Digital Commons Network^™

Predicting Flavonoid Ugt Regioselectivity With Graphical Residue Models And Machine Learning., Arthur Rhydon Jackson

Electronic Theses and Dissertations

Machine learning is applied to a challenging and biologically significant protein classification problem: the prediction of flavonoid UGT acceptor regioselectivity from primary protein sequence. Novel indices characterizing graphical models of protein residues are introduced. The indices are compared with existing amino acid indices and found to cluster residues appropriately. A variety of models employing the indices are then investigated by examining their performance when analyzed using nearest neighbor, support vector machine, and Bayesian neural network classifiers. Improvements over nearest neighbor classifications relying on standard alignment similarity scores are reported.

An Investigation Into Rewriting A Security Policy For Loreto College, Paul M. Mwai

Regis University Student Publications (comprehensive collection)

Computers as well as the networking environments in which they operate have evolved into highly sophisticated and complex systems. The intricacy of these systems and especially the relationship between them forms the greatest area of vulnerabilities for organizations. (Whitman and Mattord, 2004) Information needs to be transmitted to and from the organization, and thus may be vulnerable within certain stages along the communications line. If at any stage of the process, the information is compromised, it could have a negative impact on the entire organization. Protective measures such as disaster recover plans, encryption/ decryption, and information system security controls, can …

Realizing The Technical Advantages Of Star Transformation, Karen L. Darling

Regis University Student Publications (comprehensive collection)

Data warehousing and business intelligence go hand in hand, each gives the other purpose for development, maintenance and improvement. Both have evolved over a few decades and build upon initial development. Management initiatives further drive the need and complexity of business intelligence, while in turn expanding the end user community so that business change, results and strategy are affected at the business unit level. The literature, including a recent business intelligence user survey, demonstrates that query performance is the most significant issue encountered. Oracle's data warehouse 10g.2 is examined with improvements to query optimization via "best practice" through Star Transformation. …

Large-Scale Distributed Coalition Formation, Daniel R. Karrels

Theses and Dissertations

The CyberCraft project is an effort to construct a large scale Distributed Multi-Agent System (DMAS) to provide autonomous Cyberspace defense and mission assurance for the DoD. It employs a small but flexible agent structure that is dynamically reconfigurable to accommodate new tasks and policies. This document describes research into developing protocols and algorithms to ensure continued mission execution in a system of one million or more agents, focusing on protocols for coalition formation and Command and Control. It begins by building large-scale routing algorithms for a Hierarchical Peer to Peer structured overlay network, called Resource-Clustered Chord (RC-Chord). RC-Chord introduces the …

Interactive Football Summarization, Brandon B. Moon

Theses and Dissertations

Football fans do not have the time to watch every game in its entirety and need an effective solution that summarizes them the story of the game. Human-generated summaries are often too short, requiring time and resources to create. We utilize the advantages of Interactive TV to create an automatic football summarization service that is cohesive, provides context, covers the necessary plays, and is concise. First, we construct a degree of interest function that ranks each play based on detailed, play-by-play game events as well as viewing statistics collected from an interactive viewing environment. This allows us to select the …

Bisecting Document Clustering Using Model-Based Methods, Aaron Samuel Davis

Theses and Dissertations

We all have access to large collections of digital text documents, which are useful only if we can make sense of them all and distill important information from them. Good document clustering algorithms that organize such information automatically in meaningful ways can make a difference in how effective we are at using that information. In this paper we use model-based document clustering algorithms as a base for bisecting methods in order to identify increasingly cohesive clusters from larger, more diverse clusters. We specifically use the EM algorithm and Gibbs Sampling on a mixture of multinomials as the base clustering algorithms …

Noninvasive Estimation Of Pulmonary Artery Pressure Using Heart Sound Analysis, Aaron W. Dennis

