Computer Sciences Commons^™

Using An Ontology To Improve The Web Search Experience, Tian Tian

Dissertations

The search terms that a user passes to a search engine are often ambiguous, referring to homonyms. The results in these cases are a mixture of links to documents that contain different meanings of the search terms. Current search engines provide suggested query completions in a dropdown list. However, such lists are not well organized, mixing completions for different meanings. In addition, the suggested search phrases are not discriminating enough. Moreover, current search engines often return an unexpected number of results. Zero hits are naturally undesirable, while too many hits are likely to be overwhelming and of low precision.

This …

Design And Implementation Of A Cyberinfrastructure For Rna Motif Search, Prediction And Analysis, Dongrong Wen

Dissertations

RNA secondary and tertiary structure motifs play important roles in cells. However, very few web servers are available for RNA motif search and prediction. In this dissertation, a cyberinfrastructure, named RNAcyber, capable of performing RNA motif search and prediction, is proposed, designed and implemented.

The first component of RNAcyber is a web-based search engine, named RmotifDB. This web-based tool integrates an RNA secondary structure comparison algorithm with the secondary structure motifs stored in the Rfam database. With a user-friendly interface, RmotifDB provides the ability to search for ncRNA structure motifs in both structural and sequential ways. The second component of …

Approximate String Matching Methods For Duplicate Detection And Clustering Tasks, Oleksandr Rudniy

Dissertations

Approximate string matching methods are utilized by a vast number of duplicate detection and clustering applications in various knowledge domains. The application area is expected to grow due to the recent significant increase in the amount of digital data and knowledge sources. Despite the large number of existing string similarity metrics, there is a need for more precise approximate string matching methods to improve the efficiency of computer-driven data processing, thus decreasing labor-intensive human involvement.

This work introduces a family of novel string similarity methods, which outperform a number of effective well-known and widely used string similarity functions. The new …

An Examination Of Coordination Among Friends And Strangers From A Coordination Theory Perspective, Christopher D. Wamble

Theses

Within mobile social coordination, there is a field of study known as outeraction, the communicative processes used by people to manage future interactions. It is an important area of research because it identifies how informal interactions support complex collaboration between individuals and groups. Outeraction is primarily conducted through the interpersonal communication channels of texting, instant messaging (IM), face-to-face, and mobile phone or Skype conversations. Currently this area of research in mobile outeraction support systems is weak. It lacks a firm foundation in system building, has very few if any conceptual frameworks, and little empirical knowledge of user requirements and attitudes …

Extensions Of Snomed Taxonomy Abstraction Networks Supporting Auditing And Complexity Analysis, Duo Wei

Dissertations

The Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT) has been widely used as a standard terminology in various biomedical domains. The enhancement of the quality of SNOMED contributes to the improvement of the medical systems that it supports.

In previous work, the Structural Analysis of Biomedical Ontologies Center (SABOC) team has defined the partial-area taxonomy, a hierarchical abstraction network consisting of units called partial-areas. Each partial-area comprises a set of SNOMED concepts exhibiting a particular relationship structure and being distinguished by a unique root concept. In this dissertation, some extensions and applications of the taxonomy framework are considered. …

Security Systems Based On Gaussian Integers : Analysis Of Basic Operations And Time Complexity Of Secret Transformations, Aleksey Koval

Dissertations

Many security algorithms currently in use rely heavily on integer arithmetic modulo prime numbers. Gaussian integers can be used with most security algorithms that are formulated for real integers. The aim of this work is to study the benefits of common security protocols with Gaussian integers. Although the main contribution of this work is to analyze and improve the application of Gaussian integers for various public key (PK) algorithms, Gaussian integers were studied in the context of image watermarking as well.

The significant benefits of the application of Gaussian integers become apparent when they are used with Discrete Logarithm Problem …

Investigation On Advanced Image Search Techniques, Abhishek Verma

Dissertations

Content-based image search for retrieval of images based on the similarity in their visual contents, such as color, texture, and shape, to a query image is an active research area due to its broad applications. Color, for example, provides powerful information for image search and classification. This dissertation investigates advanced image search techniques and presents new color descriptors for image search and classification and robust image enhancement and segmentation methods for iris recognition.

