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Peptide-based hidden Markov model for peptide fingerprint mapping.

Description: Peptide mass fingerprinting (PMF) was the first automated method for protein identification in proteomics, and it remains in common usage today because of its simplicity and the low equipment costs for generating fingerprints. However, one of the problems with PMF is its limited specificity and sensitivity in protein identification. Here I present a method that shows potential to significantly enhance the accuracy of peptide mass fingerprinting, using a machine learning approach based on a hidden Markov model (HMM). This method is applied to improve differentiation of real protein matches from those that occur by chance. The system was trained using 300 examples of combined real and false-positive protein identification results, and 10-fold cross-validation applied to assess model discrimination. The model can achieve 93% accuracy in distinguishing correct and real protein identification results versus false-positive matches. The receiver operating characteristic (ROC) curve area for the best model was 0.833.
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Date: December 2004
Creator: Yang, Dongmei
Partner: UNT Libraries

Freeform Cursive Handwriting Recognition Using a Clustered Neural Network

Description: Optical character recognition (OCR) software has advanced greatly in recent years. Machine-printed text can be scanned and converted to searchable text with word accuracy rates around 98%. Reasonably neat hand-printed text can be recognized with about 85% word accuracy. However, cursive handwriting still remains a challenge, with state-of-the-art performance still around 75%. Algorithms based on hidden Markov models have been only moderately successful, while recurrent neural networks have delivered the best results to date. This thesis explored the feasibility of using a special type of feedforward neural network to convert freeform cursive handwriting to searchable text. The hidden nodes in this network were grouped into clusters, with each cluster being trained to recognize a unique character bigram. The network was trained on writing samples that were pre-segmented and annotated. Post-processing was facilitated in part by using the network to identify overlapping bigrams that were then linked together to form words and sentences. With dictionary assisted post-processing, the network achieved word accuracy of 66.5% on a small, proprietary corpus. The contributions in this thesis are threefold: 1) the novel clustered architecture of the feed-forward neural network, 2) the development of an expanded set of observers combining image masks, modifiers, and feature characterizations, and 3) the use of overlapping bigrams as the textual working unit to assist in context analysis and reconstruction.
Date: August 2015
Creator: Bristow, Kelly H.
Partner: UNT Libraries

Automatic Removal of Complex Shadows From Indoor Videos

Description: Shadows in indoor scenarios are usually characterized with multiple light sources that produce complex shadow patterns of a single object. Without removing shadow, the foreground object tends to be erroneously segmented. The inconsistent hue and intensity of shadows make automatic removal a challenging task. In this thesis, a dynamic thresholding and transfer learning-based method for removing shadows is proposed. The method suppresses light shadows with a dynamically computed threshold and removes dark shadows using an online learning strategy that is built upon a base classifier trained with manually annotated examples and refined with the automatically identified examples in the new videos. Experimental results demonstrate that despite variation of lighting conditions in videos our proposed method is able to adapt to the videos and remove shadows effectively. The sensitivity of shadow detection changes slightly with different confidence levels used in example selection for classifier retraining and high confidence level usually yields better performance with less retraining iterations.
Date: August 2015
Creator: Mohapatra, Deepankar
Partner: UNT Libraries

Algorithm Optimizations in Genomic Analysis Using Entropic Dissection

Description: In recent years, the collection of genomic data has skyrocketed and databases of genomic data are growing at a faster rate than ever before. Although many computational methods have been developed to interpret these data, they tend to struggle to process the ever increasing file sizes that are being produced and fail to take advantage of the advances in multi-core processors by using parallel processing. In some instances, loss of accuracy has been a necessary trade off to allow faster computation of the data. This thesis discusses one such algorithm that has been developed and how changes were made to allow larger input file sizes and reduce the time required to achieve a result without sacrificing accuracy. An information entropy based algorithm was used as a basis to demonstrate these techniques. The algorithm dissects the distinctive patterns underlying genomic data efficiently requiring no a priori knowledge, and thus is applicable in a variety of biological research applications. This research describes how parallel processing and object-oriented programming techniques were used to process larger files in less time and achieve a more accurate result from the algorithm. Through object oriented techniques, the maximum allowable input file size was significantly increased from 200 mb to 2000 mb. Using parallel processing techniques allowed the program to finish processing data in less than half the time of the sequential version. The accuracy of the algorithm was improved by reducing data loss throughout the algorithm. Finally, adding user-friendly options enabled the program to use requests more effectively and further customize the logic used within the algorithm.
Date: August 2015
Creator: Danks, Jacob R.
Partner: UNT Libraries

