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Articles 361 - 390 of 830
Full-Text Articles in Computer Sciences
Acceleration Of Profile-Hmm Search For Protein Sequences In Reconfigurable Hardware - Master's Thesis, May 2006 , Rahul Pratap Maddimsetty
Acceleration Of Profile-Hmm Search For Protein Sequences In Reconfigurable Hardware - Master's Thesis, May 2006 , Rahul Pratap Maddimsetty
All Computer Science and Engineering Research
Profile Hidden Markov models are highly expressive representations of functional units, or motifs, conserved across protein sequences. Profile-HMM search is a powerful computational technique that is used to annotate new sequences by identifying occurrences of known motifs in them. With the exponential growth of protein databases, there is an increasing demand for acceleration of such techniques. We describe an accelerator for the Viterbi algorithm using a two-stage pipelined design in which the first stage is implemented in parallel reconfigurable hardware for greater speedup. To this end, we identify algorithmic modifications that expose a high level of parallelism and characterize their …
Preserving Performance Of Byzantine Fault Tolerant Replica Groups In The Presence Of Malicious Clients, Sajeeva L. Pallemulle, Haraldur D. Thorvaldsson, Kenneth J. Goldman
Preserving Performance Of Byzantine Fault Tolerant Replica Groups In The Presence Of Malicious Clients, Sajeeva L. Pallemulle, Haraldur D. Thorvaldsson, Kenneth J. Goldman
All Computer Science and Engineering Research
The Castro and Liskov Byzantine Fault Tolerance protocol for replicated state machines (CLBFT) provides a practical means of tolerating arbitrary replica failures in replicated passive data servers. For better performance, CLBFT uses Message Authentication Codes (MAC) instead of public Key cryptography to authenticate messages and preserves replica consistency even in the presence of malicious clients. However, CLBFT is susceptible to potential attacks by malicious clients using corrupted MACs to force replica groups into expensive configuration changes repeatedly. While not affecting correctness, this vulnerability can seriously impair the performance of the replica group. We propose modifications to CLBFT that address this …
Mixed-Integer Linear Programming Solution To Multi-Robot Task Allocation Problem, Nuzhet Atay, Burchan Bayazit
Mixed-Integer Linear Programming Solution To Multi-Robot Task Allocation Problem, Nuzhet Atay, Burchan Bayazit
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Multi-robot systems require efficient and accurate planning in order to perform mission-critical tasks. This paper introduces a mixed-integer linear programming solution to coordinate multiple heterogenenous robots for detecting and controlling multiple regions of interest in an unknown environment. The objective function contains four basic requirements of a multi-robot system serving this purpose: control regions of interest, provide communication between robots, control maximum area and detect regions of interest. Our solution defines optimum locations of robots in order to maximize the objective function while efficiently satisfying some constraints such as avoiding obstacles and staying within the speed capabilities of the robots. …
Smooth Surface Reconstruction Using Charts For Medical Data, Cindy Grimm, Tao Ju
Smooth Surface Reconstruction Using Charts For Medical Data, Cindy Grimm, Tao Ju
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We present a surface reconstruction technique that constructs a smooth analytic surface from scattered data. The technique is robust to noise and both poorly and non-uniformly sampled data, making it well-suited for use in medical applications. In addition, the surface can be parameterized in multiple ways, making it possible to represent additional data, such as electromagnetic potential, in a different (but related) coordinate system to the geometric one. The parameterization technique also supports consistent parameterizations of multiple data sets.
