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Articles 1 - 14 of 14
Full-Text Articles in Physical Sciences and Mathematics
Parallel Phylogenetic Inference, Mark J. Clement, David Mclaughlin, Quinn O. Snell, Michael Whiting
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 …
Toward Automated Abstraction For Protocols On Branching Networks, Michael D. Jones, Ganesh Gopalakrishnan
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 …
Optically Simulating A Quantum Associative Memory, Dan A. Ventura, John C. Howell, John A. Yeazell
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.
Rescaling The Energy Function In Hopfield Networks, Tony R. Martinez, Xinchuan Zeng
Rescaling The Energy Function In Hopfield Networks, Tony R. Martinez, Xinchuan Zeng
Faculty Publications
In this paper we propose an approach that rescales the distance matrix of the energy function in the Hopfield network for solving optimization problems. We rescale the distance matrix by normalizing each row in the matrix and then adjusting the parameter for the distance term. This scheme has the capability of reducing the effects of clustering in data distributions, which is one of main reasons for the formation of invalid solutions. We evaluate this approach through a large number (20,000) simulations based on 200 randomly generated city distributions of the 10-city traveling salesman problem. The result shows that, compared to …
The Inefficiency Of Batch Training For Large Training Sets, Tony R. Martinez, D. Randall Wilson
The Inefficiency Of Batch Training For Large Training Sets, Tony R. Martinez, D. Randall Wilson
Faculty Publications
Multilayer perceptrons are often trained using error backpropagation (BP). BP training can be done in either a batch or continuous manner. Claims have frequently been made that batch training is faster and/or more "correct" than continuous training because it uses a better approximation of the true gradient for its weight updates. These claims are often supported by empirical evidence on very small data sets. These claims are untrue, however, for large training sets. This paper explains why batch training is much slower than continuous training for large training sets. Various levels of semi-batch training used on a 20,000-instance speech recognition …
Almost Block Diagonal Linear Systems: Sequential And Parallel Solution Techniques, And Applications, P. Amodio, J.R. Cash, G. Roussos, R.W. Wright, G. Fairweather, I. Gladwell, G.L. Kraut, M. Paprzycki
Almost Block Diagonal Linear Systems: Sequential And Parallel Solution Techniques, And Applications, P. Amodio, J.R. Cash, G. Roussos, R.W. Wright, G. Fairweather, I. Gladwell, G.L. Kraut, M. Paprzycki
Faculty Publications
Almost block diagonal (ABD) linear systems arise in a variety of contexts, specifically in numerical methods for two-point boundary value problems for ordinary differential equations and in related partial differential equation problems. The stable, efficient sequential solution of ABDs has received much attention over the last fifteen years and the parallel solution more recently. We survey the fields of application with emphasis on how ABDs and bordered ABDs (BABDs) arise. We outline most known direct solution techniques, both sequential and parallel, and discuss the comparative efficiency of the parallel methods. Finally, we examine parallel iterative methods for solving BABD systems. …
Roughening, Deroughening, And Nonuniversal Scaling Of The Interface Width In Electrophoretic Deposition Of Polymer Chains, Frank W. Bentrem, Ras B. Pandey, Fereydoon Family
Roughening, Deroughening, And Nonuniversal Scaling Of The Interface Width In Electrophoretic Deposition Of Polymer Chains, Frank W. Bentrem, Ras B. Pandey, Fereydoon Family
Faculty Publications
Growth and roughness of the interface of deposited polymer chains driven by a field onto an impenetrable adsorbing surface are studied by computer simulations in (2 + 1) dimensions. The evolution of the interface width W shows a crossover from short-time growth described by the exponent beta(1) to a long-time growth with exponent beta(2) (>beta(1)) Tne saturated width increases, i.e., the interface roughens, with the molecular weight L-c, but the roughness exponent alpha (from W-s similar to L-alpha) becomes negative in contrast to models for particle deposition; cr depends on the chain length-a nonuniversal scaling with the substrate length …
Intelligent Selection Tools, William A. Barrett, Eric N. Mortensen, L. Jack Reese
Intelligent Selection Tools, William A. Barrett, Eric N. Mortensen, L. Jack Reese
Faculty Publications
Intelligent Scissors and Intelligent Paint are complementary interactive image segmentation tools that allow a user to quickly and accurately select objects of interest. This demonstration provides a means for participants to experience the dynamic nature of these tools.
