Physical Sciences and Mathematics Commons^™

Comparison Of Threshold Selection Methods For Microarray Gene Co-Expression Matrices, Bhavesh R. Borate, Elissa J. Chesler, Michael A. Langston, Arnold M. Saxton, Brynn H. Voy

Faculty Publications and Other Works -- EECS

Abstract

Background

Network and clustering analyses of microarray co-expression correlation data often require application of a threshold to discard small correlations, thus reducing computational demands and decreasing the number of uninformative correlations. This study investigated threshold selection in the context of combinatorial network analysis of transcriptome data.

Findings

Six conceptually diverse methods - based on number of maximal cliques, correlation of control spots with expressed genes, top 1% of correlations, spectral graph clustering, Bonferroni correction of p-values, and statistical power - were used to estimate a correlation threshold for three time-series microarray datasets. The validity of thresholds was tested by …

Biological Simulations And Biologically Inspired Adaptive Systems, Edgar Alfredo Duenez-Guzman

Doctoral Dissertations

Many of the most challenging problems in modern science lie at the interface of several fields. To study these problems, there is a pressing need for trans-disciplinary research incorporating computational and mathematical models. This dissertation presents a selection of new computational and mathematical techniques applied to biological simulations and problem solving: (i) The dynamics of alliance formation in primates are studied using a continuous time individual-based model. It is observed that increasing the cognitive abilities of individuals stabilizes alliances in a phase transition-like manner. Moreover, with strong cultural transmission an egalitarian regime is established in a few generations. (ii) A …

Sequence-Based Specification Of Embedded Systems, Jason Martin Carter

Doctoral Dissertations

Software has become integral to the control mechanism of modern devices. From transportation and medicine to entertainment and recreation, embedded systems integrate fundamentally with time and the physical world to impact our lives; therefore, product dependability and safety are of paramount importance.

Model-based design has evolved as an effective way to prototype systems and to analyze system function through simulation. This process mitigates the problems and risks associated with embedding software into consumer and industrial products. However, the most difficult tasks remain: Getting the requirements right and reducing them to precise specifications for development, and providing compelling evidence that the …

Static And Dynamic Scheduling For Effective Use Of Multicore Systems, Fengguang Song

Doctoral Dissertations

Multicore systems have increasingly gained importance in high performance computers. Compared to the traditional microarchitectures, multicore architectures have a simpler design, higher performance-to-area ratio, and improved power efficiency. Although the multicore architecture has various advantages, traditional parallel programming techniques do not apply to the new architecture efficiently. This dissertation addresses how to determine optimized thread schedules to improve data reuse on shared-memory multicore systems and how to seek a scalable solution to designing parallel software on both shared-memory and distributed-memory multicore systems.

We propose an analytical cache model to predict the number of cache misses on the time-sharing L2 cache …

An Exploration Of Monophonic Instrument Classification Using Multi-Threaded Artificial Neural Networks, Marc Joseph Rubin

Masters Theses

The use of computers for automated music analysis could benefit several aspects of academia and industry, from psychological and music research, to intelligent music selection and music copyright investigation. In the following thesis, one of the first steps of automated musical analysis, i.e., monophonic instrument recognition, was explored. A multi-threaded artificial neural network was implemented and used as the classifier in order to utilize multi-core technology and allow for faster training. The parallelized batch-mode backpropagation algorithm used provided linear speedup, an improvement to the current literature. For the classification experiments, eleven different sets of instruments were used, starting with perceptively …

Accelerated Ctis Using The Cell Processor, Thaddeus James Thompson

Masters Theses

The Computed Tomography Imaging Spectrometer (CTIS) is a device capable of simultaneously acquiring imagery from multiple bands of the electromagnetic spectrum. Due to the method of data collection from this system, a processing intensive reconstruction phase is required to resolve the image output. This paper evaluates a parallelized implementation of the Vose-Horton CTIS reconstruction algorithm using the Cell processor. In addition to demonstrating the feasibility of a mixed precision implementation, it is shown that use of the parallel processing capabilities of the Cell may provide a significant reduction in reconstruction time.

Bridging The Gap Between Systems Biology And Medicine, Gilles Clermont, Charles Auffray, Yves Moreau, David M. Rocke, Daniel Dalevi, Devdatt Dubhashi, Dana R. Marshall, Peter Raasch, Frank Dehne, Paolo Provero, Jesper Tegner, Bruce J. Aronow, Michael A. Langston, Mikael Benson

Faculty Publications and Other Works -- EECS

Abstract

Systems biology has matured considerably as a discipline over the last decade, yet some of the key challenges separating current research efforts in systems biology and clinically useful results are only now becoming apparent. As these gaps are better defined, the new discipline of systems medicine is emerging as a translational extension of systems biology. How is systems medicine defined? What are relevant ontologies for systems medicine? What are the key theoretic and methodologic challenges facing computational disease modeling? How are inaccurate and incomplete data, and uncertain biologic knowledge best synthesized in useful computational models? Does network analysis provide …

Enhancing User Queries In Scientific Visualization With Distribution Information, Christopher Johnson

Doctoral Dissertations

Scientific visualization is concerned with the graphical portrayal of data. Using symbols, color, and natural perceptual cues, humans gain insight into collections of raw numbers that may not be as efficiently processed in non-graphical formats. For simple data, visualization may require only a simple mapping between numeric values and a color scale. But modern scientific, economic, and social data is far from simple. Multiple variables, duration of time, fine resolutions, and wide sampling have yielded data sets of unprecedented complexity. The mapping between such data and its visual appearance is difficult to define. The works described here attempt to make …

Adaptive Discontinuous Galerkin Finite Element Methods, Haihang You

Doctoral Dissertations

The Discontinuous Galerkin Method is one variant of the Finite Element Methods for solving partial differential equations, which was first introduced by Reed and Hill in 1970’s [27]. Discontinuous GalerkinMethod (DGFEM) differs from the standard Galerkin FEMthat continuity constraints are not imposed on the inter-element boundaries. It results in a solution which is composed of totally piecewise discontinuous functions. The absence of continuity constraints on the inter-element boundaries implies that DG method has a great deal of flexibility at the cost of increasing the number of degrees of freedom. This flexibility is the source of many but not all of …