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Physical Sciences and Mathematics Commons

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2007

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Full-Text Articles in Physical Sciences and Mathematics

Exploration Of Dynamic Memory, Delvin Curvin Defoe Aug 2007

Exploration Of Dynamic Memory, Delvin Curvin Defoe

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Since the advent of the Java programming language and the development of real-time garbage collection, Java has become an option for implementing real-time applications. The memory management choices provided by real-time garbage collection allow for real-time eJava developers to spend more of their time implementing real-time solutions. Unfortunately, the real-time community is not convinced that real-time garbage collection works in managing memory for Java applications deployed in a real-time context. Consequently, the Real-Time for Java Expert Group formulated the Real-Time Specification for Java (RTSJ) standards to make Java a real-time programming language. In lieu of garbage collection, the RTSJ proposed ...


Unwoven Aspect Analysis, Morgan G. Deters May 2007

Unwoven Aspect Analysis, Morgan G. Deters

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Various languages and tools supporting advanced separation of concerns (such as aspect-oriented programming) provide a software developer with the ability to separate functional and non-functional programmatic intentions. Once these separate pieces of the software have been specified, the tools automatically handle interaction points between separate modules, relieving the developer of this chore and permitting more understandable, maintainable code. Many approaches have left traditional compiler analysis and optimization until after the composition has been performed; unfortunately, analyses performed after composition cannot make use of the logical separation present in the original program. Further, for modular systems that can be configured with ...


Comparing Features Of Three-Dimensional Object Models Using Registration Based On Surface Curvature Signatures, Timothy David Gatzke, Cindy M. Grimm May 2007

Comparing Features Of Three-Dimensional Object Models Using Registration Based On Surface Curvature Signatures, Timothy David Gatzke, Cindy M. Grimm

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This dissertation presents a technique for comparing local shape properties for similar three-dimensional objects represented by meshes. Our novel shape representation, the curvature map, describes shape as a function of surface curvature in the region around a point. A multi-pass approach is applied to the curvature map to detect features at different scales. The feature detection step does not require user input or parameter tuning. We use features ordered by strength, the similarity of pairs of features, and pruning based on geometric consistency to efficiently determine key corresponding locations on the objects. For genus zero objects, the corresponding locations are ...


Performance Evaluation For Hybrid Architectures, Praveen Krishnamurthy Feb 2007

Performance Evaluation For Hybrid Architectures, Praveen Krishnamurthy

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In this dissertation we discuss methologies for estimating the performance of applications on hybrid architectures, systems that include various types of computing resources (e.g. traditional general-purpose processors, chip multiprocessors, reconfigurable hardware). A common use of hybrid architectures will be to deploy coarse pipeline stages of application on "suitable" compute units with communication path for transferring data. The first problem we focus on relates to the sizing the data queues between the different processing elements of an hybrid system. Much of the discussion centers on our analytical models that can be used to derive performance metrics of interest such as ...


A Fingerspelling Sign Language Visualization , Carol S. Brickman Jan 2007

A Fingerspelling Sign Language Visualization , Carol S. Brickman

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The goal of the Fingerspell Visualization Project is to research methods to improve learning of reading skills through sign language. The techniques are centered on Fingerspelling as the method to bridge stages of skill development. Visualization of a string of text in images of a hand performing the letters of the alphabet in standardized fingerspell sign language positions provide Full Motion Learning as opposed to learning from single pictures.


Implementing Legba: Fine-Grained Memory Protection, Sheffield, Sowell, Wilson Jan 2007

Implementing Legba: Fine-Grained Memory Protection, Sheffield, Sowell, Wilson

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Fine-grained hardware protection could provide a powerful and effective means for isolating untrusted code. However, previous techniques for providing fine-grained protection in hardware have lead to poor performance. Legba has been proposed as a new caching architecture, designed to reduce the granularity of protection, without slowing down the processor. Unfortunately, the designers of Legba have not attempted an implementation. Instead, all of their analysis is based purely on simulations. We present an implementation of the Legba design on a MIPS Core Processor, along with an analysis of our observations and results.