First, several new color descriptors have been developed for color image search. Specifically, a new oRGB-SIFT descriptor, which integrates the oRGB color space and the Scale-Invariant Feature …

Development Of Advanced Algorithms To Detect, Characterize And Forecast Solar Activities, Yuan Yuan

Dissertations

Study of the solar activity is an important part of space weather research. It is facing serious challenges because of large data volume, which requires application of state-of-the-art machine learning and computer vision techniques. This dissertation targets at two essential aspects in space weather research: automatic feature detection and forecasting of eruptive events.

Feature detection includes solar filament detection and solar fibril tracing. A solar filament consists of a mass of gas suspended over the chromosphere by magnetic fields and seen as a dark, ribbon-shaped feature on the bright solar disk in Hα (Hydrogen-alpha) full-disk solar images. In this dissertation, …

Applications Of Stochastic Simulation In Two-Stage Multiple Comparisons With The Best Problem And Time Average Variance Constant Estimation, Dibyendu Chakrabarti

Dissertations

In this dissertation, we study two problems. In the first part, we consider the two-stage methods for comparing alternatives using simulation. Suppose there are a finite number of alternatives to compare, with each alternative having an unknown parameter that is the basis for comparison. The parameters are to be estimated using simulation, where the alternatives are simulated independently. We develop two-stage selection and multiple-comparison procedures for simulations under a general framework. The assumptions are that each alternative has a parameter estimation process that satisfies a random- time-change central limit theorem (CLT), and there is a weakly consistent variance estimator (WCVE) …

Active Caching For Recommender Systems, Muhammad Umar Qasim

Dissertations

Web users are often overwhelmed by the amount of information available while carrying out browsing and searching tasks. Recommender systems substantially reduce the information overload by suggesting a list of similar documents that users might find interesting. However, generating these ranked lists requires an enormous amount of resources that often results in access latency. Caching frequently accessed data has been a useful technique for reducing stress on limited resources and improving response time. Traditional passive caching techniques, where the focus is on answering queries based on temporal locality or popularity, achieve a very limited performance gain. In this dissertation, we …

Ranking Single Nucleotide Polymorphisms With Support Vector Regression In Continuous Phenotypes, Seif Shahidain

Theses

Support vector machines (SVM) have been used to improve the ranking of single nucleotide polymorphisms (SNPs) over traditional chi-square tests in disease case studies [2]. In this investigation, ranking SNPs with support vector regression (SVR) was compared to the Wald test in predicting continuous phenotypes. SVR-ranked SNPs consistently outperformed the Wald test-ranked SNPs to provide a more accurate prediction of the phenotype with fewer SNPs across several methods of prediction.

Dynamic-Parinet (D-Parinet) : Indexing Present And Future Trajectories In Networks, Mou Nandi

Theses

While indexing historical trajectories is a hot topic in the field of moving objects (MO) databases for many years, only a few of them consider that the objects movements are constrained. DYNAMIC-PARINET (D-PATINET) is designed for capturing of trajectory data flow in multiple discrete small time interval efficiently and to predict a MO’s movement or the underlying network state at a future time.

The cornerstone of D-PARINET is PARINET, an efficient index for historical trajectory data. The structure of PARINET is based on a combination of graph partitioning and a set of composite B+-tree local indexes tuned for a given …

Fast Program For Sequence Alignment Using Partition Function Posterior Probabilities, Meera Prasad

Theses

The key requirements of a good sequence alignment tool are high accuracy and fast execution. The existing Probalign program is a highly accurate tool for sequence alignment of both proteins and nucleotides. However, the time for execution is fairly high. The focus is therefore, to reduce the running time of the existing version of Probalign, maintaining its current accuracy level.