A Netcentric Scientific Research Repository

Description: The Internet and networks in general have become essential tools for disseminating in-formation. Search engines have become the predominant means of finding information on the Web and all other data repositories, including local resources. Domain scientists regularly acquire and analyze images generated by equipment such as microscopes and cameras, resulting in complex image files that need to be managed in a convenient manner. This type of integrated environment has been recently termed a netcentric sci-entific research repository. I developed a number of data manipulation tools that allow researchers to manage their information more effectively in a netcentric environment. The specific contributions are: (1) A unique interface for management of data including files and relational databases. A wrapper for relational databases was developed so that the data can be indexed and searched using traditional search engines. This approach allows data in databases to be searched with the same interface as other data. Fur-thermore, this approach makes it easier for scientists to work with their data if they are not familiar with SQL. (2) A Web services based architecture for integrating analysis op-erations into a repository. This technique allows the system to leverage the large num-ber of existing tools by wrapping them with a Web service and registering the service with the repository. Metadata associated with Web services was enhanced to allow this feature to be included. In addition, an improved binary to text encoding scheme was de-veloped to reduce the size overhead for sending large scientific data files via XML mes-sages used in Web services. (3) Integrated image analysis operations with SQL. This technique allows for images to be stored and managed conveniently in a relational da-tabase. SQL supplemented with map algebra operations is used to select and perform operations on sets of images.
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Date: December 2006
Creator: Harrington, Brian
Partner: UNT Libraries

Mediation on XQuery Views

Description: The major goal of information integration is to provide efficient and easy-to-use access to multiple heterogeneous data sources with a single query. At the same time, one of the current trends is to use standard technologies for implementing solutions to complex software problems. In this dissertation, I used XML and XQuery as the standard technologies and have developed an extended projection algorithm to provide a solution to the information integration problem. In order to demonstrate my solution, I implemented a prototype mediation system called Omphalos based on XML related technologies. The dissertation describes the architecture of the system, its metadata, and the process it uses to answer queries. The system uses XQuery expressions (termed metaqueries) to capture complex mappings between global schemas and data source schemas. The system then applies these metaqueries in order to rewrite a user query on a virtual global database (representing the integrated view of the heterogeneous data sources) to a query (termed an outsourced query) on the real data sources. An extended XML document projection algorithm was developed to increase the efficiency of selecting the relevant subset of data from an individual data source to answer the user query. The system applies the projection algorithm to decompose an outsourced query into atomic queries which are each executed on a single data source. I also developed an algorithm to generate integrating queries, which the system uses to compose the answers from the atomic queries into a single answer to the original user query. I present a proof of both the extended XML document projection algorithm and the query integration algorithm. An analysis of the efficiency of the new extended algorithm is also presented. Finally I describe a collaborative schema-matching tool that was implemented to facilitate maintaining metadata.
Date: December 2006
Creator: Peng, Xiaobo
Partner: UNT Libraries

Analysis of Web Services on J2EE Application Servers

Description: The Internet became a standard way of exchanging business data between B2B and B2C applications and with this came the need for providing various services on the web instead of just static text and images. Web services are a new type of services offered via the web that aid in the creation of globally distributed applications. Web services are enhanced e-business applications that are easier to advertise and easier to discover on the Internet because of their flexibility and uniformity. In a real life scenario it is highly difficult to decide which J2EE application server to go for when deploying a enterprise web service. This thesis analyzes the various ways by which web services can be developed & deployed. Underlying protocols and crucial issues like EAI (enterprise application integration), asynchronous messaging, Registry tModel architecture etc have been considered in this research. This paper presents a report by analyzing what various J2EE application servers provide by doing a case study and by developing applications to test functionality.
Date: May 2004
Creator: Gosu, Adarsh Kumar
Partner: UNT Libraries

Adaptive Planning and Prediction in Agent-Supported Distributed Collaboration.

