Dynamic Rebinding for Marshalling and Update, Via Redex-Time and Destruct-Time Reduction - Sewell,Peter; Stoyle,Gareth; Hicks, Michael W.; Bierman,Gavin; Wansbrough,Keith (Journal of Functional Programming, 2008)
Most programming languages adopt static binding, but for distributed programming an exclusive reliance on static binding is too restrictive: dynamic binding is required in various guises, for example, when a marshalled value is received from the network, containing identifiers that must be rebound to local resources. Typically, it is provided only by ad hoc mechanisms that lack clean semantics. In this paper, we adopt a foundational approach, developing core dynamic rebinding mechanisms as extensions to the simply typed call-by-value λ calculus. To do so, we must first explore refinements of the call-by-value reduction strategy that delay instantiation, to ensure computations make use of the most recent versions of rebound definitions. We introduce redex-time and destruct-time strategies. The latter forms the basis for a λmarsh calculus that supports dynamic rebinding of marshalled values, while remaining as far as possible statically typed. We sketch an extension of λmarsh with concurrency and communication, giving examples showing how wrappers for encapsulating untrusted code can be expressed. Finally, we show that a high-level semantics for dynamic updating can also be based on the destruct-time strategy, defining a λupdate calculus with simple primitives to provide type-safe updating of running code. We show how the ideas of this simple calculus extend to more real-world, module-level dynamic updating in the style of Erlang. We thereby establish primitives and a common semantic foundation for a variety of real-world dynamic rebinding requirements.

Effective label acquisition for collective classification - Bilgic,Mustafa; Getoor, Lise (Proceedings of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining, 2008)
Information diffusion, viral marketing, and collective classification all attempt to model and exploit the relationships in a network to make inferences about the labels of nodes. A variety of techniques have been introduced and methods that combine attribute information and neighboring label information have been shown to be effective for collective labeling of the nodes in a network. However, in part because of the correlation between node labels that the techniques exploit, it is easy to find cases in which, once a misclassification is made, incorrect information propagates throughout the network. This problem can be mitigated if the system is allowed to judiciously acquire the labels for a small number of nodes. Unfortunately, under relatively general assumptions, determining the optimal set of labels to acquire is intractable. Here we propose an acquisition method that learns the cases when a given collective classification algorithm makes mistakes, and suggests acquisitions to correct those mistakes. We empirically show on both real and synthetic datasets that this method significantly outperforms a greedy approximate inference approach, a viral marketing approach, and approaches based on network structural measures such as node degree and network clustering. In addition to significantly improving accuracy with just a small amount of labeled data, our method is tractable on large networks.
Keywords: active inference; collective classification; label acquisition

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

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

Enhancing In-Car Navigation Systems with Personal Experience - Bederson, Benjamin B.; Clamage,Aaron; Plaisant, Catherine (Transportation Research Record: Journal of the Transportation Research Board, 2008)
Computers are extremely powerful for data processing but less adept at handling problems that involve subjective reasoning. People, on the other hand, are good at such tasks. A framework is presented for adding subjective human experience to in-car navigation systems. People often rely on personal experience when planning trips, choosing the route that is fastest, prettiest, or recommended by a friend. A set of methods was developed to help people record personal driving history, add textual annotations describing subjective experiences, and share data with friends and family or even the broader community. Users can then learn from personal data or harness the multiplicity of individual experiences to enjoy new routes. This approach can be used in conjunction with traditional in-car navigation systems.

An Environment for Conducting Families of Software Engineering Experiments - Hochstein, Lorin; Nakamura,Taiga; Shull, Forrest; Zazworka, Nico; Basili, Victor R.; Zelkowitz, Marvin V (Software Development, 2008)
The classroom is a valuable resource for conducting software engineering experiments. However, coordinating a family of experiments in classroom environments presents a number of challenges to researchers. Understanding how to run such experiments, developing procedures to collect accurate data, and collecting data that is consistent across multiple studies are major problems. This paper describes an environment, the Experiment Manager that simplifies the process of collecting, managing, and sanitizing data from classroom experiments, while minimizing disruption to natural subject behavior. We have successfully used this environment to study the impact of parallel programming languages in the high‐performance computing domain on programmer productivity at multiple universities across the United States.

Environmental signatures associated with cholera epidemics - Constantin de Magny,G.; Murtugudde,R.; Sapiano,M. R. P.; Nizam,A.; Brown,C. W.; Busalacchi,A. J.; Yunus,M.; Nair,G. B.; Gil,A. I.; Lanata,C. F.; Rita R Colwell (Proceedings of the National Academy of Sciences, 2008)
The causative agent of cholera, Vibrio cholerae, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of V. cholerae, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998–2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and in situ gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of V. cholerae is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.ecology epidemiology microbiology remote sensing

Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons - Taviani,Elisa; Ceccarelli,Daniela; Lazaro,Nivalda; Bani,Stefania; Cappuccinelli,Piero; Rita R Colwell; Colombo,Mauro M. (FEMS Microbiology Ecology, 2008)
Circulation of mobile genetic elements linked to drug resistance spread was studied in Vibrio strains isolated from surface urban water (river and sea) and shellfish samples in 2002–2003 in Maputo, Mozambique. Class 1 integrons and integrating conjugative elements (ICE) were investigated by PCR and mating experiments in strains of major health interest: 10 Vibrio cholerae, six Vibrio parahaemolyticus, two Vibrio alginolyticus and one Vibrio fluvialis. Resistance to at least two antibiotics (predominantly β-lactams) was detected in all the strains, with additional resistances to sulfamethoxazole, spectinomycin, streptomycin and/or trimethoprim. Class 1 integrons contributed partially to the expression of drug resistance and were found in five isolates: four V. cholerae (blaP1 cassette, one strain also contained the dfrA15 cassette) and one V. alginolyticus (aadA2 cassette). ICEs, apparently devoid of resistance genes, were found in eight V. cholerae, three V. parahaemolyticus and one V. fluvialis isolates. A wide variability was observed by molecular characterization of ICEs. Five ICEs were included in the SXT/R391 family and seven ICEs were not classified. Our results indicate that the SXT/R391 family and related ICEs comprise a large class of polymorphic genetic elements widely circulating in environmental Vibrio strains in Africa, beside those evidently linked to drug resistance in clinical isolates.
Keywords: ICE; integron; Mozambique; Vibrio

Expanding the reach of Grid computing: combining Globus- and BOINC-based systems - Myers,D. S; Bazinet,A. L; Cummings, Michael P. (Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology, 2008)

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

Fixing ally's growing pains with velocity modeling - Bender,Adam; Sherwood,Rob; Spring, Neil (Proceedings of the 8th ACM SIGCOMM conference on Internet measurement, 2008)
Mapping the router topology is an important component of Internet measurement. Alias resolution, the process of mapping IP addresses to routers, is critical to accurate Internet mapping. Ally, a popular alias resolution tool, was developed to resolve aliases in individual ISPs, but its probabilistic accuracy and need to send O(n2) probes to infer aliases among n IP addresses make it unappealing for large-scale Internet mapping. In this paper, we present RadarGun, a tool that uses IP identifier velocity modeling to improve the accuracy and scalability of the Ally-based resolution technique. We provide analytical bounds on Ally's accuracy and validate our predicted aliases against Ally. Additionally, we show that velocity modeling requires only O(n) probes and thus scales to Internet-sized mapping efforts.
Keywords: alias resolution; ally; ip identifier; velocity modeling

A Framework for Software Engineering Experimental Replications - Mendonca,M.G.; Maldonado,J.C.; de Oliveira,M.C.F.; Carver, J.; Fabbri,C.P.F.; Shull, F.; Travassos,G.H.; Hohn,E.N.; Basili, Victor R. (Engineering of Complex Computer Systems, 2008. ICECCS 2008. 13th IEEE International Conference on, 2008)
Experimental replications are very important to the advancement of empirical software engineering. Replications are one of the key mechanisms to confirm previous experimental findings. They are also used to transfer experimental knowledge, to train people, and to expand a base of experimental evidence. Unfortunately, experimental replications are difficult endeavors. It is not easy to transfer experimental know-how and experimental findings. Based on our experience, this paper discusses this problem and proposes a Framework for Improving the Replication of Experiments (FIRE). The FIRE addresses knowledge sharing issues both at the intra-group (internal replications) and inter-group (external replications) levels. It encourages coordination of replications in order to facilitate knowledge transfer for lower cost, higher quality replications and more generalizable results.
Keywords: engineering; engineering; evidence; experimental; experimental; Experiments; experimental; for; Framework; Improving; knowledge; of; replication; replication; software; sharing; software; the; transfer; knowledge

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

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

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

Hierarchical infrastructure for internet mapping services - Brabec,F.; Samet, Hanan (Geospatial Services and Applications for the Internet, 2008)

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

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

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

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

The Lattice Project: a Grid research and production environment combining multiple Grid computing models - Bazinet,A. L; Cummings, Michael P. (Distributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting CommunitiesDistributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting Communities, 2008)

Leveraging social context for searching social media - Smith,Marc; Barash,Vladimir; Getoor, Lise; Lauw,Hady W. (Proceedings of the 2008 ACM workshop on Search in social media, 2008)
The ability to utilize and benefit from today's explosion of social media sites depends on providing tools that allow users to productively participate. In order to participate, users must be able to find resources (both people and information) that they find valuable. Here, we argue that in order to do this effectively, we should make use of a user's "social context". A user's social context includes both their personal social context (their friends and the communities to which they belong) and their community social context (their role and identity in different communities).
Keywords: social context; social media; social search

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

Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development - Wan,Le-Ben; Pan,Hua; Hannenhalli, Sridhar; Cheng,Yong; Ma,Jun; Fedoriw,Andrew; Lobanenkov,Victor; Latham,Keith E.; Schultz,Richard M.; Bartolomei,Marisa S. (Development, 2008)
CTCF is a multifunctional nuclear factor involved in epigenetic regulation. Despite recent advances that include the systematic discovery of CTCF-binding sites throughout the mammalian genome, the in vivo roles of CTCF in adult tissues and during embryonic development are largely unknown. Using transgenic RNAi, we depleted maternal stores of CTCF from growing mouse oocytes, and identified hundreds of misregulated genes. Moreover, our analysis suggests that CTCF predominantly activates or derepresses transcription in oocytes. CTCF depletion causes meiotic defects in the egg, and mitotic defects in the embryo that are accompanied by defects in zygotic gene expression, and culminate in apoptosis. Maternal pronuclear transfer and CTCF mRNA microinjection experiments indicate that CTCF is a mammalian maternal effect gene, and that persistent transcriptional defects rather than persistent chromosomal defects perturb early embryonic development. This is the first study detailing a global and essential role for CTCF in mouse oocytes and preimplantation embryos.

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

Measuring 1st order stretchwith a single filter - Bitsakos,K.; Domke, J.; Fermüller, Cornelia; Aloimonos, J. (IEEE International Conference on Acoustics, Speech and Signal Processing, 2008. ICASSP 2008, 2008)
We analytically develop a filter that is able to measure the linear stretch of the transformation around a point, and present results of applying it to real signals. We show that this method is a real-time alternative solution for measuring local signal transformations. Experimentally, this method can accurately measure stretch, however, it is sensitive to shift.
Keywords: Cepstral analysis; Educational institutions; filter; filtering theory; Fourier transforms; Frequency domain analysis; Frequency estimation; Gabor filters; Image analysis; IMAGE PROCESSING; linear stretch measurement; local signal transformation measurement; Nonlinear filters; Phase estimation; Signal analysis; Speech processing

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

Methods to directly measure the trapping potential in optical tweezers - Balijepalli,A.; LeBrun,T. W.; Gorman,J. J.; Gupta,S.K. (2008)
Techniques to measure the trapping force in an optical tweezers without any prior assumptions about the trapshape have been developed. The response of a trapped micro or nanoparticle to a step input is measured and then used to calculate the trapping force experienced by the particle as a function of it’s position in the trap. This method will provide new insight into the trapping behavior of nanoparticles, which are more weakly bound than microparticles and thereby explore larger regions of the trapping potential due to Brownian motion. Langevin dynamics simulations are presented to model the system and are used to demonstrate this technique. Preliminary experimental results are then presented to validate the simulations. Finally, the measured trapping forces, from simulations and laboratory experiments, are integrated to recover the trapping potential.

Motivating participation in internet routing overlays - Levin,Dave; Baden,Randolph; Lumezanu,Cristian; Spring, Neil; Bhattacharjee, Bobby (Proceedings of the 3rd international workshop on Economics of networked systems, 2008)
PeerWise is an Internet routing overlay that reduces end-to-end latencies by allowing peers to forward through a relay instead of connecting directly to their destinations. Fundamental to PeerWise is the notion of peering agreements between two peers, wherein they agree to forward for one another. In this paper, we consider the problem of motivating users to establish and maintain peerings in a completely decentralized, scalable manner. We show that routing overlays present unique challenges and goals. For instance, since participants can always "fall back" on standard Internet routing, we must encourage users to stay in the system and maintain long-lived peering agreements. To address these challenges, we propose two mechanisms: First, we use Service Level Agreements (SLAs) to expressively negotiate peers' demands and the recourses they will take when SLAs are violated. Second, we propose a mechanism to address SLA violations that differs from the standard notion of punishment via service degradation. Our simulation results demonstrate that our mechanism causes peers to avoid SLA violators in favor of long-lived peerings. Lastly, we discuss potential, emergent behaviors in a selfish routing overlay.
Keywords: incentives; internet routing overlays; service-level agreements

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

Mutations in the Hydrophobic Core of Ubiquitin Differentially Affect Its Recognition by Receptor Proteins - Haririnia,Aydin; Verma,Rati; Purohit,Nisha; Twarog,Michael Z.; Deshaies,Raymond J.; Bolon,Dan; Fushman, David (Journal of Molecular Biology, 2008)
Ubiquitin (Ub) is one of the most highly conserved signaling proteins in eukaryotes. In carrying out its myriad functions, Ub conjugated to substrate proteins interacts with dozens of receptor proteins that link the Ub signal to various biological outcomes. Here we report mutations in conserved residues of Ub's hydrophobic core that have surprisingly potent and specific effects on molecular recognition. Mutant Ubs bind tightly to the Ub-associated domain of the receptor proteins Rad23 and hHR23A but fail to bind the Ub-interacting motif present in the receptors Rpn10 and S5a. Moreover, chains assembled on target substrates with mutant Ubs are unable to support substrate degradation by the proteasome in vitro or sustain viability of yeast cells. The mutations have relatively little effect on Ub's overall structure but reduce its rigidity and cause a slight displacement of the C-terminal β-sheet, thereby compromising association with Ub-interacting motif but not with Ub-associated domains. These studies emphasize an unexpected role for Ub's core in molecular recognition and suggest that the diversity of protein–protein interactions in which Ub engages placed enormous constraints on its evolvability.
Keywords: hydrophobic core mutation; molecular recognition; proteasomal degradation; ubiquitin; ubiquitin receptors