The Design, Modeling, And Implementation Of Group Scheduling For Isolation Of Computations From Adversarial Interference, Terry Tidwell, Noah Watkins, Venkita Subramonian, Douglas Niehaus, Armando Gill, Migliaccio
The Design, Modeling, And Implementation Of Group Scheduling For Isolation Of Computations From Adversarial Interference, Terry Tidwell, Noah Watkins, Venkita Subramonian, Douglas Niehaus, Armando Gill, Migliaccio
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To isolate computations from denial of service (DoS) attacks and other forms of adversarial interference, it is necessary to constrain the effects of interactions among computations. This paper makes four contributions to research on isolation of computations from adversarial interference: (1) it describes the design and implementation of a kernel level scheduling policy to control the effects of adversarial attacks on computations’ execution; (2) it presents formal models of the system components that are involved in a representative DoS attack scenario; (3) it shows how model checking can be used to analyze that example scenario, under default Linux scheduling semantics …
Smooth Key-Framing Using The Image Plane, Leon Barrett, Cindy Grimm
Smooth Key-Framing Using The Image Plane, Leon Barrett, Cindy Grimm
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This paper demonstrates the use of image-space constraints for key frame interpolation. Interpolating in image-space results in sequences with predictable and controlable image trajectories and projected size for selected objects, particularly in cases where the desired center of rotation is not fixed or when the key frames contain perspective distortion changes. Additionally, we provide the user with direct image-space control over {\em how} the key frames are interpolated by allowing them to directly edit the object's projected size and trajectory. Image-space key frame interpolation requires solving the inverse camera problem over a sequence of point constraints. This is a variation …
Use Of Gene Expression Profiling And Machine Learning To Understand And Predict Primary Graft Dysfunction, Monika Ray, Sekhar Dharmarajan, Johannes Freudenberg, Weixiong Zhang, Alexander G. Patterson
Use Of Gene Expression Profiling And Machine Learning To Understand And Predict Primary Graft Dysfunction, Monika Ray, Sekhar Dharmarajan, Johannes Freudenberg, Weixiong Zhang, Alexander G. Patterson
All Computer Science and Engineering Research
No abstract provided.
Design Of Routers For Diversified Networks, Jonathan Turner
Design Of Routers For Diversified Networks, Jonathan Turner
All Computer Science and Engineering Research
No abstract provided.
Extending Byzantine Fault Tolerance To Replicated Clients, Ian Wehrman, Sajeeva L. Pallemulle, Kenneth J. Goldman
Extending Byzantine Fault Tolerance To Replicated Clients, Ian Wehrman, Sajeeva L. Pallemulle, Kenneth J. Goldman
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Byzantine agreement protocols for replicated deterministic state machines guarantee that externally requested operations continue to execute correctly even if a bounded number of replicas fail in arbitrary ways. The state machines are passive, with clients responsible for any active ongoing application behavior. However, the clients are unreplicated and outside the fault-tolerance boundary. Consequently, agreement protocols for replicated state machines do not guarantee continued correct execution of long-running client applications. Building on the Castro and Liskov Byzantine Fault Tolerance protocol for unreplicated clients (CLBFT), we present a practical algorithm for Byzantine fault-tolerant execution of long-running distributed applications in which replicated deterministic …
Design And Analysis Of An Accelerated Seed Generation Stage For Blastp On The Mercury System - Master's Thesis, August 2006, Arpith Jacob
Design And Analysis Of An Accelerated Seed Generation Stage For Blastp On The Mercury System - Master's Thesis, August 2006, Arpith Jacob
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NCBI BLASTP is a popular sequence analysis tool used to study the evolutionary relationship between two protein sequences. Protein databases continue to grow exponentially as entire genomes of organisms are sequenced, making sequence analysis a computationally demanding task. For example, a search of the E. coli. k12 proteome against the GenBank Non-Redundant database takes 36 hours on a standard workstation. In this thesis, we look to address the problem by accelerating protein searching using Field Programmable Gate Arrays. We focus our attention on the BLASTP heuristic, building on work done earlier to accelerate DNA searching on the Mercury platform. We …
Design Of A Diversified Network Substrate, Jonathan Turner
Design Of A Diversified Network Substrate, Jonathan Turner