Description: Agents that act as user assistants will become invaluable as the number of information sources continue to proliferate. Such agents can support the work of users by learning to automate time-consuming tasks and filter information to manageable levels. Although considerable advances have been made in this area, it remains a fertile area for further development. One application of agents under careful scrutiny is the automated negotiation of conflicts between different user's needs and desires. Many techniques require explicit user models in order to function. This dissertation explores a technique for dynamically constructing user models and the impact of using them to anticipate the need for negotiation. Negotiation is reduced by including an advising aspect to the agent that can use this anticipation of conflict to adjust user behavior.
Date: December 2004
Creator: Hartness, Ken T. N.
Partner: UNT Libraries

The Effects of Shoe Modification on Transverse Tibial Rotation

Description: The purpose of this study was to evaluate the amount of change in transverse tibial rotation at the knee achieved through the use of shoe modification. In addition, an attempt to evaluate the Q-angle dynamically through the stance phase to reflect changes in transverse tibial rotation was made. Ten male subjects were filmed as they ran on a treadmill at a 2.82 m/sec pace and transverse tibial rotation data was collected simultaneously from an affixed electrogoniometer at the knee joint. The subjects were tested under three conditions: 1) barefoot, 2) running shoe, and 3) shoe plus standard orthotic. The results of the study showed that an unprescribed, standard orthotic was ineffective in changing foot pronation and transverse tibial rotation at the knee. It also showed that there was no relationship between leg-heel alignment measurements of pronation and electrogoniometric measurements of transverse tibial rotation. Q-angle measurements could not be obtained from the film date due to difficulty in visualizing body landmarks.
Date: August 1984
Creator: Trudelle, Elaine
Partner: UNT Libraries

Swinging Gait Patterns and Preferred Rung Spacing During Free Choice Horizontal Ladder Traverses

Description: Fifty-one subjects each performed two trials which consisted of traversing a horizontal ladder. Film records were made of each trial using a high-speed camera. Absolute and relative temporal and kinematic parameters were obtained from the film records. The conclusions were that there was no age related interaction or differences in preferred rung spacing or contact/airborne times. A Chi-Square analysis did show a preference for a specific gait pattern for the six year old age group.
Date: August 1984
Creator: Roth, Charles H. (Charles Hillary)
Partner: UNT Libraries

An Investigation of Textural Activity and Its Hierarchical Structures in Selected Works by Krzysztof Penderecki

Description: This study focuses on temporal aspects of the music of Krzysztof Penderecki and deals with these on the level of textural activity. The analyses are based on a referential idea called a "discrete sound event," defined as an occurrence of a sound or collection of sounds which, as a unit, is distinct from the surrounding texture. These sound events are then used to appraise textural activity from layer fluctuation and composite density. The pieces selected for applying these techniques are the Threnody to the Victims of Hiroshima, from 1960, the Fluorescences, from 1961, and the 1965 Capriccio for oboe and strings.
Date: May 1986
Creator: Daley, Paul B. (Paul Byron)
Partner: UNT Libraries

Initial Starting Posture and Total Body Movement-Reaction Time for Lateral Movement

Description: Eighteen subjects each performed fifty-five trials which consisted of assuming an initial stance and then in response to a visual stimulus running to either the left or right. For each trial both the foot width spacing and orientation of the feet were varied. Direct and indirect measurements were taken of selected temporal and kinematic parameters. The conclusions were that no interactions or differences exist among foot width spacing, foot orientation, and direction of movement; the jab step start is the preferred initial movement; the preferred foot width spacing is 46.6 centimeters; the preferred angular orientation of both feet is approximately 1.36 radians.
Date: August 1983
Creator: Darnall, Sylvia Pacheco
Partner: UNT Libraries