NASDAQ Velocity and Forces: An Interactive Visualization of Activity and Change - Dao,H.T.; Bazinet,A.; Berthier,R.; Shneiderman, Ben (Journal of Universal Computer Science, 2008)

Network-Aware Join Processing in Global-Scale Database Federations - Xiaodan Wang; Burns,R.; Terzis,A.; Deshpande, Amol (IEEE 24th International Conference on Data Engineering, 2008. ICDE 2008, 2008)
We introduce join scheduling algorithms that employ a balanced network utilization metric to optimize the use of all network paths in a global-scale database federation. This metric allows algorithms to exploit excess capacity in the network, while avoiding narrow, long-haul paths. We give a two- approximate, polynomial-time algorithm for serial (left-deep) join schedules. We also present extensions to this algorithm that explore parallel schedules, reduce resource usage, and define tradeoffs between computation and network utilization. We evaluate these techniques within the SkyQuery federation of Astronomy databases using spatial-join queries submitted by SkyQuery's users. Experiments show that our algorithms realize near-optimal network utilization with minor computational overhead.
Keywords: Astronomy; Computer networks; Concurrent computing; global-scale database federations; join scheduling algorithms; network utilization; network-aware join processing; parallel schedules; polynomial-time algorithm; Polynomials; Processor scheduling; Query processing; reduce resource usage; Scheduling algorithm; Spatial databases; spatial-join queries; Telecommunication traffic; Throughput

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

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

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

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

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

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

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

Photo-based authentication using social networks - Yardi,Sarita; Feamster, Nick; Bruckman,Amy (Proceedings of the first workshop on Online social networks, 2008)
We present Lineup, a system that uses the social network graph in Facebook and auxiliary information (e.g., "tagged" user photos) to build a photo-based Web site authentication framework. Lineup's underlying mechanism leverages the concept of CAPTCHAs, programs that are designed to distinguish bots from human users. Lineup extends this functionality to help a Web site ascertain a user's identity or membership in a certain group (e.g., an interest group, invitees to a certain event) in order to infer some level of trust. Lineup works by presenting a user with photographs and asking the user to identify subjects in the photo whom a user with the appropriate identity or group membership should know. We present the design and implementation for Lineup, describe a preliminary prototype implementation, and discuss Lineup's security properties, including possible guarantees and threats.
Keywords: social networks; trust

A pilot study to compare programming effort for two parallel programming models - Hochstein, Lorin; Basili, Victor R.; Vishkin, Uzi; Gilbert,John (Journal of Systems and Software, 2008)
ContextWriting software for the current generation of parallel systems requires significant programmer effort, and the community is seeking alternatives that reduce effort while still achieving good performance. Objective Measure the effect of parallel programming models (message-passing vs. PRAM-like) on programmer effort. Design, setting, and subjects One group of subjects implemented sparse-matrix dense-vector multiplication using message-passing (MPI), and a second group solved the same problem using a PRAM-like model (XMTC). The subjects were students in two graduate-level classes: one class was taught MPI and the other was taught XMTC. Main outcome measures Development time, program correctness. Results Mean XMTC development time was 4.8 h less than mean MPI development time (95% confidence interval, 2.0–7.7), a 46% reduction. XMTC programs were more likely to be correct, but the difference in correctness rates was not statistically significant (p = .16). Conclusions XMTC solutions for this particular problem required less effort than MPI equivalents, but further studies are necessary which examine different types of problems and different levels of programmer experience.
Keywords: effort; empirical study; Message-passing; MPI; parallel programming; PRAM; XMT

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

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

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

Role of transposable elements in trypanosomatids - Bringaud,Frédéric; Ghedin,Elodie; El‐Sayed, Najib M.; Papadopoulou,Barbara (Microbes and Infection, 2008)
Transposable elements constitute 2-5% of the genome content in trypanosomatid parasites. Some of them are involved in critical cellular functions, such as the regulation of gene expression in Leishmania spp. In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions.
Keywords: Cellular function; Domestication; Evolution; Gene expression; Leishmania; Regulation of mRNA stability; Retroposon; Transposable element; Trypanosoma

A scalable key management and clustering scheme for wireless ad hoc and sensor networks - Li,Jason H.; Bhattacharjee, Bobby; Yu,Miao; Levy,Renato (Future Generation Computer Systems, 2008)
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.
Keywords: ad hoc networks; clustering; Group communications; Key management; sensor networks

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

Sequence diversity and evolution of multigene families in Trypanosoma cruzi - Cerqueira,Gustavo C.; Bartholomeu,Daniella C.; DaRocha,Wanderson D.; Hou,Lihua; Freitas-Silva,Danielle M.; Machado,Carlos Renato; El‐Sayed, Najib M.; Teixeira,Santuza M.R. (Molecular and Biochemical Parasitology, 2008)
Several copies of genes belonging to three multigene families present in the genome of Trypanosoma cruzi were sequenced and comparatively analyzed across six different strains of the parasite belonging to the T. cruzi I lineage (Colombiana, Silvio X10 and Dm28c), the T. cruzi II lineage (Esmeraldo and JG) and a hybrid strain (CL Brener). For all three gene families analyzed, our results support the division in T. cruzi I and II lineages. Furthermore, in agreement with its hybrid nature, sequences derived from the CL Brener clone clustered together with T. cruzi II sequences as well as with a third group of sequences. Paralogous sequences encoding Amastin, an amastigote surface glycoprotein and TcAG48, an antigenic RNA binding protein, which are clustered in the parasite genome, present higher intragenomic variability in T. cruzi II and CL Brener strains, when compared to T. cruzi I strains. Paralogous sequences derived from the TcADC gene family, which encode various isoforms of adenylyl cyclases and are dispersed throughout the T. cruzi genome, exhibit similar degree of variability in all strains, except in the CL Brener strain, in which the sequences were more divergent. Several factors including mutation rates and gene conversion mechanisms, acting differently within the T. cruzi population, may contribute to create such distinct levels of sequence diversity in multigene families that are clustered in the T. cruzi genome.
Keywords: Amastin; Gene conversion; Genetic diversity; Multigene families; Trypanosoma cruzi

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

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

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

Towards Design and Fabrication of a Miniature MRI-Compatible Robot for Applications in Neurosurgery - Pappafotis,Nicholas; Bejgerowski,Wojciech; Gullapalli,Rao; Simard,J. Marc; Gupta, Satyandra K.; Desai,Jaydev P. (ASME, 2008)
Brain tumors are among the most feared complications of cancer and they occur in 20–40% of adult cancer patients. Despite numerous advances in treatment, the prognosis for these patients is poor, with a median survival of 4–8 months. The primary reasons for poor survival rate are the lack of good continuous imaging modality for intraoperative intracranial procedures and the inability to remove the complete tumor tissue due to its placement in the brain and the corresponding space constraints to reach it. Intraoperative magnetic resonance imaging (MRI) supplements the surgeon's visual and tactile senses in a way that no other imaging device can achieve resulting in less trauma to surrounding healthy brain tissue during surgery. To minimize the trauma to surrounding healthy brain tissue, it would be beneficial to operate through a narrow surgical corridor dissected by the neurosurgeon. Facilitating tumor removal by accessing regions outside the direct “line-of-sight” of the neurosurgical corridor will require a highly dexterous, small cross section, and MRI-compatible robot. Developing such a robot is extremely challenging task. In this paper we report a preliminary design of 6-DOF robot for possible application in neurosurgery. The robot actuators and body parts are constructed from MRI compatible materials. The current prototype is 0.36” in diameter and weighs only 0.0289 N (2.95 grams). The device was actuated using Flexinol® which is a shape memory alloy manufactured by Dynalloy, Inc. The end-effector forces ranged from 12 mN to 50 mN depending on the robot configuration. The end-effector force to robot weight ratio varied from 0.41 to 1.73. During trials the robot motion was repeatable and the range of motion of the robot was about 90 degrees for the end-effector when one side shape memory alloy (SMA) channel was actuated. The actuation time from the start to finish was about 2.5 s.

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

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

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

Understanding the High-Performance-Computing Community: A Software Engineer's Perspective - Basili, Victor R.; Carver, J. C; Cruzes, D.; Hochstein, L. M; Hollingsworth, Jeffrey K; Shull, F.; Zelkowitz, Marvin V (Software, IEEE, 2008)
Computational scientists developing software for HPC systems face unique software engineering issues. Attempts to transfer SE technologies to this domain must take these issues into account.
Keywords: community; software; computational; engineering; engineering; software; Science; software; high-performance-computing

A Unified Framework for Multipath Routing for Unicast and Multicast Traffic - Guven,T.; La,R.J.; Shayman,M.A.; Bhattacharjee, Bobby (Networking, IEEE/ACM Transactions on, 2008)
We study the problem of load balancing the traffic from a set of unicast and multicast sessions. The problem is formulated as an optimization problem. However, we assume that the gradient of the network cost function is not available and needs to be estimated. Multiple paths are provided between a source and a destination using application-layer overlay. We propose a novel algorithm that is based on what is known as simultaneous perturbation stochastic approximation and utilizes only noisy measurements collected and reported to the sources, using an overlay architecture. We consider three network models that reflect different sets of assumptions regarding multicast capabilities of the network. Using an analytical model we first prove the almost sure convergence of the algorithm to a corresponding optimal solution under each network model considered in this paper with decreasing step sizes. Then, we establish the weak convergence (or convergence in distribution) with a fixed step size. In addition, we investigate the benefits acquired from implementing additional multicast capabilities by studying the relative performance of our algorithm under the three network models.
Keywords: application-layer; approximation; unicast; balancing; multicast; channels; stochastic; communication; multipath; cost; function; optimization; network; overlay; load; perturbation; problem; simultaneous; processes; telecommunication; routing; network; routing; telecommunication; Stochastic; traffic; traffic; multicast; traffic; multipath

Accountability as a service - Bender,Adam; Spring, Neil; Levin,Dave; Bhattacharjee, Bobby (Proceedings of the 3rd USENIX workshop on Steps to reducing unwanted traffic on the internet, 2007)
We propose that accountability be a first-class network service, independent of addressing and routing. We design a scheme for allowing accountability services, rather than connectivity-providing ISPs, to vouch for traffic, allowing victims to report abuse, filter abusive traffic, and isolate malicious senders. We discuss how accountability services may evolve, how they may facilitate new applications, and the implications of shifting the burden of network policing to a dedicated service.

Algorithms for on-line monitoring of micro spheres in an optical tweezers-based assembly cell - Peng,T.; Balijepalli,A.; Gupta,S.K.; LeBrun,T. (Journal of Computing and Information Science in Engineering, 2007)
Optical tweezers have emerged as a powerful tool for microand nanomanipulation. Using optical tweezers to perform auto- mated assembly requires on-line monitoring of components in the assembly workspace. This paper presents algorithms for estimat- ing positions and orientations of microscale and nanoscale com- ponents in the 3-Dimensional assembly workspace. Algorithms presented in this paper use images obtained by optical section microscopy. The images are first segmented to locate areas of in- terest and then image gradient information from the areas of in- terest is used to generate probable locations and orientations of components in the XY-plane. Finally, signature curves are com- puted and utilized to obtain component locations and orienta- tions in 3-D space. We have tested these algorithms with silica micro-spheres as well as metallic nanowires. We believe that the algorithms described in this paper will provide the foundation for realizing automated assembly operations in optical tweezers- based assembly cells.

Amino acid quantitative structure property relationship database: a web-based platform for quantitative investigations of amino acids - Lu,Yi; Bulka,Blazej; desJardins, Marie; Freeland,Stephen J (Protein Engineering Design and SelectionProtein Engineering, Design and Selection, 2007)
Here, we present the AA-QSPR Db (Amino Acid Quantitative Structure Property Relationship Database): a novel, freely available web-resource of data pertaining to amino acids, both engineered and naturally occurring. In addition to presenting fundamental molecular descriptors of size, charge and hydrophobicity, it also includes online visualization tools for users to perform instant, interactive analyses of amino acid sub-sets in which they are interested. The database has been designed with extensible markup language technology to provide a flexible structure, suitable for future development. In addition to providing easy access for queries by external computers, it also offers a user-friendly web-based interface that facilitates human interactions (submission, storage and retrieval of amino acid data) and an associated e-forum that encourages users to question and discuss current and future database contents.
Keywords: Amino acids; database; QSPR; XML

Automated gui testing guided by usage profiles - Brooks,Penelope A.; Memon, Atif M. (Proceedings of the twenty-second IEEE/ACM international conference on Automated software engineering, 2007)
Most software developed in recent years has a graphical userinterface (GUI). The only way for the end-user to interact with the software application is through the GUI. Hence, acceptance and system testing of the software requires GUI testing. This paper presents a new technique for testing of GUI applications. Information on the actual usage of the application, in the form of "usage profiles," is used to ensure that a new version of the application will function correctly. Usage profiles, sequences of events that end-users execute on a GUI, are used to develop a probabilistic usage model of the application. An algorithm uses the model to generate test cases that represent events the user is most likely to execute. Reverse engineering methods are used to extract the underlying structure of the application. An empirical study on four open source GUI applications reveals that test suites generated from the probabilistic model are 0.2-22% of the size of test suites produced directly from usage profiles. Furthermore, the test suites generated from the model detect more faults per test case than those detected directly from the usage profiles, and detect faults not detected by the original profiles
Keywords: event-driven software; GUI testing; usage profiles

Autonomic computing - Brabec,F.; Samet, Hanan (IEEE internet computing, 2007)

Backbone construction in selfish wireless networks - Lee,Seungjoon; Levin,Dave; Gopalakrishnan,Vijay; Bhattacharjee, Bobby (Proceedings of the 2007 ACM SIGMETRICS international conference on Measurement and modeling of computer systems, 2007)
We present a protocol to construct routing backbones in wireless networks composed of selfish participants. Backbones are inherently cooperative, so constructing them in selfish environments is particularly difficult; participants want a backbone to exist (soothers relay their packets) but do not want to join the backbone (so they do not have to relay packets for others). We model the wireless backbone as a public good and use impatience as an incentive for cooperation. To determine if and when to donate to this public good, each participant calculates how patient it should be in obtaining the public good. We quantify patience using the Volunteer's Timing Dilemma (VTD), which we extend to general multihop network settings. Using our generalized VTD analysis, each node individually computes as its dominant strategy the amount of time to wait before joining the backbone. We evaluate our protocol using both simulations and an implementation. Our results show that, even though participants in our system deliberately wait before volunteering, a backbone is formed quickly. Further, the quality of the backbone (such as the size and resulting network lifetime) is comparable to that of existing backbone protocols that assume altruistic behavior.
Keywords: incentives; public good; selfish network; volunteer's dilemma; wireless backbone

BELIV'06: beyond time and errors: novel evaluation methods for information visualization - Bertini,Enrico; Plaisant, Catherine; Santucci,Giuseppe (interactions, 2007)

