Numerical Analysis and Scientific Computing Commons^™

Algorithms For Reconstruction Of Gene Regulatory Networks From High -Throughput Gene Expression Data, Wenping Deng

Dissertations, Master's Theses and Master's Reports

Understanding gene interactions in complex living systems is one of the central tasks in system biology. With the availability of microarray and RNA-Seq technologies, a multitude of gene expression datasets has been generated towards novel biological knowledge discovery through statistical analysis and reconstruction of gene regulatory networks (GRN). Reconstruction of GRNs can reveal the interrelationships among genes and identify the hierarchies of genes and hubs in networks. The new algorithms I developed in this dissertation are specifically focused on the reconstruction of GRNs with increased accuracy from microarray and RNA-Seq high-throughput gene expression data sets.

The first algorithm (Chapter 2) …

The Application Of Gpu To Molecular Communication Studies, Tobias J. Cain

EWU Masters Thesis Collection

This thesis applies the recent trends in parallel processing, via graphics processing unit (GPU), to the field of molecular communications (MC), an investigation into communication possibilities of futuristic in vivo nanomachines. Existing MC simulations have not fully accounted for structural boundaries and the associated simulation of a massive number of messenger molecule paths for stochastic evaluation. These molecules are influenced by a Brownian motion as well as the flow of the blood, which is modeled using numerical methods based on the Fokker-Planck stochastic differential equation. By using a GPU these paths can be calculated on a massive scale, both in …

High-Order Integral Equation Methods For Quasi-Magnetostatic And Corrosion-Related Field Analysis With Maritime Applications, Robert Pfeiffer

Theses and Dissertations--Electrical and Computer Engineering

This dissertation presents techniques for high-order simulation of electromagnetic fields, particularly for problems involving ships with ferromagnetic hulls and active corrosion-protection systems.

A set of numerically constrained hexahedral basis functions for volume integral equation discretization is presented in a method-of-moments context. Test simulations demonstrate the accuracy achievable with these functions as well as the improvement brought about in system conditioning when compared to other basis sets.

A general method for converting between a locally-corrected Nyström discretization of an integral equation and a method-of-moments discretization is presented next. Several problems involving conducting and magnetic-conducting materials are solved to verify the accuracy …

Evaluating A Cluster Of Low-Power Arm64 Single-Board Computers With Mapreduce, Daniel Mcdermott

EWU Masters Thesis Collection

With the meteoric rise of enormous data collection in science, industry, and the cloud, methods for processing massive datasets have become more crucial than ever. MapReduce is a restricted programing model for expressing parallel computations as simple serial functions, and an execution framework for distributing those computations over large datasets residing on clusters of commodity hardware. MapReduce abstracts away the challenging low-level synchronization and scalability details which parallel and distributed computing often necessitate, reducing the concept burden on programmers and scientists who require data processing at-scale. Typically, MapReduce clusters are implemented using inexpensive commodity hardware, emphasizing quantity over quality due …

Pressure Measurements Inside Multiple Cavities Of A Torque Converter And Cfd Correlation, Edward De Jesus Rivera

Dissertations, Master's Theses and Master's Reports

A torque converter was instrumented with 29 pressure transducers. The pressure transducers were located in multiple cavities. The instrumented cavities included, four transducers mounted on the impeller shell, on the channel between blades. Six transducers mounted on the pressure and suction sides on the middle streamline of a turbine blade. Another seven transducers mounted on the pressure and suction sides of the core, middle and shell streamlines of a stator blade. Seven transducers mounted on the torque converter clutch cavity. Finally, five on the cavity between the pressure plate and the turbine shell. The torque converter was part of a …

Wildfire Emissions In The Context Of Global Change And The Implications For Mercury Pollution, Aditya Kumar

Dissertations, Master's Theses and Master's Reports

Wildfires are episodic disturbances that exert a significant influence on the Earth system. They emit substantial amounts of atmospheric pollutants, which can impact atmospheric chemistry/composition and the Earth’s climate at the global and regional scales. This work presents a collection of studies aimed at better estimating wildfire emissions of atmospheric pollutants, quantifying their impacts on remote ecosystems and determining the implications of 2000s-2050s global environmental change (land use/land cover, climate) for wildfire emissions following the Intergovernmental Panel on Climate Change (IPCC) A1B socioeconomic scenario.

