Digital Commons Network^™

On Modeling Protein Superfamilies With Low Primary Sequence Conservation, Stephen Scott, H. Ji, P. Wen, Dmitri E. Fomenko, Vadim N. Gladyshev

School of Computing: Technical Reports

We present several algorithms for identifying thioredoxin (Trx)-fold proteins containing a conserved CxxC motif (two cysteines separated by two residues). The low conservation of primary sequence in this protein superfamily makes conventional methods difficult to use. Therefore, we use structural properties to build our classifiers. These structural properties include secondary structure patterns as well as various properties of the residues in the protein sequences. We use this information to model Trx-fold proteins via hidden Markov models, decision trees, and algorithms in the multipleinstance learning model. In 9-fold and 12-fold jack-knife tests, some of our models performed quite well, with high …

On Generalized Multiple-Instance Learning, Stephen Scott, Jun Zhang, Joshua Brown

School of Computing: Technical Reports

We describe a generalization of the multiple-instance learning model in which a bag’s label is not based on a single instance’s proximity to a single target point. Rather, a bag is positive if and only if it contains a collection of instances, each near one of a set of target points. We list potential applications of this model (robot vision, content-based image retrieval, protein sequence identification, and drug discovery) and describe target concepts for these applications that cannot be represented in the conventional multiple-instance learning model. We then adapt a learning-theoretic algorithm for learning in this model and present empirical …

Low-Energy Bist Design For Scan-Based Logic Circuits, Bhargab B. Bhattacharya, Sharad C. Seth, Sheng Zhang

School of Computing: Conference and Workshop Papers

In a random testing environment, a significant amount of energy is wasted in the LFSR and in the CUT by useless patterns that do not contribute to fault dropping. Another major source of energy drainage is the loss due to random switching activity in the CUT and in the scan path between applications of two successive vectors. In this work, a new built-in self-test (BIST) scheme for scan-based circuits is proposed for reducing such energy consumption. A mapping logic is designed which modifies the state transitions of the LFSR such that only the useful vectors are generated according to a …

Thesis Digest: Mathematical Interpretation Of Political Power And The Arkansas State Government, Andrew King

Inquiry: The University of Arkansas Undergraduate Research Journal

On the whole, political power can he very difficult to quantify. A person may be powerful due to his or her personal charm, wealth, fame, credibility, or influential connections. Political bodies do not account for these qualities when creating voting procedures; they only assign voting rules to specific positions. For example, most would say that in the United States government that a Senator is more powerful than a Representative, but less powerful than the President, without knowing any way to quantify or verify those differences. Since the 1950's, mathematicians and political scientists have attempted to create mathematical models that partially …

Parametrically Tunable Audio Shelving And Equalizing Ladder Wave Digital Filters, S. A. Samad

Turkish Journal of Electrical Engineering and Computer Sciences

Parametrically tunable audio equalizers are conventionally realized using allpass digital filter networks. They consist of first-order shelving filters and second-order equalizing filters. In this paper, ladder wave digital filters (WDFs) with parametrically tunable coefficients are proposed as shelving and equalizing filters. Similar to the allpass realization, the transfer function power complementary property of WDFs is used to obtain efficient shelving and equalizing filters. However, unlike the allpass structures, the transfer function and the tunable parameters of the ladder WDF are derived from the analog filter equivalent of the digital shelving and equalizing filters. For the shelving WDF, the cut-off frequency …

Under The Plastic: A Quantitative Look At Dvd Video Encoding And Its Impact On Video Modeling, Wu-Chi Feng, Jin Choi, Wu-Chang Feng, Jonathan Walpole

Computer Science Faculty Publications and Presentations

In this paper, we examine the DVD encoding process and the implications this process has video modeling and network traffic analysis. We have assembled a system that allows us to extract the video data from the DVDs as they were encoded for distribution. Analyzing the resulting video trace data, we describe how DVD encodings have evolved over time. In addition, our findings show that the underlying video content is fundamentally different than those produced by basic consumer video capture boards. We demonstrate how this affects current video modeling proposals and their affect on network traffic characterization. This research is based …

Privacy-Preserving Collaborative Filtering Using Randomized Perturbation Techniques, Huseyin Polat, Wenliang Du

Electrical Engineering and Computer Science - All Scholarship

Collaborative Filtering (CF) techniques are becoming increasingly popular with the evolution of the Internet. E-commerce sites use CF systems to suggest products to customers based on like-minded customers' preferences. People use CF systems to cope with information overload. To conduct collaborative filtering, data from customers are needed. However, collecting high quality data from customers is not an easy task because many customers are so concerned about their privacy that they might decide to give false information. CF systems using these data might produce inaccurate recommendations. We propose a randomized perturbation technique to protect users' privacy while still producing accurate recommendations. …

Interacting Data Services For Distributed Earthquake Modeling, Marlon Pierce, Choonhan Youn, Geoffrey C. Fox

Electrical Engineering and Computer Science - All Scholarship

We present XML schemas and our design for related data services for describing faults and surface displacements, which we use within earthquake modeling codes. These data services are implemented using a Web services approach and are incorporated in a portal architecture with other, general purpose services for application and file management. We make use of many Web services standards, including WSDL and SOAP, with specific implementations in Java. We illustrate how these data models and services may be used to build distributed, interacting applications through data flow.

