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Parallel Phylogenetic Inference, Mark J. Clement, David Mclaughlin, Quinn O. Snell, Michael Whiting Nov 2000

Parallel Phylogenetic Inference, Mark J. Clement, David Mclaughlin, Quinn O. Snell, Michael Whiting

Faculty Publications

Recent advances in DNA sequencing technology have created large data sets upon which phylogenetic inference can be performed. However, current research is limited by the prohibitive time necessary to perform tree search on even a reasonably sized data set. Some parallel algorithms have been developed but the biological research community does not use them because they don’t trust the results from newly developed parallel software. This paper presents a new phylogenetic algorithm that allows existing, trusted phylogenetic software packages to be executed in parallel using the DOGMA parallel processing system. The results presented here indicate that data sets that currently …

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Wright State University College Of Engineering And Computer Science Bits And Pcs Newsletter, Volume 17, Number 3, November 2000, College Of Engineering And Computer Science, Wright State University Nov 2000

Wright State University College Of Engineering And Computer Science Bits And Pcs Newsletter, Volume 17, Number 3, November 2000, College Of Engineering And Computer Science, Wright State University

BITs and PCs Newsletter

A ten page newsletter created by the Wright State University College of Engineering and Computer Science that addresses the current affairs of the college.

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The Computational Complexity Of N-K Fitness Functions, Alden H. Wright, Richard K. Thompson, Jian Zhang Nov 2000

The Computational Complexity Of N-K Fitness Functions, Alden H. Wright, Richard K. Thompson, Jian Zhang

Computer Science Faculty Publications

N-K fitness landscapes have been widely used as examples and test functions in the field of evolutionary computation. Thus, the computational complexity of these landscapes as optimization problems is of interest. We investigate the computational complexity of the problem of optimizing the N-K fitness functions and related fitness functions. We give an algorithm to optimize adjacent-model N-K fitness functions which is polynomial in N. We show that the decision problem corresponding to optimizing random-model N-K fitness functions is NP-complete for K > 1 and is polynomial for K = 1. If the restriction that the ith component function depends …

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Web Schemas In Whoweda, Sourav S. Bhowmick, Wee Keong Ng, Sanjay Kumar Madria Nov 2000

Web Schemas In Whoweda, Sourav S. Bhowmick, Wee Keong Ng, Sanjay Kumar Madria

Computer Science Faculty Research & Creative Works

The term schema denotes whatever way a data model chooses to model its data. In this paper we discuss schemas of a set of HTML or XML documents retrieved from the Web in the context of our web warehousing system called WHOWEDA (Warehouse of Web Data). Web schemas are used to bind a web table that contains a collection of interlinked web documents called web tuples. These schemas specify some of the metadata, content and structural properties (in the form of predicates) shared by some of the Web documents and hyperlinks in the web table. They also summarize the hyperlink …

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A Survey Of Context-Aware Mobile Computing Research, Guanling Chen, David Kotz Nov 2000

A Survey Of Context-Aware Mobile Computing Research, Guanling Chen, David Kotz

Computer Science Technical Reports

Context-aware computing is a mobile computing paradigm in which applications can discover and take advantage of contextual information (such as user location, time of day, nearby people and devices, and user activity). Since it was proposed about a decade ago, many researchers have studied this topic and built several context-aware applications to demonstrate the usefulness of this new technology. Context-aware applications (or the system infrastructure to support them), however, have never been widely available to everyday users. In this survey of research on context-aware systems and applications, we looked in depth at the types of context used and models of …

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Toward Automated Abstraction For Protocols On Branching Networks, Michael D. Jones, Ganesh Gopalakrishnan Nov 2000

Toward Automated Abstraction For Protocols On Branching Networks, Michael D. Jones, Ganesh Gopalakrishnan

Faculty Publications

We have used various manual abstraction techniques to formally verify a transaction ordering property for an IO protocol over bus/bridge networks. In the context of network protocol verification, an abstraction is needed to reduce the unbounded number of network configurations to a small number of representative networks that can be checked using algorithmic methods. The manually derived abstraction was both brittle and difficult to validate. In this report, we discuss the need for abstraction techniques in the formal verification of protocols over networks and present our recent efforts to create an automatic abstraction technique for network protocols using predicate abstraction …