Mlds: A Flexible Location Directory Service For Tiered Sensor Networks, Sangeeta Bhattacharya, Chien-Liang Fok, Chenyang Lu, Gruia-Catalin Roman Jan 2007

Mlds: A Flexible Location Directory Service For Tiered Sensor Networks, Sangeeta Bhattacharya, Chien-Liang Fok, Chenyang Lu, Gruia-Catalin Roman

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Many emergent distributed sensing applications need to keep track of mobile entities across multiple sensor networks connected via an IP network. To simplify the realization of such applications, we present MLDS, a Multi-resolution Location Directory Service for tiered sensor networks. MLDS provides a rich set of spatial query services ranging from simple queries about entity location, to complex nearest neighbor queries. Furthermore, MLDS supports multiple query granularities which allow an application to achieve the desired tradeoff between query accuracy and communication cost. We implemented MLDS on Agimone, a unified middleware for sensor and IP networks. We then deployed and evaluated ...


Real-Time Query Scheduling For Wireless Sensor Networks, Octav Chipara, Chenyang Lu, Gruia-Catalin Roman Jan 2007

Real-Time Query Scheduling For Wireless Sensor Networks, Octav Chipara, Chenyang Lu, Gruia-Catalin Roman

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Recent years have seen the emergence of wireless sensor network (WSN) systems that require high data rate real-time communication. This paper proposes Real-Time Query Scheduling (RTQS), a novel approach to conflict-free transmission scheduling for real-time queries in WSNs. We show that there is an inherent trade-off between prioritization and throughput in conflict-free query scheduling. RTQS provides three new real-time scheduling algorithms. The non-preemptive query scheduling algorithm achieves high throughput while introducing priority inversions. The preemptive query scheduling algorithm eliminates priority inversion at the cost of reduced throughput. The slack stealing query scheduling algorithm combines the benefits of preemptive and non-preemptive ...


A Duality Theory With Zero Duality Gap For Nonlinear Programming, Yixin Chen Jan 2007

A Duality Theory With Zero Duality Gap For Nonlinear Programming, Yixin Chen

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Duality is an important notion for constrained optimization which provides a theoretical foundation for a number of constraint decomposition schemes such as separable programming and for deriving lower bounds in space decomposition algorithms such as branch and bound. However, the conventional duality theory has the fundamental limit that it leads to duality gaps for nonconvex optimization problems, especially discrete and mixed-integer problems where the feasible sets are nonconvex. In this paper, we propose a novel extended duality theory for nonlinear optimization that overcomes some limitations of previous dual methods. Based on a new dual function, the extended duality theory leads ...


Network Access In A Diversified Internet, M. Wilson, F. Kuhns, J. Turner Jan 2007

Network Access In A Diversified Internet, M. Wilson, F. Kuhns, J. Turner

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There is a growing interest in virtualized network infrastructures as a means to enable experimental evaluation of new network architectures on a realistic scale. The National Science Foundation's GENI initiative seeks to develop a national experimental facility that would include virtualized network platforms that can support many concurrent experimental networks. Some researchers seek to make virtualization a central architectural component of a future Internet, so that new network architectures can be introduced at any time, without the barriers to entry that currently make this difficult. This paper focuses on how to extend the concept of virtualized networking through LAN-based ...


Optimal Discrete Rate Adaptation For Distributed Real-Time Systems With End-To-End Tasks, Yingming Chen, Chenyang Lu, Xenofon Koutsoukos Jan 2007

Optimal Discrete Rate Adaptation For Distributed Real-Time Systems With End-To-End Tasks, Yingming Chen, Chenyang Lu, Xenofon Koutsoukos

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Many distributed real-time systems face the challenge of dynamically maximizing system utility in response to fluctuations in system workload. We present the MultiParametric Rate Adaptation (MPRA) algorithm for discrete rate adaptation in distributed real-time systems with end-to-end tasks. The key novelty and advantage of MPRA is that it can efficiently produce optimal solutions in response to workload changes such as dynamic task arrivals. Through oline preprocessing MPRA transforms a NP-hard utility optimization problem to a set of simple linear functions in different regions expressed in term of CPU utilization changes caused by workload variations. At run time MPRA produces optimal ...