Theses and Dissertations

Right-heart catheterization is the most accurate method for estimating pulmonary artery pressure (PAP). Because it is an invasive procedure it is expensive, exposes patients to the risk of infection, and is not suited for long-term monitoring situations. Medical researchers have shown that PAP influences the characteristics of heart sounds. This suggests that heart sound analysis is a potential noninvasive solution to the PAP estimation problem. This thesis describes the development of a prototype system, called PAPEr, which estimates PAP noninvasively using heart sound analysis. PAPEr uses patient data with machine learning algorithms to build models of how PAP affects heart …

Integrating Information Theory Measures And A Novel Rule-Set-Reduction Tech-Nique To Improve Fuzzy Decision Tree Induction Algorithms, Nael Mohammed Abu-Halaweh

Computer Science Dissertations

Machine learning approaches have been successfully applied to many classification and prediction problems. One of the most popular machine learning approaches is decision trees. A main advantage of decision trees is the clarity of the decision model they produce. The ID3 algorithm proposed by Quinlan forms the basis for many of the decision trees’ application. Trees produced by ID3 are sensitive to small perturbations in training data. To overcome this problem and to handle data uncertainties and spurious precision in data, fuzzy ID3 integrated fuzzy set theory and ideas from fuzzy logic with ID3. Several fuzzy decision trees algorithms and …

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 …

Exercise Power Grid Display And Web Interface, Alexander (Alex) Chernetz

Computer Engineering

The 2008-2009 expansion of the Recreation Center at Cal Poly includes three new rooms with cardiovascular fitness equipment. As part of its ongoing commitment to sustainable development, the new machines connect to the main power grid and generate power during a workout. This document explains the process of quantifying and expressing the power generated using two interfaces: an autonomous display designed for a television with a text size and amount of detail adaptable to multiple television sizes and viewing distances, and an interactive, more detailed Web interface accessible with any Java-capable computer system or browser.

An Evaluation Of Potential Technologies For A Web Based Development Environment For Cs1 Students, Manuel Garcia

Computer Science and Software Engineering

The goal of this senior project was to design a web-based integrated development environment that would incorporate Web-CAT. Web-CAT is an automated testing tool designed by Stephen Edwards at Virginia Tech University, to help beginning students learn test-driven development. This tool runs on a server where a professor assigns usernames and passwords to students so they can submit code. This program can assist professors in grading, and students in showing errors in code. The development environment design waskept simple to create less confusion for beginning programming students. This development environment will be online to give all students universal access and …

Metabolic Network Alignments And Their Applications, Qiong Cheng

Computer Science Dissertations

The accumulation of high-throughput genomic and proteomic data allows for the reconstruction of the increasingly large and complex metabolic networks. In order to analyze the accumulated data and reconstructed networks, it is critical to identify network patterns and evolutionary relations between metabolic networks. But even finding similar networks becomes computationally challenging. The dissertation addresses these challenges with discrete optimization and the corresponding algorithmic techniques. Based on the property of the gene duplication and function sharing in biological network,we have formulated the network alignment problem which asks the optimal vertex-to-vertex mapping allowing path contraction, vertex deletion, and vertex insertions. We have …

A Cognitive Model For Problem Solving In Computer Science, Jennifer Parham

All Dissertations

According to industry representatives, computer science education needs to emphasize the processes involved in solving computing problems rather than their solutions. Most of the current assessment tools used by universities and computer science departments analyze student answers to problems rather than investigating the processes involved in solving them. Approaching assessment from this perspective would reveal potential errors leading to incorrect solutions.
This dissertation proposes a model describing how people solve computational problems by storing, retrieving, and manipulating information and knowledge. It describes how metacognition interacts with schemata representing conceptual and procedural knowledge, as well as with the external sources of …

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 …

Anomaly Detection Techniques For Ad Hoc Networks, Chaoli Cai

Dissertations

Anomaly detection is an important and indispensable aspect of any computer security mechanism. Ad hoc and mobile networks consist of a number of peer mobile nodes that are capable of communicating with each other absent a fixed infrastructure. Arbitrary node movements and lack of centralized control make them vulnerable to a wide variety of unknown and known attacks from inside as well as from outside. In this dissertation we propose two efficient statistical techniques for anomaly detection for these networks.

