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Full-Text Articles in Physical Sciences and Mathematics
Cian: A Language And Middleware For Collaboration In Ad Hoc Networks, Rohan Sen, Gruia-Catalin Roman, Andrew Frank
Cian: A Language And Middleware For Collaboration In Ad Hoc Networks, Rohan Sen, Gruia-Catalin Roman, Andrew Frank
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Designing software that supports collaboration among multiple users in mobile ad hoc networks is challenging due to the dynamic network topology and inherent unpredictability of the environment. However, as we increasingly migrate to using mobile computing platforms, there is a pertinent need for software that can support a wide range of collaborative activities anywhere and at any time without relying on any external infrastructure. In this paper, we adopt the workflow model to represent the structure of an activity that involves multiple tasks being performed in a structured, collaborative fashion by multiple users. Using the workflow model as a base, …
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. …
Virtualization For A Network Processor Runtime System, Brandon Heller, Jonathan Turner, John Dehart, Patrick Crowley
Virtualization For A Network Processor Runtime System, Brandon Heller, Jonathan Turner, John Dehart, Patrick Crowley
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The continuing ossification of the Internet is slowing the pace of network innovation. Network diversification presents one solution to this problem, by virtualizing the network at multiple layers. Diversified networks consist of a shared physical substrate, virtual routers (metarouters), and virtual links (metalinks). Virtualizing routers enables smooth and incremental upgrades to new network services. Our current priority for a diversified router prototype is to enable reserved slices of the network for researchers to perform repeatable, high-speed network experiments. General-purpose processors have well established techniques for virtualization, but do not scale efficiently to multi-gigabit speeds. To achieve these speeds, we employ …
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 …
Design Of Routers For Diversified Networks, Jonathan Turner
Design Of Routers For Diversified Networks, Jonathan Turner
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No abstract provided.
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 …
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
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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 …
Discovering Weak Community Structures In Large Biological Networks , Jianhua Ruan, Weixiong Zhang
Discovering Weak Community Structures In Large Biological Networks , Jianhua Ruan, Weixiong Zhang
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Identifying intrinsic structures in large networks is a fundamental problem in many fields, such as biology, engineering and social sciences. Motivated by biology applications, in this paper we are concerned with identifying community structures, which are densely connected sub-graphs, in large biological networks. We address several critical issues for finding community structures. First, biological networks directly constructed from experimental data often contain spurious edges and may also miss genuine connections. As a result, community structures in biological networks are often weak. We introduce simple operations to capture local neighborhood structures for identifying weak communities. Second, we consider the issue of …
Design And Evaluation Of A Blast Ungapped Extension Accelerator, Master's Thesis, Joseph M. Lancaster
Design And Evaluation Of A Blast Ungapped Extension Accelerator, Master's Thesis, Joseph M. Lancaster
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The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data is becoming an increasingly difficult task. This thesis focuses on accelerating the most widely-used software tool for analyzing genomic data, BLAST. This thesis presents Mercury BLAST, a novel method for accelerating searches through massive DNA databases. Mercury BLAST takes a streaming approach to the BLAST computation by offloading the performance-critical sections onto reconfigurable hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of …
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.
Automatic Application-Specific Customization Of Softcore Processor Microarchitecture, Masters Thesis, May 2006, Shobana Padmanabhan
Automatic Application-Specific Customization Of Softcore Processor Microarchitecture, Masters Thesis, May 2006, Shobana Padmanabhan
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Applications for constrained embedded systems are subject to strict runtime and resource utilization bounds. With soft core processors, application developers can customize the processor for their application, constrained by available hardware resources but aimed at high application performance. The more reconfigurable the processor is, the more options the application developers will have for customization and hence increased potential for improving application performance. However, such customization entails developing in-depth familiarity with all the parameters, in order to configure them effectively. This is typically infeasible, given the tight time-to-market pressure on the developers. Alternatively, developers could explore all possible configurations, but being …
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 …
Distributed Utilization Control For Real-Time Clusters With Load Balancing, Yong Fu, Hongan Wang, Chenyang Lu, Ramu S. Chandra
Distributed Utilization Control For Real-Time Clusters With Load Balancing, Yong Fu, Hongan Wang, Chenyang Lu, Ramu S. Chandra
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Recent years have seen rapid growth of online services that rely on large-scale server clusters to handle high volume of requests. Such clusters must adaptively control the CPU utilizations of many processors in order to maintain desired soft real-time performance and prevent system overload in face of unpredictable workloads. This paper presents DUC-LB, a novel distributed utilization control algorithm for cluster-based soft real-time applications. Compared to earlier works on utilization control, a distinguishing feature of DUC-LB is its capability to handle system dynamics caused by load balancing, which is a common and essential component of most clusters today. Simulation results …
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.