An Adaptive Qos Routing Protocol With Dispersity For Ad-Hoc Networks, Youngki Hwang, Pramod Varshney

Electrical Engineering and Computer Science - All Scholarship

In this paper, we present the design and simulation of a bandwidth constrained multiple path on-demand routing protocol for ad-hoc networks to support end-to-end Quality of Service, which is known as the Adaptive Dispersity QoS Routing (ADQR) Protocol. We propose a route discovery algorithm to find multiple disjoint paths with longerlived connections, where each path also specifies associated network resource information. This provides an efficient approach for network resource reservation combined with data dispersion and for route maintenance. A longerlived path generally involves less route maintenance, resulting in an increase of bandwidth utilization. We propose a route maintenance algorithm to …

Example Protein Folds, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO/CS 471: Algorithms for Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

The Structure And Functions Of Proteins, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO 271/CS 399: Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

An Additive Schwarz Preconditioner For The Spectral Element Ocean Model Formulation Of The Shallow Water Equations, Craig C. Douglas, Gundolf Haase, Mohamed Iskandarani

Computer Science Faculty Publications

We discretize the shallow water equations with an Adams-Bashford scheme combined with the Crank-Nicholson scheme for the time derivatives and spectral elements for the discretization in space. The resulting coupled system of equations will be reduced to a Schur complement system with a special structure of the Schur complement. This system can be solved with a preconditioned conjugate gradients, where the matrix-vector product is only implicitly given. We derive an overlapping block preconditioner based on additive Schwarz methods for preconditioning the reduced system.

Digitization In An Archival Environment, Sally Mckay

E-JASL: Electronic Journal of Academic and Special Librarianship (1999-2009, Volumes 1-10)

Introduction

Cultural institutions such as museums, libraries, archives, and historical societies house remarkable collections of cultural artifacts. It is the responsibility of the staff working for those institutions to preserve, protect and provide responsible stewardship for the materials, and to the best of their ability, provide continued long-term access (Russell, 2000).

Advances in technology allow institutions to provide expanded access and education; however, there are important priorities that must be addressed prior to embarking on a digital conversion project.

Digitization in an archival environment includes taking a physical object or analog item, such as an art object, a tape recording, …

Double-Tree Scan: A Novel Low-Power Scan-Path Architecture, Bhargab B. Bhattacharya, Sharad C. Seth, Sheng Zhang

School of Computing: Conference and Workshop Papers

In a scan-based system with a large number of flip-flops, a major component of power is consumed during scan-shift and clocking operation in test mode. In this paper, a novel scan-path architecture called double-tree scan (DTS) is proposed that drastically reduces the scan-shift and clock activity during testing. The inherent combinatorial properties of double-tree structure are employed to design the scan architecture, clock gating logic, and a simple shift controller. The design is independent of the structure of the circuit-under-test (CUT) or its test set. It provides a significant reduction both in instantaneous and average power needed for clocking and …

Priority-Based Lambda Scheduler, Kalpana Ganesan, Byrav Ramamurthy

School of Computing: Conference and Workshop Papers

Optical networks provide a new dimension to meet the demands of exponentially growing traffic. Optical packet switching requires a good switch architecture, which eliminates the O/E/O conversion as much as possible. Wavelength Division Multiplexing (WDM) provides a breakthrough to exploit the huge bandwidth of the optical fiber. Different applications have different requirements, which necessitate employing differentiated services. This paper presents the idea of a priority-based λ-scheduler, where the packets are differentiated into different classes and services are provided accordingly. For example, class 0 can correspond to non real time applications like email and ftp, while class 1 can correspond to …

Learning Monotone Dnf Using Spp Teaching Assistant, N. V. Vinodchandran

School of Computing: Technical Reports

In this paper we prove a new upper bound on learning monotone DNF formulae in an exact learning model called the teaching assistant model. This model, introduced in one of our earlier works, uses teaching assistant classes for classifying the complexity of learning problems. Teaching assistant classes are a learning-theoretic analog of complexity classes. We show that monotone DNF are learnable using a teaching assistant in the class SPP. On the other hand, concept classes such as k-CNF or Boolean circuits are not learnable using an SPP teaching assistant unless Np SPP. We also observe that the recent SPP algorithm …

The Foldings Of A Square To Convex Polyhedra, Rebecca Alexander, Heather Dyson, Joseph O'Rourke

Computer Science: Faculty Publications

The structure of the set of all convex polyhedra foldable from a square is detailed. It is proved that five combinatorially distinct nondegenerate polyhedra, and four different flat polyhedra, are realizable. All the polyhedra are continuously deformable into each other, with the space of polyhedra having the topology of four connected rings.

Jade Software: Getting Ready To Tackle America, Sir Gilbert Simpson, Laurence Weinstein

New England Journal of Entrepreneurship

Interview by Laurence Weinstein of Sir Gilbert Simpson, founder and CEO of Jade Software in New Zealand.