In order to take into account incomplete testing samples and the interaction among multiple features, we present BANBAD •- a …

Visuohaptic Simulation Of A Borescope For Aircraft Engine Inspection, Deepak Vembar

All Dissertations

Consisting of a long, fiber optic probe containing a small CCD camera controlled by hand-held articulation interface, a video borescope is used for remote visual inspection of hard to reach components in an aircraft. The knowledge and psychomotor skills, specifically the hand-eye coordination, required for effective inspection are hard to acquire through limited exposure to the borescope in aviation maintenance schools. Inexperienced aircraft maintenance technicians gain proficiency through repeated hands-on learning in the workplace along a steep learning curve while transitioning from the classroom to the workforce.
Using an iterative process combined with focused user evaluations, this dissertation details the …

Examining The Dynamics Of Managing Information Systems Development Projects: A Control Loss Perspective, Ravi Narayanaswamy

All Dissertations

The failure rate of information systems development (ISD) projects continues to pose a big challenge for organizations. The success rate of ISD projects is less then forty percent. Factors such as disagreements and miscommunications among project manager and team members, poor monitoring and intermediary problems contribute to project failure.
Agency theory and leader member exchange (LMX) theories offer potential explanations for project failure. In particular, three monitoring strategies - control strategy, decision rights, and influence tactics were found to be effective in promoting project success. LMX theorists suggest that achieving congruence between the manager and subordinate regarding each other actions …

An Animation Framework For Improving The Comprehension Of Tinyos Programs, Sravanthi Dandamudi

All Theses

To meet the increasing demand for monitoring of the physical world, there has been an increase in the development of wireless sensor network applications. The TinyOS platform has emerged as a de facto standard for developing these applications. The platform offers a number of advantages, with its support for concurrency, power-efficient operation, and resource-constrained hardware chief among them. However, the benefits come at a price. Even without the TinyOS platform, the inherent parallel and distributed nature of these applications makes it difficult for developers to reason about program behavior. Further, the TinyOS programming model adopts
asynchronous, split-phase execution semantics. Developers …

Semantic Search, Anup Sawant

All Theses

The thesis describes a Semantic approach towards web search through a stand-alone Java application. An Ontology Web Language(OWL) model is used to build a knowledge database related to different types of Organisms. The goal is to guide the Google web search engine using this OWL model. In the rst approach towards Semantic web search, an inference engine called CLIPS is used and in the second aproach, the Protege-OWL API is used. The thesis goes in detail about the design,
working and comparison of these two approaches. The thesis also deals with design approach for enhancement of the OWL model, once …

A Parallel Computing Test Bed For Performing An Unsupervised Fluoroscopic Analysis Of Knee Joint Kinematics, Renu Ramanatha

Boise State University Theses and Dissertations

Fluoroscopic analysis of knee joint kinematics involves accurately determining the position and orientation of bones in the knee joint. This data can be derived using the static 3-D CT scan images and 2-D video fluoroscopy images together. This involves generating hypothetical digitally reconstructed radiographs (DRR) from the CT scan image with known position and orientation and comparing them to the original fluoroscopic frame. This represents a search problem in which, among all the DRRs possible from a CT image, the image that most closely matches the target fluoroscopy frame of the knee joint has to be found.

