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Full-Text Articles in Engineering
Fpga Acceleration Of The Phylogenetic Likelihood Function For Bayesian Mcmc Inference Methods, Stephanie Zierke, Jason D. Bakos
Fpga Acceleration Of The Phylogenetic Likelihood Function For Bayesian Mcmc Inference Methods, Stephanie Zierke, Jason D. Bakos
Faculty Publications
Background
Likelihood (ML)-based phylogenetic inference has become a popular method for estimating the evolutionary relationships among species based on genomic sequence data. This method is used in applications such as RAxML, GARLI, MrBayes, PAML, and PAUP. The Phylogenetic Likelihood Function (PLF) is an important kernel computation for this method. The PLF consists of a loop with no conditional behavior or dependencies between iterations. As such it contains a high potential for exploiting parallelism using micro-architectural techniques. In this paper, we describe a technique for mapping the PLF and supporting logic onto a Field Programmable Gate Array (FPGA)-based co-processor. By leveraging …
High-Performance Heterogeneous Computing With The Convey Hc-1, Jason D. Bakos
High-Performance Heterogeneous Computing With The Convey Hc-1, Jason D. Bakos
Faculty Publications
Unlike other socket-based reconfigurable coprocessors, the Convey HC-1 contains nearly 40 field-programmable gate arrays, scatter-gather memory modules, a high-capacity crossbar switch, and a fully coherent memory system.
Integrated Circuit Implementation For A Gan Hfet Driver Circuit, Bo Wang, Jason D. Bakos, Antonello Monti
Integrated Circuit Implementation For A Gan Hfet Driver Circuit, Bo Wang, Jason D. Bakos, Antonello Monti
Faculty Publications
This paper presents the design and implementation of a new integrated circuit (IC) that is suitable for driving the new generation of high-frequency GaN HFETs. The circuit, based upon a resonant switching transition technique, is first briefly described and then discussed in detail, focusing on the design process practical considerations. A new level-shifter topology, used to generate the zero and negative gate-source voltages required to switch the GaN HFET, is introduced and analyzed. The experimental measurements included in this paper report the results of tests carried out on an IC designed and fabricated as part of the multiproject die in …
Exploiting Matrix Symmetry To Improve Fpgaaccelerated Conjugate Gradient, Jason D. Bakos, Krishna K. Nagar
Exploiting Matrix Symmetry To Improve Fpgaaccelerated Conjugate Gradient, Jason D. Bakos, Krishna K. Nagar
Faculty Publications
In this paper we describe a new approach for accelerating the Conjugate Gradient (CG) method using an FPGA co-processor. As in previous approaches, our co-processor performs a double-precision sparse matrix-vector multiplication. However, our implementation doubles the amount of computation per unit of input data by exploiting the symmetry of the input matrix and computing the upper and lower triangle of the input matrix in parallel. Using a Virtex-2 Pro 100 FPGA, we have achieved an observed computational throughput of 1155 MFLOPS.
Agents And Service-Oriented Computing For Autonomic Computing: A Research Agenda, Frances M.T. Brazier, Jeffrey O. Kephart, H. Van Dyke Parunak, Michael N. Huhns
Agents And Service-Oriented Computing For Autonomic Computing: A Research Agenda, Frances M.T. Brazier, Jeffrey O. Kephart, H. Van Dyke Parunak, Michael N. Huhns
Faculty Publications
Autonomic computing is the solution proposed to cope with the complexity of today's computing environments. Self-management, an important element of autonomic computing, is also characteristic of single and multiagent systems, as well as systems based on service-oriented architectures. Combining these technologies can be profitable for all - in particular, for the development of autonomic computing systems.
