Computer Sciences Commons^™

Evolution Of Complex Features In Digital Organisms, Javier A. Magana

Theses and Dissertations - UTB/UTPA

This thesis examines how complex features evolve in digital organisms, and how capabilities that evolved earlier provide a scaffold for evolving new features. I wanted to see how the organisms used previous adaptations to succeed in new environments, and how significant are these previous adaptations. The system used is the Avida platform, which is software that implements Darwinian evolution on self-replicating digital organisms. First, the system is seeded with ancestors that can only replicate, which gave a baseline for the quality of the task at the end of evolution. Second, the system used ancestors from a simpler environment as seeds. …

Document Collection Visualization And Clustering Using An Atom Metaphor For Display And Interaction, Khanh V. Nghi

Theses and Dissertations - UTB/UTPA

Visual Data Mining have proven to be of high value in exploratory data analysis and data mining because it provides an intuitive feedback on data analysis and support decision-making activities. Several visualization techniques have been developed for cluster discovery such as Grand Tour, HD-Eye, Star Coordinates, etc. They are very useful tool which are visualized in 2D or 3D; however, they have not simple for users who are not trained. This thesis proposes a new approach to build a 3D clustering visualization system for document clustering by using k-mean algorithm. A cluster will be represented by a neutron (centroid) and …

Generalizing Agent Plans And Behaviors With Automated Staged Observation In The Real-Time Strategy Game Starcraft, Zackary A. Gill

Theses and Dissertations - UTB/UTPA

In this thesis we investigate the processes involved in learning to play a game. It was inspired by two observations about how human players learn to play. First, learning the domain is intertwined with goal pursuit. Second, games are designed to ramp up in complexity, walking players through a gradual cycle of acquiring, refining, and generalizing knowledge about the domain. This approach does not rely on traces of expert play. We created an integrated planning, learning and execution system that uses StarCraft as its domain. The planning module creates command/event groupings based on the data received. Observations of unit behavior …

A Comparison Of Display Techniques For Large Graphs, Ana Rocio Pena

Theses and Dissertations - UTB/UTPA

Visualizing information focuses on the display of data in order to provide the user a representation that provides understanding of the data. Information visualization systems typically couple interaction mechanisms for providing overviews of the data with more detailed information through a zooming interface. This thesis compares three different techniques for displaying graphs provided by the prefuse visualization system: force-directed node positioning, radial node positioning, and a tree view of graphs. Using a large, real world data set from the South Texas College’s Distance Education department, the three visualization techniques are compared for a set of tasks that users routinely need …

A New Algorithm For Dna Motif Detection, Ran Ding

Theses and Dissertations - UTB/UTPA

Nowadays, people are more and more concentrated on the research of deoxyribonucleic acid(DNA). And a very important problem is how to identify the DNA performance. A DNA sequence contains lots of genes, and every gene has a regulatory region. This regulatory region contains the transcription factor binding sites (TFBS) which is also known as motif. How to identify this motif becomes a very important problem. There are many efficient methods and tools are dedicated to the research of DNA motif detection. In this paper, we will introduce a new method of DNA motif detection which basically is an advanced approximate …

Measuring The Impact Of Narrative On Player's Presence And Immersion In A First Person Game Environment, Raul Huerta

Theses and Dissertations - UTB/UTPA

In the virtual environments (VE) literature, presence has been described as the feeling whereby an individual feels as if he or she is actually in the VE. In the videogame literature, the related concept of immersion is viewed as an effect facilitating player engagement. This thesis examines how narrative and graphics quality influence presence and immersion in a first person game. Three levels of narrative and graphics quality are used in an empirical study: text narrative with high quality graphics, no text narrative with high quality graphics, and no text narrative with low quality graphics. Results showed that there is …

Utpb: A Benchmark For Scientific Workflow Provenance Storage And Querying Systems, Carlos F. Gomez

Theses and Dissertations - UTB/UTPA

A crucial challenge for scientific workflow management systems is to support the efficient and scalable storage and querying of large provenance datasets that record the history of in silico experiments. As new provenance management systems are being developed, it is important to have benchmarks that can evaluate these systems and provide an unbiased comparison. In this paper, based on the requirements for scientific workflow provenance systems, we design an extensible benchmark that features a collection of techniques and tools for workload generation, query selection, performance measurement, and experimental result interpretation.