Each image in …

Evaluation Of Windows Servers Security Under Icmp And Tcp Denial Of Service Attacks, Hari Krishnea Vallalacheruvu

Theses and Dissertations - UTB/UTPA

Securing server from Distributed denial of service (DDoS) attacks is a challenging task for network operators. DDOS attacks are known to reduce the performance of web based applications and reduce the number of legitimate client connections. In this thesis, we evaluate performance of a Windows server 2003 under these attacks. In this thesis, we also evaluate and compare effectiveness of three different protection mechanisms, namely SYN Cache, SYN Cookie and SYN proxy protection methods, to protect against TCP SYN DDoS attacks. It is found that the SYN attack protection at the server is more effective at lower loads of SYN …

S2st: A Relational Rdf Database Management System, Anthony T. Piazza

Theses and Dissertations - UTB/UTPA

The explosive growth of RDF data on the Semantic Web drives the need for novel database systems that can efficiently store and query large RDF datasets. To achieve good performance and scalability of query processing, most existing RDF storage systems use a relational database management system as a backend to manage RDF data. In this paper, we describe the design and implementation of a Relational RDF Database Management System. Our main research contributions are: (1) We propose a formal model of a Relational RDF Database Management System (RRDBMS), (2) We propose generic algorithms for schema, data and query mapping, (3) …

Covert Botnet Design And Defense Analysis, Brandon Lyle Shirley

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Intrusion defense system (IDS) development has been largely reactionary in nature. This is especially troubling given that botnets are capable of compromising and controlling thousands of computers before security professionals develop a mitigation technique. As new exploits are created, new mitigation techniques are developed to detect infections and, where possible, remove them. This thesis breaks from this tradition of reacting to malware. Instead, it looks at possible malicious software models through analyzing existing defense systems for exploitable weaknesses.

First, this thesis presents a new specialized botnet that circumvents current network intrusion detection mechanisms. The proposed botnet coordinates external communication among …

Evaluating Head Gestures For Panning 2-D Spatial Information, Matthew O. Derry

Master's Theses

New, often free, spatial information applications such as mapping tools, topological imaging, and geographic information systems are becoming increasingly available to the average computer user. These systems, which were once available only to government, scholastic, and corporate institutions with highly skilled operators, are driving a need for new and innovative ways for the average user to navigate and control spatial information intuitively, accurately, and efficiently. Gestures provide a method of control that is well suited to navigating the large datasets often associated with spatial information applications. Several different types of gestures and different applications that navigate spatial data are examined. …

Automation In Cs1 With The Factoring Problem Generator, Joshua B. Parker

Master's Theses

As the field of computer science continues to grow, the number of students enrolled in related programs will grow as well. Though one-on-one tutoring is one of the more effective means of teaching, computer science instructors will have less and less time to devote to individual students. To address this growing concern, many tools that automate parts of an instructor’s job have been proposed. These tools can assist instructors in presenting concepts and grading student work, and they can help students learn to program more effectively. A growing group of intelligent tutoring systems attempts to tie all of this functionality …

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.

Open Access Fiber To The Home Networking, Roger E. Timmerman

Theses and Dissertations

The concept of open-access networks appeals to communities that want to invest in and improve their access to modern telecommunications services. By investing in, or building their own open-access telecommunications networks, communities can create an environment where several telecommunications service providers can co-exist on a common open-access infrastructure. This model promotes innovation and competition among several smaller service providers rather than having a monopoly or oligopoly from those companies that can afford the investment of infrastructure in the community. This research provides an analysis of two large open-access fiber-to-the-home networks in Utah to determine a set of recommendations and best-practices …

A Neural Network Approach To Border Gateway Protocol Peer Failure Detection And Prediction, Cory B. White

Master's Theses

The size and speed of computer networks continue to expand at a rapid pace, as do the corresponding errors, failures, and faults inherent within such extensive networks. This thesis introduces a novel approach to interface Border Gateway Protocol (BGP) computer networks with neural networks to learn the precursor connectivity patterns that emerge prior to a node failure. Details of the design and construction of a framework that utilizes neural networks to learn and monitor BGP connection states as a means of detecting and predicting BGP peer node failure are presented. Moreover, this framework is used to monitor a BGP network …