Computer Sciences Commons^™

A Framework To Support Spatial, Temporal And Thematic Analytics Over Semantic Web Data, Matthew Steven Perry

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Spatial and temporal data are critical components in many applications. This is especially true in analytical applications ranging from scientific discovery to national security and criminal investigation. The analytical process often requires uncovering and analyzing complex thematic relationships between disparate people, places and events. Fundamentally new query operators based on the graph structure of Semantic Web data models, such as semantic associations, are proving useful for this purpose. However, these analysis mechanisms are primarily intended for thematic relationships. This dissertation proposes a framework built around the RDF data model for analysis of thematic, spatial and temporal relationships between named entities. …

Algorithmic Techniques Employed In The Isolation Of Codon Usage Biases In Prokaryotic Genomes, Douglas W. Raiford Iii

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While genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons is preferred. Isolation of translational efficiency bias can have important …

Energy Efficient Image Video Sensor Networks, Paul Anthony Bender

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Image Video Sensor Networks are emerging applications for sensor network technologies. The relatively large size of the data collected by image video sensors presents new challenges for the sensor network in terms of energy consumption and channel capacity. We address each of these issues through the use of a high density network deployment utilizing some nodes as dedicated relay nodes.

A high density network allows network nodes to reduce their transmission power. This reduction in transmission power allows each node to conserve power and simultaneously increases the potential for spatially concurrent transmissions within the network, resulting in improved network throughputs. …

Object Similarity Through Correlated Third-Party Objects, Ting Sa

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Given a pair of objects, it is of interest to know how they are related to each other and the strength of their similarity. Many previous studies focused on two types of similarity measures: The first type is based on closeness of attribute values of two given objects, and the second type is based on how often the two objects co-occur in transactions/tuples.

In this thesis we study a new behavior-based similarity measure, which evaluates similarity between two objects by considering how similar their correlated third-party object sets are. Behavior-based similarity can help us find pairs of objects that have …

Analysis And Transformation Of Post-Conditions, Abhinav Vasikarla

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Software engineers have been trying for years to develop a software synthesis system that can transform a formal specification model to a design model from which executable code can be generated. AFIT wide spectrum object modeling environment (AWESOME) is one result of their research. AWESOME presents a formal model as an abstract syntax tree. This model consists mainly of object class specifications. The methods in these classes are specified using pre and post-conditions. The intent of this thesis is to support the transformation of post-conditions to code statements. A post-condition is first categorized as dependent or independent relative to other …

Performance And Complexity Co-Evaluations Of Mpeg4-Als Compression Standard For Low-Latency Music Compression, Isaac Kevin Matthew

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In this thesis compression ratio and latency of different classical audio music tracks are analyzed with various encoder options of MPEG4ALS. Different tracks of audio music tracks are tested with MPEG4-ALS coder with different options to find the optimum values for various parameters to obtain maximum compression ratio with minimum CPU time (encoder and decoder time). Optimum frame length for which the compression ratio saturates for music audio is found out by analyzing the results when different classical music tracks are experimented with various frame lengths. Also music tracks with varying sampling rate are tested and the compression ratio and …

An Analog Evolvable Hardware Device For Active Control, Saranyan A. Vigraham

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The field of Evolvable Hardware (EH) has recently gained a lot of interest due to the novel methodology it offers for designing electrical circuits and machines. EH techniques involve configuring a reconfigurable hardware platform with the aid of learning engines such as evolutionary algorithms. The EH devices normally act as closed loop controllers with the capability of learning necessary control laws adaptively. Current EH practices have several shortcomings, which have restricted their use as reliable controllers. This dissertation will present an improved EH device based on behavioral reconfigurability that addresses the current open challenges in the field of analog Evolvable …

Classification Of Microarray Data To Predict Toxic Exposure, Tarek A. Seleem

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This thesis presents a software system for the analysis of microarray data. Microarrays are a relatively new technology that can be used to examine the state of the genome of an organism at some instant in time. The challenge is the amount of natural variation in biological systems limits our ability to identify specific genes that may be sensitive to changes in an organism's physiology or its environment. The analysis software consists of three modules. The first module filters microarray data to reduce the complexity of the problem. The second module selects subsets of genes for evaluation using a genetic …

