Computer Sciences Commons^™

Biomedical Relationship Extraction From Literature Based On Bio-Semantic Token Subsequences, Ying Xie, Jayasimha R. Katukuri, Vijay V. Raghavan

Faculty Articles

Relationship Extraction (RE) from biomedical literature is an important and challenging problem in both text mining and bioinformatics. Although various approaches have been proposed to extract protein?protein interaction types, their accuracy rates leave a large room for further exploring. In this paper, two supervised learning algorithms based on newly defined "bio-semantic token subsequence" are proposed for multi-class biomedical relationship classification. The first approach calculates a "bio-semantic token subsequence kernel", whereas the second one explicitly extracts weighted features from bio-semantic token subsequences. The two proposed approaches outperform several alternatives reported in literature on multi-class protein?protein interaction classification.

Eliciting User Requirements Using Appreciative Inquiry, Carol Kernitzki Gonzales

CGU Theses & Dissertations

Many software development projects fail because they do not meet the needs of users, are over-budget, and abandoned. To address this problem, the user requirements elicitation process was modified based on principles of Appreciative Inquiry. Appreciative Inquiry, commonly used in organizational development, aims to build organizations, processes, or systems based on success stories using a hopeful vision for an ideal future. Spanning five studies, Appreciative Inquiry was evaluated for its effectiveness with eliciting user requirements. In the first two cases, it was compared with traditional approaches with end-users and proxy-users. The third study was a quasi-experiment comparing the use of …

Application-Level Optimization Of End-To-End Data Transfer Throughput, Esma Yildirim

LSU Doctoral Dissertations

For large-scale distributed applications, effective use of available network throughput and optimization of data transfer speed is crucial for end-to-end application performance. Today, many regional and national optical networking initiatives such as LONI, ESnet and Teragrid provide high speed network connectivity to their users. However, majority of the users fail to obtain even a fraction of the theoretical speeds promised by these networks due to issues such as sub-optimal protocol tuning, disk bottleneck on the sending and/or receiving ends, and processor limitations. This implies that having high speed networks in place is important but not sufficient for the improvement of …

An Online Ballistics Imaging System For Firearm Identification, Zhihu Huang, Jinsong Leng

Research outputs pre 2011

Since the traditional ballistics imaging system is dependent upon the expertise and experience of end-user, an intelligent ballistics imaging system is highly demanded to overcome the drawbacks of traditional techniques. This paper aims to develop a novel ballistics imaging system so as to combine the traditional functions with new features such as the line-scan image module, the characteristics extraction module, and the intelligent image processing module. With the help of these features, the new system can identify firearm more efficiently and effectively than the traditional techniques.

Application Of A Data Mining Framework For The Identification Of Agricultural Production Areas In Wa, Yunous Vagh, Leisa Armstrong, Dean Diepeveen

Research outputs pre 2011

This paper will propose a data mining framework for the identification of agricultural production areas ill WA. The data mining (DM) framework was developed with the aim of enhancing the analysis of agricultural datasets compared to currently used statistical methods. The DM framework is a synthesis of different technologies brought together for the purpose of enhancing the interrogation of these datasets. The DM framework is based on the data, information, knowledge and wisdom continuum as a horizontal axis, with DM and online analytical processing (OLAP) forming the vertical axis. In addition the DM framework incorporates aspects of data warehousing phases, …

A Mobile Intelligent Interruption Management System, Sina Zulkernain, Praveen Madiraju, Sheikh Iqbal Ahamed, Karl Stamm

Mathematics, Statistics and Computer Science Faculty Research and Publications

Mobile phones have become the most hated device that people cannot live without. For its primary usage as a communication device, it has surpassed any other medium. But it comes with a high price, interruption, anywhere anytime. These unwanted interruptions cause loss of productivity and also mostly not beneficial to the immediate task at hand, and moving them few minutes into the future can increase productivity. Considering receiver’s unavailability, it is possible to manage cell phone disruptions using advanced features like sensing capability, ubiquitous computing and context aware systems. This paper proposes the architecture of a system named Mobile Intelligent …

Digraphs With Isomorphic Underlying And Domination Graphs: 4-Cycles And Pairs Of Paths, Kim A. S. Factor, Larry J. Langley

Mathematics, Statistics and Computer Science Faculty Research and Publications

A domination graph of a digraph D, dom(D), is created using the vertex set of D, V(D). There is an edge uv in dom(D) whenever (u, z) or (v, z) is in the arc set of D, A(D), for every other vertex z ε V(D). For only some digraphs D has the structure of dom(D) been characterized. Examples of this are tournaments and regular digraphs. The authors have characterizations for the structure of digraphs D for …