A global fire emissions model is developed to compile global wildfire emission inventories for major atmospheric …

Quantifying Effects Of Using Thermally Thin Fuel Approximations On Modelling Fire Propagation In Woody Fuels, David Blasen, Jesse Johnson, William Jolly, Russell Parsons

Graduate Student Theses, Dissertations, & Professional Papers

In this paper, we quantify the effects of the thermally thin fuel approximations commonly made in numerical models that eliminate temperature gradients within a heated object. This assumption is known to affect the modeled ignition and burn behavior, but there is little research on its impact, particularly in larger fuels or in numerical models including moisture and chemical decomposition of fuels.

We begin by comparing modeled to observed ignition times and burn rates. To constrain variability in the material properties of wood and focus on variability caused by fuels assumed to be thermally thin, we conduct experiments using thermogravimetric analysis …

Guidelines And Considerations For The Use Of System Suitability And Quality Control Samples In Mass Spectrometry Assays Applied In Untargeted Clinical Metabolomic Studies, David Broadhurst, Royston Goodacre, Stacey N. Reinke, Julia Kuligowski, Ian Wilson, Matthew Lewis, Warwick Dunn

Research outputs 2014 to 2021

Background

Quality assurance (QA) and quality control (QC) are two quality management processes that are integral to the success of metabolomics including their application for the acquisition of high quality data in any high-throughput analytical chemistry laboratory. QA defines all the planned and systematic activities implemented before samples are collected, to provide confidence that a subsequent analytical process will fulfil predetermined requirements for quality. QC can be defined as the operational techniques and activities used to measure and report these quality requirements after data acquisition.

Aim of review

This tutorial review will guide the reader through the use of system …

Sports Analytics With Computer Vision, Colby T. Jeffries

Senior Independent Study Theses

Computer vision in sports analytics is a relatively new development. With multi-million dollar systems like STATS’s SportVu, professional basketball teams are able to collect extremely fine-detailed data better than ever before. This concept can be scaled down to provide similar statistics collection to college and high school basketball teams. Here we investigate the creation of such a system using open-source technologies and less expensive hardware. In addition, using a similar technology, we examine basketball free throws to see whether a shooter’s form has a specific relationship to a shot’s outcome. A system that learns this relationship could be used to …

Big Networks: Analysis And Optimal Control, Hung The Nguyen

Theses and Dissertations

The study of networks has seen a tremendous breed of researches due to the explosive spectrum of practical problems that involve networks as the access point. Those problems widely range from detecting functionally correlated proteins in biology to finding people to give discounts and gain maximum popularity of a product in economics. Thus, understanding and further being able to manipulate/control the development and evolution of the networks become critical tasks for network scientists. Despite the vast research effort putting towards these studies, the present state-of-the-arts largely either lack of high quality solutions or require excessive amount of time in real-world …

Identifying And Computing The Exact Core-Determining Class, Ye Luo, Hai Wang

Research Collection School Of Computing and Information Systems

The indeterministic relations between unobservable events andobserved outcomes in partially identified models can be characterized bya bipartite graph. Given a probability measure on observed outcomes, theset of feasible probability measures on unobservable events can be definedby a set of linear inequality constraints, according to Artstein’s Theorem.This set of inequalities is called the “core-determining class”. However, thenumber of inequalities defined by Artstein’s Theorem is exponentially increasing with the number of unobservable events, and many inequalitiesmay in fact be redundant. In this paper, we show that the “exact coredetermining class”, i.e., the smallest possible core-determining class, canbe characterized by a set of …

Competency Analytics Tool: Analyzing Curriculum Using Course Competencies, Swapna Gottipati, Venky Shankararaman

Research Collection School Of Computing and Information Systems

The applications of learning outcomes and competency frameworks have brought better clarity to engineering programs in many universities. Several frameworks have been proposed to integrate outcomes and competencies into course design, delivery and assessment. However, in many cases, competencies are course-specific and their overall impact on the curriculum design is unknown. Such impact analysis is important for analyzing, discovering gaps and improving the curriculum design. Unfortunately, manual analysis is a painstaking process due to large amounts of competencies across the curriculum. In this paper, we propose an automated method to analyze the competencies and discover their impact on the overall …

