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Computer Engineering

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2007

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Full-Text Articles in Engineering

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

All Computer Science and Engineering Research

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 genome. …

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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

All Computer Science and Engineering Research

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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Efficient Fair Algorithms For Message Communication, Sergey Gorinsky, Eric J. Friedman, Shane Henderson, Christoph Jechlitschek Jan 2007

Efficient Fair Algorithms For Message Communication, Sergey Gorinsky, Eric J. Friedman, Shane Henderson, Christoph Jechlitschek

All Computer Science and Engineering Research

A computer network serves distributed applications by communicating messages between their remote ends. Many such applications desire minimal delay for their messages. Beside this efficiency objective, allocation of the network capacity is also subject to the fairness constraint of not shutting off communication for any individual message. Processor Sharing (PS) is a de facto standard of fairness but provides significantly higher average delay than Shortest Remaining Processing Time (SRPT), which is an optimally efficient but unfair algorithm. In this paper, we explore efficient fair algorithms for message communication where fairness means that no message is delivered later than under PS. …

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Context-Aware Publish Subscribe In Mobile Ad Hoc Networks, Davide Frey, Gruia-Catalin Roman Jan 2007

Context-Aware Publish Subscribe In Mobile Ad Hoc Networks, Davide Frey, Gruia-Catalin Roman

All Computer Science and Engineering Research

The publish-subscribe communication paradigm is enjoying increasing popularity thanks to its ability to simplify the development of complex distributed applications. However, existing solutions in the publish-subscribe domain address only part of the challenges associated with the development of applications in dynamic scenarios such as mobile ad hoc networks. Mobile applications must be able to assist users in a variety of situations, responding not only to their inputs but also to the characteristics of the environment in which they operate. In this paper, we address these challenges by extending the publish-subscribe paradigm with the ability to manage and exploit context information …

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Roadmap Analysis Of Protein-Protein Interactions. Master's Thesis, August 2007, Brian C. Haynes Jan 2007

Roadmap Analysis Of Protein-Protein Interactions. Master's Thesis, August 2007, Brian C. Haynes

All Computer Science and Engineering Research

The ability to effectively model the interaction between proteins is an important and open problem. In molecular biology it is well accepted that from sequence arises form and from form arises function but relating structure to function remains a challenge. The function of a given protein is defined by its interactions. Likewise a malfunction or a change in protein-protein interactions is a hallmark of many diseases. Many researchers are studying the mechanisms of protein-protein interactions and one of the overarching goals of the community is to predict whether two proteins will bind, and if so what the final conformation will …

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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

All Computer Science and Engineering Research

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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Evolvable Reconfigurable Hardware Framework For Edge Detection, Nader I. Rafla Jan 2007

Evolvable Reconfigurable Hardware Framework For Edge Detection, Nader I. Rafla

Electrical and Computer Engineering Faculty Publications and Presentations

Systems on Reconfigurable Chips contain rich resources of logic, memory, and processor cores on the same fabric. This platform is suitable for implementation of Evolvable Reconfigurable Hardware Architectures (ERHA). It is based on the idea of combining reconfigurable Field Programmable Gate Arrays (FPGA) along with genetic algorithms (GA) to perform the reconfiguration operation. This architecture is a suitable candidate for implementation of early-processing stage operators of image processing such as filtering and edge detection. However, there are still fundamental issues need to be solved regarding the on-chip reprogramming of the logic. This paper presents a framework for implementing an evolvable …

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Clarifications Of Rule 2 In Teaching Geometric Dimensioning And Tolerancing, Cheng Lin, Alok Verma Jan 2007

Clarifications Of Rule 2 In Teaching Geometric Dimensioning And Tolerancing, Cheng Lin, Alok Verma

Engineering Technology Faculty Publications

Geometric dimensioning and tolerancing is a symbolic language used on engineering drawings and computer generated three-dimensional solid models for explicitly describing nominal geometry and its allowable variation. Application cases using the concept of Rule 2 in the Geometric Dimensioning and Tolerancing (GD&T) are presented. The rule affects all fourteen geometric characteristics. Depending on the nature and location where each feature control frame is specified, interpretation on the applicability of Rule 2 is quite inconsistent. This paper focuses on identifying the characteristics of a feature control frame to remove this inconsistency. A table is created to clarify the confusions for students …

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A Vector Based Method Of Ontology Matching, Z. Eidoon, N. Yazdani, Farhad Oroumchian Jan 2007