Emergent Task Allocation For Mobile Robots Through Intentions And Directives, Nuzhet Atay, Burchan Bayazit Jan 2007

Emergent Task Allocation For Mobile Robots Through Intentions And Directives, Nuzhet Atay, Burchan Bayazit

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Multi-robot systems require efficient and accurate planning in order to perform mission-critical tasks. However, algorithms that find the optimal solution are usually computationally expensive and may require a large number of messages between the robots as the robots need to be aware of the global spatiotemporal information. In this paper, we introduce an emergent task allocation approach for mobile robots. Each robot uses only the information obtained from its immediate neighbors in its decision. Our technique is general enough to be applicable to any task allocation scheme as long as a utilization criteria is given. We demonstrate that our approach ...


Expression Profiling Of Human Donor Lungs To Understand Primary Graft Dysfunction After Lung Transplantation, Monika Ray, Sekhar Dharmarajan, Johannes Freudenberg, Weixiong Zhang, Alexander G. Patterson Jan 2007

Expression Profiling Of Human Donor Lungs To Understand Primary Graft Dysfunction After Lung Transplantation, Monika Ray, Sekhar Dharmarajan, Johannes Freudenberg, Weixiong Zhang, Alexander G. Patterson

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Lung transplantation is the treatment of choice for end-stage pulmonary diseases. A limited donor supply has resulted in 4000 patients on the waiting list. Currently, 10-20% of donor organs offered for transplantation are deemed suitable under the selection criteria, of which 15-25% fails due to primary graft dysfunction (PGD). This has resulted in increased efforts to search for alternative donor lungs selection criteria. In this study, we attempt to further our understanding of PGD by observing the changes in gene expression across donor lungs that developed PGD versus those that did not. Our second goal is to use a machine ...


Determining Alpha-Helix Correspondence For Protein Structure Prediction From Cryo-Em Density Maps, Master's Thesis, May 2007, Sasakthi S. Abeysinghe Jan 2007

Determining Alpha-Helix Correspondence For Protein Structure Prediction From Cryo-Em Density Maps, Master's Thesis, May 2007, Sasakthi S. Abeysinghe

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Determining protein structure is an important problem for structural biologists, which has received a significant amount of attention in the recent years. In this thesis, we describe a novel, shape-modeling approach as an intermediate step towards recovering 3D protein structures from volumetric images. The input to our method is a sequence of alpha-helices that make up a protein, and a low-resolution volumetric image of the protein where possible locations of alpha-helices have been detected. Our task is to identify the correspondence between the two sets of helices, which will shed light on how the protein folds in space. The central ...


Splice: A Standardized Peripheral Logic And Interface Creation Engine, Justin Thiel Jan 2007

Splice: A Standardized Peripheral Logic And Interface Creation Engine, Justin Thiel

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Recent advancements in FPGA technology have allowed manufacturers to place general-purpose processors alongside user-configurable logic gates on a single chip. At first glance, these integrated devices would seem to be the ideal deployment platform for hardware-software co-designed systems, but some issues, such as incompatibility across vendors and confusion over which bus interfaces to support, have impeded adoption of these platforms. This thesis describes the design and operation of Splice, a software-based code generation tool intended to address these types of issues by providing a bus-independent structure that allows end-users to easily integrate their customized peripheral logic into embedded systems. To ...