K-Nearest Keyword Search In Rdf Graphs, Eugenio De Hoyos

Theses and Dissertations - UTB/UTPA

We formulate and tackle a flexible and useful query, namely k-nearest keyword (k-NK) query, which can identify the relationship between vertices (or keywords) in an RDF graph, where users are only required to specify two query keywords q and w (without knowing the domain knowledge). In particular, a k-NK query returns k closest pairs of vertices (ui; vi) in the RDF graph such that vertices ui and vi contain keywords q and w, respectively, and vi has the smallest (shortest path) distance to ui (i.e., vi is the nearest neighbor of ui). In order to efficiently answer k-NK queries, in …

Benchmarking Bottom-Up And Top-Down Strategies To Sparql-To-Sql Query Translation, Andrii Kashliev

Theses and Dissertations - UTB/UTPA

Many researchers have proposed using conventional relational databases to store and query large Semantic Web datasets. The most complex component of this approach is SPARQL-to-SQL query translation. Existing algorithms perform this translation using either bottom-up or top-down strategy and result in semantically equivalent but syntactically different relational queries. Do relational query optimizers always produce identical query execution plans for semantically equivalent bottom-up and top-down queries? Which of the two strategies yields faster SQL queries? To address these questions, this work studies bottom-up and top-down translations of SPARQL queries with nested optional graph patterns. This work presents: (1) A basic graph …

Intractability Of Integration And Derivative For Multivariate Polynomial And Trigonometric Function, Liang Ding

Theses and Dissertations - UTB/UTPA

We study the hardness of some basic linear operators which involve high dimension integration or derivative. For a multivariate polynomial ��(��1, ⋯ , ����) which has format ∏ ∑ ��1, we show that there is no any factor polynomial time approximation for the integration of ��(��1, ⋯ , ����) in the unit cube [0,1] �� unless P = NP. In addition to polynomials, we extend the discussion to nonlinear function. For a trigonometric function ��(��1, ⋯ , ����) of format ∏ ∑ �������� ∗ , we show that it is #P-hard to compute derivative ����(��) (��1,⋯,����) ����1⋯������ at the origin …

Narrative Analysis And Computational Model To Predict Interestingness Of Narratives, Laxman Thapa

Theses and Dissertations - UTB/UTPA

In this research, I present results demonstrating the classification of the specially generated narratives by a machine agent by listening to human subject describing the same sets of the events. These classifications are based on human ratings of interestingness for many different recountings of the same stories. The classification is performed on various features selected after analyzing the different possible feature that affect on the interestingness of narratives. The features were extracted from the surface text as well as from annotations of how each narration relates to the content of the known story. I present the annotation process and resulting …

Partition A 3-Colorable Graph Into A Small Bipartite Subgraph And A Large Independent Set, Qing Wang

Theses and Dissertations - UTB/UTPA

Exact algorithms have made a little progress for the 3-coloring problem: improved from to since 1976. The best exact algorithm for the 3-coloring problem is by Beigel and Eppstein, and its analysis is very complicated. We study the parameterized 3-coloring problem: partitioning a 3-colorable graph into a bipartite subgraph and an independent set. Taking the size of the bipartite subgraph as the parameter k, we propose the first parameter algorithm of complexity . Our algorithm can solve the 3-coloring problem faster than the best exact algorithm for graphs with k ≤ 0.527n where n is the graph size. Our study …

Distributed Storage And Queryng Techniques For A Semantic Web Of Scientific Workflow Provenance, Jaime Alberto Navarro

Theses and Dissertations - UTB/UTPA

In scientific workflow environments, scientists depend on provenance, which records the history of an experiment. Resource Description Framework is frequently used to represent provenance based on vocabularies such as the Open Provenance Model. For complex scientific workflows that generate large amounts of RDF triples, single-machine provenance management becomes inadequate over time. In this thesis, we research how HBase capabilities can be leveraged for distributed storage and querying of provenance data represented in RDF. We architect the ProvBase system that incorporates an HBase/Hadoop backend, propose a storage schema to hold provenance triples, and design querying algorithms to evaluate SPARQL queries in …

New Algorithms For Protein Structure Comparison And Protein Structure Prediction, Zaixin Lu

Theses and Dissertations - UTB/UTPA

Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore algorithms of protein structure alignment, protein similarity search and protein structure prediction are very helpful for protein biologists. We developed new algorithms for the problems in this field. The algorithms are tested with structures from the Protein Data Bank (PDB) and SCOP, a Structure Classification of Protein Database. The experimental results show that our tools are more efficient than some well known systems for finding similar protein structures and predicting protein structures.

