Physical Sciences and Mathematics Commons^™

Alignment-Free Methods And Its Applications, Ramez Mina

Student Work

Comparing biological sequences remains one of the most vital activities in Bioinformatics. Comparing biological sequences would address the relatedness between species, and find similar structures that might lead to similar functions.

Sequence alignment is the default method, and has been used in the domain for over four decades. It gained a lot of trust, but limitations and even failure has been reported, especially with the new generated genomes. These new generated genomes have bigger size, and to some extent suffer errors. Such errors come mainly as a result from the sequencing machine. These sequencing errors should be considered when submitting …

Application Oriented Analysis Of Large Scale Datasets, Prashant Shivaji Paymal

Student Work

Diverse application areas, such as social network, epidemiology, and software engineering consist of systems of objects and their relationships. Such systems are generally modeled as graphs. Graphs consist of vertices that represent the objects, and edges that represent the relationships between them. These systems are data intensive and it is important to correctly analyze the data to obtain meaningful information. Combinatorial metrics can provide useful insights for analyzing these systems. In this thesis, we use the graph based metrics such as betweenness centrality, clustering coefficient, articulation points, etc. for analyzing instances of large change in evolving networks (Software Engineering), and …

On-Line Banking Systems: Are They Sustainable?, Satish Mahadevan Srinivasan, Sachin Pawaskar, Abhishek Tripathi, Lotfollah Najjar

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

Although the trend for on-line banking has increased in recent years, the customers have not shown enthusiastic participation in the past and in present. Since the sustainability of a bank supporting on-line-banking service depends on what capacity it can attract new customers, retain already existing customers and how well can it extend its services to the current and future customer base. This investigation is focused on examining if there is any significant difference among the factors namely the transactional security, information design, navigational design, visual design, web site trust, web site satisfaction and e-loyalty over sustainability of on-line banking for …

On Elementary Loops Of Logic Programs, Martin Gerber, Joohyung Lee, Yuliya Lierler

Computer Science Faculty Publications

Using the notion of an elementary loop, Gebser and Schaub (2005. Proceedings of the Eighth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR'05), 53–65) refined the theorem on loop formulas attributable to Lin and Zhao (2004) by considering loop formulas of elementary loops only. In this paper, we reformulate the definition of an elementary loop, extend it to disjunctive programs, and study several properties of elementary loops, including how maximal elementary loops are related to minimal unfounded sets. The results provide useful insights into the stable model semantics in terms of elementary loops. For a nondisjunctive program, …

Using Semantic Templates To Study Vulnerabilities Recorded In Large Software Repositories, Yan Wu

Student Work

Software vulnerabilities allow an attacker to reduce a system's Confidentiality, Availability, and Integrity by exposing information, executing malicious code, and undermine system functionalities that contribute to the overall system purpose and need. With new vulnerabilities discovered everyday in a variety of applications and user environments, a systematic study of their characteristics is a subject of immediate need for the following reasons:

• The high rate in which information about past and new vulnerabilities are accumulated makes it difficult to absorb and comprehend.
• Rather than learning from past mistakes, similar types of vulnerabilities are observed repeatedly.
• As the scale and complexity of …

The Global Geek: Language Training For It Students’ Study Abroad In Austria And Germany, Gwyneth E. Cliver, Deepak Khazanchi

Information Systems and Quantitative Analysis Faculty Publications

The Modern Language Association’s (MLA) urgent appeal for the restructuring of the undergraduate language curriculum, “Foreign Languages and Higher Education: New Structures for a Changed World,” emphasizes a need for language departments to enrich their upper-division course offerings beyond the traditional literary studies model in order to attract and retain broader interest in language learning among students with diverse academic interests and needs. Citing the National Science Foundation’s 2003 Survey of College Graduates, it stresses that only 6.1% of undergraduates whose primary major is a foreign language later achieve doctorate degrees and concludes that departments should provide upper-division language courses …

Creating An International Joint Certificate In It Administration, Peter Wolcott

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

The University of Nebraska at Omaha (UNO) and the University of Agder (UiA), Norway, are collaborating on the creation of an undergraduate certificate in Information Technology Administration. The certificate is designed for students who are interested in managing the complex technical infrastructure of today's organizations. The certificate will consist of approximately 15 credit hours of hands-on courses, covering such areas as systems administration, network administration, database administration, security administration, and distributed systems. All courses will be offered online, using a variety of collaboration tools and teaching techniques that reflect the best of current practice. Students will take courses taught by …

Collaborative Learning In Software Development Teams, Matthew Hale, Rose Gamble, Kimberly Wilson, Anupama Narayan

Interdisciplinary Informatics Faculty Proceedings & Presentations

Recently Web 2.0 has emerged as a framework to study collaborative learning. Assessing learning in team projects is one mechanism used to improve teaching methodologies and tool support. Web 2.0 technologies enable automated assessment capabilities, leading to both rapid and incremental feedback. Such feedback can catch problems in time for pedagogic adjustment, to better guide students toward reaching learning objectives. Our courseware, SEREBRO, couples a social, tagging enabled, idea network with a range of modular toolkits, such as wikis, feeds and project management tools into a Web 2.0 environment for collaborating teams. In this paper, we first refine a set …