Splice: A Standardized Peripheral Logic And Interface Creation Engine, Master's Thesis, May 2007, Justin Thiel Jan 2007

Splice: A Standardized Peripheral Logic And Interface Creation Engine, Master's Thesis, May 2007, Justin Thiel

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Recent advancements in FPGA technology have allowed manufacturers to place general-purpose processors alongside user-configurable logic gates on a single chip. At first glance, these integrated devices would seem to be the ideal deployment platform for hardware-software co-designed systems, but some issues, such as incompatibility across vendors and confusion over which bus interfaces to support, have impeded adoption of these platforms. This thesis describes the design and operation of Splice, a software-based code generation tool intended to address these types of issues by providing a bus-independent structure that allows end-users to easily integrate their customized peripheral logic into embedded systems. To ...


Price Of Asynchrony: Queuing Under Ideally Smooth Congestion Control, Maxim Podlesny, Sergey Gorinsky Jan 2007

Price Of Asynchrony: Queuing Under Ideally Smooth Congestion Control, Maxim Podlesny, Sergey Gorinsky

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The ability of TCP (Transmission Control Protocol) or alternative congestion control algorithms to operate successfully in networks with small link buffers has recently become a subject of intensive research. In this paper, we investigate fundamental limitations on minimum buffer requirements for any congestion control. We present an idealized protocol where all flows always transmit at their fair rates. The ideally smooth congestion control causes link queuing only due to asynchrony of flow arrivals, which is intrinsic to computer networks. Our analysis and simulations for different distributions of flow interarrival times agree that the buffer size needed for a fixed loss ...


Curing Regular Expressions Matching Algorithms From Insomnia, Amnesia, And Acalulia, Sailesh Kumar, Balakrishnan Chandrasekaran, Jonathan Turner, George Varghese Jan 2007

Curing Regular Expressions Matching Algorithms From Insomnia, Amnesia, And Acalulia, Sailesh Kumar, Balakrishnan Chandrasekaran, Jonathan Turner, George Varghese

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The importance of network security has grown tremendously and a collection of devices have been introduced, which can improve the security of a network. Network intrusion detection systems (NIDS) are among the most widely deployed such system; popular NIDS use a collection of signatures of known security threats and viruses, which are used to scan each packet's payload. Today, signatures are often specified as regular expressions; thus the core of the NIDS comprises of a regular expressions parser, such parsers are traditionally implemented as finite automata. Deterministic Finite Automata (DFA) are fast, therefore they are often desirable at high ...


Hexa: Compact Data Structures For Faster Packet Processing, Sailesh Kumar, Jonathan Turner, Patrick Crowley, Michael Mitzenmacher Jan 2007

Hexa: Compact Data Structures For Faster Packet Processing, Sailesh Kumar, Jonathan Turner, Patrick Crowley, Michael Mitzenmacher

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Directed graphs with edge labels are used in packet processing algorithms for a variety of network applications. In this paper we present a novel representation for such graph that significantly reduces the memory required for such graphs. This approach called History-based Encoding, eXecution and Addressing (HEXA) challenges the conventional assumption that graph data structures must store pointers of log2n bits to identify successor nodes. HEXA takes advantage of implict information to reduce the information that must be stored explicitly. We demonstrate that the binary tries used for IP route lookup can be implemented using just two bytes per stored prefix ...


Architecture For Document Clustering In Reconfigurable Hardware, Master's Thesis, December 2006, Adam G. Covington Jan 2007

Architecture For Document Clustering In Reconfigurable Hardware, Master's Thesis, December 2006, Adam G. Covington

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High-performance document clustering systems enable similar documents to automatically self-organize into groups. In the past, the large amount of computational time needed to cluster documents prevented practical use of such systems with a large number of documents. A full hardware implementation of K-means clustering has been designed and implemented in reconfigurable hardware that rapidly clusters a half million documents. Documents and concepts are represented as vectors with 4000 dimensions. The circuit was implemented in Field Programmable Gate Array (FPGA) logic and uses four parallel cosine distance metrics to cluster document vectors together. An exploration of the effect of the integer ...