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Extensible Mpeg-4 Textual Format (Xmt), Michelle Kim, Steve Wood, Lai-Tee Cheok Nov 2000

Extensible Mpeg-4 Textual Format (Xmt), Michelle Kim, Steve Wood, Lai-Tee Cheok

Research Collection School Of Computing and Information Systems

This paper describes the Extensible MPEG-4 Textual format (XMT), a framework for representing MPEG-4 scene description using a textual syntax. The XMT allows the content authors to exchange their content with other authors, tools or service providers, and facilitates interoperability with both the X3D, developed by the Web3D consortium, and the Synchronized Multimedia Integration Language (SM1L) from the W3C consortium.

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Automated Systematic Testing For Constraint-Based Interactive Services, Patrice Godefroid, Lalita Jategaonkar Jagadeesan, Radha Jagadeesan, Konstantin Laufer Nov 2000

Automated Systematic Testing For Constraint-Based Interactive Services, Patrice Godefroid, Lalita Jategaonkar Jagadeesan, Radha Jagadeesan, Konstantin Laufer

Computer Science: Faculty Publications and Other Works

Constraint-based languages can express in a concise way the complex logic of a new generation of interactive services for applications such as banking or stock trading, that must support multiple types of interfaces for accessing the same data. These include automatic speech-recognition interfaces where inputs may be provided in any order by users of the service. We study in this paper how to systematically test event-driven applications developed using such languages. We show how such applications can be tested automatically, without the need for any manually-written test cases, and effi- ciently, by taking advantage of their capability of taking unordered …

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Performance Enhancement By Memory Reduction, Yonghong Song, Rong Xu, Cheng Wang, Zhiyuan Li Nov 2000

Performance Enhancement By Memory Reduction, Yonghong Song, Rong Xu, Cheng Wang, Zhiyuan Li

Department of Computer Science Technical Reports

No abstract provided.

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Gasturbnlab Simulation Of Instability In A Gas Turbine, A. C. Catlin, S. Fleeter, Elias N. Houstis, John R. Rice, C. Zhou Nov 2000

Gasturbnlab Simulation Of Instability In A Gas Turbine, A. C. Catlin, S. Fleeter, Elias N. Houstis, John R. Rice, C. Zhou

Department of Computer Science Technical Reports

No abstract provided.

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Traffic Conditioner Design For Assured Forwarding In Differentiated Services Network, Ahsan Habib, Sonja Fahmy, Bharat Bhargava Nov 2000

Traffic Conditioner Design For Assured Forwarding In Differentiated Services Network, Ahsan Habib, Sonja Fahmy, Bharat Bhargava

Department of Computer Science Technical Reports

No abstract provided.

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Using 'Drop-Biasing' To Stabilize The Occupancy Of Random-Drop Queues With Tcp Traffic, Archan Misra, Teunis Ott, John Baras Nov 2000

Using 'Drop-Biasing' To Stabilize The Occupancy Of Random-Drop Queues With Tcp Traffic, Archan Misra, Teunis Ott, John Baras

Research Collection School Of Computing and Information Systems

The paper describes how the use of ‘drop-biasing’, a technique to control the distribution of the gap between consecutive packet losses in random drop queues (such as RED) can be used to reduce the variability of the queue occupancy with TCP traffic. Reducing the variance of the queue occupancy reduces delay jitter for buffered packets, as well as decreases the likelihood of buffer underflow. We find that modifying the packet drop probabilities to ensure a minimum separation between consecutive packet drops serves to decrease the variability in the queue occupancy. This is really achieved as a result of the increased …

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Information Retrieval And Mining In High Dimensional Databases, Xiong Wang Oct 2000

Information Retrieval And Mining In High Dimensional Databases, Xiong Wang

Dissertations

This dissertation is composed of two parts. In the first part, we present a framework for finding information (more precisely, active patterns) in three dimensional (3D) graphs. Each node in a graph is an undecoraposable or atomic unit and has a label. Edges are links between the atomic units. Patterns are rigid substructures that may occur in a graph after allowing for an arbitrary number of whole-structure rotations and translations as well as a small number (specified by the user) of edit operations in the patterns or in the graph. (When a pattern appears in a graph only after the …