Augmenting Online Learning With Real-Time Conferencing: Experiences From An International Course, Bjørn Erik Munkvold, Ilze Zigurs, Deepak Khazanchi

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

This paper reports experiences from the use of real-time conferencing to support synchronous class interaction in an international online course. Through combination of video, audio, application sharing and chat, the students and instructors engaged in weekly interactions in a virtual classroom. This created an environment for rich interaction, augmenting the traditional use of course repositories. Further, this gave the students hands-on experience with real-time conferencing tools which are increasingly common in the workplace. The paper also discusses experienced challenges related to combining the use of multiple synchronous communication channels and presents implications for further use of real-time conferencing in online …

Centinela: A Human Activity Recognition System Based On Acceleration And Vital Sign Data, Óscar D. Lara, Alfredo J. Perez, Miguel A. Labrador, José D. Posada

Computer Science Faculty Publications

This paper presents Centinela, a system that combines acceleration data with vital signs to achieve highly accurate activity recognition. Centinela recognizes five activities: walking, running, sitting, ascending, and descending. The system includes a portable and unobtrusive real-time data collection platform, which only requires a single sensing device and a mobile phone. To extract features, both statistical and structural detectors are applied, and two new features are proposed to discriminate among activities during periods of vital sign stabilization. After evaluating eight different classifiers and three different time window sizes, our results show that Centinela achieves up to 95.7% overall accuracy, which …

An Investigation Of Microenterprise Capability-Building Via Access And Use Of Technology, Travis Godwin Good

Student Work

Micro-enterprises (businesses with one to five employees) lie at the heart of the American economy but are not well-researched. It is believed that technology adoption has the potential to spark strong growth among micro-enterprises, but current technology adoption models are tailored for large businesses and do not consider the human, social, and economic inputs peculiar to micro-enterprises. This research investigates how access to, and use of technology may lead micro enterprises to build capabilities that will help them increase their net income and hire more employees. Framed as a specification of Amartya Sen’s capability perspective, this research seeks, through a …

Transition Systems For Model Generators — A Unifying Approach, Yuliya Lierler, Miroslaw Truszczyński

Computer Science Faculty Publications

A fundamental task for propositional logic is to compute models of propositional formulas. Programs developed for this task are called satisfiability solvers. We show that transition systems introduced by Nieuwenhuis, Oliveras, and Tinelli to model and analyze satisfiability solvers can be adapted for solvers developed for two other propositional formalisms: logic programming under the answerset semantics, and the logic PC(ID). We show that in each case the task of computing models can be seen as “satisfiability modulo answer-set programming,” where the goal is to find a model of a theory that also is an answer set of a certain program. …

Multi-Robot Coalition Formation For Distributed Area Coverage, Ke Cheng

Student Work

The problem of distributed area coverage using multiple mobile robots is an important problem in distributed multi-robot sytems. Multi-robot coverage is encountered in many real world applications, including unmanned search & rescue, aerial reconnaissance, robotic demining, inspection of engineering structures, and automatic lawn mowing. To achieve optimal coverage, robots should move in an efficient manner and reduce repeated coverage of the same region that optimizes a certain performance metric such as the amount of time or energy expended by the robots. This dissertation especially focuses on using mini-robots with limited capabilities, such as low speed of the CPU and limited …

Wopr In Search Of Better Strategies For Board Games, Ben Horner

Student Work

Board games have been challenging intellects and capturing imaginations for more than five thousand years. Researchers have been producing artificially intelligent players for more than fifty. Common artificial intelligence techniques applied to board games use alpha-beta pruning tree search techniques. This paper supplies a frame- work that accommodates many of the diverse aspects of board games, as well as exploring several alternatives for searching out ever better strategies. Techniques examined include optimizing artificial neural networks using genetic algorithms and backpropagation.

Applications Of Hidden Markov Models In Microarray Gene Expression Data, Huimin Geng, Xutao Deng, Hesham Ali

Computer Science Faculty Publications

Hidden Markov models (HMMs) are well developed statistical models to capture hidden information from observable sequential symbols. They were first used in speech recognition in 1970s and have been successfully applied to the analysis of biological sequences since late 1980s as in finding protein secondary structure, CpG islands and families of related DNA or protein sequences [1]. In a HMM, the system being modeled is assumed to be a Markov process with unknown parameters, and the challenge is to determine the hidden parameters from the observable parameters. In this chapter, we described two applications using HMMs to predict gene functions …

Dynamic Reconfiguration In Modular Self-Reconfigurable Robots Using Multi-Agent Coalition Games, Zachary Ramaekers

Student Work

In this thesis, we consider the problem of autonomous self-reconfiguration by modular self-reconfigurable robots (MSRs). MSRs are composed of small units or modules that can be dynamically configured to form different structures, such as a lattice or a chain. The main problem in maneuvering MSRs is to enable them to autonomously reconfigure their structure depending on the operational conditions in the environment. We first discuss limitations of previous approaches to solve the MSR self-reconfiguration problem. We will then present a novel framework that uses a layered architecture comprising a conventional gait table-based maneuver to move the robot in a fixed …

