Computer Engineering Commons^™

Multi-Break Rearrangements And Breakpoint Re-Uses: From Circular To Linear Genomes, Max A. Alekseyev

Faculty Publications

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Alekseyev and Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion …

Improving Reversal Median Computation Using Commuting Reversals And Cycle Information, William Arndt, Jijun Tang

Faculty Publications

In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods for reconstructing phylogeny from genome rearrangements include distance-based methods, MCMC methods, and direct optimization methods. The latter, pioneered by Sankoff and extended with the software suites GRAPPA and MGR, is the most accurate approach, but is very limited due to the difficulty of its scoring procedure—it must solve multiple instances of the reversal median problem to compute the score of a given tree. The reversal median problem is known to be NP-hard and all …

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 …

Phylogenetic Reconstruction From Transpositions, Feng Yue, Meng Zhang, Jijun Tang

Faculty Publications

Background
Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangement of these entities through computational means. As a result, genome rearrangement data has attracted increasing attentions from both biologists and computer scientists as a new type of data for phylogenetic analysis. The main events of genome rearrangements include inversions, transpositions and transversions. To date, GRAPPA and MGR are the most accurate …

Gene Rearrangement Analysis And Ancestral Order Inference From Chloroplast Genomes With Inverted Repeat, Feng Yue, Liying Cui, Claude W. Depamphilis, Bernard M.E. Moret, Jijun Tang

Faculty Publications

Background
Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction.

Results
We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR …

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

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.

Are There Rearrangement Hotspots In The Human Genome?, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of chromosome evolution. Despite the fact that RBM had prophetic prediction power, it was recently refuted by Pevzner and Tesler [4], who introduced the fragile breakage model (FBM), postulating that the human genome is a mosaic of solid regions (with low propensity for rearrangements) and fragile regions (rearrangement hotspots). However, the rebuttal …

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 …

Localization With Limited Sensing, Jason M. O'Kane, Steven M. Lavalle

Faculty Publications

Localization is a fundamental problem for many kinds of mobile robots. Sensor systems of varying ability have been proposed and successfully used to solve the problem. This paper probes the lower limits of this range by describing three extremely simple robot models and addresses the active localization problem for each. The robot, whose configuration is composed of its position and orientation, moves in a fully-known, simply connected polygonal environment. We pose the localization task as a planning problem in the robot's information space, which encapsulates the uncertainty in the robot's configuration. We consider robots equipped with: 1) angular and linear …

Fpga Acceleration Of Gene Rearrangement Analysis, Jason D. Bakos

Faculty Publications

In this paper we present our work toward FPGA acceleration of phylogenetic reconstruction, a type of analysis that is commonly performed in the fields of systematic biology and comparative genomics. In our initial study, we have targeted a specific application that reconstructs maximum-parsimony (MP) phylogenies for gene-rearrangement data. Like other prevalent applications in computational biology, this application relies on a control-dependent, memory-intensive, and non-arithmetic combinatorial optimization algorithm. To achieve hardware acceleration, we developed an FPGA core design that implements the application's primary bottleneck computation. Because our core is lightweight, we are able to synthesize multiple cores on a single FPGA. …

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. …

Whole Genome Duplications And Contracted Breakpoint Graphs, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

The genome halving problem, motivated by the whole genome duplication events in molecular evolution, was solved by El-Mabrouk and Sankoff in the pioneering paper [SIAM J. Comput., 32 (2003), pp. 754–792]. The El-Mabrouk–Sankoff algorithm is rather complex, inspiring a quest for a simpler solution. An alternative approach to the genome halving problem based on the notion of the contracted breakpoint graph was recently proposed in [M. A. Alekseyev and P. A. Pevzner, IEEE/ACM Trans. Comput. Biol. Bioinformatics, 4 (2007), pp. 98–107]. This new technique reveals that while the El-Mabrouk–Sankoff result is correct in most cases, it does not hold in …

Colored De Bruijn Graphs And The Genome Halving Problem, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

Breakpoint graph analysis is a key algorithmic technique in studies of genome rearrangements. However, breakpoint graphs are defined only for genomes without duplicated genes, thus limiting their applications in rearrangement analysis. We discuss a connection between the breakpoint graphs and de Bruijn graphs that leads to a generalization of the notion of breakpoint graph for genomes with duplicated genes. We further use the generalized breakpoint graphs to study the Genome Halving Problem (first introduced and solved by Nadia El-Mabrouk and David Sankoff). The El-Mabrouk-Sankoff algorithm is rather complex, and, in this paper, we present an alternative approach that is based …

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

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

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 …

Adaptive Evolution Of Chloroplast Genome Structure Inferred Using A Parametric Bootstrap Approach, Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David B. Stern, Claude W. Depamphilis

Faculty Publications

Background
Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the …

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

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

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

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

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.

Every Polynomial-Time 1-Degree Collapses If And Only If P=Pspace, Stephen A. Fenner, Stuart A. Kurtz, James S. Royer

Faculty Publications

No abstract provided.

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

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 …

Identity Management, Duncan A. Buell, Ravi Sandhu

Faculty Publications

No abstract provided.

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 …

The Zen Of The Web, Jeff Heflin, Michael N. Huhns

Faculty Publications

No abstract provided.

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.