A Special-Purpose Architecture For Solving The Breakpoint Median Problem, Jason D. Bakos, Panormitis E. Elenis
A Special-Purpose Architecture For Solving The Breakpoint Median Problem, Jason D. Bakos, Panormitis E. Elenis
Faculty Publications
In this paper, we describe the design for a co-processor for whole-genome phylogenetic reconstruction. Our current design performs a parallelized breakpoint median computation, which is an expensive component of the overall application. When implemented on a field-programmable gate array (FPGA), our hardware breakpoint median achieves a maximum speedup of 1005times over software. When the coprocessor is used to accelerate the entire reconstruction procedure, we achieve a maximum application speedup of 417times. The results in this paper suggest that FPGA-based acceleration is a promising approach for computationally expensive phylogenetic problems, in spite of the fact that the involved algorithms are based …
Evaluating Shape Correspondence For Statistical Shape Analysis: A Benchmark Study, Brent C. Munsell, Pahal Dalal, Song Wang
Evaluating Shape Correspondence For Statistical Shape Analysis: A Benchmark Study, Brent C. Munsell, Pahal Dalal, Song Wang
Faculty Publications
This paper introduces a new benchmark study to evaluate the performance of landmark-based shape correspondence used for statistical shape analysis. Different from previous shape-correspondence evaluation methods, the proposed benchmark first generates a large set of synthetic shape instances by randomly sampling a given statistical shape model that defines a ground-truth shape space. We then run a test shape-correspondence algorithm on these synthetic shape instances to identify a set of corresponded landmarks. According to the identified corresponded landmarks, we construct a new statistical shape model, which defines a new shape space. We finally compare this new shape space against the ground-truth …
Globally Optimal Grouping For Symmetric Closed Boundaries By Combining Boundary And Region Information, Joachim S. Stahl, Song Wang
Globally Optimal Grouping For Symmetric Closed Boundaries By Combining Boundary And Region Information, Joachim S. Stahl, Song Wang
Faculty Publications
Many natural and man-made structures have a boundary that shows a certain level of bilateral symmetry, a property that plays an important role in both human and computer vision. In this paper, we present a new grouping method for detecting closed boundaries with symmetry. We first construct a new type of grouping token in the form of symmetric trapezoids by pairing line segments detected from the image. A closed boundary can then be achieved by connecting some trapezoids with a sequence of gap-filling quadrilaterals. For such a closed boundary, we define a unified grouping cost function in a ratio form: …
Web-Scale Workflow: Integrating Distributed Services, M. Brian Blake, Michael N. Huhns
Web-Scale Workflow: Integrating Distributed Services, M. Brian Blake, Michael N. Huhns
Faculty Publications
Modular applications, components, and services are all ways of describing the product of an organization's efforts to embody its capabilities in autonomous software modules. In fact, the integration of services using well-established workflow paradigms could amplify an organization's capabilities with the creation of a full-blown, inter-organizational system of systems. This is the essence of Web-scale workflows. Considering the recent popularity and acceptance of service-oriented technologies, the application of such distributed systems is only limited by imagination, but it's also important to understand existing research challenges and their implications to various Web-scale workflow domains.
Edge Grouping Combining Boundary And Region Information, Joachim S. Stahl, Song Wang
Edge Grouping Combining Boundary And Region Information, Joachim S. Stahl, Song Wang
Faculty Publications
This paper introduces a new edge-grouping method to detect perceptually salient structures in noisy images. Specifically, we define a new grouping cost function in a ratio form, where the numerator measures the boundary proximity of the resulting structure and the denominator measures the area of the resulting structure. This area term introduces a preference towards detecting larger-size structures and, therefore, makes the resulting edge grouping more robust to image noise. To find the optimal edge grouping with the minimum grouping cost, we develop a special graph model with two different kinds of edges and then reduce the grouping problem to …
Lightweight Error Correction Coding For System-Level Interconnects, Jason D. Bakos, Donald M. Chiarulli, Steven P. Levitan
Lightweight Error Correction Coding For System-Level Interconnects, Jason D. Bakos, Donald M. Chiarulli, Steven P. Levitan
Faculty Publications
"Lightweight hierarchical error control coding (LHECC)" is a new class of nonlinear block codes that is designed to increase noise immunity and decrease error rate for high-performance chip-to-chip and on-chip interconnects. LHECC is designed such that its corresponding encoder and decoder logic may be tightly integrated into compact, high-speed, and low-latency I/O interfaces. LHECC operates over a new channel technology called multi-bit differential signaling (MBDS). MBDS channels utilize a physical-layer channel code called "N choose M (nCm)" encoding, where each channel is restricted to a symbol set such that half of the bits in each symbol are set to one. …