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

Boycotting and extorting nodes in an internetwork - Levin,D.; Bender,A.; Lumezanu,C.; Spring, Neil; Bhattacharjee, Bobby (NetE-con+ IBC, 2007)

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

Cell breathing in wireless LANs: Algorithms and evaluation - Hajiaghayi, Mohammad T.; Mirrokni,S. V.; Saberi,A.; Bahl,P.; Jain,K.; Qiu,L. (IEEE Transactions on Mobile Computing, 2007)

Children's interests and concerns when using the international children's digital library: a four-country case study - Druin, Allison; Weeks,A.; Massey,S.; Bederson, Benjamin B. (Proceedings of the 7th ACM/IEEE-CS joint conference on Digital libraries, 2007)

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

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

Client-Based Spatial Browsing on the World Wide Web - Brabec,Frantisek; Samet, Hanan (IEEE Internet Computing, 2007)
Being able to visualize both spatial and nonspatial data is becoming increasingly important to today's Internet users. Spatial data viewers and query tools can aid in visualization, but they should also let users access data instantly and with minimal effort. The authors explore new ways to allow visualization of data stored in a central server database on a simple client. They also consider usage scenarios in which transferring the whole database to the client for processing isn't feasible due to the amount of data on the server, insufficient computing power on the client, and a slow link between the two.
Keywords: client-server spatial browsing; geographic information systems (GIS); Spatial databases; web access; web-based mapping

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

Collective entity resolution in relational data - Bhattacharya,Indrajit; Getoor, Lise (ACM Trans. Knowl. Discov. Data, 2007)
Many databases contain uncertain and imprecise references to real-world entities. The absence of identifiers for the underlying entities often results in a database which contains multiple references to the same entity. This can lead not only to data redundancy, but also inaccuracies in query processing and knowledge extraction. These problems can be alleviated through the use of entity resolution. Entity resolution involves discovering the underlying entities and mapping each database reference to these entities. Traditionally, entities are resolved using pairwise similarity over the attributes of references. However, there is often additional relational information in the data. Specifically, references to different entities may cooccur. In these cases, collective entity resolution, in which entities for cooccurring references are determined jointly rather than independently, can improve entity resolution accuracy. We propose a novel relational clustering algorithm that uses both attribute and relational information for determining the underlying domain entities, and we give an efficient implementation. We investigate the impact that different relational similarity measures have on entity resolution quality. We evaluate our collective entity resolution algorithm on multiple real-world databases. We show that it improves entity resolution performance over both attribute-based baselines and over algorithms that consider relational information but do not resolve entities collectively. In addition, we perform detailed experiments on synthetically generated data to identify data characteristics that favor collective relational resolution over purely attribute-based algorithms.
Keywords: data cleaning; entity resolution; graph clustering; record linkage

Combining Collective Classification and Link Prediction - Bilgic,M.; Namata,G.M.; Getoor, Lise (Data Mining Workshops, 2007. ICDM Workshops 2007. Seventh IEEE International Conference on, 2007)
The problems of object classification (labeling the nodes of a graph) and link prediction (predicting the links in a graph) have been largely studied independently. Commonly, object classification is performed assuming a complete set of known links and link prediction is done assuming a fully observed set of node attributes. In most real world domains, however, attributes and links are often missing or incorrect. Object classification is not provided with all the links relevant to correct classification and link prediction is not provided all the labels needed for accurate link prediction. In this paper, we propose an approach that addresses these two problems by interleaving object classification and link prediction in a collective algorithm. We investigate empirically the conditions under which an integrated approach to object classification and link prediction improves performance, and find that performance improves over a wide range of network types, and algorithm settings.
Keywords: algorithm; link; classification; classification; graph; collective; prediction; object; theory; pattern

Combining motion from texture and lines for visual navigation - Bitsakos,K.; Li Yi; Fermüller, Cornelia (IEEE/RSJ International Conference on Intelligent Robots and Systems, 2007. IROS 2007, 2007)
Two novel methods for computing 3D structure information from video for a piecewise planar scene are presented. The first method is based on a new line constraint, which clearly separates the estimation of distance from the estimation of slant. The second method exploits the concepts of phase correlation to compute from the change of image frequencies of a textured plane, distance and slant information. The two different estimates together with structure estimates from classical image motion are combined and integrated over time using an extended Kalman filter. The estimation of the scene structure is demonstrated experimentally in a motion control algorithm that allows the robot to move along a corridor. We demonstrate the efficacy of each individual method and their combination and show that the method allows for visual navigation in textured as well as un-textured environments.
Keywords: 3D structure information; CAMERAS; Computer vision; extended Kalman filter; Frequency; image frequencies; Image motion analysis; Image texture; Kalman filters; Layout; motion control; Motion estimation; Navigation; Optical computing; phase correlation; piecewise planar scene; Robustness; Simultaneous localization and mapping; Speech processing; textured plane; video signal processing; visual navigation

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

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

Data Management in the Worldwide Sensor Web - Balazinska,Magdalena; Deshpande, Amol; Franklin,Michael J.; Gibbons,Phillip B.; Gray,Jim; Hansen,Mark; Liebhold,Michael; Nath,Suman; Szalay,Alexander; Tao,Vincent (IEEE Pervasive Computing, 2007)
Advances in hardware and miniaturization technologies have led to a rapid increase in the number of large-scale sensor network deployments around the world, bringing us closer to the vision of a worldwide sensor web. Exploiting the sensor web to its full potential, however, raises several hard data management challenges. Addressing these challenges requires a concerted multidisciplinary effort encompassing many computer science fields. This article outlines some of the key data management challenges of a worldwide sensor web. It also presents recent advances in data management research that aim to address these challenges. Hopefully, the scientific, ubiquitous computing, and sensor network communities will adopt some of these solutions for managing their data. The article also attempts to bring many of the remaining open issues to the attention of the database community. This article is part of a special issue on Building a Sensor-Rich World.
Keywords: data modeling; data streams; data uncertainty; distributed systems; interoperability; sensor networks

Dataflow-based mapping of computer vision algorithms onto FPGAs - Sen,M.; Corretjer,I.; Haim,F.; Saha,S.; Schlessman,J.; Lv,T.; Bhattacharyya, Shuvra S.; Wolf,W. (EURASIP Journal on Embedded Systems, 2007)

Description of Computer Science Higher Education in Sub-Saharan Africa: Initial Explorations - Marshini Chetty; Buckhalter, Celeste; Best, Michael L.; Grinter, Rebecca E.; Guzdial, Mark (2007)
Many countries in Sub-Saharan Africa (SSA) are in need oftechnology innovators who are equipped to leverage technologies in locally relevant domains such as health, government and education. To create skilled graduates who can build and shape locally relevant technologies, higher education institutes in Africa must have Computer Science (CS) education programs that meet local needs, for example, to satisfy the demand for entrepreneurs to build industry and strengthen an economy. This paper characterizes the current state of CS education in SSA in order to identify opportunities for addressing education challenges and to make suggestions that may improve the Information and Communication Technology (ICT) infrastructure in this region. We present the results of a survey of CS educators in SSA institutions of higher education, which was aimed at exploring the issues they face. In addition to the continued chronic under-funding of SSA education, we found that universities in SSA have smaller departments, less focus on Human Computer Interaction (HCI) and offer a variety of courses aside from undergraduate Bachelors degrees. We discuss directions to improve CS curricula through investing in locally tailored courses and changing perceptions of the value of SSA CS higher education programs, standards and educators. Further, we reflect on the challenges of conducting research on SSA. We conclude that further research in this area is needed to build on the ideas we offer here to continue to strengthen CS higher education in SSA.
Keywords: Sub-Saharan Africa; Undergraduate computing education

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

Distributed Ranked Search - Gopalakrishnan,Vijay; Morselli,Ruggero; Bhattacharjee, Bobby; Keleher,Pete; Srinivasan, Aravind (High Performance Computing – HiPC 2007High Performance Computing – HiPC 2007, 2007)
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 results, not necessarily 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 decentralized setting. We analyze the overhead of our approach, and quantify 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 scale with little overhead to large systems, and b) the accuracy of the results obtained using distributed ranking is comparable to that of a centralized implementation.

Distributed ranked search - Gopalakrishnan,V.; Morselli,R.; Bhattacharjee, Bobby; Keleher,P.; Srinivasan, Aravind (High Performance Computing–HiPC 2007, 2007)
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 results, not necessarily 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 decentralized setting. We analyze the overhead of our approach, and quantify 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 scale with little overhead to large systems, and b) the accuracy of the results obtained using distributed ranking is comparable to that of a centralized implementation.

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

EcoLens: Integration and interactive visualization of ecological datasets - Parr,Cynthia Sims; Lee,Bongshin; Bederson, Benjamin B. (Ecological Informatics, 2007)
Complex multi-dimensional datasets are now pervasive in science and elsewhere in society. Better interactive tools are needed for visual data exploration so that patterns in such data may be easily discovered, data can be proofread, and subsets of data can be chosen for algorithmic analysis. In particular, synthetic research such as ecological interaction research demands effective ways to examine multiple datasets. This paper describes our integration of hundreds of food-web datasets into a common platform, and the visualization software, EcoLens, we developed for exploring this information. This publicly-available application and integrated dataset have been useful for our research predicting large complex food webs, and EcoLens is favorably reviewed by other researchers. Many habitats are not well represented in our large database. We confirm earlier results about the small size and lack of taxonomic resolution in early food webs but find that they and a non-food-web source provide trophic information about a large number of taxa absent from more modern studies. Corroboration of Tuesday Lake trophic links across studies is usually possible, but lack of links among congeners may have several explanations. While EcoLens does not provide all kinds of analytical support, its label- and item-based approach is effective at addressing concerns about the comparability and taxonomic resolution of food-web data.
Keywords: Data integration; Food webs; Taxonomy; Visualization

Efficient Indexing For Articulation Invariant Shape Matching And Retrieval - Biswas,S.; Aggarwal,G.; Chellapa, Rama (Computer Vision and Pattern Recognition, 2007. CVPR '07. IEEE Conference on, 2007)
Most shape matching methods are either fast but too simplistic to give the desired performance or promising as far as performance is concerned but computationally demanding. In this paper, we present a very simple and efficient approach that not only performs almost as good as many state-of-the-art techniques but also scales up to large databases. In the proposed approach, each shape is indexed based on a variety of simple and easily computable features which are invariant to articulations and rigid transformations. The features characterize pairwise geometric relationships between interest points on the shape, thereby providing robustness to the approach. Shapes are retrieved using an efficient scheme which does not involve costly operations like shape-wise alignment or establishing correspondences. Even for a moderate size database of 1000 shapes, the retrieval process is several times faster than most techniques with similar performance. Extensive experimental results are presented to illustrate the advantages of our approach as compared to the best in the field.
Keywords: alignment; image; articulation; geometric; invariant; matching; image; matching; indexing; invariant; relationships; shape-wise; retrieval; indexing; retrieval; pairwise; SHAPE

Efficient lookup on unstructured topologies - Morselli,R.; Bhattacharjee, Bobby; Marsh,M.A.; Srinivasan, Aravind (IEEE Journal on Selected Areas in Communications, 2007)
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 LMS. 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: Computer science; DHT; distributed algorithms; Distributed computing; distributed hash table; Least squares approximation; LMS; local minima search; lookup protocol; Network topology; node failures; Peer to peer computing; Performance analysis; Protocols; replication strategy; Resilience; Robustness; table lookup; telecommunication network topology; unstructured network topology

Efficient parallel memory organization for turbo decoders - Salmela,P.; Gu,R.; Bhattacharyya, Shuvra S.; Takala,J. (Red, 2007)

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

Empirical studies to build a science of computer science - Basili, Victor R.; Zelkowitz, Marvin V (Communications of the ACM, 2007)
We learn to develop software by building, testing, and evolving models.

Energy-aware data compression for wireless sensor networks - Puthenpurayil,S.; Gu,R.; Bhattacharyya, Shuvra S. (Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on, 2007)

An energy-driven design methodology for distributing DSP applications across wireless sensor networks - Shen,C. C; Plishker,W.; Bhattacharyya, Shuvra S.; Goldsman,N. (Proceedings of RTSS, 2007)

An Environment of Conducting Families of Software Engineering Experiments - Hochstein, Lorin; Nakamura,Taiga; Shull, Forrest; Zazworka, Nico; Voelp,Martin; Zelkowitz, Marvin V; Basili, Victor R. (University of Maryland, College Park, 2007)
The classroom is a valuable resource for conducting software engineering experiments. However, coordinating a family of experiments in classroom environments presents a number of challenges to researchers. This paper describes an environment that simplifies the process of collecting, managing and sanitizing data from classroom experiments, while minimizing disruption to natural subject behavior. We have successfully used this environment to study the impact of parallel programming languages on programmer productivity at multiple universities across the United States.
Keywords: collecting data; managing data; parallel programming languages; sanitizing data; software engineering experiments; universities

Evolution of genes and genomes on the Drosophila phylogeny - Clark,Andrew G.; Eisen,Michael B.; Smith,Douglas R.; Bergman,Casey M.; Oliver,Brian; Markow,Therese A.; Kaufman,Thomas C.; Kellis,Manolis; Gelbart,William; Iyer,Venky N.; Pollard,Daniel A.; Sackton,Timothy B.; et al. (Nature, 2007)
Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Evolution of genes and genomes on the Drosophila phylogeny - Clark, A.G.; Eisen,M. B; Smith,D. R; Bergman, C.M.; Oliver, B.; Markow, T.A.; Kaufman, T.C.; Kellis, M.; Gelbart, W.; Iyer, V.N.; others (Nature, 2007)

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

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

Exploiting approximate transitivity of trust - Morselli,Ruggero; Bhattacharjee, Bobby; Katz, Jonathan; Marsh,Michael (Broadband Communications, Networks and Systems, 2007. BROADNETS 2007. Fourth International Conference on, 2007)
Social networks, of which webs of trust are a particular type, have been shown to be effective ways of moving information with minimal external configuration, setup, or management. For applications requiring information assurance, a web of trust is an appealing system architecture, since trust is an inherent component of both the network design and assurance. The trust in a typical web of trust is not transitive, however, making the construction of an application with strong assurance difficult or impossible. Instead, in this paper we examine a notion of weak assurance that can be provided by a web of trust, and might be #x201C;good enough #x201D; for many applications. As a motivating example, and to provide a more concrete basis for exposition, we present KeyChains, a peer-to-peer system that operates over a distributed web of trust to provide fully decentralized public key publishing and retrieval. In addition to weak assurance guarantees, KeyChains also provides an audit trail for public keys retrieved. Our analysis and simulations show that the resulting system is both efficient and secure.