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A diversified network substrate enables multiple end-to-end metanetworks to co-exist within a shared physical infrastructure. Metanetworks are implemented by metarouters, hosted by substrate routers, and metarouters are connected by metalinks. The substrate allocates resources (both link bandwidth and processing resources) to metarouters based on advance reservations received from metanetwork planning systems. It also enables dynamic creation of access metalinks, connecting end systems to metarouters, and supports mobility of end systems under the control of their metanetworks. This report defines a model for a diversified internet and presents a detailed design of the substrate that enables metanetworks to co-exist. The design …
Discovering Functional Modules By Clustering Gene Co-Expression Networks, Jianhua Ruan, Weixiong Zhang
Discovering Functional Modules By Clustering Gene Co-Expression Networks, Jianhua Ruan, Weixiong Zhang
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Identification of groups of functionally related genes from high throughput gene expression data is an important step towards elucidating gene functions at a global scale. Most existing approaches treat gene expression data as points in a metric space, and apply conventional clustering algorithms to identify sets of genes that are close to each other in the metric space. However, they usually ignore the topology of the underlying biological networks. In this paper, we propose a network-based clustering method that is biologically more realistic. Given a gene expression data set, we apply a rank-based transformation to obtain a sparse co-expression network, …
Fast Packet Classification Using Bloom Filters, Sarang Dharmapurikar, Haoyu Song, Jonathan Turner, John Lockwood
Fast Packet Classification Using Bloom Filters, Sarang Dharmapurikar, Haoyu Song, Jonathan Turner, John Lockwood
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While the problem of general packet classification has received a great deal of attention from researchers over the last ten years, there is still no really satisfactory solution. Ternary Content Addressable Memory (TCAM), although widely used in practice, is both expensive and consumes a lot of power. Algorithmic solutions, which rely on commodity memory chips, are relatively inexpensive and power-efficient, but have not been able to match the generality and performance of TCAMs. In this paper we propose a new approach to packet classification, which combines architectural and algorithmic techniques. Our starting point is the well-known crossproducting algorithm, which is …
Acceleration Of Gapped Alignment In Blastp Using The Mercury System, Brandon B. Harris
Acceleration Of Gapped Alignment In Blastp Using The Mercury System, Brandon B. Harris
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Protein databases have grown exponentially over the last decade. This exponential growth has made extracting valuable information from these databases increasingly time consuming. This project presents a new method of accelerating a commonly used program for performing similarity searching on protein databases, BLASTP. This project describes the design and implementation of Mercury BLASTP, a customized hardware accelerated variant of BLASTP. This project focuses on the gapped alignment stage of Mercury BLASTP and provides design details and implementation results.
A Unified Architecture For Flexible Radio Power Management In Wireless Sensor Networks, Kevin Klues, Guoliang Xing, Chenyang Lu
A Unified Architecture For Flexible Radio Power Management In Wireless Sensor Networks, Kevin Klues, Guoliang Xing, Chenyang Lu
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A challenge for many wireless sensor networks is to remain operational for long periods of time on a very limited power supply. While many power management protocols have been proposed, a solution does not yet exist that allows them to be seamlessly integrated into the existing systems. In this paper we study the architectural support required to resolve this issue. We propose a framework that separates sleep scheduling from the basic MAC layer functionality and provide a set of unified interfaces between them. This framework enables different sleep scheduling policies to be easily implemented on top of multiple MAC layers. …
Flexible Maximum Urgency First Scheduling For Distributed Real-Time Systems, Yingming Chen, Chenyang Lu
Flexible Maximum Urgency First Scheduling For Distributed Real-Time Systems, Yingming Chen, Chenyang Lu
All Computer Science and Engineering Research
No abstract provided.
A Thesis On Sketch-Based Techniques For Mesh Deformation And Editing, Raquel Bujans
A Thesis On Sketch-Based Techniques For Mesh Deformation And Editing, Raquel Bujans
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The goal of this research is to develop new and more intuitive ways for editing a mesh from a static camera angle. I present two ways to edit a mesh via a simple sketching system. The first method is a gray-scale editor which allows the user to specify a fall off function for the region being deformed. The second method is a profile editor in which the user can re-sketch a mesh’s profile. Lastly, the types of edits possible will be discussed and our results will be presented.