Jamming Sensor Networks: Attack And Defense Strategies, Wenyuan Xu, Wade Trappe, Yanyong Zhang
Jamming Sensor Networks: Attack And Defense Strategies, Wenyuan Xu, Wade Trappe, Yanyong Zhang
Faculty Publications
Wireless sensor networks are built upon a shared medium that makes it easy for adversaries to conduct radio interference, or jamming, attacks that effectively cause a denial of service of either transmission or reception functionalities. These attacks can easily be accomplished by an adversary by either bypassing MAC-layer protocols or emitting a radio signal targeted at jamming a particular channel. In this article we survey different jamming attacks that may be employed against a sensor network. In order to cope with the problem of jamming, we discuss a two-phase strategy involving the diagnosis of the attack, followed by a suitable …
A Reconfigurable Distributed Computing Fabric Exploiting Multilevel Parallelism, Charles L. Cathey, Jason D. Bakos, Duncan A. Buell
A Reconfigurable Distributed Computing Fabric Exploiting Multilevel Parallelism, Charles L. Cathey, Jason D. Bakos, Duncan A. Buell
Faculty Publications
This paper presents a novel reconfigurable data flow processing architecture that promises high performance by explicitly targeting both fine- and course-grained parallelism. This architecture is based on multiple FPGAs organized in a scalable direct network that is substantially more interconnect-efficient than currently used crossbar technology. In addition, we discuss several ancillary issues and propose solutions required to support this architecture and achieve maximal performance for general-purpose applications; these include supporting IP, mapping techniques, and routing policies that enable greater flexibility for architectural evolution and code portability.
Convergence Of Ipsec In Presence Of Resets, Chin-Tser Huang, Mohamed G. Gouda, E.N. Elnozahy
Convergence Of Ipsec In Presence Of Resets, Chin-Tser Huang, Mohamed G. Gouda, E.N. Elnozahy
Faculty Publications
IPsec is the current security standard for the Internet Protocol IP. According to this standard, a selected computer pair (p, q) in the Internet can be designated a “security association”. This designation guarantees that all sent IP messages whose original source is computer p and whose ultimate destination is computer q cannot be replayed in the future (by an adversary between p and q) and still be received by computer q as fresh messages from p. This guarantee is provided by adding increasing sequence numbers to all IP messages sent from p to q. Thus, p needs to always remember …
Concurrent Multiple- Issue Negotiation For Internet-Based Services, Jiangbo Dang, Michael N. Huhns
Concurrent Multiple- Issue Negotiation For Internet-Based Services, Jiangbo Dang, Michael N. Huhns
Faculty Publications
Negotiation is a technique for reaching a mutually beneficial agreement among autonomous entities. In an Internet-based services context, multiple entities are negotiating simultaneously. The concurrent negotiation protocol extends existing negotiation protocols, letting both service requestors and service providers manage several negotiation processes in parallel. Colored Petri nets, which have greater expressive power than finite state machines and offer support for concurrency, represent the negotiation protocol and facilitate the analysis of desirable properties.
Salient Closed Boundary Extraction With Ratio Contour, Song Wang, Toshiro Kubota, Jeffrey Mark Siskind, Jun Wang
Salient Closed Boundary Extraction With Ratio Contour, Song Wang, Toshiro Kubota, Jeffrey Mark Siskind, Jun Wang
Faculty Publications
We present ratio contour, a novel graph-based method for extracting salient closed boundaries from noisy images. This method operates on a set of boundary fragments that are produced by edge detection. Boundary extraction identifies a subset of these fragments and connects them sequentially to form a closed boundary with the largest saliency. We encode the Gestalt laws of proximity and continuity in a novel boundary-saliency measure based on the relative gap length and average curvature when connecting fragments to form a closed boundary. This new measure attempts to remove a possible bias toward short boundaries. We present a polynomial-time algorithm …
Research Directions For Service-Oriented Multiagent Systems, Michael N. Huhns, Munindar P. Singh, Mark Burstein, Keith Decker, Edmund Durfee, Tim Finin, Les Gasser, Hrishikesh Goradia, Nick Jennings, Kiran Lakkaraju, Hideyuki Nakashima, H. Van Dyke Parunak, Jeffrey S. Rosenschein, Alicia Ruvinsky, Gita Sukthankar, Samarth Swarup, Katia Sycara, Milind Tambe, Tom Wagner, Laura Zavala, Mas Research Roadmap Project
Research Directions For Service-Oriented Multiagent Systems, Michael N. Huhns, Munindar P. Singh, Mark Burstein, Keith Decker, Edmund Durfee, Tim Finin, Les Gasser, Hrishikesh Goradia, Nick Jennings, Kiran Lakkaraju, Hideyuki Nakashima, H. Van Dyke Parunak, Jeffrey S. Rosenschein, Alicia Ruvinsky, Gita Sukthankar, Samarth Swarup, Katia Sycara, Milind Tambe, Tom Wagner, Laura Zavala, Mas Research Roadmap Project
Faculty Publications
Today's service-oriented systems realize many ideas from the research conducted a decade or so ago in multiagent systems. Because these two fields are so deeply connected, further advances in multiagent systems could feed into tomorrow's successful service-oriented computing approaches. This article describes a 15-year roadmap for service-oriented multiagent system research.