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Immaccs: An Experimental Multi-Agent C2 System, Jens G. Pohl, Anthony A. Wood, Kym Jason Pohl Oct 2000

Immaccs: An Experimental Multi-Agent C2 System, Jens G. Pohl, Anthony A. Wood, Kym Jason Pohl

Collaborative Agent Design (CAD) Research Center

The Integrated Marine Multi-Agent Command and Control System (IMMACCS) is a multi-agent, distributed software system, designed to provide a Common Tactical Picture (CTP) with integrated and meaningful decision-support facilities to authorized operators at any access node. IMMACCS has been implemented as a three-tier architecture that distinguishes between information, logic and presentation. It utilizes an object-serving communication facility with subscription and multi-casting capabilities that is based on the Common Object Request Broker Architecture (CORBA). With an emphasis on application, IMMACCS was designed and implemented in concert with its military users as an integral component of experiments conceived by the Marine Corps …

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Semi-Regular Mesh Extraction From Volumes, Z. J. Wood, M. Desbrun, P. Schroder, D. Breen Oct 2000

Semi-Regular Mesh Extraction From Volumes, Z. J. Wood, M. Desbrun, P. Schroder, D. Breen

Computer Science and Software Engineering

We present a novel method to extract iso-surfaces from distance volumes. It generates high quality semi-regular multiresolution meshes of arbitrary topology. Our technique proceeds in two stages. First, a very coarse mesh with guaranteed topology is extracted. Subsequently an iterative multi-scale force-based solver refines the initial mesh into a semi-regular mesh with geometrically adaptive sampling rate and good aspect ratio triangles. The coarse mesh extraction is performed using a new approach we call surface wavefront propagation. A set of discrete iso-distance ribbons are rapidly built and connected while respecting the topology of the iso-surface implied by the data. Subsequent multi-scale …

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Robotic System Sensitivity To Neural Network Learning Rate: Theory, Simulation, And Experiments, Christopher M. Clark, James K. Mills Oct 2000

Robotic System Sensitivity To Neural Network Learning Rate: Theory, Simulation, And Experiments, Christopher M. Clark, James K. Mills

Computer Science and Software Engineering

Selection of neural network learning rates to obtain satisfactory performance from neural network controllers is a challenging problem. To assist in the selection of learning rates, this paper investigates robotic system sensitivity to neural network (NN) learning rate. The work reported here consists of experimental and simulation results. A neural network controller module, developed for the purpose of experimental evaluation of neural network controller performance of a CRS Robotics Corporation A460 robot, allows testing of NN controllers using real-time iterative learning. The A460 is equipped with a joint position proportional, integral, and derivative (PID) controller. The neural network module supplies …

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The Cracker Patch Choice: An Analysis Of Post Hoc Security Techniques, Crispin Cowan, Heather Hinton, Calton Pu, Jonathan Walpole Oct 2000

The Cracker Patch Choice: An Analysis Of Post Hoc Security Techniques, Crispin Cowan, Heather Hinton, Calton Pu, Jonathan Walpole

Computer Science Faculty Publications and Presentations

It has long been known that security is easiest to achieve when it is designed in from the start. Unfortunately, it has also become evident that systems built with security as a priority are rarely selected for wide spread deployment, because most consumers choose features, convenience, and performance over security. Thus security officers are often denied the option of choosing a truly secure solution, and instead must choose among a variety of post hoc security adaptations. We classify security enhancing methods, and compare and contrast these methods in terms of their effectiveness vs. cost of deployment. Our analysis provides practitioners …

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Editorial, Sanjay Kumar Madria, Mukesh Mohania, Bharat Bhargava Oct 2000

Editorial, Sanjay Kumar Madria, Mukesh Mohania, Bharat Bhargava

Computer Science Faculty Research & Creative Works

No abstract provided.