Algorithmic Temperature 1 Self-Assembly, Yunhui Fu

Theses and Dissertations - UTB/UTPA

We investigate the power of the Wang tile self-assembly model at temperature 1, a threshold value that permits attachment between any two tiles that share even a single bond. When restricted to deterministic assembly in the plane, no temperature 1 assembly system has been shown to build a shape with a tile complexity smaller than the diameter of the shape. Our work shows a sharp contrast in achievable tile complexity at temperature 1 if either growth into the third dimension or a small probability of error are permitted. Motivated by applications in nanotechnology and molecular computing, and the plausibility of …

Parameterized Algorithm For 3-Sat, Yi Gao

Theses and Dissertations - UTB/UTPA

The SAT problem is the classical NP-complete problem. In the past, many methods have been proposed for solving this problem. We investigated a new method for 3-SAT problem, which is a fixed parameterized algorithm proposed in this paper first. This method uses a fixed parameter k, where k is the number of true values in an assignment for checking whether the formula is satisfied or not. The complexity of our algorithm is O(3k ), which is exponentially independent of the number of variables. Theoretical analysis shows that when k is small, this method has smaller search space and higher speed.

Dna Staged Self-Assembly At Temperature 1, Nicholas H. Guiterrez

Theses and Dissertations - UTB/UTPA

We introduce alternate temperature 1 self-assembly constructions of an n x n square by efficiently utilizing bins and stages to achieve desirable results. These bins are able to contain a variety of tiles or supertiles, which are then mixed together in a pre-determined sequence of distinct stages. The basic 2D tile assembly model at temperature 1 uses 2n-1 tile types to construct a square. The model only utilizes one bin and occurs all in one stage. We will demonstrate how the use of bins and stages will allow for the construction of these squares more efficiently.

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) …

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 …

Image Up-Sampling Using The Discrete Wavelet Transform, Laleh Asgharian

Theses and Dissertations - UTB/UTPA

Image up-sampling is an effective technique, useful in today's digital image processing applications and rendering devices. In image up-sampling, an image is enhanced from a lower resolution to a higher resolution with the degree of enhancement depending upon application requirements. It is known that the traditional interpolation based approaches for up-sampling, such as the Bilinear or Bicubic interpolations, blur the resultant images along edges and image features. Furthermore, in color imagery, these interpolation-based up-sampling methods may have color infringing artifacts in the areas where the images contain sharp edges and fine textures. We present an interesting up-sampling algorithm based on …

An Improvement And A Generalization Of Zippel's Sparse Multivariate Polynomial Interpolation Algorithm, Michael D. Brazier

Theses and Dissertations - UTB/UTPA

The algorithm most often used for the problem of interpolating sparse multivariate polynomials from their values is Zippel's probabilistic algorithm (1988). The algorithm evaluates the function to be interpolated at a significant number of points, and for many problems of interest processing evaluations dominates the running time. This thesis presents an improvement of Zippel's algorithm, which decreases the number of evaluations needed for an interpolation by using transposed Vandermonde systems for the univariate interpolation step of Zippel's algorithm. The technique also allows a more general form of the algorithm: it becomes possible to interpolate more than one variable within a …

Improving The Performance Of Nested Loop Algorithm Using Separators, Nachiappan N. Nachiappan

Theses and Dissertations - UTB/UTPA

This thesis studies the properties of distance-based outliers and a better detection method for large multi-dimensional datasets. Outlier detection is an important task to find out the objects that deviate in a high ratio from the rest of the objects. The proposed algorithm breaks the data set into divisions and sets the area of access for each division, thus reducing the unnecessary access for a major set of elements. This algorithm reduces the run time of the existing algorithm by using separators. Datasets of varying sizes have been tested to analyze the empirical values of these procedures. Effective data structures …

Entropy-Based 2d Image Dissimilarity Measure, Meng-Hung Wu

Theses and Dissertations - UTB/UTPA

Traditional histogram or statistics based 2D image similarity/dissimilarity metrics fail to handle conjugate pair of black and white images, due to the lack of spatial information in the measurement. Recently proposed Compression-based Dissimilarity Measure (CDM) [1] based on the concept of Kolmogorov complexity has provided a different paradise for similarity measurement. However, without a clear definition how to “concatenate” two 2D images, CDM has difficulties to directly apply with 2D images. In this thesis, an entropy -based 2D image dissimilarity measure is proposed within the same Kolmogorov complexity paradise. The spatial relationship between images is embedded in our metric, and …

