of our proposal.
Keywords: BGP; interdomain routing; routing architecture

The CBP Parameter: A Module Characterization Approach for DSP Software Optimization - Bhattacharyya, Shuvra S.; Murthy,P. K (The Journal of VLSI Signal Processing, 2004)

Challenges in Measuring HPCS Learner Productivity in an Age of Ubiquitous Computing: The HPCS Program - Asgari, S.; Basili, Victor R.; Carver, J.; Hochstein, L.; Hollingsworth, Jeffrey K; Zelkowitz, Marvin V (In Proceedings of ICSE Workshop on High Productivity Computing. May 2004, 2004)

Characterization of the Overall Rotational Diffusion of a Protein From 15N Relaxation Measurements and Hydrodynamic Calculations - Blake-Hall,Jennifer; Walker,Olivier; Fushman, David (Protein NMR Techniques, 2004)
In this chapter, we discuss experimental and theoretical methods for characterizing the overall rotational diffusion of molecules in solution. The methods are illustrated for the B3 domain of protein G, a small protein with rotational anisotropy of D par / D perp = 1.4. The rotational diffusion tensor of the protein is determined directly from 15 N relaxation measurements. The experimental data are treated assuming various possible models for the overall tumbling: isotropic, axially symmetric, and fully anisotropic, and the results of these analyses are compared to determine an adequate diffusion model for the protein. These experimentally derived characteristics of the protein are compared with the results of theoretical calculations of the diffusion tensor using various hydrodynamic models, to find optimal models and parameter sets for theoretical predictions. We also derive model-free characteristics of internal backbone motions in the protein, to show that different models for the overall motion can result in significantly different pictures of motion. This emphasizes the necessity of accurately characterizing the overall tumbling of a molecule to determine its local dynamics.
Keywords: Biomedical and Life Sciences

CHARMED: A multi-objective co-synthesis framework for multi-mode embedded systems - Kianzad,V.; Bhattacharyya, Shuvra S. (Application-Specific Systems, Architectures and Processors, 2004. Proceedings. 15th IEEE International Conference on, 2004)

Compact procedural implementation in DSP software synthesis through recursive graph decomposition - Ko,M. Y; Murthy,P. K; Bhattacharyya, Shuvra S. (Software and compilers for embedded systems: 8th international workshop, SCOPES 2004, Amsterdam, The Netherlands, September 2-3, 2004: proceedings, 2004)

Compound eye sensor for 3D ego motion estimation - Neumann, J.; Fermüller, Cornelia; Aloimonos, J.; Brajovic,V. (2004 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2004. (IROS 2004). Proceedings, 2004)
We describe a compound eye vision sensor for 3D ego motion computation. Inspired by eyes of insects, we show that the compound eye sampling geometry is optimal for 3D camera motion estimation. This optimality allows us to estimate the 3D camera motion in a scene-independent and robust manner by utilizing linear equations. The mathematical model of the new sensor can be implemented in analog networks resulting in a compact computational sensor for instantaneous 3D ego motion measurements in full six degrees of freedom.
Keywords: 3D camera motion estimation; CAMERAS; compound eye vision sensor; Computer vision; Equations; Eyes; Geometry; Image sensors; Insects; linear equations; Motion estimation; robot vision; Robustness; sampling geometry; Sampling methods; Sensor phenomena and characterization

A cooperative bulk transfer protocol - Sherwood,R.; Braud,R.; Bhattacharjee, Bobby (IEEE Infocom, 2004)

Data Centric Cache Measurement on the Intel ltanium 2 Processor - Buck, Bryan R; Hollingsworth, Jeffrey K (Proceedings of the 2004 ACM/IEEE conference on Supercomputing, 2004)
Processor speed continues to increase faster than the speed of access to main memory, making effective use of memory caches more important. Information about an applicationýs interaction with the cache is therefore critical to performance tuning. To be most useful, tools that measure this information should relate it to the source code level data structures in an application. We describe how to gather such information by using hardware performance counters to sample cache miss addresses, and present a new tool named Cache Scope that does this using the Intel Itanium 2 performance monitors. We present experimental results concerning Cache Scopeýs accuracy and perturbation of cache behavior. We also describe a case study of using Cache Scope to tune two applications, achieving 24% and 19% reductions in running time.

Data sciences technology for homeland security information management and knowledge discovery - Kolda,T.; Brown,D; Corones,J.; Critchlow,T.; Eliassi-Rad,T.; Getoor, Lise; Hendrickson,B.; Kumar, V.; Lambert,D.; Matarazzo,C. (Report of the DHS Workshop Data Sciences, Jointly Released by Sandia National Laboratories and Lawrence Livermore National Laboratory, Alexandria, Va, 2004)

DateLens: A fisheye calendar interface for PDAs - Bederson, Benjamin B.; Clamage,A.; Czerwinski,M.P.; Robertson,G.G. (ACM Transactions on Computer-Human Interaction (TOCHI), 2004)

Deduplication and group detection using links - Bhattacharya,I.; Getoor, Lise (KDD workshop on link analysis and group detection, 2004)
Clustering is a fundamental problem in data mining. Tradi-tionally, clustering is done based on the similarity of the at- tribute values of the entities to be clustered. More recently, there has been greater interest in clustering relational and structured data. Often times this data is best described as a graph, in which there are both entities, described by a collec- tion of attributes, and links between entities, representing the relations between them. Clustering in these scenarios becomes more complex, as we should also take into account the similarity of the entity links when we are clustering. We propose novel distance measures for clustering linked data, and show how they can be used to solve two important data mining tasks, entity deduplication and group discovery.

Determining Causes and Severity of End-User Frustration - Ceaparu,Irina; Lazar,Jonathan; Bessiere,Katie; Robinson,John; Shneiderman, Ben (International Journal of Human-Computer Interaction, 2004)
Although computers are beneficial to individuals and society, frequently users encounter frustrating experiences when using computers. This study represents an attempt to measure, in 111 participants, the frequency, the cause, and the level of severity of frustrating experiences. The data show that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were Web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47% to 53% of time spent on a computer, depending on the location and study method. After extreme cases were discarded, the time lost was still above 38%. These disturbing results should be a basis for future study.Although computers are beneficial to individuals and society, frequently users encounter frustrating experiences when using computers. This study represents an attempt to measure, in 111 participants, the frequency, the cause, and the level of severity of frustrating experiences. The data show that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were Web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47% to 53% of time spent on a computer, depending on the location and study method. After extreme cases were discarded, the time lost was still above 38%. These disturbing results should be a basis for future study.