A Vector Based Method Of Ontology Matching, Z. Eidoon, N. Yazdani, Farhad Oroumchian

University of Wollongong in Dubai - Papers

Semantic interoperability is highly influenced by similarities and differences which exist between ontologies. Ontology matching as a solution for finding corresponding concepts among ontologies has emerged to facilitate semantic based negotiations of applications. This paper presents a method of ontology matching which is based on vectorizing ontologies and estimating their similarity degree. A post processing with two heuristic rules also has been employed to improve the results. The proposed method is successfully applied to the test suit of Ontology Alignment Evaluation Initiative 2005 [10] and compared to results obtained by other methods. In general the preliminary results are encouraging and …

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Whole Genome Duplications And Contracted Breakpoint Graphs, Max A. Alekseyev, Pavel A. Pevzner Jan 2007

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 …

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Colored De Bruijn Graphs And The Genome Halving Problem, Max A. Alekseyev, Pavel A. Pevzner Jan 2007

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 …

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Study Of Soliton Stabilization In D+1 Dimensions Using Novel Analytical And Numerical Techniques, George Nehmetallah, Partha P. Banerjee Jan 2007

Study Of Soliton Stabilization In D+1 Dimensions Using Novel Analytical And Numerical Techniques, George Nehmetallah, Partha P. Banerjee

Electrical and Computer Engineering Faculty Publications

In this Chapter, we provide a brief review of the underlying nonlinear Schrödinger and associated equations that model spatio-temporal propagation in one and higher dimensions in a nonlinear dispersive environment. Particular attention is given to fast adaptive numerical techniques to solve such equations, and in the presence of dispersion and nonlinearity management, saturating nonlinearity and nonparaxiality. A unique variational approach is also outlined which helps in determining the ranges of nonlinearity and dispersion parameters to ensure stable solutions of the nonlinear equations. The propagation of 3+1 dimensional spatio-temporal pulses, or optical bullets is also modeled using a fast adaptive split-step …

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Byzantine Fault Tolerant Coordination For Web Services Atomic Transactions, Wenbing Zhao Jan 2007

Byzantine Fault Tolerant Coordination For Web Services Atomic Transactions, Wenbing Zhao

Electrical and Computer Engineering Faculty Publications

In this paper, we present the mechanisms needed for Byzantine fault tolerant coordination of Web services atomic transactions. The mechanisms have been incorporated into an open-source framework implementing the standard Web services atomic transactions specification. The core services of the framework, namely, the activation service, the registration service, the completion service, and the distributed commit service, are replicated and protected with our Byzantine fault tolerance mechanisms. Such a framework can be useful for many transactional Web services that require high degree of security and dependability.

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Introduction: Special Issue For The Selected Papers In The Fourth International Conference On Intelligent Multimedia Computing And Networking (Immcn) 2005, Chong-Wah Ngo, Hong-Va Leong Jan 2007

Introduction: Special Issue For The Selected Papers In The Fourth International Conference On Intelligent Multimedia Computing And Networking (Immcn) 2005, Chong-Wah Ngo, Hong-Va Leong

Research Collection School Of Computing and Information Systems

This special issue introduces seven papers selected from the IMMCN’ 2005, covering a wide range of emerging topics in multimedia field. These papers receive high scores and good comments from the reviewers in their respective areas of intelligent and nextgeneration networking, technology and application, multimedia coding, content analysis and retrieval. The seven papers are extended to 20 pages and then gone through another review process before the final publication. In this issue, we have two papers for video streaming, two papers for multimedia applications, one paper for video coding, and two papers for image and video retrieval.

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Dit Frequency Based Incremental Attribute Selection For Gre., John D. Kelleher Jan 2007

Dit Frequency Based Incremental Attribute Selection For Gre., John D. Kelleher

Conference papers

The DIT system uses an incremental greedy search to generate descriptions, (similar to the incremental algorithm described in (Dale and Reiter, 1995) ) incremental algorithm). The selection of the next attribute to be tested for inclusion in the description is ordered by the absolute frequency of each attribute in the training corpus. Attributes are selected in descending order of frequency (i.e. the attribute that occurred most frequently in the training corpus is selected first).