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, …
A Theory Of Load Adjustments And Its Implications For Congestion Control, Sergey Gorinsky, Manfred Georg, Maxim Podlesny, Christoph Jechlitschek
A Theory Of Load Adjustments And Its Implications For Congestion Control, Sergey Gorinsky, Manfred Georg, Maxim Podlesny, Christoph Jechlitschek
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Multiplicative Increase (MI), Additive Increase (AI), and Multiplicative Decrease (MD) are linear adjustments used extensively in networking. However, their properties are not fully understood. We analyze responsiveness (time for the total load to reach the target load), smoothness (maximal size of the total load oscillations after reaching the target load), fairing speed (speed of convergence to equal individual loads) and scalabilities of MAIMD algorithms, which generalize AIMD algorithms via optional inclusion of MI. We prove that an MAIMD can provide faster asymptotic fairing than a less smooth AIMD. Furthermore, we discover that loads under a specific MAIMD converge from any …
Three Dimensional Panoramic Fast Flourescence Imaging Of Cardiac Arryhtymias In The Rabbit Heart, Fujian Qu, Vladimir P. Nikolski, Cindy Grimm, Igor R. Efimov
Three Dimensional Panoramic Fast Flourescence Imaging Of Cardiac Arryhtymias In The Rabbit Heart, Fujian Qu, Vladimir P. Nikolski, Cindy Grimm, Igor R. Efimov
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Cardiac high spatio-temporal optical mapping provides a unique opportunity to investigate the dynamics of propagating waves of excitation during ventricular arrhythmia and defibrillation. However, studies using single camera imaging systems are hampered by the inability to monitor electrical activity from the entire surface of the heart. We have developed a three dimensional panoramic imaging system which allows high-resolution and high-dynamic-range optical mapping from the entire surface of the heart. Rabbit hearts (n=4) were Langendorff perfused and imaged by the system during sinus rhythm, epicardial pacing, and arrhythmias. The reconstructed 3D electrical activity provides us with a powerful tool to investigate …
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 …
Activepdf-Toolk, Washington University In St. Louis Computer Science Engineering Department
Activepdf-Toolk, Washington University In St. Louis Computer Science Engineering Department
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This document provides information for deploying activePDF Toolkit Professional in a development environment. This document is organized into four sections: Getting Started, Tutorials, Technical Reference and the Toolkit Appendices. The Getting Started section covers setup and installation, includes a product overview and information related to operating Toolkit Professional. Tutorials includes examples of many Toolkit features, including PDF generation and form filling. All of the tutorials can be used with activePDF Toolkit. Technical Reference provides detailed information on Toolkit’s objects, subobjects, methods and properties.