A fast implementation of the ISODATA clustering algorithm - Memarsadeghi,N.; Mount, Dave; Netanyahu,N. S; Le Moigne,J.; de Berg,M. (International Journal of Computational Geometry and Applications, 2007)
Clustering is central to many image processing and remote sensing applications. isodatais one of the most popular and widely used clustering methods in geoscience applications, but it can run slowly, particularly with large data sets. We present a more efficient approach to isodata clustering, which achieves better running times by storing the points in a kd-tree and through a modification of the way in which the algorithm estimates the dispersion of each cluster. We also present an approximate version of the algorithm which allows the user to further improve the running time, at the expense of lower fidelity in computing the nearest cluster center to each point. We provide both theoretical and empirical justification that our modified approach produces clusterings that are very similar to those produced by the standard isodata approach. We also provide empirical studies on both synthetic data and remotely sensed Landsat and MODIS images that show that our approach has significantly lower running times.

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

Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses - Salzberg,Steven L.; Kingsford, Carl; Cattoli,Giovanni; Spiro,David J.; Janies,Daniel A.; Aly,Mona Mehrez; Brown,Ian H.; Couacy-Hymann,Emmanuel; De Mia,Gian Mario; Dung,Do Huu; Guercio,Annalisa; Joannis,Tony; et al. (Emerging Infectious DiseasesEmerg Infect Dis, 2007)
Although linked, these viruses are distinct from earlier outbreak strains., To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted.

Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex - Yang,Shuzhang; Wang,Kai; Valladares,Otto; Hannenhalli, Sridhar; Bucan,Maja (Genome Biology, 2007)
The prefrontal cortex is important in regulating sleep and mood. Diurnally regulated genes in the prefrontal cortex may be controlled by the circadian system, by sleep:wake states, or by cellular metabolism or environmental responses. Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances.

Geometrical algorithms for automated design of side actions in injection moulding of complex parts - Banerjee,Ashis Gopal; Gupta, Satyandra K. (Computer-Aided Design, 2007)
This paper describes algorithms for generating shapes of side actions to minimize a customizable injection moulding cost function. Given a set of undercut facets on a polyhedral part and the main mold opening directions, our approach works in the following manner: first, we compute candidate retraction space for every undercut facet. This space represents the set of candidate translation vectors that can be used by the side action to completely disengage from the undercut facet. As the next step, we generate a discrete set of feasible, nondominated retractions. Then we group the undercut facets into undercut regions by performing state space search over such retractions. This search step is performed by minimizing the given moulding cost function. After identifying the undercut regions, we generate the shapes of individual side actions. We believe that the results presented in this paper will provide the foundations for developing fully automated software for designing side actions.
Keywords: Configuration spaces; Geometrical reasoning; Mould design

Get Your Experience Factory Ready for the Next Decade–Ten Years after "How to Build and Run One" - Basili, Victor R.; Bomarius,Frank; Feldmann,Raimund L. (Companion to the proceedings of the 29th International Conference on Software Engineering, 2007)
This one-day tutorial aims at industry practitioners, managers and developers alike, who want to learn more about how to successfully design, implement and run an Experience Factory, to systematically build up and manage the experience of an organization. State-of- the art methods and techniques on how to initially set-up or to further develop and improve an organization's Experience Factory are discussed. Participants should come from organizations (not only from the software domain) that are interested in implementing an Experience Factory to help effectively support improvement activities (such as TQM, ISO 9000, CMMI, SPICE, or TSP) to gain competitive advantages.

Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services - Bazinet,A. L; Myers,D. S; Fuetsch,J.; Cummings, Michael P. (Future Generation Comp Syst, 2007)
The Grid Services Base Library (GSBL) is a procedural application programming interface (API) that abstracts many of the high-level functions performed by Globus Grid services, thus dramatically lowering the barriers to writing Grid services. The library has been extensively tested and used for computational biology research in a Globus Toolkit-based Grid system, in which no fewer than twenty Grid services written with this API are deployed.

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

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

Holding the Internet Accountable - Andersen,David; Balakrishnan,Hari; Feamster, Nick; Koponen,Teemu; Moon,Daekyong; Shenker,Scott (Proc. 6th ACM Workshop on Hot Topics in Networks (Hotnets-VI), 2007)
Today’s IP network layer provides little to no protection against misconfiguration or malice. Despite some progress in improving the robustness and security of the IP layer, misconfigurations and attacks still occur frequently. We show how a network layer that provides accountability, i.e., the ability to associate each action with the responsible entity, provides a firm foundation for defenses against misconfiguration and malice. We present the design of a network layer that incorporates accountability called AIP (Accountable Internet Protocol) and show how its features—notably, its use of self-certifying addresses— can improve both source accountability (the ability to trace actions to a particular end host and stop that host from misbehaving) and control-plane accountability (the ability to pinpoint and prevent attacks on routing).

Human Values for Shaping the Made World - Shneiderman, Ben (Human-Computer Interaction – INTERACT 2007Human-Computer Interaction – INTERACT 2007, 2007)
Interface design principles have been effective in shaping new desktop applications, web-based resources, and mobile devices. Usability and sociability promote successful online communities and social network services. The contributions of human-computer interaction researchers have been effective in raising the quality of design of many products and services. As our influence grows, we can play an even more profound role in guaranteeing that enduring human values are embedded in the next generation of technology. This talk identifies which goals are realistic, such as universality, responsibility, trust, empathy, and privacy, and how we might ensure that they become part of future services and systems.

Hybrid Detectors for Subpixel Targets - Broadwater, J.; Chellapa, Rama (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2007)
Subpixel detection is a challenging problem in hyperspectral imagery analysis. Since the target size is smaller than the size of a pixel, detection algorithms must rely solely on spectral information. A number of different algorithms have been developed over the years to accomplish this task, but most detectors have taken either a purely statistical or a physics-based approach to the problem. We present two new hybrid detectors that take advantage of these approaches by modeling the background using both physics and statistics. Results demonstrate improved performance over the well-known AMSD and ACE subpixel algorithms in experiments that include multiple targets, images, and area types - especially when dealing with weak targets in complex backgrounds.
Keywords: ACE subpixel algorithm; AMSD subpixel algorithm; hybrid detectors; hyperspectral imagery analysis; physics; statistics; subpixel target detection; subspace detection; object detection; spectral analysis; statistical analysis; target tracking; Algorithms; Artificial In; Automated; Reproducibility of Results; Sensitivity and Specificity; Signal Processing; Computer-Assisted; Computer-Assisted; Models; Computer-Assisted; Pattern Recognition; Statistical; Image Enhancement; Image Interpretation; Statistical; Numerical Analysis

Implications of Autonomy for the Expressiveness of Policy Routing - Feamster, Nick; Johari,R.; Balakrishnan,H. (Networking, IEEE/ACM Transactions on, 2007)
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 in the 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 ldquonext-hop rankings,rdquo 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 imposes strong restrictions on the rankings ASes are allowed to choose. We discuss the implications of these results for the future of interdomain routing.
Keywords: autonomous systems; global Internet connectivity; interdomain routing system; Internet; next-hop rankings; routing protocol; routing protocols; routing stability; stable path assignment

Incorporating manufacturability considerations during design of injection molded multi-material objects - Banerjee,Ashis; Li,Xuejun; Fowler,Greg; Gupta, Satyandra K. (Research in Engineering Design, 2007)
The presence of an already molded component during the second and subsequent molding stages makes multi-material injection molding different from traditional injection molding process. Therefore, designing multi-material molded objects requires addressing many additional manufacturability considerations. In this paper, we first present an approach to systematically identifying potential manufacturability problems that are unique to the multi-material molding processes and design rules to avoid these problems. Then we present a comprehensive manufacturability analysis approach that incorporates both the traditional single material molding rules as well as the specific rules that have been identified for multi-material molding. Our analysis shows that sometimes the traditional rules need to be suppressed or modified. Lastly, for each of the new manufacturability problem, this paper describes algorithms for automatically detecting potential occurrences and generating redesign suggestions. These algorithms have been implemented in a computer-aided manufacturability analysis system. The approach presented in this paper is applicable to multi-shot and over molding processes. We expect that the manufacturability analysis techniques presented in this paper will help in decreasing the product development time for the injection molded multi-material objects.
Keywords: engineering

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

Kernel fully constrained least squares abundance estimates - Broadwater, J.; Chellapa, Rama; Banerjee, A.; Burlina, P. (Geoscience and Remote Sensing Symposium, 2007. IGARSS 2007. IEEE International, 2007)
A critical step for fitting a linear mixing model to hyperspectral imagery is the estimation of the abundances. The abundances are the percentage of each end member within a given pixel; therefore, they should be non-negative and sum to one. With the advent of kernel based algorithms for hyperspectral imagery, kernel based abundance estimates have become necessary. This paper presents such an algorithm that estimates the abundances in the kernel feature space while maintaining the non-negativity and sum-to-one constraints. The usefulness of the algorithm is shown using the AVIRIS Cuprite, Nevada image.
Keywords: abundance; algorithm; kernel; analysis; AVIRIS; based; constrained; constraint; feature; constraint; spectral; estimates; linear; extraction; geophysical; feature; fully; image; hyperspectral; imagery; kernel; least; mixing; model; nonnegativity; processing; geophysical; processing; multidimensional; processing; spectral; signal; space; kernel; squares; techniques; image; unmixing; sum-to-one

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

Layout-Accurate Design and Implementation of a High-Throughput Interconnection Network for Single-Chip Parallel Processing - Balkan,A.O.; Horak,M.N.; Gang Qu; Vishkin, Uzi (High-Performance Interconnects, 2007. HOTI 2007. 15th Annual IEEE Symposium on, 2007)
A mesh of trees (MoT) on-chip interconnection network has been proposed recently to provide high throughput between memory units and processors for single-chip parallel processing (Balkan et al., 2006). In this paper, we report our findings in bringing this concept to silicon. Specifically, we conduct cycle-accurate Verilog simulations to verify the analytical results claimed in (Balkan et al., 2006). We synthesize and obtain the layout of the MoT interconnection networks of various sizes. To further improve throughput, we investigate different arbitration primitives to handle load and store, the two most common memory operations. We also study the use of pipeline registers in large networks when there are long wires. Simulation based on full network layout demonstrates that significant throughput improvement can be achieved over the original proposed MoT interconnection network. The importance of this work lies in its validation of performance features of the MoT interconnection network, as they were previously shown to be competitive with traditional network solutions. The MoT network is currently used in an eXplicit multi-threading (XMT) on-chip parallel processor, which is engineered to support parallel programming. In that context, a 32-terminal MoT network could support up to 512 on-chip XMT processors. Our 8-terminal network that could serve 8 processor clusters (or 128 total processors), was also accepted recently for fabrication.
Keywords: description; design; mesh; interconnection; languages; multi-threading; multiprocessor; MoT; multi-threading; layout-accurate; network; on-chip; network; Verilog; networks; parallel; of; on-chip; Parallel; processing; processing; hardware; processor; parallel; processors; on-chip; programming; pipeline; registers; single-chip; simulations; eXplicit; TREES; XMT

Local strategy learning in networked multi-agent team formation - Bulka,Blazej; Gaston,Matthew; desJardins, Marie (Autonomous Agents and Multi-Agent Systems, 2007)
Networked multi-agent systems are comprised of many autonomous yet interdependent agents situated in a virtual social network. Two examples of such systems are supply chain networks and sensor networks. A common challenge in many networked multi-agent systems is decentralized team formation among the spatially and logically extended agents. Even in cooperative multi-agent systems, efficient team formation is made difficult by the limited local information available to the individual agents. We present a model of distributed multi-agent team formation in networked multi-agent systems, describe a policy learning framework for joining teams based on local information, and give empirical results on improving team formation performance. In particular, we show that local policy learning from limited information leads to a significant increase in organizational team formation performance compared to a random policy.

Low-overhead run-time scheduling for fine-grained acceleration of signal processing systems - Boutellier,J.; Bhattacharyya, Shuvra S.; Silvén,O. (Signal Processing Systems, 2007 IEEE Workshop on, 2007)

Measurement and analysis of online social networks - Mislove,Alan; Marcon,Massimiliano; Gummadi,Krishna P.; Druschel,Peter; Bhattacharjee, Bobby (Proceedings of the 7th ACM SIGCOMM conference on Internet measurement, 2007)
Online social networking sites like Orkut, YouTube, and Flickr are among the most popular sites on the Internet. Users of these sites form a social network, which provides a powerful means of sharing, organizing, and finding content and contacts. The popularity of these sites provides an opportunity to study the characteristics of online social network graphs at large scale. Understanding these graphs is important, both to improve current systems and to design new applications of online social networks. This paper presents a large-scale measurement study and analysis of the structure of multiple online social networks. We examine data gathered from four popular online social networks: Flickr, YouTube, LiveJournal, and Orkut. We crawled the publicly accessible user links on each site, obtaining a large portion of each social network's graph. Our data set contains over 11.3 million users and 328 million links. We believe that this is the first study to examine multiple online social networks at scale. Our results confirm the power-law, small-world, and scale-free properties of online social networks. We observe that the indegree of user nodes tends to match the outdegree; that the networks contain a densely connected core of high-degree nodes; and that this core links small groups of strongly clustered, low-degree nodes at the fringes of the network. Finally, we discuss the implications of these structural properties for the design of social network based systems.
Keywords: analysis; measurement; social networks

Multi-Dimensional Range Query over Encrypted Data - Elaine Shi; Bethencourt, J.; Chan, T.-H.H.; Song, Dawn; Perrig, A. (2007)
We design an encryption scheme called multi-dimensional range query over encrypted data (MRQED), to address the privacy concerns related to the sharing of network audit logs and various other applications. Our scheme allows a network gateway to encrypt summaries of network flows before submitting them to an untrusted repository. When network intrusions are suspected, an authority can release a key to an auditor, allowing the auditor to decrypt flows whose attributes (e.g., source and destination addresses, port numbers, etc.) fall within specific ranges. However, the privacy of all irrelevant flows are still preserved. We formally define the security for MRQED and prove the security of our construction under the decision bilinear Diffie-Hellman and decision linear assumptions in certain bilinear groups. We study the practical performance of our construction in the context of network audit logs. Apart from network audit logs, our scheme also has interesting applications for financial audit logs, medical privacy, untrusted remote storage, etc. In particular, we show that MRQED implies a solution to its dual problem, which enables investors to trade stocks through a broker in a privacy-preserving manner.
Keywords: auditing; cryptography; data privacy; decision bilinear Diffie-Hellman; decision linear assumptions; encrypted data; multi-dimensional range query; network audit logs; network gateway; network intrusions

Mutatis Mutandis: Safe and predictable dynamic software updating - Stoyle,Gareth; Hicks, Michael W.; Bierman,Gavin; Sewell,Peter; Neamtiu,Iulian (ACM Trans. Program. Lang. Syst., 2007)
This article presents Proteus, a core calculus that models dynamic software updating, a service for fixing bugs and adding features to a running program. Proteus permits a program's type structure to change dynamically but guarantees the updated program remains type-correct by ensuring a property we call con-freeness. We show how con-freeness can be enforced dynamically, and how it can be approximated via a novel static analysis. This analysis can be used to assess the implications of a program's structure on future updates in order to make update success more predictable. We have implemented Proteus for C, and briefly discuss our implementation which we have tested on several well-known programs.
Keywords: capability; dynamic software updating; proteus; Type inference; updateability analysis

NetLens: Iterative Exploration of Content-Actor Network Data - Kang,Hyunmo; Plaisant, Catherine; Lee,Bongshin; Bederson, Benjamin B. (Information VisualizationInformation Visualization, 2007)
Networks have remained a challenge for information retrieval and visualization because of the rich set of tasks that users want to accomplish. This paper offers an abstract Content-Actor network data model, a classification of tasks, and a tool to support them. The NetLens interface was designed around the abstract Content-Actor network data model to allow users to pose a series of elementary queries and iteratively refine visual overviews and sorted lists. This enables the support of complex queries that are traditionally hard to specify. NetLens is general and scalable in that it applies to any data set that can be represented with our abstract data model. This paper describes the use of NetLens with a subset of the ACM Digital Library consisting of about 4000 papers from the CHI conference written by about 6000 authors, and reports on a usability study with nine participants.
Keywords: content-actor network data; digital library; incremental data exploration; iterative query refinement; User interfaces

NetLens: iterative exploration of content-actor network data - Kang,H.; Plaisant, Catherine; Lee,B.; Bederson, Benjamin B. (Information Visualization, 2007)

New records of phytoplankton for Bangladesh. 3. Volvocales - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasmin,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Plant Taxonomy, 2007)
This study presents 21 species of Chlamydomonas, four species of Carteria, two species of each of Nephroselmis, Pyramidomonas and Scherffelia, and Collodictyon triciliatum, Polytoma minus, Tetrachloridium ? allorgei and Tetraselmis cordiformis. These species have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal districts in Bangladesh.