Local Out-Tournaments With Upset Tournament Strong Components I: Full And Equal {0,1}-Matrix Ranks, Kim A. S. Factor, Rebecca M. Kohler, Jason M. Derby

Mathematics, Statistics and Computer Science Faculty Research and Publications

A digraph D is a local out-tournament if the outset of every vertex is a tournament. Here, we use local out-tournaments, whose strong components are upset tournaments, to explore the corresponding ranks of the adjacency matrices. Of specific interest is the out-tournament whose adjacency matrix has boolean, nonnegative integer, term, and real rank all equal to the number of vertices, n. Corresponding results for biclique covers and partitions of the digraph are provided.

Digraphs With Isomorphic Underlying And Domination Graphs: Pairs Of Paths, Kim A. S. Factor, Larry J. Langley

Mathematics, Statistics and Computer Science Faculty Research and Publications

A domination graph of a digraph D, dom (D), is created using thc vertex set of D and edge uv ϵ E (dom (D)) whenever (u, z) ϵ A (D) or (v, z) ϵ A (D) for any other vertex z ϵ A (D). Here, we consider directed graphs whose underlying graphs are isomorphic to their domination graphs. Specifically, digraphs are completely characterized where UG^c (D) is the union of two disjoint paths.

Lower Semimodular Inverse Semigroups, Ii, Peter R. Jones, Kyeong Hee Cheong

Mathematics, Statistics and Computer Science Faculty Research and Publications

The authors’ description of the inverse semigroups S for which the lattice ℒℱ(S) of full inverse subsemigroups is lower semimodular is used to describe those for which (a) the lattice ℒ(S) of all inverse subsemigroups or (b) the lattice �o(S) of convex inverse subsemigroups has that property. In each case, we show that this occurs if and only if the entire lattice is a subdirect product of ℒℱ(S) with ℒ(E _S ), or �o(E _S ), respectively, where E _S is the semilattice of idempotents of …

Automation Process For Morphometric Analysis Of Volumetric Ct Data From Pulmonary Vasculature In Rats, Rahul Shingrani, Gary S. Krenz, Robert Molthen

Mathematics, Statistics and Computer Science Faculty Research and Publications

With advances in medical imaging scanners, it has become commonplace to generate large multidimensional datasets. These datasets require tools for a rapid, thorough analysis. To address this need, we have developed an automated algorithm for morphometric analysis incorporating A Visualization Workshop computational and image processing libraries for three-dimensional segmentation, vascular tree generation and structural hierarchical ordering with a two-stage numeric optimization procedure for estimating vessel diameters. We combine this new technique with our mathematical models of pulmonary vascular morphology to quantify structural and functional attributes of lung arterial trees. Our physiological studies require repeated measurements of vascular structure to determine …

Cnareporter: A Computational Tool For The Generation Of Clinical Reports Of Genomic Alterations, Yuri Kotliarov, Serdar Bozdag, Hangjiong Cheng, Stefan Wuchty, Jean-Claude Zenklusen, Howard A. Fine

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background: Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patient's genomic profile for diagnostic and potential treatment purposes increasingly gain importance. Results: We developed CNAReporter, a software tool that allows users to visualize SNP-specific data obtained from Affymetrix arrays and generate PDF-reports as output. We combined standard algorithms for the analysis of chromosomal alterations, utilizing the widely applied GenePattern framework. …

Not Every Co-Existential Map Is Confluent, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

A continuous surjection between compacta is co-existential if it is the second of two maps whose composition is a standard ultracopower projection. Co-existential maps are always weakly confluent, and are even monotone when the range space is locally connected; so it is a natural question to ask whether they are always confluent. Here we give a negative answer. This is an interesting question, mainly because of the fact that most theorems about confluent maps have parallel versions for co-existential maps---notably, both kinds of maps preserve hereditary indecomposability. Where the known parallels break down is in the question of chainability. It …

Information Sharing Across Private Databases, Swapnil Suresh Samant

Open Access Theses & Dissertations

While the explosion of availability of information has become invaluable in modern society, it has also raised valid concerns about erosion of privacy. More and more, different entities are encouraged to share information in order to discover potential security risks, health pattern, or social behavior trends. However, some of this information is sensitive. Owners of information may be unwilling to share their whole databases with other entities, either to protect the privacy of the records, or because of the proprietary nature of the information.