Automatic Tagging of Communication Data

Description: Globally distributed software teams are widespread throughout industry. But finding reliable methods that can properly assess a team's activities is a real challenge. Methods such as surveys and manual coding of activities are too time consuming and are often unreliable. Recent advances in information retrieval and linguistics, however, suggest that automated and/or semi-automated text classification algorithms could be an effective way of finding differences in the communication patterns among individuals and groups. Communication among group members is frequent and generates a significant amount of data. Thus having a web-based tool that can automatically analyze the communication patterns among global software teams could lead to a better understanding of group performance. The goal of this thesis, therefore, is to compare automatic and semi-automatic measures of communication and evaluate their effectiveness in classifying different types of group activities that occur within a global software development project. In order to achieve this goal, we developed a web-based component that can be used to help clean and classify communication activities. The component was then used to compare different automated text classification techniques on various group activities to determine their effectiveness in correctly classifying data from a global software development team project.
Date: August 2012
Creator: Hoyt, Matthew Ray
Partner: UNT Libraries

The Effects of Surface Type on Experienced Foot Contact Pressures and Lower Limb Functioning During Running Performance

Description: The purpose of this study was to examine the effects of different surfaces on lower limb motion and encountered pressures at two locations on the plantar surface of the right foot. Nine females performed five trials for each of four surface conditions. The results provided no evidence for surface-related changes in experienced foot contact pressures. Both asphalt and grass surfaces resulted in the shortest relative time of forefoot immobility. No surface related differences were found for the range of pronation.
Date: December 1983
Creator: Denniston, Nancy L. (Nancy Louise)
Partner: UNT Libraries

The Effects of Shoe Type on Foot Functioning and Contact Pressures During Walking Performances

Description: The purpose of this study was to evaluate the functional effectiveness of a selection of women's walking shoes with particular attention being directed towards an assessment of specific shoe modifications which were included in a prototype model to theoretically reduce the undesirable characteristics associated with flexible shoes. Nine female subjects performed three trials for each of five shoe conditions. The prototype model decreased the encountered pressures and pressure integrals in the region of the second metatarsal-phalangeal joint. The use of the prototype shoe did not appear to unduly affect the gait of the subject.
Date: August 1982
Creator: Raley, Brenda F.
Partner: UNT Libraries

The Effect of Roughness Elements on the Magnus Characteristics of Rotating Spherical Projectiles

Description: Thirty trials of each of three roughness conditions were examined. The first condition consisted of a baseball pitched so that two of the roughness elements opposed the flow. The second condition consisted of a pitched baseball with four of the roughness elements opposing the flow. The third consisted of a pitched uniformly rough sphere. The conclusions were that roughness elements increase horizontal flight deviations when a baseball rotates about a vertical axis; roughness elements on the surface of a baseball may cause a decrease in the encountered drag forces; linear velocity has a dominating effect on the trajectory of a spinning baseball; previously developed mathematical models do not adequately predict flight deviations.
Date: December 1982
Creator: Smith, Michael A. (Michael Albert)
Partner: UNT Libraries

A Study of Lean Body Mass in Estimating Basal Metabolic Rate

Description: The primary purpose of the study was to determine if measured LBM could be used as a more powerful predictor of BMR than could surface area (SA) as calculated by the formula of DuBois and DuBois (1916). It was also of interest to develop a prediction equation for BMR using multiple regression analysis. Data from 82 women and 76 men were included in the study. Pearson product-moment correlations indicated that LBM was a better predictor for BMR than SA on either of the principal SA prediction equations, those of Aub and DuBois (1917) and Harris and Benedict (1919). Age, sex, and fat weight were not found to contribute significantly to prediction when included by multiple regression analyses. Linear equations for BMR as a function of LBM were developed for each sex. Tables based on these equations were also generated as a quick reference for clinicians.
Date: May 1985
Creator: Lachenbruch, Charles
Partner: UNT Libraries

A Comparison of Two Methods of Training Naive Users in the Use of a Microcomputer System