Design And Evaluation Of Packet Classification Systems, Doctoral Dissertation, December 2006, Haoyu Song
Design And Evaluation Of Packet Classification Systems, Doctoral Dissertation, December 2006, Haoyu Song
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Although many algorithms and architectures have been proposed, the design of efficient packet classification systems remains a challenging problem. The diversity of filter specifications, the scale of filter sets, and the throughput requirements of high speed networks all contribute to the difficulty. We need to review the algorithms from a high-level point-of-view in order to advance the study. This level of understanding can lead to significant performance improvements. In this dissertation, we evaluate several existing algorithms and present several new algorithms as well. The previous evaluation results for existing algorithms are not convincing because they have not been done in …
Hail: An Algorithm For The Hardware Accelerated Identification Of Languages, Master's Thesis, May 2006, Charles M. Kastner
Hail: An Algorithm For The Hardware Accelerated Identification Of Languages, Master's Thesis, May 2006, Charles M. Kastner
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This thesis examines in detail the Hardware-Accelerated Identification of Languages (HAIL) project. The goal of HAIL is to provide an accurate means to identify the language and encoding used in streaming content, such as documents passed over a high-speed network. HAIL has been implemented on the Field-programmable Port eXtender (FPX), an open hardware platform developed at Washington University in St. Louis. HAIL can accurately identify the primary languages and encodings used in text at rates much higher than what can be achieved by software algorithms running on microprocessors.
A Query-Centric Approach To Supporting The Development Of Context-Aware Applications For Mobile Ad Hoc Networks, Doctoral Dissertation, August 2006, Jamie Payton
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The wide-spread use of mobile computing devices has led to an increased demand for applications that operate dependably in opportunistically formed networks. A promising approach to supporting software development for such dynamic settings is to rely on the context-aware computing paradigm, in which an application views the state of the surrounding ad hoc network as a valuable source of contextual information that can be used to adapt its behavior. Collecting context information distributed across a constantly changing network remains a significant technical challenge. This dissertation presents a query-centered approach to simplifying context interactions in mobile ad hoc networks. Using such …
Unified Power Management In Wireless Sensor Networks, Doctoral Dissertation, August 2006, Guoliang Xing
Unified Power Management In Wireless Sensor Networks, Doctoral Dissertation, August 2006, Guoliang Xing
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Radio power management is of paramount concern in wireless sensor networks (WSNs) that must achieve long lifetimes on scarce amount of energy. Previous work has treated communication and sensing separately, which is insufficient for a common class of sensor networks that must satisfy both sensing and communication requirements. Furthermore, previous approaches focused on reducing energy consumption in individual radio states resulting in suboptimal solutions. Finally, existing power management protocols often assume simplistic models that cannot accurately reflect the sensing and communication properties of real-world WSNs. We develop a unified power management approach to address these issues. We first analyze the …
Competent Program Evolution, Doctoral Dissertation, December 2006, Moshe Looks
Competent Program Evolution, Doctoral Dissertation, December 2006, Moshe Looks
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Heuristic optimization methods are adaptive when they sample problem solutions based on knowledge of the search space gathered from past sampling. Recently, competent evolutionary optimization methods have been developed that adapt via probabilistic modeling of the search space. However, their effectiveness requires the existence of a compact problem decomposition in terms of prespecified solution parameters. How can we use these techniques to effectively and reliably solve program learning problems, given that program spaces will rarely have compact decompositions? One method is to manually build a problem-specific representation that is more tractable than the general space. But can this process be …
Limit Crossing For Decision Problems, Sharlee Climer, Weixiong Zhang
Limit Crossing For Decision Problems, Sharlee Climer, Weixiong Zhang
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Limit crossing is a methodology in which modified versions of a problem are solved and compared, yielding useful information about the original problem. Pruning rules that are used to exclude portions of search trees are excellent examples of the limit-crossing technique. In our previous work, we examined limit crossing for optimization problems. In this paper, we extend this methodology to decision problems. We demonstrate the use of limit crossing in our design of a tool for identifying K-SAT backbones. This tool is guaranteed to identify all of the backbone variables by solving at most n+1 formulae, where n is the …
A Proposed Architecture For The Geni Backbone Platform, Jonathan Turner
A Proposed Architecture For The Geni Backbone Platform, Jonathan Turner