3d Outside Cell Interference Factor For An Air-Ground Cdma ‘Cellular’ System, David W. Matolak
3d Outside Cell Interference Factor For An Air-Ground Cdma ‘Cellular’ System, David W. Matolak
Faculty Publications
We compute the outside-cell interference factor of a code-division multiple-access (CDMA) system for a three-dimensional (3-D) air-to-ground (AG) "cellular-like" network consisting of a set of uniformly distributed ground base stations and airborne mobile users. The CDMA capacity is roughly inversely proportional to the outside-cell interference factor. It is shown that for the nearly free-space propagation environment of these systems, the outside-cell interference factor can be larger than that for terrestrial propagation models (as expected) and depends approximately logarithmically upon both the cell height and cell radius.
Bounding Interval Rational Bézier Curves With Interval Polynomial Bézier Curves, Thomas W. Sederberg, Falai Chen, Wenping Lou
Bounding Interval Rational Bézier Curves With Interval Polynomial Bézier Curves, Thomas W. Sederberg, Falai Chen, Wenping Lou
Faculty Publications
In this paper, we put forward and study the problem of bounding an interval rational Bézier curve with an interval polynomial Bézier curve. We propose three different methods—Hybrid Method, Perturbation Method and Linear Programming Method to solve this problem. Examples are illustrated to compare the three different methods. The empirical results show that the Perturbation Method and the Linear Programming Method produce much tighter bounds than the Hybrid Method, though they are computationally several times more expensive.
Alternate Path Routing For Multicast, Daniel Zappala
Alternate Path Routing For Multicast, Daniel Zappala
Faculty Publications
Alternate path routing has been well-explored in telecommunication networks as a means of decreasing the call blocking rate and increasing network utility. However, aside from some work applying these concepts to unicast flows, alternate path routing has received little attention in the Internet community. We describe and evaluate an architecture for alternate path routing for multicast flows. For path installation, we design a receiver-oriented alternate path protocol and prove that it reconfigures multicast trees without introducing loops. For path computation, we propose a scalable local search heuristic that allows receivers to find alternate paths using only partial network information. We …
Designing Human-Centered Automation: Tradeoffs In Collision Avoidance System Design, Michael A. Goodrich, Erwin R. Boer
Designing Human-Centered Automation: Tradeoffs In Collision Avoidance System Design, Michael A. Goodrich, Erwin R. Boer
Faculty Publications
Technological advances have made plausible the design of automated systems that share responsibility with a human operator. The decision to use automation to assist or replace a human operator in safety-critical tasks must account for not only the technological capabilities of the sensor and control subsystems, but also the autonomy, capabilities, and preferences of the human operator. By their nature, such human-centered automation problems have multiple attributes: an attribute reflecting human goals and capabilities, and an attribute reflecting automation goals and capabilities. Although good theories exist that describe portions of human behavior generation, in the absence of a general theory …
Learning Quantum Operators, Dan A. Ventura
Learning Quantum Operators, Dan A. Ventura
Faculty Publications
Consider the system Fx = w where F is unknown. We examine the possibility of learning the operator F inductively, drawing analogies with ideas from classical computational learning.
Estimating Tessellation Parameter Intervals For Rational Curves And Surfaces, Thomas W. Sederberg, Jianmin Zheng
Estimating Tessellation Parameter Intervals For Rational Curves And Surfaces, Thomas W. Sederberg, Jianmin Zheng
Faculty Publications
This paper presents a method for determining a priori a constant parameter interval with which a rational curve or surface can be tessellated such that the deviation of the curve or surface from its piecewise linear approximation is within a specified tolerance. The parameter interval is estimated based on information about the second order derivatives in the homogeneous coordinates, instead of using affine coordinates directly. This new step size can be found with roughly the same amount of computation as the step size presented in [Cheng 1992], though it can be proven to always be larger than Cheng's step size. …