On Optimal Survivability Design In Wdm Optical Networks Under Scheduled Traffic Models, Tianjian Li

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Wavelength division multiplexing (WDM) optical networks are widely viewed as the most appropriate choice for future Internet backbone with the potential to fulfill the ever-growing demands for bandwidth. WDM divides the enormous bandwidth of an optical fiber into many non-overlapping wavelength channels, each of which may operate at the rate of 10 Gigabit per second or higher. A failure in a network such as a cable cut may result in a tremendous loss of data. Therefore, survivability is a very important issue in WDM optical networks. The objective of this dissertation is to address the survivability provisioning problem in WDM …

Transformation Of Formally Defined Post-Conditions Into Target Language Statements, Swetha Padma Parvathaneni

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For years software engineering researchers have been trying to come up with a software synthesis system that can transform a formal specification model into a design model from which executable code can be generated. AFIT Wide Spectrum Object Modeling Environment (AWSOME) is one such formal based software synthesis system. In this system formal specifications written in AWL are parsed into an AST (Abstract Syntax Tree). The intent of this thesis is to demonstrate the transformation of the postconditions of a method into target language statements. The methods in the classes are specified using pre-conditions and post-conditions. Transforms are developed to …

Role-Based Access Control For The Open Grid Services Architecture - Data Access And Integration (Ogsa-Dai), Anil L. Pereira

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Grid has emerged recently as an integration infrastructure for the sharing and coordinated use of diverse resources in dynamic, distributed virtual organizations (VOs). A Data Grid is an architecture for the access, exchange, and sharing of data in the Grid environment. In this dissertation, role-based access control (RBAC) systems for heterogeneous data resources in Data Grid systems are proposed. The Open Grid Services Architecture - Data Access and Integration (OGSA-DAI) is a widely used framework for the integration of heterogeneous data resources in Grid systems.

However, in the OGSA-DAI system, access control causes substantial administration overhead for resource providers in …

Data Mining And Analysis On Multiple Time Series Object Data, Chunyu Jiang

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Huge amount of data is available in our society and the need for turning such data into useful information and knowledge is urgent. Data mining is an important field addressing that need and significant progress has been achieved in the last decade. In several important application areas, data arises in the format of Multiple Time Series Object (MTSO) data, where each data object is an array of time series over a large set of features and each has an associated class or state. Very little research has been conducted towards this kind of data. Examples include computational toxicology, where each …

Xml Integrated Environment For Service-Oriented Data Management, Marwan Younes Maarouf

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The proliferation of XML as a family of related standards including a markup language (XML), formatting semantics (XSL style sheets), a linking syntax (XLINK), and appropriate data schema standards have emerged as a de facto standard for encoding and sharing data between various applications. XML is designed to be simple, easily parsed and self-describing. XML is based on and support the idea of separation of concerns: information content is separated from information rendering, and relationships between data elements are provided via simple nesting and references. As the XML content grows, the ability to handle schemaless XML documents becomes more critical …

High Performance Text Document Clustering, Yanjun Li

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Data mining, also known as knowledge discovery in database (KDD), is the process to discover interesting unknown knowledge from a large amount of data. Text mining is to apply data mining techniques to extract interesting and nontrivial information and knowledge from unstructured text. Text clustering is one of important techniques of text mining, which is the unsupervised classification of similar documents into different groups.

This research focuses on improving the performance of text clustering. We investigated the text clustering algorithms in four aspects: document representation, documents closeness measurement, high dimension reduction and parallelization. We propose a group of high performance …

An Analysis Of Neutral Drift's Effect On The Evolution Of A Ctrnn Locomotion Controller With Noisy Fitness Evaluation, Gregory Robert Kramer

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This dissertation focuses on the evolution of Continuous Time Recurrent Neural Networks (CTRNNs) as controllers for control systems. Existing research suggests that the process of neutral drift can greatly benefit evolution for problems whose fitness landscapes contain large-scale neutral networks. CTRNNs are known to be highly degenerate, providing a possible source of large-scale landscape neutrality, and existing research suggests that neutral drift benefits the evolution of simple CTRNNs. However, there has been no in-depth examination of the effects of neutral drift on complex CTRNN controllers, especially in the presence of noisy fitness evaluation. To address this problem, this dissertation presents …

Computational Methods For The Objective Review Of Forensic Dna Testing Results, Jason R. Gilder