Description: The problem addressed in this study is the need for efficient and economic methods to train naive college students to operate microcomputers as a necessary step in their acquisition of computer proficiency. Two methods of training were compared. These were training by live demonstration and training by videotape. These methods were considered economically viable because each could be presented in a classroom and neither required a one-to-one student-to-computer or student-to-tutor ratio. Four sections of an introductory computer science class were used in the study. Two classes were presented each treatment. The effectiveness of the presentations was measured by means of a written quiz administered immediately after the presentation and by the number of microcomputer system operation tasks successfully completed during an individual laboratory session. The computer anxiety level of each participant was measured prior to the presentation to determine if anxiety was a factor in finding the best training method. When scores of naive users who saw the videotape were compared with the scores of naive users who saw the live demonstration, no significant differences were found. However, when novice users (those who had some previous experience with operating or programming a microcomputer) were included, the group that saw the videotape scored significantly higher on the written quiz than the group that saw the live demonstration. A two by two analysis of variance showed no significant interactions between anxiety and treatment. User satisfaction was found to be significantly higher for the videotape group than for the live demonstration group. This study concluded with the recommendation that the Computer Science Department of North Texas State University utilize videotapes to train students in introductory classes to use a microcomputer system. This recommendation was based on the superior test results for naive and novice users who saw the videotape, the user satisfaction scores ...
Date: May 1986
Creator: Wallace, Susan Ree Heil
Partner: UNT Libraries

Reverse Transfer Students: Students Who Transfer from Area Universities to the Junior College

Description: A study was conducted to identify demographic and academic characteristics of students transferring from North Texas area senior colleges to Tarrant County Junior College (Texas) in the Fall 1984 semester. Academic characteristics were measured at the point of transfer and during subsequent junior college enrollment(s) through Spring 1989. Transcripts of 608 reverse transfer students were examined. Non-Completers, students who transferred prior to completing a baccalaureate degree, were identified as 77% of the population; students who transferred after earning a degree were 22%. Of the Non Completer students, 35% transferred as Poor Students (transfer GPA of 0.00-1.99), 23% as Fair Students (2.00-2.79) and 19% as Good Students (2.80-4.00). The reverse transfer students were 52% male. Most (87%) were white, with 6% black, 4% Hispanic, and 3% other ethnic. They varied in age from 18 to 81: 24% were younger than 21, 31% were 21-25, 45% older than 25. Poor Students earned a cumulative junior college GPA 1.29 higher than transfer GPA; Fair Student GPA was .63 higher; Good Student GPA decreased by .01. The change was significant at the .01 level for Poor and for Fair students. Poor arid Fair students who stopped out "for at least two years prior to transfer increased GPA by .58 more than the GPA of immediate transfers; those who changed from an academic program to vocational or avocational courses increased GPA by .46 more than those who did not. The differences were found to be significant at the .01 level. Too few Poor and Fair Students (11%) enrolled in remediation to allow statistical measurement, but Poor Student junior college GPA was found to be 1.41 higher than university transfer GPA. Degree students were found to be older than the average reverse transfer, to be 91% white and 52% male, and to be good students with ...
Date: August 1990
Creator: Jackson, Cathie J. (Cathie Jean)
Partner: UNT Libraries

Information Seeking in a Virtual Learning Environment

Description: Duplicating a time series study done by Kuhlthau and associates in 1989, this study examines the applicability of the Information Search Process (ISP) Model in the context of a virtual learning environment. This study confirms that students given an information seeking task in a virtual learning environment do exhibit the stages indicated by the ISP Model. The six-phase ISP Model is shown to be valid for describing the different stages of cognitive, affective, and physical tasks individuals progress through when facing a situation where they must search for information to complete an academic task in a virtual learning environment. The findings in this study further indicate there is no relationship between the amount of computer experience subjects possess and demonstrating the patterns of thoughts, feelings, and actions described by the ISP Model. The study demonstrates the ISP Model to be independent of the original physical library environments where the model was developed. An attempt is made to represent the ISP model in a slightly different manner that provides more of the sense of motion and interaction among the components of thoughts, feelings, and action than is currently provided for in the model. The study suggests that the development of non-self-reporting data collection techniques would be useful in complementing and furthering research to enhance and refine the representation of the ISP Model. Additionally, expanding the research to include the examination of group interaction is called for to enhance the ISP Model and develop further applications that could potentially aid educational delivery in all types of learning environments.
Date: August 1999
Creator: Byron, Suzanne M.
Partner: UNT Libraries