Sir Gil Simpson is one of New Zealand’s pioneers in software development, having started in the field in 1967. He holds steadfast to his dream that one day his approach to software programming will take hold around the world. Simpson has just opened up the company’s first office in the United States; he expects his first significant foray into this country will be a successful one.

Fragment Assembly Of Dna, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO/CS 471: Algorithms for Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Semantic Web Processes, Jorge Cardoso, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Pid Stabilization Of A Position-Controlled Robot Manipulator Acting Independently Of In Collaboration With Human Arm, Anindo Roy, Kamran Iqbal

Journal of the Arkansas Academy of Science

In this paper we develop framework for PID stabilization of a robot manipulator when using an object independently or in collaboration with a human arm. In both applications, the manipulator is equipped with a wrist sensor represented by an impedance. A second order manipulator transfer function along each coordinate direction is assumed. The aim of the paper is to design a PID controller when measurement of contact force, available via wrist sensor, is used to command the position controlled manipulator to a desired position and/or force profile. Necessary and sufficient conditions for stability of the closed loop system are developed …

Heterogenous Network Management, Kenneth Carey

Theses

Enterprise level system development, integrating a broad range of arctures and legacy systems, has received significant attention over the last few yentegrated chain management, which allows companies to see their full manufactu inventory and sales channels, has driven much of this work. Delivering quality IP 1 wireless access is forcing similar integration in 2.5G and 3G telecom archires. Such integration has resulted in the emergence of multi-protocol heterogeneietworks, combining IP core backbones, legacy databases and switchinghnology. Heterogeneous networks, due to their diversity of equipment and suppoDrotocols, introduce challenges for today's network administrators, particularly ii areas of device configuration and alarm …

Sedimentological And Plant Taphonomic Evaluation Of The Early Middle Devonian Trout Valley Formation, Jonathan Allen

Honors Theses

The Trout Valley Formation of Emsian-Eifelian age, outcropped in Baxter State Park, Maine, consists offluvial and coastal deposits preserving early land plants. Massive, crudely bedded conglomerate represents deposits of proximal braided channels on an alluvial fan complex. Lithic sandstone bodies in channel-form geometries represent deposits of river channels draining the Acadian highlands whereas associated siltstones represent overbank deposits, intertidal flats, and tidal channels. Localized lenticular quartz arenites represent nearshore shelf bar deposits that were storm influenced. The majority of plant assemblages preserved mainly in siltstone lithologies are allochthonous and parautochthonous, with only one autochthonous assemblage identified in the sequence. Plant …

Wright State University College Of Engineering And Computer Science Bits And Pcs Newsletter, Volume 19, Number 3, January 2003, College Of Engineering And Computer Science, Wright State University

BITs and PCs Newsletter

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

A Gentle Introduction To (Or Review Of) Fundamentals Of Chemistry And Organic Chemistry, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for CS 790: Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Sequence Alignments And Database Searches, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for Intro to Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Physical Mapping Of Dna, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO/CS 471: Algorithms for Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

The Staging Transformation Approach To Mixing Initiative, Robert Capra, Michael Narayan, Saverio Perugini, Naren Ramakrishnan, Manuel A. Pérez-Quiñones

Computer Science Faculty Publications

Mixed-initiative interaction is an important facet of many conversational interfaces, flexible planning architectures, intelligent tutoring systems, and interactive information retrieval systems. Software systems for mixed-initiative interaction must enable us to both operationalize the mixing of initiative (i.e., support the creation of practical dialogs) and to reason in real-time about how a flexible mode of interaction can be supported (e.g., from a meta-dialog standpoint). In this paper, we present the staging transformation approach to mixing initiative, where a dialog script captures the structure of the dialog and dialog control processes are realized through generous use of program transformation techniques (e.g., partial …

Personalizing Interactions With Information Systems, Saverio Perugini, Naren Ramakrishnan

Computer Science Faculty Publications

Personalization constitutes the mechanisms and technologies necessary to customize information access to the end-user. It can be defined as the automatic adjustment of information content, structure, and presentation tailored to the individual. In this chapter, we study personalization from the viewpoint of personalizing interaction. The survey covers mechanisms for information-finding on the web, advanced information retrieval systems, dialog-based applications, and mobile access paradigms. Specific emphasis is placed on studying how users interact with an information system and how the system can encourage and foster interaction. This helps bring out the role of the personalization system as a facilitator which reconciles …

Patterns Of Curriculum Design, Doug Blank, Deepak Kumar

Computer Science Faculty Research and Scholarship

We present a perspective on the design of a curriculum for a new computer science program at a women s liberal arts college. The design incorporates lessons learned at the college in its successful implementation of other academic programs, incorporation of best practices in curriculum design at other colleges, results from studies performed on various computer science programs, and a significant number of our own ideas. Several observations and design decisions are presented as curriculum design patterns. The goal of making the design patterns explicit is to encourage a discussion on curriculum design that goes beyond the identification of core …