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Since the advent of criminal investigations, investigators have sought a "gold standard" for the evaluation of forensic evidence. Currently, deoxyribonucleic acid (DNA) technology is the most reliable method of identification. Short Tandem Repeat (STR) DNA genotyping has the potential for impressive match statistics, but the methodology not infallible. The condition of an evidentiary sample and potential issues with the handling and testing of a sample can lead to significant issues with the interpretation of DNA testing results. Forensic DNA interpretation standards are determined by laboratory validation studies that often involve small sample sizes. This dissertation presents novel methodologies to address …

Summaritive Digest For Large Document Repositories With Application To E-Rulemaking, Lijun Chen

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Large document repositories need to be organized and summarized to make them more accessible and understandable. Such needs exist in many applications, including web search, e-rulemaking (electronic rulemaking) and document archiving. Even though much has been done in the areas of document clustering and summarization, there are still many new challenges and issues that need to be addressed as the repositories become larger, more prevalent and dynamic. In this dissertation, we investigate more informative ways to organize and summarize large document repositories, especially e-rulemaking feedback repositories (ERFRs), so that the large repositories can be managed and digested more efficiently and …

Analysis Of Very Large Scale Image Data Using Out-Of-Core Technique And Automated 3d Reconstruction Using Calibrated Images, Chandrashekara Hassan Raju

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Analysis of large scale volumetric data sets is very important from the researcher's and technological point of view as it helps in understanding and analyzing the original data. For example, when analyzing volumetric images from cast arteries of pigs, it is essential to apply a suitable segmentation in order to retrieve morphometric data from the scanned image. Due to improved scanning technology, such as MicroCT, these scanned images can get as large as several gigabytes in size. In order to analyze such large scale data sets on common desktop computers is a challenge due to limited main memory. By using …

Gpu-Assisted Rendering Of Large Tree-Shaped Data Sets, Pallavi Ramachandra Mangalvedkar

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Due to their complexity, medical data sets can easily comprise of several gigabytes in size. For example, geometric representations of a coronary arterial tree spanning vessels from the large proximal coronary arteries down to the capillary level consist of 6 gigabytes or more of geometry data, depending on the accuracy of the geometric representation. Visualization of such large data sets using the CPU alone can be inefficient and time consuming since they require special out-of-core techniques due to the size of the data set. The usage of the GPU can help render such data sets faster compared to CPU-based implementations …

Design And Implementation Of Timeline Application For News Documents, Mastan Vali Shaik

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The growing News document archive emphasizes the need for efficient techniques to retrieve and visualize its content. We present a timeline based graphical interface for this purpose. The timeline is a graph of number of documents supporting association between entity (event, country, person, etc) etc and event (entity, country, person, etc) with respect to dates. The query is formulated based on entity, event, country, and person metadata extracted from the text of the News documents by analyzing the documents using proprietary name-entity recognizers. The timeline also provides a means to index and access relevant documents. Associations inferred on the basis …

Fuel Flow Control Issue In Jet Engines: An Evolvable Hardware Approach, Kshitij S. Deshpande

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Dealing with unexpected dynamic loads in Jet and Turbine engines have always been a matter of concern and an active area of research. This thesis is an initial attempt to apply Evolvable Hardware methods for augmenting classical control methods in a generic turbine engine model. In this work, the Air Force Research Laboratory Generic Turbine Engine Model was converted into C and interfaced with a simulation of a EH VLSI control chip currently under development. The simulated EH device was allowed to evolve to augment the simulated engine's standard FADEC controller so that the whole system could tolerate unexpected, large …

Comparative Microarray Data Mining, Shihong Mao

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As a revolutionary technology, microarrays have great potential to provide genome-wide patterns of gene expression, to make accurate medical diagnosis, and to explore genetic causes underlying diseases. It is commonly believed that suitable analysis of microarray datasets can lead to achieve the above goals. While much has been done in microarray data mining, few previous studies, if any, focused on multiple datasets at the comparative level. This dissertation aims to fill this gap by developing tools and methods for set-based comparative microarray data mining. Specifically, we mine highly differentiative gene groups (HDGGs) from given datasets/classes, evaluate the concordance of datasets …

A Hybrid Approach To Retrieving Web Documents And Semantic Web Data, Trivikram Immaneni