Infusing Automatic Question Generation with Natural Language Understanding

Description: Automatically generating questions from text for educational purposes is an active research area in natural language processing. The automatic question generation system accompanying this dissertation is MARGE, which is a recursive acronym for: MARGE automatically reads generates and evaluates. MARGE generates questions from both individual sentences and the passage as a whole, and is the first question generation system to successfully generate meaningful questions from textual units larger than a sentence. Prior work in automatic question generation from text treats a sentence as a string of constituents to be rearranged into as many questions as allowed by English grammar rules. Consequently, such systems overgenerate and create mainly trivial questions. Further, none of these systems to date has been able to automatically determine which questions are meaningful and which are trivial. This is because the research focus has been placed on NLG at the expense of NLU. In contrast, the work presented here infuses the questions generation process with natural language understanding. From the input text, MARGE creates a meaning analysis representation for each sentence in a passage via the DeconStructure algorithm presented in this work. Questions are generated from sentence meaning analysis representations using templates. The generated questions are automatically evaluated for question quality and importance via a ranking algorithm.
Date: December 2016
Creator: Mazidi, Karen
Partner: UNT Libraries

SEM Predicting Success of Student Global Software Development Teams

Description: The extensive use of global teams to develop software has prompted researchers to investigate various factors that can enhance a team’s performance. While a significant body of research exists on global software teams, previous research has not fully explored the interrelationships and collective impact of various factors on team performance. This study explored a model that added the characteristics of a team’s culture, ability, communication frequencies, response rates, and linguistic categories to a central framework of team performance. Data was collected from two student software development projects that occurred between teams located in the United States, Panama, and Turkey. The data was obtained through online surveys and recorded postings of team activities that occurred throughout the global software development projects. Partial least squares path modeling (PLS-PM) was chosen as the analytic technique to test the model and identify the most influential factors. Individual factors associated with response rates and linguistic characteristics proved to significantly affect a team’s activity related to grade on the project, group cohesion, and the number of messages received and sent. Moreover, an examination of possible latent homogeneous segments in the model supported the existence of differences among groups based on leadership style. Teams with assigned leaders tended to have stronger relationships between linguistic characteristics and team performance factors, while teams with emergent leaders had stronger. Relationships between response rates and team performance factors. The contributions in this dissertation are three fold. 1) Novel analysis techniques using PLS-PM and clustering, 2) Use of new, quantifiable variables in analyzing team activity, 3) Identification of plausible causal indicators for team performance and analysis of the same.
Date: May 2015
Creator: Brooks, Ian Robert
Partner: UNT Libraries

Predictive Modeling for Persuasive Ambient Technology

Description: Computer scientists are increasingly aware of the power of ubiquitous computing systems that can display information in and about the user's environment. One sub category of ubiquitous computing is persuasive ambient information systems that involve an informative display transitioning between the periphery and center of attention. The goal of this ambient technology is to produce a behavior change, implying that a display must be informative, unobtrusive, and persuasive. While a significant body of research exists on ambient technology, previous research has not fully explored the different measures to identify behavior change, evaluation techniques for linking design characteristics to visual effectiveness, nor the use of short-term goals to affect long-term behavior change. This study uses the unique context of noise-induced hearing loss (NIHL) among collegiate musicians to explore these issues through developing the MIHL Reduction Feedback System that collects real-time data, translates it into visuals for music classrooms, provides predictive outcomes for goalsetting persuasion, and provides statistical measures of behavior change.
Date: August 2015
Creator: Powell, Jason W.
Partner: UNT Libraries

A Pattern Oriented Data Structure for Interactive Computer Music

Description: This essay describes a pattern oriented data structure, or PODS, as a system for storing computer music data. It organizes input by sequences or patterns that recur, while extensively interlinking the data. The interlinking process emulates cognitive models, while the pattern processing draws specifically from music cognition. The project aims at creating open source external objects for the Max/MSP software environment. The computer code for this project is in the C and Objective-C computer programming languages.
Date: May 2011
Creator: Lockhart, Adam
Partner: UNT Libraries