New records of phytoplankton for Bangladesh. 4. Chlorococcales - Khondker,Moniruzzaman; Bhuiyan,Rauf Ahmed; Yeasim,Jenat; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Bangladesh Journal of Plant Taxonomy, 2007)
This study presents three species from each of Schroederia, Monoraphidium and Ankistrodesmus, two species and one variety of Dictyosphaerium, two varieties of Pediastrum, and Tetraedron arthrodesmiforme var. contorta, Chlorotetraedron polymorphum, Myrmecia aquatica, Oocystis tainoensis, Nephrocytium spirale, Kirchneriella irregularis, Coelastrum indicum and Scenedesmus similagineus. These taxa have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal Districts in Bangladesh.

Object recognition using linear subspaces - Jacobs, David W.; Basri,Ronen The Weizmann Institute (2007)
Abstract of EP1204069A method for choosing an image from a plurality of three-dimensional models which is most similar to an input image is provided. The method includes the steps of: (a) providing a database of the plurality of three-dimensional models; (b) providing an input image; (c) positioning each three-dimensional model relative to the input image; (d) for each three-dimensional model, determining a rendered image that is most similar to the input image by: (d)(i) computing a linear subspace that describes an approximation to the set of all possible rendered images that each three-dimensional model can produce under all possible lighting conditions where each point in the linear subspace represents a possible image; and one of(d)(ii) finding the point on the linear subspace that is closest to the input image or finding a rendered image in a subset of the linear subspace obtained by projecting the set of images that are generated by positive lights onto the linear subspace; (e) computing a measure of similarly between the input image and each rendered image; and (f) selecting the three-dimensional model corresponding to the rendered image whose measure of similarity is most similar to the input image. Step (d) is preferably repeated for each of a red, green, and blue color component for each three-dimensional model. The linear subspace is preferably either four-dimensional or nine-dimensional.

Online collective entity resolution - Bhattacharya,I.; Getoor, Lise (PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE, 2007)
Entity resolution is a critical component of data integration where the goal is to reconcile database references correspond- ing to the same real-world entities. Given the abundance of publicly available databases that have unresolved entities, we motivate the problem of quick and accurate resolution for an- swering queries over such ‘unclean’ databases. Since collec- tive entity resolution approaches — where related references are resolved jointly — have been shown to be more accu- rate than independent attribute-based resolution, we focus on adapting collective resolution for answering queries. We pro- pose 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 pre- serving the gains of collective resolution. This work extends work presented in (Bhattacharya, Licamele, & Getoor 2006).

Parameterized Looped Schedules for Compact Representation of Execution Sequences in DSP Hardware and Software Implementation - Ming-Yung Ko; Zissulescu,C.; Puthenpurayil,S.; Bhattacharyya, Shuvra S.; Kienhuis,B.; Deprettere,E. F (IEEE Transactions on Signal Processing, 2007)
In this paper, we present a technique for compact representation of execution sequences in terms of efficient looping constructs. Here, by a looping construct, we mean a compact way of specifying a finite repetition of a set of execution primitives. Such compaction, which can be viewed as a form of hierarchical run-length encoding (RLE), has application in many very large scale integration (VLSI) signal processing contexts, including efficient control generation for Kahn processes on field-programmable gate arrays (FPGAs), and software synthesis for static dataflow models of computation. In this paper, we significantly generalize previous models for loop-based code compaction of digital signal processing (DSP) programs to yield a configurable code compression methodology that exhibits a broad range of achievable tradeoffs. Specifically, we formally develop and apply to DSP hardware and software synthesis a parameterizable loop scheduling approach with compact format, dynamic reconfigurability, and low-overhead decompression
Keywords: Application software; array signal processing; code compression methodology; compact representation; Compaction; data compression; Design automation; Digital signal processing; digital signal processing chips; DSP; DSP hardware; embedded systems; Encoding; Field programmable gate arrays; field-programmable gate arrays (FPGAs); FPGA; Hardware; hierarchical runlength encoding; high-level synthesis; Kahn process; loop-based code compaction; looping construct; parameterized loop schedules; program compilers; reconfigurable design; runlength codes; scheduling; Signal generators; Signal processing; Signal synthesis; software engineering; software implementation; static dataflow models; Very large scale integration; VLSI

Photometric stereo with general, unknown lighting - Basri,R.; Jacobs, David W.; Kemelmacher,I. (International Journal of Computer Vision, 2007)
Work on photometric stereo has shown how to recover the shape and reflectance properties of an object using multiple images taken with a fixed viewpoint and variable lighting conditions. This work has primarily relied on known lighting conditions or the presence of a single point source of light in each image. In this paper we show how to perform photometric stereo assuming that all lights in a scene are distant from the object but otherwise unconstrained. Lighting in each image may be an unknown and may include arbitrary combination of diffuse, point and extended sources. Our work is based on recent results showing that for Lambertian objects, general lighting conditions can be represented using low order spherical harmonics. Using this representation we can recover shape by performing a simple optimization in a low-dimensional space. We also analyze the shape ambiguities that arise in such a representation. We demonstrate our method by reconstructing the shape of objects from images obtained under a variety of lightings. We further compare the reconstructed shapes against shapes obtained with a laser scanner.

Probabilistic design of multimedia embedded systems - Hua,S.; Qu,G.; Bhattacharyya, Shuvra S. (ACM Transactions on Embedded Computing Systems (TECS), 2007)

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

Protocols in the use of empirical software engineering artifacts - Basili, Victor R.; Zelkowitz, Marvin V; Sjøberg,D. I.K; Johnson,P.; Cowling,A. J (Empirical Software EngineeringEmpirical Software Engineering, 2007)
If empirical software engineering is to grow as a valid scientific endeavor, the ability to acquire, use, share, and compare data collected from a variety of sources must be encouraged. This is necessary to validate the formal models being developed within computer science. However, within the empirical software engineering community this has not been easily accomplished. This paper analyses experiences from a number of projects, and defines the issues, which include the following: (1) How should data, testbeds, and artifacts be shared? (2) What limits should be placed on who can use them and how? How does one limit potential misuse? (3) What is the appropriate way to credit the organization and individual that spent the effort collecting the data, developing the testbed, and building the artifact? (4) Once shared, who owns the evolved asset? As a solution to these issues, the paper proposes a framework for an empirical software engineering artifact agreement. Such an agreement is intended to address the needs for both creator and user of such artifacts and should foster a market in making available and using such artifacts. If this framework for sharing software engineering artifacts is commonly accepted, it should encourage artifact owners to make the artifacts accessible to others (gaining credit is more likely and misuse is less likely). It may be easier for other researchers to request artifacts since there will be a well-defined protocol for how to deal with relevant matters.

PUTOP: turning predominant senses into a topic model for word sense disambiguation - Jordan Boyd-Graber; Blei,David (Proceedings of the 4th International Workshop on Semantic Evaluations, 2007)
We extend on McCarthy et al.'s predominant sense method to create an unsupervised method of word sense disambiguation that uses automatically derived topics using Latent Dirichlet allocation. Using topic-specific synset similarity measures, we create predictions for each word in each document using only word frequency information. It is hoped that this procedure can improve upon the method for larger numbers of topics by providing more relevant training corpora for the individual topics. This method is evaluated on SemEval-2007 Task 1 and Task 17.

Report on the Fourth International Workshop on Data Management for Sensor Networks (DMSN 2007) - Balazinska,Magdalena; Deshpande, Amol; Labrinidis,Alexandros; Luo,Qiong; Madden,Samuel; Yang,Jun (SIGMOD Rec., 2007)
Sensor networks enable an unprecedented level of access to the physical world, and hold tremendous potential to revolutionize many application domains. Research on sensor networks spans many areas of computer science, and there are now major conferences, e.g., IPSN and SenSys, devoted to sensor networks. However, there is no focused forum for discussion of early and innovative work on data management in sensor networks. The International Workshop on Data Management for Sensor Networks (DMSN), inaugurated in 2004, aims to fill this significant gap in the database and sensor network communities.

Robust Routing with Unknown Traffic Matrices - Tabatabaee,V.; Kashyap,A.; Bhattacharjee, Bobby; La,R.J.; Shayman,M.A. (INFOCOM 2007. 26th IEEE International Conference on Computer Communications. IEEE, 2007)
In this paper, we present an algorithm for intra-domain traffic engineering. We assume that the traffic matrix, which specifies traffic load between every source-destination pair in the network, is unknown and varies with time, but that always lies inside an explicitly defined region. Our goal is to compute a fixed robust routing with best worst case performance for all traffic matrices inside the bounding region. We formulate this problem as a semi-infinite programming problem. Then, we focus on a special case with practical merits, where (1) the traffic matrix region is assumed to be a polytope specified by a finite set of linear inequalities, and (2) our objective is to find the routing that minimizes the maximum link utilization. Under these assumptions, the problem can be formulated as a polynomial size linear programming (LP) problem with finite number of constraints. We further consider two specific set of constraints for the traffic matrix region. The first set is based on the hose model and limits the total traffic rate of network point of presence (PoP) nodes. The second set is based on the pipe model and limits the traffic between source-destination pairs. We study the effectiveness of each set of constraints using extensive simulations.
Keywords: engineering; linear; inequalities; maximum; intradomain; linear; link; matrices; linear; matrix; network; nodes; polynomial; of; point; presence; problem; traffic; Programming; programming; semiinfinite; programming; telecommunication; region; unknown; routing; telecommunication; size; traffic; traffic; utilization; network

SAAR: A shared control plane for overlay multicast - Nandi,A.; Ganjam,A.; Druschel,P.; Ng,T. S.E; Stoica,I.; Zhang,H.; Bhattacharjee, Bobby (Proceedings of 4th USENIX Symposium on Networked Systems Design & Implementation, 2007)
Many cooperative overlay multicast systems of diverse designs have been implemented and deployed. In this paper, we explore a new architecture for overlay multicast: we factor out the control plane into a separate overlay that provides a single primitive: a configurable anycast for peer selection. This separation of control and data overlays has several advantages. Data overlays can be optimized for efficient content delivery, while the control overlay can be optimized for flexible and efficient peer selection. Several data channels can share a control plane for fast switching among content channels, which is particularly important for IPTV. And, the control overlay can be reused in multicast systems with different data plane organizations.We designed and evaluated a decentralized control overlay for endsystem multicast. The overlay proactively aggregates system state and implements a powerful anycast primitive for peer selection. We demonstrate that SAAR's efficiency in locating peers reduces channel switching time, improves the quality of content delivery, and reduces overhead, even under dynamic conditions and at scale. An experimental evaluation demonstrates that the system can efficiently support single-tree, multi-tree and block-based multicast systems.

Schistosoma mansoni genome: Closing in on a final gene set - Haas,Brian J.; Berriman,Matthew; Hirai,Hirohisa; Cerqueira,Gustavo G.; LoVerde,Philip T.; El‐Sayed, Najib M. (Experimental Parasitology, 2007)
The Schistosoma mansoni genome sequencing consortium has recently released the latest versions of the genome assembly as well as an automated preliminary gene structure annotation. The combined datasets constitute a vast resource for researchers to exploit in a variety of post-genomic studies with an emphasis of transcriptomic and proteomic tools. Here we present an innovative method used for combining diverse sources of evidence including ab initio gene predictions, protein and transcript sequence homologies, and cross-genome sequence homologies between S. mansoni and Schistosoma japonicum to define a comprehensive list of protein-coding genes.
Keywords: Annotation; Gene finding; Genome; Schistosoma mansoni

A Secure DHT via the Pigeonhole Principle - Baden,Randy; Bender,Adam; Levin,Dave; Sherwood,Rob; Spring, Neil; Bhattacharjee, Bobby (Technical Reports of the Computer Science Department, CS-TR-4884, 2007)
The standard Byzantine attack model assumes no more than some fixedfraction of the participants are faulty. This assumption does not accurately apply to peer-to-peer settings, where Sybil attacks and botnets are realistic threats. We propose an attack model that permits an arbitrary number of malicious nodes under the assumption that each node can be classified based on some of its attributes, such as autonomous system number or operating system, and that the number of classes with malicious nodes is bounded (e.g., an attacker may exploit at most a few operating systems at a time). In this model, we present a secure DHT, evilTwin, which replaces a single, large DHT with sufficiently many smaller instances such that it is impossible for an adversary to corrupt every instance. Our system ensures high availability and low-latency lookups, is easy to implement, does not require a complex Byzantine agreement protocol, and its proof of security is a straightforward application of the pigeonhole principle. The cost of security comes in the form of increased storage and bandwidth overhead; we show how to reduce these costs by replicating data and adaptively querying participants who historically perform well. We use implementation and simulation to show that evilTwin imposes a relatively small additional cost compared to conventional DHTs.
Keywords: Technical Report