We consider the following problem. How can we compute the intersection and the equijoin of databases …

Pwisegen: A Genetic Algorithms-Based Framework For Pairwise Test Set Generation, Pedro Flores

Open Access Theses & Dissertations

Pairwise testing is a combinatorial testing approach that can be used to reduce the number of test cases dramatically for a software system. It specializes in the type of testing where the outcome of a system depends on the combination of several input parameters. This technique is widely used when there is not enough time to try out all possible combinations of the input parameters involved, because that would be very time consuming. The purpose of pairwise testing technique is to avoid testing all possible value combinations that a system can receive, and to preferably take a representative sample of …

Modeling Geographic Awareness Of Road Networks For Consistency Verification, Ari Kassin

Open Access Theses & Dissertations

Problems related to transportation and inspection of valuable or sensitive assets such as commercial products and materials, cultural items and works of art, and hazardous materials share similarities and can be modeled by a core set of abstract entities including a payload, a vehicle, a driver, and an inspector. To make the load handling capabilities of security monitoring and inspection systems more scalable, security can be increased by reducing the variability of transportation routes to a finite set of authorized routes between trip origin and destination locations. Then trip anomalies, which are unexpected trip variations, can be used in inspection …

Function Point Analysis In Computer Science Capstone Projects, Evelyn Torres

Open Access Theses & Dissertations

Capstone projects at the Computer Science Department at the University of Texas at El Paso allow students to demonstrate their knowledge of software engineering. During the capstone project, students work on a project that simulates industry; students have a client and a supervising team. Before a project is implemented, professors must assess the project to ensure consistency with previous projects and a significant experience for the students. Currently, a project is assessed primarily on past experiences. In industry, agreeing to completing and delivering a project without assessing the scope and estimating the project cost is neither acceptable nor profitable. Similarly …

Stochastic Optimization For Learning-Based Super-Resolution: Algorithms And Applications, Jun Zheng

Open Access Theses & Dissertations

Human beings get much of their information visually and depend on perception of images for many critical tasks, such as object identification, medical image analysis, photography, etc. In many visual-based applications, higher resolution images are required for perceiving and receiving critical information. A high resolution image can contribute to a better identification of a suspect's face, or a more accurate localization of a tumor in a mammogram, or a more pleasing view in high definition television, and so on. However, it is hard to obtain the high resolution images needed for some applications, for example, the cost of sensors increases …

Geometrical Structure And Analysis Of Association Rule, Rajat Sar

Master's Projects

Association rule mining helps us to identify the association between items from a large transactional data set. It has always been a time consuming process because of repeatedly scanning of the data set. Apriori Algorithm [1] and FP-Tree Algorithm [2] are the two methods to find out the association of items in a large transactional item set. Both the above algorithm works differently (Apriori follows Bottom-Up Approach & FP-Tree follows Top-Down Approach) in order to get the association. Associations of items generated from the above two algorithms can be represented in geometry. The geometrical form of associations is called Simplical …

Detecting Undetectable Computer Viruses, Sujandharan Venkatachalam

Master's Projects

Signature-based detection relies on patterns present in viruses and provides a relatively simple and efficient method for detecting known viruses. At present, most anti-virus systems rely primarily on signature detection. Metamorphic viruses are one of the most difficult types of viruses to detect. Such viruses change their internal structure, which provides an effective means of evading signature detection. Previous work has provided a rigorous proof that a fairly simple metamorphic engine can generate viruses that will evade any signature-based detection. In this project, we first implement a metamorphic engine that is provably undetectable—in the sense of signature-based detection. We then …

Geometrical Structure And Analysis Of Association Rules, Sar Rajat

Master's Projects

Association rule mining helps us to identify the association between items from a large transactional data set. It has always been a time consuming process because of repeatedly scanning of the data set. Apriori Algorithm [1] and FP-Tree Algorithm [2] are the two methods to find out the association of items in a large transactional item set. Both the above algorithm works differently (Apriori follows Bottom-Up Approach & FP-Tree follows Top-Down Approach) in order to get the association. Associations of items generated from the above two algorithms can be represented in geometry. The geometrical form of associations is called Simplical …

Improved Software Activation Using Multithreading, Jian Rui Zhang

Master's Projects

Software activation is an anti-piracy technology designed to verify that software products have been legitimately licensed [1]. It is supposed to be quick and simple while simultaneously protecting customer privacy. The most common form of software activation is through the entering of legitimate product serial numbers by users, which sometimes are also known as product keys. This technique is employed by various software, from small shareware programs to large commercial programs such as Microsoft Office. However, software activation based on a serial number appears to be weak, as various cracks for a majority of programs are available and can be …