The thesis conducts a detail analysis of the performance of Probalign to bring down the running time of the existing code. A modified version of Probalign, Version 1.4 is released. A new program for sequence alignment with faster computation is …

A Molecular Dynamics Simulation Based Principal Component Analysis Framework For Computation Of Multi-Scale Modeling Of Protein And Its Interaction With Solvent, Tao Wu

Dissertations

This dissertation presents a new computational framework for calculating the normal modes and interactions of proteins, macromolecular assemblies and surrounding solvents. The framework employs a combination of molecular dynamics simulation (MD) and principal component analysis (PCA). It enables the capture and visualization of the molecules' normal modes and interactions over time scales that are computationally challenging. It also provides a starting point for experimental and further computational studies of protein conformational changes.

A protein's function is sometimes linked to its conformational flexibility. Normal mode analysis (NMA) and various extensions of it have provided insights into the conformational fluctuations associated with …

Face Recognition Using Multiple Features In Different Color Spaces, Zhiming Liu

Dissertations

Face recognition as a particular problem of pattern recognition has been attracting substantial attention from researchers in computer vision, pattern recognition, and machine learning. The recent Face Recognition Grand Challenge (FRGC) program reveals that uncontrolled illumination conditions pose grand challenges to face recognition performance. Most of the existing face recognition methods use gray-scale face images, which have been shown insufficient to tackle these challenges. To overcome this challenging problem in face recognition, this dissertation applies multiple features derived from the color images instead of the intensity images only.

First, this dissertation presents two face recognition methods, which operate in different …

Aminormotiffinder - A Graph Grammar Based Tool To Effectively Search A Minor Motifs In 3d Rna Molecules, Ankur Malhotra

Theses

RNA Motifs are three dimensional folds that play important role in RNA folding and its interaction with other molecules. They basically have modular structure and are composed of conserved building blocks dependent upon the sequence. Their automated in silico identification remains a challenging task. Existing motif identification tools does not correctly identify motifs with large structure variations. Here a “graph rewriting” based method is proposed to identify motifs in real three dimensional structures. The unique encoding of A Minor Searcher takes into consideration the non canonical base pairs and also multipairing of RNA structural motifs. The accuracy is demonstrated by …

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 …

Processing Techniques For Partial Tree-Pattern Queries On Xml Data, Pawel Placek

Dissertations

In recent years, eXtensible Markup Language (XML) has become a de facto standard for exporting and exchanging data on the Web. XML structures data as trees. Querying capabilities are provided through patterns matched against the XML trees. Research on the processing of XML queries has focused mainly on tree-pattern queries. Tree-pattern queries are not appropriate for querying XML data sources whose structure is not fully known to the user, or for querying multiple data sources which structure information differently. Recently, a class of queries, called Partial Tree-Pattern Queries (PTPQs) was identified. A central feature of PTPQs is that the structure …

In-Group / Out-Group Dynamics And Effectiveness In Partially Distributed Teams, Faina Privman

Dissertations

When organizations collaborate they often do so using partially distributed teams (PDTs). In a Partially Distributed Team there exist at least two distinct sub-groups. In addition, at least one of the sub-groups has two or more members that are geographically co-located. Co-located members can meet face to face; chat in the hallway; have lunch together; and otherwise socialize with one another. On the other hand, remote members must rely on technology to communicate and work together. This distinct characteristic of partially distributed teams makes them especially susceptible to the In-Group / Out Group dynamic (Huang and Ocker, 2006). This dynamic …

Design Development And Evaluation Of Collario, A Group Support System For Collaborative Scenario Creation, Xiang Yao

Dissertations

In the fields of Emergency Management and Business Continuity Planning, scenarios are a widely used tool for planning, training and knowledge sharing purposes. The ability to create and discuss emergency scenarios in virtual teams can lead to many potential applications, such as discussing emergency scenarios by world-wide experts, conducting on-line exercises, and creating Communities of Practices. Existing scenario creation systems, like NxMsel provided by FEMA, allow distributed groups to create scenarios together. However, collaborative support in these systems is generally limited.

This dissertation explores an innovative solution to provide various types of collaboration support around a knowledge structure and uses …