Naboh System: Gathering Intelligence From Traffic Patterns, Angelica M. Delgado

Theses and Dissertations - UTB/UTPA

Network traffic anomalies are important indicators of problematic traffic over a network. Network activity has patterns associated with it depending on the applications running on the local hosts connected to the network. There are traffic parameters into which network traffic of a local host can be divided: bandwidth usage, number of remote hosts that a local host is connecting to and vice versa, and number of ports used by the local host. This thesis develops a system for detecting and profiling network anomalies by analyzing traffic parameters using intelligent computational techniques. The developed system gathers intelligence by examining only the …

Empirical Performance Analysis Of Two Algorithms For Mining Intentional Knowledge Of Distance-Based Outliers, Enbamoorthy Prasanthi

Theses and Dissertations - UTB/UTPA

This thesis studies the empirical analysis of two algorithms, Uplattice and Jumplattice for mining intentional knowledge of distance-based outliers [19]. These algorithms detect strongest and weak outliers among them. Finding outliers is an important task required in major applications such as credit-card fraud detection, and the NHL statistical studies. Datasets of varying sizes have been tested to analyze the empirical values of these two algorithms. Effective data structures have been used to gain efficiency in memory-performance. The two algorithms provide intentional knowledge of the detected outliers which determines as to why an identified outlier is exceptional. This knowledge helps the …

Compensation For Automatic White Balance Correction With Histogram Equalization, David D. Kirtley

Theses and Dissertations - UTB/UTPA

Histogram equalization rather than hard scaling can be used as an effective technique to counter automatic white balance correction in video processing to facilitate motion detection in video sequences. Benefits of this method are less user interaction needed by not needing to preview the image to select a scaling area and reduction of the non-focused changes in the video caused by using a scaling area. Reduced interaction lends itself to data mining of video.

Design And Evaluation Of High-Performance Packet Switching Schemes, Taner Doganer

Theses and Dissertations - UTB/UTPA

The design of high-performance packet switches is essential to efficiently handle the exponential growth of data traffic in the next generation Internet. Shared-memory-based packet switches are known to provide the best possible delay-throughput performance and the lowest packet-loss rate compared with packet switches using other buffering strategies. However, scalability of shared-memory-based switching systems has been restricted by high memory bandwidth requirements, segregation of memory space and centralized control of switching functions that causes the switch performance to degrade as a shared-memory switch is grown in size. The new class of sliding-window based packet switches are known to overcome these problems …

Parametric Classification In Domains Of Characters, Numerals, Punctuation, Typefaces And Image Qualities, Osama Ahmed Khan

Theses and Dissertations - UTB/UTPA

This thesis contributes to the Optical Font Recognition problem (OFR), by developing a classifier system to differentiate ten typefaces using a single English character ‘e’. First, features which need to be used in the classifier system are carefully selected after a thorough typographical study of global font features and previous related experiments. These features have been modeled by multivariate normal laws in order to use parameter estimation in learning. Then, the classifier system is built up on six independent schemes, each performing typeface classification using a different method. The results have shown a remarkable performance in the field of font …

Visualization Of Internet Web Pages Based On Authority And Word Frequency, David Navarro

Theses and Dissertations - UTB/UTPA

The growth, accessibility, and integration of the World Wide Web with contemporary information utilization provides a rich domain in which to explore information retrieval systems. One approach in the evolution of retrieval systems couples successful and long-standing techniques of information retrieval with new techniques, such as visualization. The system developed and reported in this thesis takes this approach. It builds upon well-known techniques of information retrieval including stemming, keyword matching, and cosine similarity. It also incorporates the new and relatively successful hubs and authority approach, which describes Web documents by their reference by other documents. Finally, it develops a new …

Data Analysis In The Antes System, Yavuz Tor

Theses and Dissertations - UTB/UTPA

Acanthosis nigricans is a skin condition that can be used as an indicator for the risk of developing type 2 diabetes in the future. Border Health Office, in University of Texas - Pan American, organizes screenings in schools for acanthosis nigricans. Screening results are, then, collected and evaluated in the Border Health Office. The ANTES System is a computer system that stores and manages the data collected in those screenings.

This study is on the analysis of those collected data to track the progress of data entry, to evaluate the progress on obesity and related problems, and to discover the …