Security In Peer-To-Peer Sip Voip, Richa Marwaha

Master's Projects

VoIP (Voice over Internet Protocol) is one of the fastest growing technologies in the world. It is used by people all over the world for communication. But with the growing popularity of internet, security is one of the biggest concerns. It is important that the intruders are not able to sniff the packets that are transmitted over the internet through VoIP. Session Initiation Protocol (SIP) is the most popular and commonly used protocol of VoIP. Now days, companies like Skype are using Peer-to-Peer SIP VoIP for faster and better performance. Through this project I am improving an already existing Peer-to-Peer …

Clustering And Validation Of Microarray Data Using Consensus Clustering, Sarbinder Kallar

Master's Projects

Clustering is a popular method to glean useful information from microarray data. Unfortunately the results obtained from the common clustering algorithms are not consistent and even with multiple runs of different algorithms a further validation step is required. Due to absence of well defined class labels, and unknown number of clusters, the unsupervised learning problem of finding optimal clustering is hard. Obtaining a consensus of judiciously obtained clusterings not only provides stable results but also lends a high level of confidence in the quality of results. Several base algorithm runs are used to generate clusterings and a co-association matrix of …

Email Data Mining: An Approach To Construct An Organization Position-Wise Structure While Performing Email Analysis, Bhargav Vadher

Master's Projects

In this age of social networking, it is necessary to define the relationships among the members of a social network. Various techniques are already available to define user- to-user relationships across the network. Over time, many algorithms and machine learning techniques were applied to find relationships over social networks, yet very few techniques and information are available to define a relation directly over raw email data. Few educational societies have developed a way to mine the email log files and have found the inter-relation between the users by means of clusters. Again, there is no solid technique available that can …

The Activelecture System, Sanuja Dabade

Master's Projects

For an instructor, it has always been a challenging task to keep students engaged during the lecture and assess them in real time. Instructors use different methodologies to address the challenge of keeping students engaged during the class and increase their participation. Widely used methodologies for active learning include clickers and Tablet PCs. Clickers are small handheld devices which are used to collect student responses and present these responses graphically. Tablet PCs provide a functionality to use natural handwriting to provide feedback. Web browsers are a cost effective approaches. I have used a web based technology to create active learning …

Bookmarklet Builder For Offline Data Retrieval, Sheetal Naidu

Master's Projects

Bookmarklet Builder for Offline Data Retrieval is a computer application which will allow users to view websites even when they are offline. It can be stored as a URL of a bookmark in the browser. Bookmarklets exist for storing single web pages in hand-held devices and these web pages are stored as PDF files. In this project we have developed a tool that can save entire web page applications as bookmarklets. This will enable users to use these applications even when they are not connected to the Internet. The main technology beyond Javascript used to achieve this is the data: …

Parallel Programming Recipes, Thuy C. Nguyenphuc

Master's Projects

Parallel programming has become vital for the success of commercial applications since Moore’s Law will now be used to double the processors (or cores) per chip every technology generation. The performance of applications depends on how software executions can be mapped on the multi-core chip, and how efficiently they run the cores. Currently, the increase of parallelism in software development is necessary, not only for taking advantage of multi-core capability, but also for adapting and surviving in the new silicon implementation. This project will provide the performance characteristics of parallelism for some common algorithms or computations using different parallel languages. …

How Smart Is Your Android Smartphone?, Deepika Mulani

Master's Projects

Smart phones are ubiquitous today. These phones generally have access to sensitive personal information and, consequently, they are a prime target for attackers. A virus or worm that spreads over the network to cell phone users could be particularly damaging. Due to a rising demand for secure mobile phones, manufacturers have increased their emphasis on mobile security. In this project, we address some security issues relevant to the current Android smartphone framework. Specifically, we demonstrate an exploit that targets the Android telephony service. In addition, as a defense against the loss of personal information, we provide a means to encrypt …

Document Builder, Thien Tran

Master's Projects

In this paper, we consider problems related to on-demand content publishing and maintenance. Specifically, we are concerned with the recent concept of structural Content Management Systems (CMS) and its design principles. We focus on Apache Ant, a popular document generator tool for the Java development industry. However, Ant has not been widely extended beyond its capacity to deal with computer programs, which limits its utility. We analyze the Ant build script structure, study its usage, and implement an on-demand document generator for Ant. The focus is to provide a better document build model based on Ant, which can provide document …