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Wright State University College Of Engineering And Computer Science Bits And Pcs Newsletter, Volume 17, Number 2, October 2000, College Of Engineering And Computer Science, Wright State University Oct 2000

Wright State University College Of Engineering And Computer Science Bits And Pcs Newsletter, Volume 17, Number 2, October 2000, College Of Engineering And Computer Science, Wright State University

BITs and PCs Newsletter

A ten page newsletter created by the Wright State University College of Engineering and Computer Science that addresses the current affairs of the college.

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Performance Analysis Of Mobile Agents For Filtering Data Streams On Wireless Networks, David Kotz, George Cybenko, Robert S. Gray, Guofei Jiang, Ronald A. Peterson, Martin O. Hofmann, Daria A. Chacon, Kenneth R. Whitebread Oct 2000

Performance Analysis Of Mobile Agents For Filtering Data Streams On Wireless Networks, David Kotz, George Cybenko, Robert S. Gray, Guofei Jiang, Ronald A. Peterson, Martin O. Hofmann, Daria A. Chacon, Kenneth R. Whitebread

Computer Science Technical Reports

Wireless networks are an ideal environment for mobile agents, since their mobility allows them to move across an unreliable link to reside on a wired host, next to or closer to the resources that they need to use. Furthermore, client-specific data transformations can be moved across the wireless link and run on a wired gateway server, reducing bandwidth demands. In this paper we examine the tradeoffs faced when deciding whether to use mobile agents in a data-filtering application where numerous wireless clients filter information from a large data stream arriving across the wired network. We develop an analytical model and …

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A Formal Semantics For Spki, Jon Howell, David Kotz Oct 2000

A Formal Semantics For Spki, Jon Howell, David Kotz

Dartmouth Scholarship

We extend the logic and semantics of authorization due to Abadi, Lampson, et al. to support restricted delegation. Our formal model provides a simple interpretation for the variety of constructs in the Simple Public Key Infrastructure (SPKI), and lends intuition about possible extensions. We discuss both extensions that our semantics supports and extensions that it cautions against.

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End-To-End Authorization, Jon Howell, David Kotz Oct 2000

End-To-End Authorization, Jon Howell, David Kotz

Dartmouth Scholarship

Many boundaries impede the flow of authorization information, forcing applications that span those boundaries into hop-by-hop approaches to authorization. We present a unified approach to authorization. Our approach allows applications that span administrative, network, abstraction, and protocol boundaries to understand the end-to-end authority that justifies any given request. The resulting distributed systems are more secure and easier to audit. \par We describe boundaries that can interfere with end-to-end authorization, and outline our unified approach. We describe the system we built and the applications we adapted to use our unified authorization system, and measure its costs. We conclude that our system …

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Classes Of Logic Programs Which Possess Unique Supported Models, Anthony K. Seda, Pascal Hitzler Oct 2000

Classes Of Logic Programs Which Possess Unique Supported Models, Anthony K. Seda, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Logic programming is concerned with the use of logic as a programming language. The main manifestation of this computing paradigm is in the various versions of Prolog which are now available, in which computation is viewed as deduction from sets of Horn clauses, although there is also growing interest in the related form known as answer set programming, see [10]. The reference [1] contains a good survey of the growth of logic programming over the last twenty-five years both as a stand-alone programming language and as a software component of large information systems. One advantage a logic program P has …

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Mol: Method Of Lines Application, John R. Rice, Mikel Luján Oct 2000

Mol: Method Of Lines Application, John R. Rice, Mikel Luján

Department of Computer Science Technical Reports

No abstract provided.

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Studies Related To The Design And Implementation Of A Magnetic Suspension And Balance System, Syed Adeel Akhtar Jafri Oct 2000

Studies Related To The Design And Implementation Of A Magnetic Suspension And Balance System, Syed Adeel Akhtar Jafri

Electrical & Computer Engineering Theses & Dissertations

This thesis presents studies related to the magnetic suspension and balance system (MSBS) of the Princeton/ONR High Reynolds Number Testing Facility (HRTF). The main motivation for developing the MSBS is to provide interference free aero/hydrodynamic testing of submersible models, which will lead to more accurate measurements. From the controls point of view, the main specification of the MSBS is to robustly control the position of a submersible model in five degrees of freedom (DOF), including three translational as well as pitching and yawing positions. The MSBS should not only regulate the submersible model's position but should also allow for small …