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

Semantics-Preserving Design of Embedded Control Software from Synchronous Models - Mangeruca,L.; Baleani,M.; Ferrari,A.; Sangiovanni-Vincentelli,A. (Software Engineering, IEEE Transactions on, 2007)
The design of embedded controllers is experiencing a growth in complexity as embedded systems increase their functionality while they become ubiquitous in electronic appliances, cars, airplanes, etc. As requirements become more challenging, mathematical models gain importance for mastering complexity. Among the different computational models proposed, synchronous models have proved to be the most widely used for control dominated applications. While synchronous models simplify the way of dealing with concurrency by decoupling functional and timing aspects, their software implementation on multitasking and multiprocessor platforms is far from straightforward, because of the asynchronous nature of most industrial software platforms. Known solutions in the literature either restrict the solution space or focus on special cases. We present a method for preserving the synchronous semantics through buffer-based intertask communication mechanisms, grounded on an abstraction of the target platform. This allows us to deal with any task set and, most importantly, being independent of the implementation, to explore the design space effectively.
Keywords: embedded control software; embedded systems; multiprocessing programs; multiprocessor; multitasking; semantics-preserving design; software engineering; software implementation; systems analysis

Semi-automatic photo annotation strategies using event based clustering and clothing based person recognition - Suh,B.; Bederson, Benjamin B. (Interacting with Computers, 2007)

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

Similarity-Based Forecasting with Simultaneous Previews: A River Plot Interface for Time Series Forecasting - Buono,P.; Plaisant, Catherine; Simeone,A.; Aris,A.; Shneiderman, Ben; Shmueli,G.; Jank,W. (Information Visualization, 2007. IV '07. 11th International Conference, 2007)
Time-series forecasting has a large number of applications. Users with a partial time series for auctions, new stock offerings, or industrial processes desire estimates of the future behavior. We present a data driven forecasting method and interface called similarity-based forecasting (SBF). A pattern matching search in an historical time series dataset produces a subset of curves similar to the partial time series. The forecast is displayed graphically as a river plot showing statistical information about the SBF subset. A forecasting preview interface allows users to interactively explore alternative pattern matching parameters and see multiple forecasts simultaneously. User testing with 8 users demonstrated advantages and led to improvements.
Keywords: data driven forecasting method; data visualisation; Data visualization; Economic forecasting; forecasting preview interface; Graphical user interfaces; historical time series dataset; Laboratories; new stock offerings; partial time series; pattern matching; pattern matching search; Predictive models; river plot interface; Rivers; similarity-based forecasting; Smoothing methods; Technological innovation; Testing; time series; time series forecasting; Weather forecasting

Stochastic Communication: A New Paradigm for Fault-Tolerant Networks-on-Chip - Bogdan, Paul; Dumitraş Tudor; Marculescu, Radu (VLSI Design, 2007)
As CMOS technology scales down into the deep-submicron (DSM) domain, the costs of design and verification for Systems-on-Chip (SoCs) are rapidly increasing. Relaxing the requirement of 100% correctness for devices and interconnects drastically reduces the costs of design but, at the same time, requires SoCs to be designed with some degree of system-level fault-tolerance. Towards this end, this paper introduces a novel communication paradigm for SoCs, called stochastic communication. This scheme separates communication from computation by allowing the on-chip interconnect to be designed as a reusable IP and also provides a built-in tolerance to DSM failures, without a significant performance penalty. By using this communication scheme, a large percentage of data upsets, packet losses due to buffers overflow, and severe levels of synchronization failures can be tolerated, while providing high levels of performance.

Supporting elementary-age children's searching and browsing: Design and evaluation using the international children's digital library - Hutchinson,H.B.; Druin, Allison; Bederson, Benjamin B. (Journal of the American Society for Information Science and Technology, 2007)

Symmetric Objects are Hardly Ambiguous - Aggarwal,G.; Biswas,S.; Chellapa, Rama (Computer Vision and Pattern Recognition, 2007. CVPR '07. IEEE Conference on, 2007)
Given any two images taken under different illumination conditions, there always exist a physically realizable object which is consistent with both the images even if the lighting in each scene is constrained to be a known point light source at infinity. In this paper, we show that images are much less ambiguous for the class of bilaterally symmetric Lambertian objects. In fact, the set of such objects can be partitioned into equivalence classes such that it is always possible to distinguish between two objects belonging to different equivalence classes using just one image per object. The conditions required for two objects to belong to the same equivalence class are very restrictive, thereby leading to the conclusion that images of symmetric objects are hardly ambiguous. The observation leads to an illumination-invariant matching algorithm to compare images of bilaterally symmetric Lambertian objects. Experiments on real data are performed to show the implications of the theoretical result even when the symmetry and Lambertian assumptions are not strictly satisfied.
Keywords: algorithm; symmetric; bilaterally; images; image; Lambertian; MATCHING; matching; objects; objects; illumination-invariant; objects; symmetric; symmetric

A taxonomy for medical image registration acceleration techniques - Plishker,W.; Dandekar,O.; Bhattacharyya, Shuvra S.; Shekhar,R. (Life Science Systems and Applications Workshop, 2007. LISA 2007. IEEE/NIH, 2007)

Test suite prioritization by interaction coverage - Bryce,Renée C.; Memon, Atif M. (Workshop on Domain specific approaches to software test automation: in conjunction with the 6th ESEC/FSE joint meeting, 2007)
Event-driven software (EDS) is a widely used class of software that takes sequences of events as input, changes state, and outputs new event sequences. Managing the size of tests suites for EDS is difficult as the number of event combinations and sequences grow exponentially with the number of events. We propose a new testing technique that extends software interaction testing. Traditional software interaction testing systematically examines all t-way interactions of parameters for a program. This paper extends the notion to t-way interactions over sequences of events. The technique applies to many classes of software; we focus on that of EDS. As a proof-of-concept, we prioritize existing test suites for four GUI-based programs by t-way interaction coverage. We compare the rate of fault detection with that of several other prioritization criteria. Results show that prioritization by interaction coverage has the fastest rate of fault detection in half of our experiments, making the most impact when tests have high interaction coverage.
Keywords: t-way interaction coverage; combinatorial interaction testing; covering arrays; event driven software; test suite prioritization

Thumbspace: Generalized one-handed input for touchscreen-based mobile devices - Karlson,A.K.; Bederson, Benjamin B. (Proceedings of the 11th IFIP TC 13 international conference on Human-computer interaction, 2007)

A topic model for word sense disambiguation - Jordan Boyd-Graber; Blei,D.; Zhu,X. (Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL), 2007)

Towards a heterogeneous medical image registration acceleration platform - Plishker,W.; Dandekar,O.; Bhattacharyya, Shuvra S.; Shekhar,R. (Biomedical Circuits and Systems Conference, 2007. BIOCAS 2007. IEEE, 2007)

Towards the development of a virtual environment-based training system for mechanical assembly operations - Brough,John; Schwartz,Maxim; Gupta, Satyandra K.; Anand,Davinder; Kavetsky,Robert; Pettersen,Ralph (Virtual Reality, 2007)
In this paper, we discuss the development of Virtual Training Studio (VTS), a virtual environment-based training system that allows training supervisors to create training instructions and allows trainees to learn assembly operations in a virtual environment. Our system is mainly focused on the cognitive side of training so that trainees can learn to recognize parts, remember assembly sequences, and correctly orient the parts during assembly operations. Our system enables users to train using the following three training modes: (1) Interactive Simulation, (2) 3D Animation, and (3) Video. Implementing these training modes required us to develop several new system features. This paper presents an overview of the VTS system and describes a few main features of the system. We also report user test results that show how people train using our system. The user test results indicate that the system is able to support a wide variety of training preferences and works well to support training for assembly operations.
Keywords: Computer science

Using Content-Addressable Networks for Load Balancing in Desktop Grids - Kim,Jik-Soo; Keleher,Peter; Marsh,Michael; Bhattacharjee, Bobby; Sussman, Alan (Instititue for Advanced Computer Studies, Univ of Maryland, College Park, 2007)
Desktop grids combine Peer-to-Peer and Grid computing techniques to improvethe robustness, reliability and scalability of job execution infrastructures. However, efficiently matching incoming jobs to available system resources and achieving good load balance in a fully decentralized and heterogeneous computing environment is a challenging problem. In this paper, we extend our prior work with a new decentralized algorithm for maintaining approximate global load information, and a job pushing mechanism that uses the global information to push jobs towards underutilized portions of the system. The resulting system more effectively balances load and improves overall system throughput. Through a comparative analysis of experimental results across different system configurations and job profiles, performed via simulation, we show that our system can reliably execute Grid applications on a distributed set of resources both with low cost and with good load balance.
Keywords: Technical Report

Using virtual demonstrations for creating multi-media training instructions - Schwartz,M.; Gupta,S.K.; Anand,D. K.; Brough,J. E.; Kavetsky,R. (2007)
Often generating training instructions for virtual environments is a long and tedious process. In thispaper, we discuss the development of a virtual environment (VE) instruction generating tool called Virtual Author which is the main component of the Virtual Training Studio (VTS). VTS is a virtual environment-based training system that provides instructors with a tool to create training instructions and allows trainees to learn assembly operations in a personal virtual environment. The Virtual Author tool is designed to allow an instructor to perform virtual demonstrations using CAD models in the virtual environment in order to quickly generate VE-based training instructions for use in VTS. This paper describes the algorithms used to carry out motion smoothening of instructor’s actions, automated text instruction generation based on part and assembly motions, and extraction of alignment constraints from 3D CAD models to support instruction generation. We also present examples to illustrate how the use of the Virtual Author tool leads to a significant reduction in the training instruction generation time.

Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes - Minkah,Nana; Hwang,Young; Perry,Kay; Van Duyne,Gregory D.; Hendrickson,Robert; Lefkowitz,Elliot J.; Hannenhalli, Sridhar; Bushman,Frederic D. (Virology, 2007)
Topoisomerase enzymes regulate superhelical tension in DNA resulting from transcription, replication, repair, and other molecular transactions. Poxviruses encode an unusual type IB topoisomerase that acts only at conserved DNA sequences containing the core pentanucleotide 5'-(T/C)CCTT-3'. In X-ray structures of the variola virus topoisomerase bound to DNA, protein-DNA contacts were found to extend beyond the core pentanucleotide, indicating that the full recognition site has not yet been fully defined in functional studies. Here we report quantitation of DNA cleavage rates for an optimized 13 bp site and for all possible single base substitutions (40 total sites), with the goals of understanding the molecular mechanism of recognition and mapping topoisomerase sites in poxvirus genome sequences. The data allow a precise definition of enzyme-DNA interactions and the energetic contributions of each. We then used the resulting "action matrix" to show that favorable topoisomerase sites are distributed all along the length of poxvirus DNA sequences, consistent with a requirement for local release of superhelical tension in constrained topological domains. In orthopox genomes, an additional central cluster of sites was also evident. A negative correlation of predicted topoisomerase sites was seen relative to early terminators, but no correlation was seen with early or late promoters. These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo.
Keywords: Annotation of topoisomerase sites; Sequence specific recognition; Topoisomerase IB; Variola virus

Visual Mining of Multi-Modal Social Networks at Different Abstraction Levels - Singh,L.; Beard,M.; Getoor, Lise; Blake,M.B. (Information Visualization, 2007. IV '07. 11th International Conference, 2007)
Social networks continue to become more and more feature rich. Using local and global structural properties and descriptive attributes are necessary for more sophisticated social network analysis and support for visual mining tasks. While a number of visualization tools for social network applications have been developed, most of them are limited to uni-modal graph representations. Some of the tools support a wide range of visualization options, including interactive views. Others have better support for calculating structural graph properties such as the density of the graph or deploying traditional statistical social network analysis. We present Invenio, a new tool for visual mining of socials. Invenio integrates a wide range of interactive visualization options from Prefuse, with graph mining algorithm support from JUNG. While the integration expands the breadth of functionality within the core engine of the tool, our goal is to interactively explore multi-modal, multi-relational social networks. Invenio also supports construction of views using both database operations and basic graph mining operations.
Keywords: computing; database; interactive; graph; management; mining; data; network; structural; property; visual; sciences; social; systems; graph; systems; social; theory; interactive; visualisation; database; visualization; multimodal

Voila: Efficient feature-value acquisition for classification - Bilgic,M.; Getoor, Lise (PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE, 2007)
We address the problem of efficient feature-value acquisi- tion for classification in domains in which there are varying costs associated with both feature acquisition and misclassi- fication. The objective is to minimize the sum of the infor- mation acquisition cost and misclassification cost. Any de- cision theoretic strategy tackling this problem needs to com- pute value of information for sets of features. Having cal- culated this information, different acquisition strategies are possible (acquiring one feature at time, acquiring features in sets, etc.). However, because the value of information cal- culation for arbitrary subsets of features is computationally intractable, most traditional approaches have been greedy, computing values of features one at a time. We make the problem of value of information calculation tractable in prac- tice by introducing a novel data structure called the Value of Information Lattice (VOILA). VOILA exploits dependencies between missing features and makes sharing of information value computations between different feature subsets possi- ble. To the best of our knowledge, performance differences between greedy acquisition, acquiring features in sets, and a mixed strategy have not been investigated empirically in the past, due to inherit intractability of the problem. With the help of VOILA, we are able to evaluate these strategies on five real world datasets under various cost assumptions. We show that VOILA reduces computation time dramatically. We also show that the mixed strategy outperforms both greedy acqui- sition and acquisition in sets.

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

An Adaptive Threshold Method for Hyperspectral Target Detection - Broadwater, J.; Chellapa, Rama (Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on, 2006)
In this paper, we present a new approach to automatically determine a detector threshold. This research problem is especially important in hyperspectral target detection as targets are typically very similar to the background. While a number of methods exist to determine the threshold, these methods require either large amounts of data or make simplifying assumptions about the background distribution. We use a method called inverse blind importance sampling which requires few samples and makes no a-priori assumptions about the background statistics. Results show the promise of this algorithm to determine thresholds for fixed false alarm densities in hyperspectral detectors
Keywords: adaptive; blind; detection; detection; inverse; importance; method; background; processing; importance; sampling; geophysical; sampling; object; signal; statistics; hyperspectral; target; threshold

Adding dense, weighted connections to wordnet - Jordan Boyd-Graber; Fellbaum,C.; Osherson,D.; Schapire,R. (Proceedings of the Third International WordNet Conference, 2006)
WORDNET, a ubiquitous tool for natural language processing, suffers from sparsity of connectionsbetween its component concepts (synsets). Through the use of human annotators, a subset of the connections between 1000 hand-chosen synsets was assigned a value of “evocation” representing how much the first concept brings to mind the second. These data, along with existing similarity measures, constitute the basis of a method for predicting evocation between previously unrated pairs.

Algorithms for on-line monitoring of components in an optical tweezers-based assembly cell - Peng,T.; Balijepalli,A.; Gupta,S.K.; LeBrun,T. W. (2006)
Optical tweezers have emerged as a powerful tool for microand nanomanipulation. Using optical tweezers to perform auto- mated assembly requires on-line monitoring of components in the assembly workspace. This paper presents algorithms for estimat- ing positions and orientations of microscale and nanoscale com- ponents in the 3-Dimensional assembly workspace. Algorithms presented in this paper use images obtained by optical section microscopy. The images are first segmented to locate areas of in- terest and then image gradient information from the areas of in- terest is used to generate probable locations and orientations of components in the XY-plane. Finally, signature curves are com- puted and utilized to obtain component locations and orienta- tions in 3-D space. We have tested these algorithms with silica micro-spheres as well as metallic nanowires. We believe that the algorithms described in this paper will provide the foundation for realizing automated assembly operations in optical tweezers- based assembly cells.

