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2007

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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 …

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Extending Bpel For Interoperable Pervasive Computing, Gregory Hackmann, Christopher Gill, Christopher Gill, Gruia-Catalin Roman Jan 2007

Extending Bpel For Interoperable Pervasive Computing, Gregory Hackmann, Christopher Gill, Christopher Gill, Gruia-Catalin Roman

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The widespread deployment of mobile devices like PDAs and mobile phones has created a vast computation and communication platform for pervasive computing applications. However, these devices feature an array of incompatible hardware and software architectures, discouraging ad-hoc interactions among devices. The Business Process Execution Language (BPEL) allows users in wired computing settings to model applications of significant complexity, leveraging Web standards to guarantee interoperability. However, BPEL's inflexible communication model effectively prohibits its deployment on the kinds of dynamic wireless networks used by most pervasive computing devices. This paper presents extensions to BPEL that address these restrictions, transforming BPEL into a …

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Mercury Blast Dictionaries: Analysis And Performance Measurement, Jeremy Buhler Jan 2007

Mercury Blast Dictionaries: Analysis And Performance Measurement, Jeremy Buhler

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This report describes a hashing scheme for a dictionary of short bit strings. The scheme, which we call near-perfect hashing, was designed as part of the construction of Mercury BLAST, an FPGA-based accelerator for the BLAST family of biosequence comparison algorithms. Near-perfect hashing is a heuristic variant of the well-known displacement hashing approach to building perfect hash functions. It uses a family of hash functions composed from linear transformations on bit vectors and lookups in small precomputed tables, both of which are especially appropriate for implementation in ardware logic. We show empirically that for inputs derived from genomic DNA sequences, …

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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 access …

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Fair Efficiency, Or Low Average Delay Without Starvation, Christoph Jechlitschek, Sergey Gorinsky Jan 2007

Fair Efficiency, Or Low Average Delay Without Starvation, Christoph Jechlitschek, Sergey Gorinsky

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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. While SRPT (Shortest Remaining Processing Time) is an optimally efficient algorithm that minimizes average delay of messages, large messages might starve under SRPT in heavy load conditions. PS (Processor Sharing) and ViFi (Virtual Finish Time First) are fair but yield higher average delays than under SRPT. We explore the class of fair algorithms further and prove that no online algorithm in this class is optimally efficient. Then, …

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The Effect Of Object Color On Depth Ordering, Reynold Bailey, Cindy Grimm, Christopher Davoli, Richard Abrams Jan 2007

The Effect Of Object Color On Depth Ordering, Reynold Bailey, Cindy Grimm, Christopher Davoli, Richard Abrams

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The relationship between color and perceived depth for realistic, colored objects with varying shading was explored. Background: Studies have shown that warm-colored stimuli tend to appear nearer in depth than cool-colored stimuli. The majority of these studies 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 were typically highly saturated. Although such stimuli are useful for isolating and studying depth cues in certain contexts, they leave …

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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 …

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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 …

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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 …

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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 …

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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 …

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Dna Repair In Incipient Alzheimer's Disease, Monika Ray, Weixiong Zhang Jan 2007

Dna Repair In Incipient Alzheimer's Disease, Monika Ray, Weixiong Zhang

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Alzheimer’s disease (AD) is a progressive neurodegenerative disorder currently with no cure. Understanding the pathogenesis in the early stages of late-onset AD can help gain important mechanistic insights into this disease as well as aid in effective drug development. The analysis of incipient AD is steeped in difficulties due to its slight pathological and genetic differences from normal ageing. The difficulty also lies in the choice of analysis techniques as statistical power to analyse incipient AD with a small sample size, as is common in pilot studies, can be low if the proper analytical tool is not employed. In this …

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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 network …

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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 …

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Single Cell Expression Profiling Reveals Major Disruption Of Dna Repair Capacity In Incipient Alzheimer's Disease, Monika Ray, Weixiong Zhang Jan 2007

Single Cell Expression Profiling Reveals Major Disruption Of Dna Repair Capacity In Incipient Alzheimer's Disease, Monika Ray, Weixiong Zhang

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Understanding the pathogenesis in the early stages of late-onset Alzheimer's disease (LOAD) can help in gaining important mechanistic insights into this devastating neurodegenerative disorder. Alzheimer's disease (AD) is characterised by extensive cell death with disease progression. In this paper laser capture microdissection (LCM) based gene expression profiling, which is able to profile gene expression in a single cell type, is employed to analyse the gene expression regulation of incipient AD. Our analysis shows that LCM based gene expression profiling of neurons has a critical advantage over the conventional gene expression profiling method which uses samples of mixed cell types and …

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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 …

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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 …

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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 …

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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 …

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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 …

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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.

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Lower Bounds On Queuing And Loss At Highly Multiplexed Links, Maxim Podlesny, Sergey Gorinsky Jan 2007

Lower Bounds On Queuing And Loss At Highly Multiplexed Links, Maxim Podlesny, Sergey Gorinsky

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Explicit and delay-driven congestion control protocols strive to preclude overflow of link buffers by reducing transmission upon incipient congestion. In this paper, we explore fundamental limitations of any congestion control with respect to minimum queuing and loss achievable at highly multiplexed links. We present and evaluate an idealized protocol where all flows always transmit at equal rates. The ideally smooth congestion control causes link queuing only due to asynchrony of flow arrivals, which is intrinsic to computer networks. With overprovisioned buffers, our analysis and simulations for different smooth distributions of flow interarrival times agree that minimum queuing at a fully …

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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 …

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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.

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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 …

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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 …

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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 …

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Perpetual: Byzantine Fault Tolerance For Federated Distributed Applications, Sajeeva L. Pallemulle, Haraldur D. Thorvaldsson, Kenneth J. Goldman Jan 2007

Perpetual: Byzantine Fault Tolerance For Federated Distributed Applications, Sajeeva L. Pallemulle, Haraldur D. Thorvaldsson, Kenneth J. Goldman

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Modern distributed applications rely upon the functionality of services from multiple providers. Mission-critical services, possibly shared by multiple applications, must be replicated to guarantee correct execution and availability in spite of arbitrary (Byzantine) faults. Furthermore, shared services must enforce strict fault isolation policies to prevent cascading failures across organizational and application boundaries. Most existing protocols for Byzantine fault-tolerant execution do not support interoperability between replicated services while others provide poor fault isolation. Moreover, existing protocols place impractical limitations on application development by disallowing long-running threads of computation, asynchronous operation invocation, and asynchronous request processing. We present Perpetual, a protocol that …

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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, …

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Mobile Wireless Sensor Network Connectivity Repair With K-Redundanc, Nuzhet Atay, Burchan Bayazit Jan 2007

Mobile Wireless Sensor Network Connectivity Repair With K-Redundanc, Nuzhet Atay, Burchan Bayazit

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Connectivity is an important requirement for wireless sensor networks especially in real-time monitoring and data transfer applications. However, node movements and failures change the topology of the initial deployed network, which can result in partitioning of the communication graph. In this paper, we present a method for maintaining and repairing the communication network of a dynamic mobile wireless sensor network. We assume that we cannot control the motion of wireless sensor nodes, but there are robots whose motion can be controlled by the wireless sensor nodes to maintain and repair the connectivity of the network. At the heart of our …

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