A Semantic Web Services Architecture, Mark Burstein, Christoph Bussler, Michal Zaremba, Tim Finn, Michael N. Huhns, Massimo Paolucci, Amit P. Sheth, Stuart Williams
A Semantic Web Services Architecture, Mark Burstein, Christoph Bussler, Michal Zaremba, Tim Finn, Michael N. Huhns, Massimo Paolucci, Amit P. Sheth, Stuart Williams
Faculty Publications
The semantic Web services initiative architecture (SWSA) committee has created a set of architectural and protocol abstractions that serve as a foundation for semantic Web service technologies. This article summarizes the committee's findings, emphasizing its review of requirements gathered from several different environments. We also identify the scope and potential requirements for a semantic Web services architecture.
Service-Oriented Computing: Key Concepts And Principles, Michael N. Huhns, Munindar P. Singh
Service-Oriented Computing: Key Concepts And Principles, Michael N. Huhns, Munindar P. Singh
Faculty Publications
Traditional approaches to software development - the ones embodied in CASE tools and modeling frameworks - are appropriate for building individual software components, but they are not designed to face the challenges of open environments. Service-oriented computing provides a way to create a new architecture that reflects components' trends toward autonomy and heterogeneity. We thus emphasize SOC concepts instead of how to deploy Web services in accord with current standards. To begin the series, we describe the key concepts and abstractions of SOC and the elements of a corresponding engineering methodology.
Multiagent Systems With Workflows, José M. Vidal, Paul A. Buhler, Christian Stahl
Multiagent Systems With Workflows, José M. Vidal, Paul A. Buhler, Christian Stahl
Faculty Publications
Industry and researchers have two different visions for the future of Web services. Industry wants to capitalize on Web service technology to automate business processes via centralized workflow enactment. Researchers are interested in the dynamic composition of Web services. We show how these two visions are points in a continuum and discuss a possible path for bridging the gap between them.
Image Segmentation With Ratio Cut, Song Wang, Jeffrey Mark Siskind
Image Segmentation With Ratio Cut, Song Wang, Jeffrey Mark Siskind
Faculty Publications
This paper proposes a new cost function, cut ratio, for segmenting images using graph-based methods. The cut ratio is defined as the ratio of the corresponding sums of two different weights of edges along the cut boundary and models the mean affinity between the segments separated by the boundary per unit boundary length. This new cost function allows the image perimeter to be segmented, guarantees that the segments produced by bipartitioning are connected, and does not introduce a size, shape, smoothness, or boundary-length bias. The latter allows it to produce segmentations where boundaries are aligned with image edges. Furthermore, the …
The Zen Of The Web, Jeff Heflin, Michael N. Huhns
The Zen Of The Web, Jeff Heflin, Michael N. Huhns
Faculty Publications
No abstract provided.
