Physical Sciences and Mathematics Commons^™

Natural Selection On Mrna Secondary Structure And Its Correlation With Protein Functional Groups, Suresh Solaimuthu

Dissertations

Natural selection may occur at multiple levels of the biological hierarchy, including at the molecular level. It may occur on any phenotypic trait that evidences variation and that is heritable. This research uses computational methods to investigate whether the stability of the secondary structures of mRNAs has been the subject of natural selection.

The DNA sequence that codes for a particular target protein is only partially determined by that protein, since the redundancy of the genetic code permits multiple possible synonymous codons for each peptide. An RNA transcript of a DNA protein template (gene) folds back on itself through complementary …

Variance Reduction Techniques For Estimating Quantiles And Value-At-Risk, Fang Chu

Dissertations

Quantiles, as a performance measure, arise in many practical contexts. In finance, quantiles are called values-at-risk (VARs), and they are widely used in the financial industry to measure portfolio risk. When the cumulative distribution function is unknown, the quantile can not be computed exactly and must be estimated. In addition to computing a point estimate for the quantile, it is important to also provide a confidence interval for the quantile as a way of indicating the error in the estimate. A problem with crude Monte Carlo is that the resulting confidence interval may be large, which is often the case …

New Data Structures, Models, And Algorithms For Real-Time Resource Management, Xinfa Hu

Dissertations

Real-time resource management is the core and critical task in real-time systems. This dissertation explores new data structures, models, and algorithms for real-time resource management.

At first, novel data structures, i.e., a class of Testing Interval Trees (TITs), are proposed to help build efficient scheduling modules in real-time systems. With a general data structure, i.e., the TIT* tree, the average costs of the schedulability tests in a wide variety of real-time systems can be reduced. With the Testing Interval Tree for Vacancy analysis (TIT-V), the complexities of the schedulability tests in a class of parallel/distributed real-time systems can be effectively …

Type-1 Diabetes Risk Prediction Using Multiple Kernel Learning, Paras Garg

Theses

This thesis presents an analysis of multiple kernel learning (MKL) for type-1 diabetes risk prediction. MKL combines different models and representation of data to find a linear combination of these representations of the data. MKL has been successfully been implemented in image detection, splice site detection, ribosomal and membrane protein prediction, etc. In this thesis, this method was applied for Genome-wide association study (GWAS) for classifying cases and controls.

This thesis has shown that combined kernel does not perform better than the individual kernels and that MKL does not select the best model for this problem. Also, the effect of …

Algorithms In Comparative Genomics, Satish Chikkagoudar

Dissertations

The field of comparative genomics is abundant with problems of interest to computer scientists. In this thesis, the author presents solutions to three contemporary problems: obtaining better alignments for phylogeny reconstruction, identifying related RNA sequences in genomes, and ranking Single Nucleotide Polymorphisms (SNPs) in genome-wide association studies (GWAS).

Sequence alignment is a basic and widely used task in bioinformatics. Its applications include identifying protein structure, RNAs and transcription factor binding sites in genomes, and phylogeny reconstruction. Phylogenetic descriptions depend not only on the employed reconstruction technique, but also on the underlying sequence alignment. The author has studied and established a …

Understanding Cognitive Differences In Processing Competing Visualizations Of Complex Systems, Madhavi Mukul Chakrabarty

Dissertations

Node-link diagrams are used represent systems having different elements and relationships among the elements. Representing the systems using visualizations like node-link diagrams provides cognitive aid to individuals in understanding the system and effectively managing these systems. Using appropriate visual tools aids in task completion by reducing the cognitive load of individuals in understanding the problems and solving them. However, the visualizations that are currently developed lack any cognitive processing based evaluation. Most of the evaluations (if any) are based on the result of tasks performed using these visualizations. Therefore, the evaluations do not provide any perspective from the point of …

Job Seeking And Job Application In Social Networking Sites : Predicting Job Seekers' Behavioral Intentions, Maria Marcella Plummer

Dissertations

Social networking sites (SNSs) are revolutionizing the way in which employers and job seekers connect and interact with each other. Despite the reported benefits of SNSs with respect to finding a job, there are issues such as privacy concerns that might be deterring job seekers from using these sites in their attempts to secure a job. It is therefore important to understand the factors that are salient in predicting job seekers' use of SNSs in applying for jobs.

In this research, a theoretical model was developed to explicate job seekers' intentions to use SNSs to apply for jobs. Two aspects …

Semantics And Efficient Evaluation Of Partial Tree-Pattern Queries On Xml, Xiaoying Wu

Dissertations

Current applications export and exchange XML data on the web. Usually, XML data are queried using keyword queries or using the standard structured query language XQuery the core of which consists of the navigational query language XPath. In this context, one major challenge is the querying of the data when the structure of the data sources is complex or not fully known to the user. Another challenge is the integration of multiple data sources that export data with structural differences and irregularities. In this dissertation, a query language for XML called Partial Tree-Pattern Query (PTPQ) language is considered. PTPQs generalize …

Virtual World Commerce Adoption (Vwca) : A Case Study Of Second Life Investigating The Impacts Of Perceived Affordances, Trust, And Need Satisfaction, Kamolbhan Olapiriyakul

Dissertations

Virtual worlds are computer-simulated worlds in which multi-players can simultaneously interact in a rich graphical environment. The development of virtual worlds, along with the massive growth of users, creates opportunities for business organizations. This dissertation involves many studies regarding virtual world adoption in business by virtual consumers.

Most of the research in Information Systems (IS) was conducted investigating factors influencing technology adoption, such as ease of use and usefulness, subjective norms and behavioral controls, self-efficacy, performance and effort expectancy, flow, etc. However, most of these research studies focused neither on design aspects related to affordances nor users' goal-oriented behaviors, such …

In Silico Prediction Of Non-Coding Rnas Using Supervised Learning And Feature Ranking Methods, Stephen J. Griesmer

Theses

This thesis presents a novel method, RNAMultifold, for development of a non-coding RNA (ncRNA) classification model based on features derived from folding the consensus sequence of multiple sequence alignments using different folding programs: RNAalifold, CentroidFold, and RSpredict. The method ranks these folding features according to a Class Separation Measure (CSM) that quantifies the ability of the features to differentiate between samples from positive and negative test sets. The set of top-ranked features is then used to construct classification models: Naive Bayes, Fisher Linear Discriminant, and Support Vector Machine (SVM). These models are compared to the performance of the same models …

Social Group Discovery Using Using Co-Location Traces, Steve Mardenfeld

Theses

Social information can be used to enhance existing applications and services or can be utilized to devise entirely new applications. Examples of such applications include recommendation systems, peer-to-peer networks, opportunistic data dissemination in ad hoc networks, or mobile friend finder. Social information can be collected from either online or mobile sources.

This thesis focuses on identifying social groups based on data collected from mobile phones. These data can be either location or co-location traces. Unfortunately, location traces require a localization system for every mobile device, and users are reluctant to share absolute location due to privacy concerns. On the other …