Anonymous multi-attribute encryption with range query and conditional decryption - Bethencourt, J.; Chan, H.; Perrig, A.; Elaine Shi; Song,D. (Carnegie Mellon University, 2006)
We introduce the concept of Anonymous Multi-Attribute Encryption with Range Query and Con-ditional Decryption (AMERQCD). In AMERQCD, a plaintext is encrypted under a point in multi- dimensional space. To a computationally bounded adversary, the ciphertext hides both the plaintext and the point under which it is encrypted. In a range query, a master key owner releases the decryp- tion key for an arbitrary hyper-rectangle in space, thus allowing decryption of ciphertexts previ- ously encrypted under any point within the hyper-rectangle. However, a computationally bounded adversary cannot learn any information on ciphertexts outside the range covered by the decryption key (except the fact that they do not lie within this range). We give an efficient construction based on the Decision Bilinear Diffie-Hellman (D-BDH) and Decision Linear (D-Linear) assumption.

Bio-inspired, Modular, and Multifunctional Thermal and Impact Protected (TIPed) Embedded Sensing Controls Actuation Power Element (ESCAPE) Structures - Gyger Jr,L. S.; Spranklin,B. W.; Gupta,S.K.; Bruck,H. A. (2006)
There is a great deal of interest in creating new structural concepts, such as snake robots, from analogousbiological systems. These biological systems are typically composed of materials that serve multiple functions. For example, the skin of a snake is a system consisting of a soft, hyperelastic covering, with nerves providing thermal and pressure sensitivity, and a hard, scaly coating to resist wear and tear from hard particles such as sand. Therefore, bio-inspired structures can also be composed of multifunctional materials. There are currently many approaches to fabricating bio-inspired structures with conventional materials. These concepts typically utilize a system-of-systems design approach where the structure will be composed of a structural framework, an actuation system, a power source for the actuation system, controllers, and external sensors. The drawbacks to these structures include the need to assemble all of the components, interfaces between components that can compromise reliability, constraints on scaling down the structure, and very high power consumption and power generation requirements. These problems have been addressed by developing a new scalable approach to creating multifunctional materials for bio-inspired structures where the controllers, actuators, and sensors are integrated into a modular, multifunctional structure. This approach is facilitated by using multi-material multi-stage molding processes with fully embedded electronic systems, and has resulted in new Thermal and Impact Protected (TIPed) Embedded Sensing Controls Actuation Power Element (ESCAPE) Structures for compact and rugged robotic applications.

CAM04-6: Single-Path Routing of Time-varying Traffic - Kashyap,A.; Bhattacharjee, Bobby; La,R.; Shayman,M.; Tabatabaee,V. (Global Telecommunications Conference, 2006. GLOBECOM '06. IEEE, 2006)
We consider the problem of finding a single-path intra-domain routing for time-varying traffic. We characterize the traffic variations by a finite set of traffic profiles with given non-zero fractions of occurrence. Our goal is to optimize the average performance over all of these traffic profiles. We solve the optimal multi-path version of this problem using linear programming and develop heuristic single-path solutions using randomized rounding and iterated rounding. We analyze our single-path heuristic (finding the optimal single-path routing is NP-hard), and prove that the randomized rounding algorithm has a worst case performance bound of O(log(KN)/log(log(KN))) compared to the optimal multi-path routing with a high probability, where K is the number of traffic profiles, and N the number of nodes in the network. Further, our simulations show the iterated rounding heuristics perform close to the optimal multi-path routing on a wide range of measured ISP topologies, in both the average and the worst-case. Overall, these results are extremely positive since they show that in a wide-range of practical situations, it is not necessary to deploy multi-path routing; instead, an appropriately computed single-path routing is sufficient to provide good performance.
Keywords: algorithm; linear; algorithm; time-varying; algorithms; telecommunication; bound; IP; case; complexity; iterative; intra-domain; IP; methods; linear; multipath; network; network; ISP; networks; Internet; computational; optimal; performance; problem; heuristic; profile; worst; programming; optimal; programming; probability; randomised; rounding; routing; iterated; routing; probability; randomized; routing; telecommunication; single-path; topology; NP-hard; topology; telecommunication; traffic; traffic

A case study of tangible flags: a collaborative technology to enhance field trips - Chipman,G.; Druin, Allison; Beer,D.; Fails,J. A; Guha,M.L.; Simms,S. (Proceedings of the 2006 conference on Interaction design and children, 2006)

A client-driven approach for channel management in wireless LANs - Mishra,A.; Brik,V.; Banerjee,S.; Srinivasan, Aravind; Arbaugh, William A. (IEEE Infocom, 2006)
We propose an efficient client-based approach for channel man-agement (channel assignment and load balancing) in 802.11-based WLANs that lead to better usage of the wireless spectrum. This approach is based on a “conflict set coloring” formulation that jointly performs load balancing along with channel assignment. Such a formulation has a number of advantages. First, it explicitly captures interference effects at clients. Next, it intrinsically ex- poses opportunities for better channel re-use. Finally, algorithms 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 addi- tion to single network scenarios, the conflict set coloring formu- lation is well suited for channel assignment where multiple wire- less networks share and contend for spectrum in the same physical space. Our results over a wide range of both simulated topologies and in-building testbed experiments indicate that our approach improves application level performance at the clients by upto three times (and atleast 50%) in comparison to current best-known tech- niques.

Client-driven channel management for wireless LANs - Mishra,Arunesh; Brik,Vladimir; Banerjee,Suman; Srinivasan, Aravind; Arbaugh, William A. (SIGMOBILE Mob. Comput. Commun. Rev., 2006)
With the explosive growth in the density of 802.11 access points (APs) in the form of hotspots and public/home access networks, coordinating the shared use of spectrum has become an important problem. The irregular coverage topologies present in WLANs due to the vagaries of the indoor RF environment make the channel assignment algorithms in cellular networks inapplicable [1, 2].

A Communication Interface for Multiprocessor Signal Processing Systems - Sankalita Saha; Bhattacharyya, Shuvra S.; Wayne Wolf (Proceedings of the 2006 IEEE/ACM/IFIP Workshop on Embedded Systems for Real Time Multimedia, 2006)
Parallelization of embedded software is often desirable for power/performance-related considerations for computation-intensive applications that frequently occur in the signal-processing domain. Although hardware support for parallel computation is increasingly available in embedded processing platforms, there is a distinct lack of effective software support. One of the most widely known efforts in support of parallel software is the message passing interface (MPI). However, MPI suffers from several drawbacks with regards to customization to specialized parallel processing contexts, and performance degradation for communication-intensive applications. In this paper, we propose a new interface, the signal passing interface (SPI), that is targeted toward signal processing applications and addresses the limitations of MPI for this important domain of embedded software by integrating relevant properties of MPI and coarse-grain dataflow modeling. SPI is much easier and more intuitive to use, and due to its careful specialization, more performance-efficient for the targeted application domain. We present our preliminary version of SPI, along with experiments using SPI on a practical face detection system that demonstrate the capabilities of SPI
Keywords: application program interfaces; Application software; coarse-grain dataflow modeling; Computer applications; Concurrent computing; Context; data flow graphs; Embedded computing; Embedded software; face detection system; Hardware; Message passing; message passing interface; MPI; Multiprocessing systems; multiprocessor signal processing system; PARALLEL PROCESSING; signal passing interface; Signal processing; SPI

Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis - Campbell,Matthew A.; Haas,Brian J.; Hamilton,John P.; Mount, Stephen M.; Buell,C. Robin (BMC Genomics, 2006)
Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST) libraries. We employed the Program to Assemble Spliced Alignments (PASA) to identify and analyze alternatively spliced isoforms in both species.

Compression techniques for minimum energy consumption - Puthenpurayil,S.; Gu,R.; Bhattacharyya, Shuvra S. (25th Army Science Conference, 2006)

Configuration and representation of large-scale dataflow graphs using the dataflow interchange format - Corretjer,I.; Hsu,C.; Bhattacharyya, Shuvra S. (Proceedings of the IEEE Workshop on Signal Processing Systems, Banff, Canada, 2006)

Conservation Patterns in cis-Elements Reveal Compensatory Mutations - Evans,Perry; Donahue,Greg; Hannenhalli, Sridhar (Comparative GenomicsComparative Genomics, 2006)
Transcriptional regulation critically depends on proper interactions between transcription factors (TF) and their cognate DNA binding sites or cis elements. A better understanding and modelling of the TF-DNA interaction is an important area of research. The Positional Weight Matrix (PWM) is the most common model of TF-DNA binding and it presumes that the nucleotide preferences at individual positions within the binding site are independent. However, studies have shown that this independence assumption does not always hold. If the nucleotide preference at one position depends on the nucleotide at another position, a chance mutation at one position should exert selection pressures at the other position. By comparing the patterns of evolutionary conservation at individual positions within cis elements, here we show that positional dependence within binding sites is highly prevalent. We also show that dependent positions are more likely to be functional, as evidenced by a higher information content and higher conservation. We discuss two examples—Elk-1 and SAP-1 where the inferred compensatory mutation is consistent with known TF-DNA crystal structure.

Contention-conscious transaction ordering in multiprocessor DSP systems - Khandelia,M.; Bambha,N. K; Bhattacharyya, Shuvra S. (IEEE Transactions on Signal Processing, 2006)
This paper explores the problem of efficiently ordering interprocessor communication (IPC) operations in statically scheduled multiprocessors for iterative dataflow graphs. In most digital signal processing (DSP) applications, the throughput of the system is significantly affected by communication costs. By explicitly modeling these costs within an effective graph-theoretic analysis framework, we show that ordered transaction schedules can significantly outperform self-timed schedules even when synchronization costs are low. However, we also show that when communication latencies are nonnegligible, finding an optimal transaction order given a static schedule is an NP-complete problem, and that this intractability holds both under iterative and noniterative execution. We develop new heuristics for finding efficient transaction orders, and perform an extensive experimental comparison to gauge the performance of these heuristics.
Keywords: contention-conscious transaction ordering; Costs; data flow graphs; Dataflow; Delay; Digital signal processing; digital signal processing chips; Embedded system; graph-theoretic analysis; Instruments; Internet telephony; interprocessor communication; iterative dataflow graphs; iterative methods; Message passing; multiprocessor; multiprocessor DSP systems; NP-complete problem; Processor scheduling; scheduling; Signal processing; synchronization; Throughput

Cooperative peer groups in NICE - Sherwood,Rob; Lee,Seungjoon; Bhattacharjee, Bobby (Computer Networks, 2006)
We present a distributed scheme for trust inference in peer-to-peer networks. Our work is in the context of the NICE system, which is a platform for implementing cooperative applications over the Internet. We describe a technique for efficiently storing user reputation information in a completely decentralized manner, and show how this information can be used to efficiently identify non-cooperative users in NICE. We present a simulation-based study of our algorithms, in which we show our scheme scales to thousands of users using modest amounts of storage, processing, and bandwidth at any individual node. Lastly we show that our scheme is robust and can form cooperative groups in systems where the vast majority of users are malicious.
Keywords: distributed algorithms; P2P; Reputation base trust

Cross-Language Access to Recorded Speech in the MALACH Project - Oard, Douglas; Demner-Fushman,Dina; Hajič,Jan; Ramabhadran,Bhuvana; Gustman,Samuel; Byrne,William; Soergel,Dagobert; Dorr, Bonnie J; Resnik, Philip; Picheny,Michael (Text, Speech and DialogueText, Speech and Dialogue, 2006)
The MALACH project seeks to help users find information in a vast multilingual collections of untranscribed oral history interviews. This paper introduces the goals of the project and focuses on supporting access by users who are unfamiliar with the interview language. It begins with a review of the state of the art in crosslanguage speech retrieval; approaches that will be investigated in the project are then described. Czech was selected as the first non-English language to be supported, so results of an initial experiment with Czech/English cross-language retrieval are reported.

Data redistribution and remote method invocation for coupled components - Bertrand,Felipe; Bramley,Randall; Bernholdt,David E.; Kohl,James A.; Sussman, Alan; Larson,Jay W.; Damevski,Kostadin B. (Journal of Parallel and Distributed Computing, 2006)
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.
Keywords: Common component architecture; Model coupling; Parallel data redistribution; Parallel remote method invocation

Dataflow transformations in high-level DSP system design - Saha,S.; Puthenpurayil,S.; Bhattacharyya, Shuvra S. (Proceedings of the International Symposium on System-on-Chip, Tampere, Finland, 2006)

D-Dupe: An Interactive Tool for Entity Resolution in Social Networks - Bilgic,M.; Licamele,L.; Getoor, Lise; Shneiderman, Ben (Visual Analytics Science And Technology, 2006 IEEE Symposium On, 2006)
Visualizing and analyzing social networks is a challenging problem that has been receiving growing attention. An important first step, before analysis can begin, is ensuring that the data is accurate. A common data quality problem is that the data may inadvertently contain several distinct references to the same underlying entity; the process of reconciling these references is called entity-resolution. D-Dupe is an interactive tool that combines data mining algorithms for entity resolution with a task-specific network visualization. Users cope with complexity of cleaning large networks by focusing on a small subnetwork containing a potential duplicate pair. The subnetwork highlights relationships in the social network, making the common relationships easy to visually identify. D-Dupe users resolve ambiguities either by merging nodes or by marking them distinct. The entity resolution process is iterative: as pairs of nodes are resolved, additional duplicates may be revealed; therefore, resolution decisions are often chained together. We give examples of how users can flexibly apply sequences of actions to produce a high quality entity resolution result. We illustrate and evaluate the benefits of D-Dupe on three bibliographic collections. Two of the datasets had already been cleaned, and therefore should not have contained duplicates; despite this fact, many duplicates were rapidly identified using D-Dupe's unique combination of entity resolution algorithms within a task-specific visual interface
Keywords: algorithm; data; analysis; social; computing; user; D-Dupe; interactive; interface; data; interfaces; mining; mining; interactive; network; problem; entity; QUALITY; resolution; entity-resolution; social; sciences; systems; social; tool; data; visual; visualization; task-specific

Decentralized message ordering for publish/subscribe systems - Lumezanu,Cristian; Spring, Neil; Bhattacharjee, Bobby (Proceedings of the ACM/IFIP/USENIX 2006 International Conference on Middleware, 2006)
We describe a method to order messages across groups in a publish/subscribe system without centralized control or large vector timestamps. We show that our scheme is practical---little state is required; that it is scalable---the maximum message load is limited by receivers; and that it performs well---the paths messages traverse to be ordered are not made much longer than necessary. Our insight is that only messages to groups that overlap in membership can be observed to arrive out of order: sequencing messages to these groups is sufficient to provide a consistent order, and when publishers subscribe to the groups to which they send, this message order is a causal order.