Consensus Software: Robustness And Social Good, Michael N. Huhns
Consensus Software: Robustness And Social Good, Michael N. Huhns
Faculty Publications
In this column I explore some far-reaching issues of software development that lie at the intersection of robust software and sociopolitical systems. These two areas might seem unrelated-and most software developers would likely be horrified to have politics intrude on their programming efforts-but the intersection occurs through these premises: software systems administer and control much of our societal infrastructure; people would appreciate and better accept that control if they had input into the nature of the control and the systems' behavior; designers can make software systems more robust through redundancy, in which different versions of software components might cover for …
Massive Deliberation, William H. Turkett Jr., John R. Rose, Michael N. Huhns
Massive Deliberation, William H. Turkett Jr., John R. Rose, Michael N. Huhns
Faculty Publications
Agents are proliferating on the Web, making it conceivable that their collective reasoning ability might someday be harnessed for robust decision-making. The hope is that massive deliberation power can soon help solve problems that require knowledge, reasoning, and intelligence. Until recently, working individually or in small groups, agents across the Web could barely communicate and could only reason under conditions of severely bounded rationality. Projects such as Agentcities showed that widespread heterogeneous agents could collaborate on specific predefined tasks and provide diverse agent-based services. When the tasks are dynamic, of long duration, and ill defined, however, success requires planning that …
Identity Management, Duncan A. Buell, Ravi Sandhu
Identity Management, Duncan A. Buell, Ravi Sandhu
Faculty Publications
No abstract provided.
The Sentient Web, Michael N. Huhns
The Sentient Web, Michael N. Huhns
Faculty Publications
In a startling revelation, a team of university scientists has reported that a network of computers has become conscious and sentient, and is beginning to assume control of online information system. In spite of the ominous tone typically chosen for dramatic effect, a sentient Web would be more helpful and much easier for people to use. An agent is an active, persistent software component that perceives, reasons, and acts, and whose actions include communication. Agents inherently take intentional actions based on sensory information and memories of past actions. All agents have necessary communication ability, but they do not necessarily possess …
Commitments Among Agents, Ashok U. Mallya, Michael N. Huhns
Commitments Among Agents, Ashok U. Mallya, Michael N. Huhns
Faculty Publications
Commitments are a powerful representation for modeling multiagent interactions. Previous approaches have considered the semantics of commitments and how to check compliance with them. However, these approaches do not capture some of the subtleties that arise in real-life applications such as e-commerce, in which contracts and institutions have implicit temporal references. In this column, we describe a rich representation for the temporal content of commitments that lets us capture realistic contracts and avoid ambiguities. Consequently, this approach lets us reason about whether, and at what point, a commitment is satisfied or breached, and whether it is or ever becomes unenforceable.
Being And Acting Rational, Michael N. Huhns
Being And Acting Rational, Michael N. Huhns
Faculty Publications
Rationality alone is insufficient to specify agent design. Using economic theory, we can program agents to behave in ways that maximize their utility while responding to environmental changes. However, economic models for agents, although general in principle, are typically limited in practice because the value functions that are tractable essentially reduce an agent to acting selfishly. Building a stable social system from a collection of agents motivated by self-serving interests is difficult. Finally, understanding rationality and knowledge requires interdisciplinary results from artificial intelligence, distributed.
On Localized Control In Qos Routing, Srihari Nelakuditi, Srivatsan Varadarajan, Zhi-Li Zhang
On Localized Control In Qos Routing, Srihari Nelakuditi, Srivatsan Varadarajan, Zhi-Li Zhang
Faculty Publications
In this note, we study several issues in the design of localized quality-of-service (QoS) routing schemes that make routing decisions based on locally collected QoS state information (i.e., there is no network-wide information exchange among routers). In particular, we investigate the granularity of local QoS state information and its impact on the design of localized QoS routing schemes from a theoretical perspective. We develop two theoretical models for studying localized proportional routing: one using the link-level information and the other using path-level information. We compare the performance of these localized proportional routing models with that of a global optimal proportional …
A Localized Adaptive Proportioning Approach To Qos Routing, Srihari Nelakuditi, Zhi-Li Zhang
A Localized Adaptive Proportioning Approach To Qos Routing, Srihari Nelakuditi, Zhi-Li Zhang
Faculty Publications
In QoS routing, paths for flows are selected based on knowledge of resource availability at network nodes and the QoS requirements of flows. Several QoS routing schemes have been proposed that differ in the way they gather information about the network state and select paths based on this information. We broadly categorize these schemes into best path routing and proportional routing. The best path routing schemes gather global network state information and always select the best path for an incoming I-low,based on this global view. It has been shown that best path routing schemes require frequent exchange of network state, …