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Mediating Between Qualitative And Quantitative Representations For Task-Orientated Human-Robot Interaction., Michael Brenner, John D. Kelleher, Nick Hawes, Jeremy Wyatt Jan 2007

Mediating Between Qualitative And Quantitative Representations For Task-Orientated Human-Robot Interaction., Michael Brenner, John D. Kelleher, Nick Hawes, Jeremy Wyatt

Conference papers

In human-robot interaction (HRI) it is essential that the robot interprets and reacts to a human’s utterances in a manner that reflects their intended meaning. In this paper we present a collection of novel techniques that allow a robot to interpret and execute spoken commands describing manipulation goals involving qualitative spatial constraints (e.g. “put the red ball near the blue cube”). The resulting implemented system integrates computer vision, potential field models of spatial relationships, and action planning to mediate between the continuous real world, and discrete, qualitative representations used for symbolic reasoning.

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A Cognitive Robotics Approach To Comprehending Human Language And Behaviors, Deryle W. Lonsdale, D. Paul Benjamin, Damian Lyons Jan 2007

A Cognitive Robotics Approach To Comprehending Human Language And Behaviors, Deryle W. Lonsdale, D. Paul Benjamin, Damian Lyons

Faculty Publications

The ADAPT project is a collaboration of researchers in linguistics, robotics and artificial intelligence at three universities. We are building a complete robotic cognitive architecture for a mobile robot designed to interact with humans in a range of environments, and which uses natural language and models human behavior. This paper concentrates on the HRI aspects of ADAPT, and especially on how ADAPT models and interacts with humans.

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Directflow: A Domain-Specific Language For Information-Flow Systems, Andrew P. Black, Chuan-Kai Lin Jan 2007

Directflow: A Domain-Specific Language For Information-Flow Systems, Andrew P. Black, Chuan-Kai Lin

Computer Science Faculty Publications and Presentations

Programs that process streams of information are commonly built by assembling reusable information-flow components. In some systems the components must be chosen from a pre-defined set of primitives; in others the programmer can create new custom components using a general-purpose programming language. Neither approach is ideal: restricting programmers to a set of primitive components limits the expressivity of the system, while allowing programmers to define new components in a general-purpose language makes it difficult or impossible to reason about the composite system. We advocate defining information-flow components in a domain-specific language (DSL) that enables us to infer the properties of …

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Pi-Calculus In Logical Form, Marcello M. Bonsangue, Alexander Kurz Jan 2007

Pi-Calculus In Logical Form, Marcello M. Bonsangue, Alexander Kurz

Engineering Faculty Articles and Research

Abramsky’s logical formulation of domain theory is extended to encompass the domain theoretic model for picalculus processes of Stark and of Fiore, Moggi and Sangiorgi. This is done by defining a logical counterpart of categorical constructions including dynamic name allocation and name exponentiation, and showing that they are dual to standard constructs in functor categories. We show that initial algebras of functors defined in terms of these constructs give rise to a logic that is sound, complete, and characterises bisimilarity. The approach is modular, and we apply it to derive a logical formulation of pi-calculus. The resulting logic is a …

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Mandating Access To Telecom And The Internet: The Hidden Side Of Trinko, Daniel F. Spulber, Christopher S. Yoo Jan 2007

Mandating Access To Telecom And The Internet: The Hidden Side Of Trinko, Daniel F. Spulber, Christopher S. Yoo

All Faculty Scholarship

Antitrust has long played a major role in telecommunications policy, demonstrated most dramatically by the equal access mandate imposed during the breakup of AT&T. In this Article we explore the extent to which antitrust can continue to serve as a source of access mandates following the Supreme Court's 2004 Trinko decision. Although Trinko sharply criticized access remedies and antitrust courts' ability to enforce them, it is not yet clear whether future courts will interpret the opinion as barring all antitrust access claims. Even more importantly, the opinion contains language hinting at possible bases for differentiating among different types of access, …

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Keeping The Internet Neutral?: Tim Wu And Christopher Yoo Debate, Tim Wu, Christopher S. Yoo Jan 2007

Keeping The Internet Neutral?: Tim Wu And Christopher Yoo Debate, Tim Wu, Christopher S. Yoo

All Faculty Scholarship

"Net neutrality" has been among the leading issues of telecommunications policy this decade. Is the neutrality of the Internet fundamental to its success, and worth regulating to protect, or simply a technical design subject to improvement? In this debate-form commentary, Tim Wu and Christopher Yoo make clear the connection between net neutrality and broader issues of national telecommunications policy.

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