Collaboration Patterns In Software Developer Network, Didi Surian, Ee-Peng Lim, David Lo

Research Collection School Of Computing and Information Systems

In this entry, we mine collaboration patterns from a large software developer network (Surian et al. 2010). We consider high- and low-level patterns. High-level patterns correspond to various network-level statistics that we observe to hold in this network. Low-level patterns are topological subgraph patterns that are frequently observed among developers collaborating in the network. Mining topological subgraph patterns are difficult as it is an NP-hard problem. To address this issue, we use a combination of frequent subgraph mining and graph matching by leveraging the power law property exhibited by a large collaboration graph. The technique is applicable to any software …

Automated Species Classification Methods For Passive Acoustic Monitoring Of Beaked Whales, John Lebien

LSU New Orleans Theses and Dissertations

The Littoral Acoustic Demonstration Center has collected passive acoustic monitoring data in the northern Gulf of Mexico since 2001. Recordings were made in 2007 near the Deepwater Horizon oil spill that provide a baseline for an extensive study of regional marine mammal populations in response to the disaster. Animal density estimates can be derived from detections of echolocation signals in the acoustic data. Beaked whales are of particular interest as they remain one of the least understood groups of marine mammals, and relatively few abundance estimates exist. Efficient methods for classifying detected echolocation transients are essential for mining long-term passive …

Underwater Acoustic Signal Analysis Toolkit, Kirk Bienvenu Jr

LSU New Orleans Theses and Dissertations

This project started early in the summer of 2016 when it became evident there was a need for an effective and efficient signal analysis toolkit for the Littoral Acoustic Demonstration Center Gulf Ecological Monitoring and Modeling (LADC-GEMM) Research Consortium. LADC-GEMM collected underwater acoustic data in the northern Gulf of Mexico during the summer of 2015 using Environmental Acoustic Recording Systems (EARS) buoys. Much of the visualization of data was handled through short scripts and executed through terminal commands, each time requiring the data to be loaded into memory and parameters to be fed through arguments. The vision was to develop …

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. Bioconductor 3.6 was released on 31 October, 2017. It is compatible with R 3.4.3 and consists of 1473 software packages, 326 experiment data packages, and 911 up-to-date annotation packages. The release announcement includes descriptions of 100 new software packages, and updated NEWS files for many additional packages. Start using Bioconductor by installing the most recent version of R and evaluating the commands

Changes On Cran, Kurt Hornik, Uwe Ligges, Achim Zeileis

The R Journal

In the past 6 months,1244 new packages were added to the CRAN package repository. 19 packages were unarchived, 55 archived and 3 removed. The following shows the growth of the number of active packages in the CRAN package repository

R Teaching Column, Matthias Gehrke, Reed Davis, Norman Matloff, Paul Thompson, Tiffany Chen, Emily Watkins, Laurel Beckett

The R Journal

The revisit package, developed as a collaborative tool for scientists, also serves as a tool for teaching statistics, in a manner that can be highly motivating for students. Using either the included case studies or datasets/code provided by the instructor, students can explore several alternate paths of analysis, such as the effects of including/excluding certain variables, employing different types of statistical methodology and so on. The package includes features that help students follow modern statistical standards and avoid various statistical errors, such as “p-hacking” and lack of attention to outlier data.

Forwards Column, Stella Bollmann, Dianne Cook, Jasmine Dumas, John Fox, Julie Josse, Oliver Keyes, Carolin Strobl, Heather Turner, Rudolf Debelak

The R Journal

Forwards is a task force that was set up by the R Foundation in 2015 to address the under representation of women that has since widened its scope to encompass other under represented groups. The task force is organised as a core team comprising leaders from a number of sub-teams that focus on particular aspects:

An Introduction To Rocker: Docker Containers For R, Carl Boettiger, Dirk Eddelbuettel

The R Journal

We describe the Rocker project, which provides a widely-used suite of Docker images with customized R environments for particular tasks. We discuss how this suite is organized, and how these tools can increase portability, scaling, reproducibility, and convenience of R users and developers.