Improving Individual Flow Performance With Multiple Queue Fair Queuing, Manfred Georg, Christopher Jechlitschek, Sergey Gorinsky Jan 2007

Improving Individual Flow Performance With Multiple Queue Fair Queuing, Manfred Georg, Christopher Jechlitschek, Sergey Gorinsky

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Fair Queuing (FQ) algorithms provide isolation between packet flows, allowing max-min fair sharing of a link even when flows misbehave. However, fairness comes at the expense of per-flow state. To keep the memory requirement independent of the flow count, the router can isolate aggregates of flows, rather than individual flows. We investigate the feasibility of protecting individual flows under such aggregate isolation in the context of Multiple Queue Fair Queuing (MQFQ), where the router maintains a fixed number of queues and associates multiple queues with each flow. MQFQ places packets in the shortest queue associated with their flow. The redundancy ...


Link Layer Support For Unified Radio Power Management In Wireless Sensor Networks, Master's Thesis, May 2007, Kevin Klues Jan 2007

Link Layer Support For Unified Radio Power Management In Wireless Sensor Networks, Master's Thesis, May 2007, Kevin Klues

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Radio power management is of paramount concern in wireless sensor networks that must achieve long lifetimes on scarce amounts of energy. While a multitude of power management protocols have been proposed in the past, the lack of system support for flexibly integrating them with a diverse set of applications and network platforms has made them difficult to use. Instead of proposing yet another power management protocol, this thesis focuses on providing link layer support towards realizing a Unified Power Management Architecture (UPMA) for flexible radio power management in wireless sensor networks. In contrast to the monolithic approaches adopted by existing ...


Scheduling Induced Bounds And The Verification Of Preemptive Real-Time Systems, Terry Tidwell, Christopher Gill, Venkita Subramonian Jan 2007

Scheduling Induced Bounds And The Verification Of Preemptive Real-Time Systems, Terry Tidwell, Christopher Gill, Venkita Subramonian

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Distributed real-time and embedded (DRE) systems have stringent constraints on timeliness and other properties whose assurance is crucial to correct system behavior. Our previous research has shown that detailed models of essential middleware mechanisms can be developed, composed, and for constrained examples verified tractably, using state of the art timed automata model checkers. However, to apply model checking to a wider range of real-time systems, particularly those involving more general forms of preemptive concurrency, new techniques are needed to address decidability and tractability concerns. This paper makes three contributions to research on formal verification and validation of DRE systems. First ...


Optimal Discrete Rate Adaptation For Distributed Real-Time Systems, Yingming Chen, Chenyang Lu, Xenofon Kutsoukos Jan 2007

Optimal Discrete Rate Adaptation For Distributed Real-Time Systems, Yingming Chen, Chenyang Lu, Xenofon Kutsoukos

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Many distributed real-time systems face the challenge of dynamically maximizing system utility in response to fluctuations in system workload. We present the MultiParametric Rate Adaptation (MPRA) algorithm for discrete rate adaptation in distributed real-time systems with end-to-end tasks. The key novelty and advantage of MPRA is that it can efficiently produce optimal solutions in response to workload variations such as dynamic task arrivals. Through offline preprocessing MPRA transforms an NP-hard utility optimization problem to the evaluation of a piecewise linear function of the CPU utilization. At run time MPRA produces optimal solutions by evaluating the function based on the CPU ...


Control Of A Robotic Arm Using Low-Dimensional Emg And Ecog Biofeedback, Timothy M. Blackely, William D. Smart Jan 2007

Control Of A Robotic Arm Using Low-Dimensional Emg And Ecog Biofeedback, Timothy M. Blackely, William D. Smart

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In this dissertation we describe a system that uses a low dimensional input derived from electromyography and electrocorticography data to control a robot. The work involves creating a system that allows signals recorded directly from a human body to allow control of a small robot arm. We compare direct joystick control with electromyogram (EMG) input to determine if one input system is superior, or if the quality of control between them is comparable. We also verify the system that is used to record the electromyogram signals is adaptable to other forms of biosignal input; in particular, direct connection to a ...