Knuth-Bendix Completion With Modern Termination Checking, Master's Thesis, August 2006, Ian Wehrman
Knuth-Bendix Completion With Modern Termination Checking, Master's Thesis, August 2006, Ian Wehrman
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Knuth-Bendix completion is a technique for equational automated theorem proving based on term rewriting. This classic procedure is parametrized by an equational theory and a (well-founded) reduction order used at runtime to ensure termination of intermediate rewriting systems. Any reduction order can be used in principle, but modern completion tools typically implement only a few classes of such orders (e.g., recursive path orders and polynomial orders). Consequently, the theories for which completion can possibly succeed are limited to those compatible with an instance of an implemented class of orders. Finding and specifying a compatible order, even among a small number …
Multimodal Congestion Control For Low Stable-State Queuing, Maxim Podlesny, Sergey Gorinsky
Multimodal Congestion Control For Low Stable-State Queuing, Maxim Podlesny, Sergey Gorinsky
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To discover an efficient fair sending rate for a flow, Transmission Control Protocol (TCP) saturates the bottleneck link and its buffer until the router discards a packet. Such TCP-caused queuing is detrimental for interactive and other delay-sensitive applications. In this paper, we present Multimodal Control Protocol (MCP) which strives to maintain low queues and avoid congestion losses at network links. The multimodal MCP engages routers and hosts in limited explicit communication. A distinguishing property of MCP is stable transmission after converging to efficient fair states. To ensure convergence to fairness, MCP incorporates an innovative mechanism that enables a flow to …
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
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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 …
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
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No abstract provided.
Dynamic Resource Management In A Static Network Operating System, Kevin Klues, Vlado Handziski, David Culler, David Gay, Phillip Levis Levis, Chenyang Lu, Adam Wolisz
Dynamic Resource Management In A Static Network Operating System, Kevin Klues, Vlado Handziski, David Culler, David Gay, Phillip Levis Levis, Chenyang Lu, Adam Wolisz
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We present novel approaches to managing three key resources in an event-driven sensornet OS: memory, energy, and peripherals. We describe the factors that necessitate using these new approaches rather than existing ones. A combination of static allocation and compile-time virtualization isolates resources from one another, while dynamic management provides the flexibility and sharing needed to minimize worst-case overheads. We evaluate the effectiveness and efficiency of these management policies in comparison to those of TinyOS 1.x, SOS, MOS, and Contiki. We show that by making memory, energy, and peripherals first-class abstractions, an OS can quickly, efficiently, and accurately adjust itself to …
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.
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 …
A View-Based Deformation Tool-Kit, Master's Thesis, August 2006, Nisha Sudarsanam
A View-Based Deformation Tool-Kit, Master's Thesis, August 2006, Nisha Sudarsanam
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Camera manipulation is a hard problem since a graphics camera is defined by specifying 11 independent parameters. Manipulating such a high-dimensional space to accomplish specific tasks is difficult and requires a certain amount of expertise. We present an intuitive interface that allows novice users to perform camera operations in terms of the change they want see in the image. In addition to developing a natural means for camera interaction, our system also includes a novel interface for viewing and organizing previously saved views. When exploring complex 3D data-sets a single view is not sufficient. Instead, a composite view built from …
Design Issues Of Reserved Delivery Subnetworks, Doctoral Dissertation, May 2006, Ruibiao Qiu
Design Issues Of Reserved Delivery Subnetworks, Doctoral Dissertation, May 2006, Ruibiao Qiu
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The lack of per-flow bandwidth reservation in today's Internet limits the quality of service that an information service provider can provide. This dissertation introduces the reserved delivery subnetwork (RDS), a mechanism that provides consistent quality of service by implementing aggregate bandwidth reservation. A number of design and deployment issues of RDSs are studied. First, the configuration problem of a single-server RDS is formulated as a minimum concave cost network flow problem, which properly reflects the economy of bandwidth aggregation, but is also an NP-hard problem. To make the RDS configuration problem tractable, an efficient approximation heuristic, largest demands first (LDF), …
Towards A Unified Radio Power Management Architecture For Wireless Sensor Networks, Kevin Klues, Guoliang Xing, Chenyang Lu
Towards A Unified Radio Power Management Architecture For Wireless Sensor Networks, Kevin Klues, Guoliang Xing, Chenyang Lu
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In many wireless sensor networks, energy is an extremely limited resource. While many different power management strategies have been proposed to help reduce the amount of energy wasted, application developers still face two fundamental challenges when developing systems with stringent power constraints. First, existing power management strategies are usually tightly coupled with network protocols and other system functionality. This monolithic approach has led to standalone solutions that cannot easily be reused or extended to other applications or platforms. Second, different power management strategies make different and sometimes even conflicting assumptions about the rest of the system with which they need …
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. …