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Side Collision Warning System For Transit Buses, Sue Mcneil, David Duggins, Christoph Mertz, Arne Suppe, Chuck Thorpe Oct 2000

Side Collision Warning System For Transit Buses, Sue Mcneil, David Duggins, Christoph Mertz, Arne Suppe, Chuck Thorpe

Research Collection School Of Computing and Information Systems

Transit buses are involved in many more accidents than other vehicles. Collision warning systems (CWS) are therefore placed most efficiently on these buses. In our project, we investigate their operating environment and available technologies to develop performance specifications for such CWS. The paper discusses our findings of transit buses driving through very cluttered surroundings and being involved in many different types of accidents where currently available CWS no not work effectively. One of the focuses of our work is pedestrians around the bus and their detection.

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On Reconfiguring Tree Linkages: Trees Can Lock, Therese Biedl, Erik D. Demaine, Martin L. Demaine, Sylvain Lazard, Anna Lubiw, Joseph O'Rourke, Steve Robbins, Ileana Streinu, Godfried Toussaint, Sue Whitesides Sep 2000

On Reconfiguring Tree Linkages: Trees Can Lock, Therese Biedl, Erik D. Demaine, Martin L. Demaine, Sylvain Lazard, Anna Lubiw, Joseph O'Rourke, Steve Robbins, Ileana Streinu, Godfried Toussaint, Sue Whitesides

Computer Science: Faculty Publications

It has recently been shown that any simple (i.e. nonintersecting) polygonal chain in the plane can be reconfigured to lie on a straight line, and any simple polygon can be reconfigured to be convex. This result cannot be extended to tree linkages: we show that there are trees with two simple configurations that are not connected by a motion that preserves simplicity throughout the motion. Indeed, we prove that an N-link tree can have 2Ω(N) equivalence classes of configurations.

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Semantic Web And Information Brokering: Opportunities, Commercialization, And Challenges, Amit P. Sheth Sep 2000

Semantic Web And Information Brokering: Opportunities, Commercialization, And Challenges, Amit P. Sheth

Kno.e.sis Publications

From the chairs' report published in SIGMOD record: The keynote address entitled 'Semantic Web and Information Brokering: Opportunities, Early Commercializations, and Challenges' was delivered by Amit Sheth (University of Georgia and Taalee Corp). Sheth characterized semantics as the next step in the evolution of the WWW and stressed the importance of semantically organized information for supporting ubiquitous, powerful, accurate and efficient access to this information. Sheth also reviewed proposals for semantic interoperability frameworks such as the DAML(DARPA Agent Mark-Up Language), the Oingo family of tools for defining concepts and extracting knowledge from large databases, as well as several scenarios on …

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Optically Simulating A Quantum Associative Memory, Dan A. Ventura, John C. Howell, John A. Yeazell Sep 2000

Optically Simulating A Quantum Associative Memory, Dan A. Ventura, John C. Howell, John A. Yeazell

Faculty Publications

This paper discusses the realization of a quantum associative memory using linear integrated optics. An associative memory produces a full pattern of bits when presented with only a partial pattern. Quantum computers have the potential to store large numbers of patterns and hence have the ability to far surpass any classical neural network realization of an associative memory. In this work two 3-qubit associative memories will be discussed using linear integrated optics. In addition, corrupted, invented and degenerate memories are discussed.

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Pushpush And Push-1 Are Np-Hard In 2d, Erik D. Demaine, Martin L. Demaine, Joseph O'Rourke Sep 2000

Pushpush And Push-1 Are Np-Hard In 2d, Erik D. Demaine, Martin L. Demaine, Joseph O'Rourke

Computer Science: Faculty Publications

We prove that two pushing-blocks puzzles are intractable in 2D. One of our constructions improves an earlier result that established intractability in 3D [OS99] for a puzzle inspired by the game PushPush. The second construction answers a question we raised in [DDO00] for a variant we call Push-1. Both puzzles consist of unit square blocks on an integer lattice; all blocks are movable. An agent may push blocks (but never pull them) in attempting to move between given start and goal positions. In the PushPush version, the agent can only push one block at a time, and moreover when a …

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