Depth estimation using the compound eye of dipteran flies - Bitsakos,Konstantinos; Fermüller, Cornelia (Biological Cybernetics, 2006)
In the neural superposition eye of a dipteran fly every ommatidium has eight photoreceptors, each associated with a rhabdomere, two central and six peripheral, which altogether result in seven functional light guides. Groups of eight rhabdomeres in neighboring ommatidia have largely overlapping fields of view. Based on the hypothesis that the light signals collected by these rhabdomeres can be used individually, we investigated the feasibility of estimating 3D scene information. According to Pick (Biol Cybern 26:215–224, 1977) the visual axes of these rhabdomeres are not parallel, but converge to a point 3–6 mm in front of the cornea. Such a structure theoretically could estimate depth in a very simple way by assuming that locally the image intensity is well approximated by a linear function of the spatial coordinates. Using the measurements of Pick (Biol Cybern 26:215–224, 1977) we performed simulation experiments to find whether this is practically possible. Our results indicate that depth estimation at small distances (up to about 1.5–2 cm) is reasonably accurate. This would allow the insect to obtain at least an ordinal spatial layout of its operational space when walking.

Distributing Google - Gopalakrishnan,V.; Bhattacharjee, Bobby; Keleher,P. (Data Engineering Workshops, 2006. Proceedings. 22nd International Conference on, 2006)
We consider the problem of wide-area large-scale text search over a peer-to-peer infrastructure. A wide-area search infrastructure with billions of documents and millions of search terms presents unique challenges in terms of the amount of state that must be maintained and updated. Distributing such a system would require tens of thousands of hosts leading to the usual problems associated with node failures, churn and data migration. Localities inherent in query patterns will cause load imbalances and hot spots that can severely impair performance. In this paper, we describe an architecture for constructing a scalable search infrastructure that is designed to cope with the challenges of scale described above. Our architecture consists of a data store layer which is used to reliably store and recompute indexes over a slow timescale and a caching layer that is used to respond to most queries. Our primary insight is that the problem of efficiently retrieving a small number of relevant results must be decoupled from the problem of reliably storing potentially huge indexes. Relevant results can be quickly retrieved from caches of ranked results, which can be replicated based upon query load. An entirely different set of mechanisms, such as encoded storage and/or data partitioning, should be used to store large indexes reliably. These indexes should only be used to compute results when there is a miss in the cache.

Effect of transport at ambient temperature on detection and isolation of Vibrio cholerae from environmental samples - Alam,M.; Sadique,A.; Bhuiyan,N. A.; Nair,G. B.; Siddique,A. K.; Sack,D. A.; Ahsan,S.; Huq,A.; Sack,R. B.; Rita R Colwell; others (Applied and environmental microbiology, 2006)
It has long been assumed that prolonged holding of environmental samples at the ambient air temperature prior to bacteriological analysis is detrimental to isolation and detection of Vibrio cholerae, the causative agent of pandemic cholera. The present study was aimed at understanding the effect of transporting environmental samples at the ambient air temperature on isolation and enumeration of V. cholerae. For water and plankton samples held at ambient temperatures ranging from 31°C to 35°C for 20 h, the total counts did not increase significantly but the number of culturable V. cholerae increased significantly compared to samples processed within 1 h of collection, as measured by culture, acridine orange direct count, direct fluorescent-antibody-direct viable count (DFA-DVC), and multiplex PCR analyses. For total coliform counts, total bacterial counts, and DFA-DVC counts, the numbers did not increase significantly, but the culturable plate counts for V. cholerae increased significantly after samples were held at the ambient temperature during transport to the laboratory for analysis. An increase in the recovery of V. cholerae O1 and improved detection of V. cholerae O1 rfb and ctxA also occurred when samples were enriched after they were kept for 20 h at the ambient temperature during transport. Improved detection and isolation of toxigenic V. cholerae from freshwater ecosystems can be achieved by holding samples at the ambient temperature, an observation that has significant implications for tracking this pathogen in diverse aquatic environments.

Efficient Circuits for Exact-Universal Computation with Qudits - Brennen,Gavin K.; Bullock,Stephen S.; O'Leary, Dianne P. (Quantum Information and Computation, 2006)

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

Efficient techniques for clustering and scheduling onto embedded multiprocessors - Kianzad,V.; Bhattacharyya, Shuvra S. (IEEE Transactions on Parallel and Distributed Systems, 2006)

An empirical study to compare two parallel programming models - Hochstein, Lorin; Basili, Victor R. (Proceedings of the eighteenth annual ACM symposium on Parallelism in algorithms and architectures, 2006)
While there are strong beliefs within the community about whether one particular parallel programming model is easier to use than another, there has been little research to analyze these claims empirically. Currently, the most popular paradigm is message-passing, as implemented by the MPI library [1]. However, MPI is considered to be difficult for developing programs, because it forces the programmer to work at a very low level of abstraction. One alternative parallel programming model is the PRAM model, which supports fine-grained parallelism and has a substantial history of algorithmic theory [2]. It is not possible to program current parallel machines using the PRAM model because modern architectures are not designed to support such a model efficiently. However, current trends towards multicore chips suggest that large-scale, fine-grained uniform-memory access parallel machines may soon be feasible. XMT-C is an extension of the C language that supports parallel directives to provide a PRAM-like model to the programmer. A prototype compiler exists that generates code which runs on a simulator for an XMT architecture [3].To better understand how much benefit a PRAM-like model could provide over a message-passing model, we conducted a feasibility study in an academic setting to compare the effort required to solve a particular problem. The questions under study were: can we measure the effort in developing a program using these two programming models and can we differentiate the amount of effort for each model?.The subjects participating in the study were divided up into two groups. One group solved a problem using the MPI library in either C,C++, or Fortran, and the other group solved the problem using XMT-C. The task was to write a function to multiply a sparse matrix with a dense vector. To obtain subjects, we leveraged existing graduate-level parallel programming courses at two different universities: University of California, Santa Barbara (UCSB), and University of Maryland (UMD). At UCSB, the students solved the problem in MPI, and at UMD, the students solved the same problem in XMT-C. The focus of the UCSB class was on developing parallel programs to run on the current generation of architectures, and the students were taught MPI, as well as other models. The focus of the UMD class was parallel algorithms in the PRAM model, and the students were taught XMT-C. The students were assigned to treatment groups by class. The study was integrated into each class, as the problem was a required assignment in each class.Subjects kept track of their effort with a self-reported effort log. We also collected automatic effort data by instrumenting the compilers, which recorded data at each compile. We computed three effort measures: self-reported, instrumented, and combined. Self-reported effort measures are based entirely on effort logs, instrumented effort measures are based entirely on timestamps from the instrumented compilers, and combined effort measures are based on compiler timestamps when the subject is working on the instrumented machine, and self-reported effort when the subject is working off the instrumented machine.The results of this preliminary study answer both of our questions in the positive. In this case, on average, students required less effort to solve the problem using XMT-C compared to MPI. The reduction in mean effort was approximately 50% for all three measures, which was statistically significant at the level of p < .05 using a t-test.This study demonstrates that the effect of programming model on effort can be directly measured through empirical studies with human subjects. While no single study can conclusively demonstrate the advantage of one programming model over another, a series of studies examining different models and different problems can provide insights into the relative strengths of parallel programming models in different contexts. The study described above is one of a series of such studies that we are currently conducting.
Keywords: effort; empirical study; HPC; Message-passing; MPI; parallel programming; PRAM; Productivity; XMT

Energy-efficient embedded software implementation on multiprocessor system-on-chip with multiple voltages - Hua,S.; Qu,G.; Bhattacharyya, Shuvra S. (ACM Transactions on Embedded Computing Systems (TECS), 2006)

Entity Resolution in Graphs - Bhattacharya,Indrajit; Getoor, Lise (Mining Graph DataMining Graph Data, 2006)
This chapter contains sections titled:Introduction Related Work Motivating Example for Graph-Based Entity Resolution Graph-Based Entity Resolution: Problem Formulation Similarity Measures for Entity Resolution Graph-Based Clustering for Entity Resolution Experimental Evaluation Conclusion References
Keywords: entity resolution in graphs; graph‐based clustering for entity resolution; graph‐based entity resolution problem

Estimation of Anthropomeasures from a Single Calibrated Camera - BenAbdelkader,C.; Davis, Larry S. (Automatic Face and Gesture Recognition, 2006. FGR 2006. 7th International Conference on, 2006)
We are interested in the recovery of anthropometric dimensions of the human body from calibrated monocular sequences, and their use in multi-target tracking across multiple cameras and identification of individual people. In this paper, we focus on two specific anthropomeasures that are relatively easy to estimate from low-resolution images: stature and shoulder breadth. Precise average estimates are obtained for each anthropomeasure by combining measurements from multiple frames in the sequence. Our contribution is two-fold: (i) a novel technique for automatic and passive estimation of shoulder breadth, that is based on modelling the shoulders as an ellipse, and (U) a novel method for increasing the accuracy of the mean estimates of both anthropomeasures. The latter is based on the observation that major sources of error in the measurements are landmark localization the 2D image and 3D modelling error, and that both of these are correlated with gait phase and body orientation with respect to the camera. Consequently, estimation error can be significantly reduced via appropriate selection or control of these two variables
Keywords: anthropomeasures; calibrated; camera; anthropometry; error; estimation; error; estimation; gait; identification; image; phase; image; recovery; image; resolution; image; resolution; monocular; restoration; image; sensors; image; sequences; sequences; single; statistics; image

Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements - Bringaud,Frédéric; Ghedin,Elodie; Blandin,Gaëlle; Bartholomeu,Daniella C.; Caler,Elisabet; Levin,Mariano J.; Baltz,Théo; El‐Sayed, Najib M. (Molecular and Biochemical Parasitology, 2006)
The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5'-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.
Keywords: Degenerate retroelement; Evolution; Ingi; L1Tc; Leishmania major; Non-LTR retrotransposon; Retroposon; Trypanosoma brucei; Trypanosoma cruzi

The evolution of the international children's digital library searching and browsing interface - Hutchinson,H.B.; Bederson, Benjamin B.; Druin, Allison (Proceedings of the 2006 conference on Interaction design and children, 2006)

Experiments to understand HPC time to development - Hochstein, Lorin; Nakamura,Taiga; Basili, Victor R.; Asgari, Sima; Zelkowitz, Marvin V; Hollingsworth, Jeffrey K; Shull, Forrest; Carver,Jeffrey; Voelp,Martin; Zazworka, Nico; Johnson,Philip (CTWatch Quarterly, 2006)
In order to understand how high performance computing (HPC) programs are developed, a series of experiments, using students in graduate level HPC classes, have been conducted at many universities in the US. In this paper we discuss the general process of conducting those experiments, give some of the early results of those experiments, and describe a web-based process we are developing that will allow us to run additional experiments at other universities and laboratories that will be easier to conduct and generate results that more accurately reflect the process of building HPC programs.
Keywords: hackystat; HPC; publications-journals

Exploring content-actor paired network data using iterative query refinement with NetLens - Lee,Bongshin; Kang,Hyunmo; Plaisant, Catherine; Bederson, Benjamin B. (Digital Libraries, 2006. JCDL '06. Proceedings of the 6th ACM/IEEE-CS Joint Conference on, 2006)
Networks have remained a challenge for information retrieval and visualization because of the rich set of tasks that users want to accomplish. This paper demonstrates a tool, NetLens, to explore a content-actor paired network data model. The NetLens interface was designed to allow users to pose a series of elementary queries and iteratively refine visual overviews and sorted lists. This enables the support of complex queries that are traditionally hard to specify in node-link visualizations. NetLens is general and scalable in that it applies to any dataset that can be represented with our abstract content-actor data model
Keywords: data; interface; libraries; query; management; model; data; models; data; NetLens; content-actor; network; pair; processing; user; query; refinement; data; retrieval; iterative; systems; visualisation; digital; visualization; information

Fair file swarming with FOX - Levin,D.; Sherwood,R.; Bhattacharjee, Bobby (Proc. 5th IPTPS, 2006)
File swarming is a popular method of coordi-nated download by which peers obtain a file from an under- provisioned server. Critical problems arise within this domain when users act selfishly, yet most systems are built with altru- ism assumed. Working under the assumption that all peers are greedy, we introduce the Fair, Optimal eXchange (FOX) protocol. FOX, in addition to effective and robust application of the tit-for-tat incentive mechanism, provides theoretically optimal download times when everyone cooperates. Under our assumption of server and peer capabilities, we develop a strong threat model that provides peers with the incentives to not deviate from the protocol. From a theoretical perspective, we prove FOX’s optimality and incentive properties, even when the network consists only of purely self-interested peers. We also discuss issues in implementing and deploying such a system, and address the cost of ensuring fairness in a domain where efficiency is so important.

File System Support for Collaboration in theWide Area - Gaburici,V.; Keleher,P.; Bhattacharjee, Bobby (Distributed Computing Systems, 2006. ICDCS 2006. 26th IEEE International Conference on, 2006)
We describe the design, implementation, and performance of MFS, a new file system designed to support efficient widearea collaboration. MFS is structured around the twin abstractions of lightweight sessions and snapshots, along with a highly configurable capability-based security architecture. Sessions simplify and clarify collaborative semantics. Snapshots allow atomic access to arbitrary collections of files, and allow sharing to be defined in a simple and expressive fashion. MFS #146;s security architecture is a layered system that allows diverse usage scenarios. Pure capability-based access allows clients to access data without needing expensive public key or authentication servers, or complicated administration. However, MFS #146;s capabilities can also be watermarked, allowing a range of services to be added on a per-mount basis, up to and including traditional user authentication based on passwords or public keys. Basing the system around the use of immutable snapshots enables the underlying system to use several performance optimizations aggressively. Performance results from our MFS prototype show that, far from adding overhead, the use of snapshots allows the system to perform comparably to NFS in the local-area case and significantly outperform existing systems in wide-area environments.

Find that photo!: interface strategies to annotate, browse, and share - Shneiderman, Ben; Bederson, Benjamin B.; Drucker,Steven M. (Communications of the ACM - Supporting exploratory search, 2006)

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

A flexible system framework for a nanoassembly cell using optical tweezers - Balijepalli,A.; LeBrun,T. W.; Gupta,S.K. (2006)
The optical tweezers instrument is a unique tool fordirected assembly of nanocomponents. In order to function as a viable nanomanufacturing tool, a software architecture is needed to run the optical tweezers hardware, provide an effective user interface, and allow automated operation. A flexible software system framework is described to utilize the optical tweezers hardware to its full potential. Initially we lay out the requirements for the system framework and define the broad architectural choices made while implementing the different modules. Implementation details of key system modules are then described. The flexible nature of the architecture is demonstrated by showing how a simulation module can be seamlessly included into the framework to replace the optical tweezers hardware as necessary. Finally, we show some representative assembly operations to demonstrate the capabilities of the system.