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The Semantic Web has been evolving into a property-linked web of RDF data, conceptually divorced from (but physically housed in) the World Wide Web of hyperlinked documents. Data Retrieval techniques are typically used to retrieve data from the Semantic Web while Information Retrieval techniques are used to retrieve documents from the Hypertext Web. Conceptually unifying the two webs enables the exploitation of their interconnections resulting in benefits to both data and document retrieval. Towards this end, we present the Unified Web model that integrates the two webs and formalizes the structure and the semantics of their interconnections. We present a …

Investigating The Male-Driven Evolution Hypothesis Using Human AluRepeat Elements, Sridhar Ramachandran

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Thousands of copies of short interspersed repeats (SINEs) are scattered essentially ran-domly through the human genome. Although copies of each repeat subfamily are identical at the time of their insertion, they become subject to individual substitutions after insertion. As the relative time of insertion is known for many of these repeats, such "junk DNA" can be used to provide a sizeable number of time-series data points for studying substitution effects in a variety of genomic contexts. This dissertation specifically discusses the usefulness of the Alufamily of SINE repeats towards addressing open problems in genomics, population genetics, and biology in …

A Computational Framework For Analyzing Chemical Modification And Limited Proteolysis Experimental Data Used For High Confidence Protein Structure Prediction, Paul E. Anderson

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Prediction of protein tertiary structure based on amino acid sequence is one of the most challenging open questions in computational molecular biology. Experimental methods for protein structure determination remain relatively time consuming and expensive, and are not applicable to all proteins. While a diverse array of algorithms have been developed for prediction of protein structure from amino acid sequence information, the accuracy and reliability of these methods are not yet comparable to experimental structure determination techniques. Computational models of protein structure can, however, be improved by the incorporation of experimental information. Relatively rapid and inexpensive protein modification experiments can be …

Specification For Visual Requirements Of Work-Centered Software Systems, James Robert Knapp

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Work-centered software systems function as inherent work-aiding systems. Based on the design concept for a work-centered support system (WCSS), these software systems support user tasks and goals through both direct and indirect aiding methods within the interface client. In order to ensure the coherent development and delivery of work-centered software products, WCSS visual interface requirements must be specified in order to capture the cognitive and work-aiding aspects of the user interface design. Without the ability to specify such original requirements, the probability of creating an accurate and effective work-centered software system is significantly reduced. A new visual requirements specification language …

A Field Programmable Gate Array Architecture For Two-Dimensional Partial Reconfiguration, Fei Wang

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Reconfigurable machines can accelerate many applications by adapting to their needs through hardware reconfiguration. Partial reconfiguration allows the reconfiguration of a portion of a chip while the rest of the chip is busy working on tasks. Operating system models have been proposed for partially reconfigurable machines to handle the scheduling and placement of tasks. They are called OS4RC in this dissertation. The main goal of this research is to address some problems that come from the gap between OS4RC and existing chip architectures and the gap between OS4RC models and practical applications. Some existing OS4RC models are based on an …

Multivariate Analysis Of Prokaryotic Amino Acid Usage Bias: A Computational Method For Understanding Protein Building Block Selection In Primitive Organisms, Douglas Whitmore Raiford Iii

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Organisms expend a significant fraction of their overall energy budget in the creation of proteins, particularly for those that are produced in large quantities. Recent research has demonstrated that genes encoding these proteins are shaped by natural selection to produce the proteins with low cost building blocks (amino acids) whenever possible. The negative correlation between protein production rate and their energetic costs has been established for two bacterial genomes: Escherichia coli and Bacillus subtilis. This thesis provides scientific validation of this theory by automating the analysis and extending the research to additional genomes. Investigations into building block selection are highly …

Pattern Recognition Via Machine Learning With Genetic Decision-Programming, Carl C. Hoff

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In the intersection of pattern recognition, machine learning, and evolutionary computation is a new search technique by which computers might program themselves. That technique is called genetic decision-programming. A computer can gain the ability to distinguish among the things that it needs to recognize by using genetic decision-programming for pattern discovery and concept learning. Those patterns and concepts can be easily encoded in the spines of a decision program (tree or diagram). A spine consists of two parts: (1) the test-outcome pairs along a path from the program's root to any of its leaves and (2) the conclusion in that …