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The GENI Project (Global Environment for Network Innovation) is a major NSF-sponsored initiative that seeks to create a national research facility to enable experimental deployment of innovative new network architectures on a sufficient scale to enable realistic evaluation. One key component of the GENI system will be the GENI Backbone Platform (GBP) that provides the resources needed to allow multiple experimental networks to co-exist within the shared GENI infrastructure. This report reviews the objectives for the GBP, reviews the key issues that affect its design and develops a detailed reference architecture in order to provide a concrete example for how …
The Real Effect Of Warm-Cool Colors, Reynold J. Bailey, Cindy M, Grimm, Chris Davoli
The Real Effect Of Warm-Cool Colors, Reynold J. Bailey, Cindy M, Grimm, Chris Davoli
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The phenomenon of warmer colors appearing nearer in depth to viewers than cooler colors has been studied extensively by psychologists and other vision researchers. The vast majority of these studies have asked human observers to view physically equidistant, colored stimuli and compare them for relative depth. However, in most cases, the stimuli presented were rather simple: straight colored lines, uniform color patches, point light sources, or symmetrical objects with uniform shading. Additionally, the colors used were typically highly saturated. Although such stimuli are useful in isolating and studying depth cues in certain contexts, they leave open the question of whether …
Tuple Space Coordination Across Space & Time, Gruia-Catalin Roman, Radu Handorean, Chenyang Lu
Tuple Space Coordination Across Space & Time, Gruia-Catalin Roman, Radu Handorean, Chenyang Lu
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CAST is a coordination model designed to support interactions among agents executing on hosts that make up a mobile ad hoc network (MANET). From an application programmer’s point of view, CAST makes it possible for operations to be executed at arbitrary locations in space, at prescribed times which may be in the future, and on remote hosts even when no end-to-end connected route exists between the initiator and target(s) of the operation. To accomplish this, CAST assumes that each host moves in space in accordance with a motion profile which is accurate but which at any given time extends into …
Fair Efficiency, Or Low Average Delay Without Starvation, Christoph Jechlitschek, Sergey Gorinksky
Fair Efficiency, Or Low Average Delay Without Starvation, Christoph Jechlitschek, Sergey Gorinksky
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Elastic applications are primarily interested in minimal delay achievable for their messages under current network load. In this paper, we investigate how to transmit such messages over a bottleneck link efficiently and fairly.
Virtualizing Network Processors, Ben Wun, Jonathan Turner, Patrick Crowley
Virtualizing Network Processors, Ben Wun, Jonathan Turner, Patrick Crowley
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This paper considers the problem of virtualizing the resources of a network processor (NP) in order to allow multiple third-parties to execute their own virtual router software on a single physical router at the same time. Our broad interest is in designing such a router capable of supporting virtual networking. We discuss the issues and challenges involved in this virtualization, and then describe specific techniques for virtualizing both the control and data-plane processors on NPs. For Intel IXP NPs in particular, we present a dynamic, macro-based technique for virtualization that allows multiple virtual routers to run on multiple data plane …
An Improved Analysis For A Greedy Remote-Clique Algorithm Using Factor-Revealing Lps, Benjamin E. Birnbaum, Kenneth J. Goldman
An Improved Analysis For A Greedy Remote-Clique Algorithm Using Factor-Revealing Lps, Benjamin E. Birnbaum, Kenneth J. Goldman
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Given a complete graph with nonnegative edge weights satisfying the triangle inequality and a positive integer p, the remote-clique problem is to find a subset of p vertices having a maximum-weight induced subgraph. A simple greedy algorithm for the problem has been shown to have an approximation ratio of 4, but a tight example has not been provided. In this paper, we use the technique of factor revealing linear programs to prove that this algorithm actually achieves an approximation ratio of 2, matching the best-known ratio for the problem. The greedy algorithm's running time of O(pn) makes it the fastest …
Agilla: A Mobile Agent Middleware For Sensor Networks, Chien-Liang Fok, Gruia-Catalin Roman, Chenyang Lu
Agilla: A Mobile Agent Middleware For Sensor Networks, Chien-Liang Fok, Gruia-Catalin Roman, Chenyang Lu
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Agilla is a mobile agent middleware for sensor networks. Mobile agents are special processes that can migrate across sensors. They increase network flexibility by enabling active in-network reprogramming. Neighbor lists and tuple spaces are used for agent coordination. Agilla was originally implemented on Mica2 motes, but has been ported to other platforms. Its Mica2 implementation consumes 41.6KB of code and 3.59KB of data memory. Agents can move five hops in less than 1.1s with over 92% success. Agilla was used to develop multiple applications related to fire detection and tracking, cargo container monitoring, and robot navigation.