Configurable Component Middleware For Distributed Real-Time Systems With Aperiodic And Periodic Tasks, Yuanfang Zhang, Christopher Gill, Chenyang Lu Jan 2007

Configurable Component Middleware For Distributed Real-Time Systems With Aperiodic And Periodic Tasks, Yuanfang Zhang, Christopher Gill, Chenyang Lu

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Many distributed real-time applications must handle mixed periodic and aperiodic tasks with diverse requirements. However, existing middleware lacks flexible configuration mechanisms needed to manage end-to-end timing easily for a wide range of different applications with both periodic and aperiodic tasks. The primary contribution of this work is the design, implementation and performance evaluation of the first configurable component middleware services for admission control and load balancing of aperiodic and periodic tasks in distributed real-time systems. Empirical results demonstrate the need for and effectiveness of our configurable component middleware approach in supporting different applications with periodic and aperiodic tasks.


Distributed Allocation Of Workflow Tasks In Manets, Rohan Sen, Gruia-Catalin Roman, Christopher Gill Jan 2007

Distributed Allocation Of Workflow Tasks In Manets, Rohan Sen, Gruia-Catalin Roman, Christopher Gill

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When multiple participants work on a workflow that represents a large, collaborative activity, it is important to have a well defined process to determine the portions of the workflow that each participant is responsible for executing. In this paper, we describe a process and related algorithms required to assign tasks in a workflow, to hosts that are willing to carry out the execution of these tasks, and thereby contributing to the completion of the activity. This problem is a stylized form of the multi-processor scheduling algorithm which has been shown to be NP-Hard. Further complicating the issue is that we ...


Configuring Low Cost Metanetworks On A Shared Substrate, Jing Lu, Jonathan Turner Jan 2007

Configuring Low Cost Metanetworks On A Shared Substrate, Jing Lu, Jonathan Turner

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In a diversified internet, meta-networks (“metanets?for short) share a common substrate and offer value-added services to millions of users around the globe. Therefore, configuring low-cost metanets with links having enough bandwidth to accommodate all anticipated user traffic is critical to the success of the metanets. In this paper, we propose a novel pruning algorithm that configures metanets on any given substrate in a cost-efficient way. In contrast to other testbed configuration systems, we solve the metanet configuration problem from a higher level specification and produces a network that is dimensioned to handle the specified traffic. To the best of ...


Customizing Component Middleware For Distributed Real-Time Systems With Aperiodic And Periodic Tasks, Yuanfang Zhang, Christopher Gill, Chenyang Lu Jan 2007

Customizing Component Middleware For Distributed Real-Time Systems With Aperiodic And Periodic Tasks, Yuanfang Zhang, Christopher Gill, Chenyang Lu

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Many distributed real-time applications must handle mixed aperiodic and periodic tasks with diverse requirements. However, existing middleware lacks flexible configuration mechanisms needed to manage end-to-end timing easily for a wide range of different applications with both aperiodic and periodic tasks. The primary contribution of this work is the design, implementation and performance evaluation of the first configurable component middleware services for admission control and load balancing of aperiodic and periodic tasks in distributed real-time systems. Empirical results demonstrate the need for, and the effectiveness of, our configurable component middleware approach in supporting different applications with aperiodic and periodic tasks.


Leveraging Est Evidence To Automatically Predict Alternatively Spliced Genes, Master's Thesis, December 2006, Robert Zimmermann Jan 2007

Leveraging Est Evidence To Automatically Predict Alternatively Spliced Genes, Master's Thesis, December 2006, Robert Zimmermann

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Current methods for high-throughput automatic annotation of newly sequenced genomes are largely limited to tools which predict only one transcript per gene locus. Evidence suggests that 20-50% of genes in higher eukariotic organisms are alternatively spliced. This leaves the remainder of the transcripts to be annotated by hand, an expensive time-consuming process. Genomes are being sequenced at a much higher rate than they can be annotated. We present three methods for using the alignments of inexpensive Expressed Sequence Tags in combination with HMM-based gene prediction with N-SCAN EST to recreate the vast majority of hand annotations in the D.melanogaster ...