Semantic Relevance Analysis Of Subject-Predicate-Object (Spo) Triples, Ranjana Kumar

Student Work

The goal of this thesis is to explore and integrate several existing measurements for ranking the relevance of a set of subject-predicate-object (SPO) triples to a given concept. As we are inundated with information from multiple sources on the World-Wide-Web, SPO similarity measures play a progressively important role in information extraction, information retrieval, document clustering and ontology learning. This thesis is applied in the Cyber Security Domain for identifying and understanding the factors and elements of sociopolitical events relevant to cyberattacks. Our efforts are towards developing an algorithm that begins with an analysis of news articles by taking into account …

An Architecture For Global Ubiquitous Sensing, Alfredo J. Perez

Computer Science Faculty Publications

A new class of wireless sensor networks has recently appeared due to the pervasiness of cellular phones with embedded sensors, mobile Internet connectivity, and location technologies. This mobile wireless sensor network has the potential to address large-scale societal problems and improve the people’s quality of life in a better, faster and less expensive fashion than current solutions based on static wireless sensor networks. Ubiquitous Sensing is the umbrella term used in this dissertation that encompasses location-based services, human-centric, and participatory sensing applications. At the same time, ubiquitous sensing applications are bringing a new series of challenging problems. This dissertation proposes …

Abstract Answer Set Solvers With Backjumping And Learning, Yuliya Lierler

Computer Science Faculty Publications

Nieuwenhuis et al. (2006. Solving SAT and SAT modulo theories: From an abstract Davis-Putnam-Logemann-Loveland procedure to DPLL(T). Journal of the ACM 53(6), 937977 showed how to describe enhancements of the Davis–Putnam–Logemann–Loveland algorithm using transition systems, instead of pseudocode. We design a similar framework for several algorithms that generate answer sets for logic programs: SMODELS, SMODELS_cc, asp-sat with Learning (CMODELS), and a newly designed and implemented algorithm sup. This approach to describe answer set solvers makes it easier to prove their correctness, to compare them, and to design new systems.

An Empirical Investigation Of Virtual World Projects And Metaverse Technology Capabilities, Dawn Owens, Alanah Davis, Deepak Khazanchi, Ilze Zigurs

Information Systems and Quantitative Analysis Faculty Publications

Metaverses are immersive three-dimensional virtual worlds (VWs) where people interact with each other and their environment, using the metaphor of the real world but without its physical limitations. Unique technology capabilities of metaverses have the potential to enhance the conduct of virtual projects, but little is known about virtual worlds in this context. Virtual project teams struggle in meeting stated project outcomes due to challenges related to communication, shared understanding, and coordination. One way to address these challenges is to consider the use of emerging technologies, such as metaverses, to minimize the impact on virtual project teams. Applying a theoretical …

Termination Of Grounding Is Not Preserved By Strongly Equivalent Transformations, Yuliya Lierler, Vladimir Lifschitz

Computer Science Faculty Proceedings & Presentations

The operation of a typical answer set solver begins with grounding—replacing the given program with a program without variables that has the same answer sets. When the given program contains function symbols, the process of grounding may not terminate. In this note we give an example of a pair of consistent, strongly equivalent programs such that one of them can be grounded by LPARSE, DLV, and gringo, and the other cannot.

Parsing Combinatory Categorial Grammar With Answer Set Programming: Preliminary Report, Yuliya Lierler, Peter Schüller

Computer Science Faculty Proceedings & Presentations

Combinatory categorial grammar (CCG) is a grammar formalism used for natural language parsing. CCG assigns structured lexical categories to words and uses a small set of combinatory rules to combine these categories to parse a sentence. In this work we propose and implement a new approach to CCG parsing that relies on a prominent knowledge representation formalism, answer set programming (ASP) — a declarative programming paradigm. We formulate the task of CCG parsing as a planning problem and use an ASP computational tool to compute solutions that correspond to valid parses. Compared to other approaches, there is no need to …

Weighted-Sequence Problem: Asp Vs Casp And Declarative Vs Problem-Oriented Solving, Yuliya Lierler, Shaden Smith, Miroslaw Truszczyński, Alex Westlund

Computer Science Faculty Proceedings & Presentations

Search problems with large variable domains pose a challenge to current answer-set programming (ASP) systems as large variable domains make grounding take a long time, and lead to large ground theories that may make solving infeasible. To circumvent the “grounding bottleneck” researchers proposed to integrate constraint solving techniques with ASP in an approach called constraint ASP (CASP). In the paper, we evaluate an ASP system CLINGO and a CASP system CLINGCON on a handcrafted problem involving large integer domains that is patterned after the database task of determining the optimal join order. We find that search methods used by CLINGO …

A Transition System For Ac Language Algorithms, Yuliya Lierler, Yaunlin Zhang

Computer Science Faculty Proceedings & Presentations

Recently a logic programming language AC was proposed by Mellarkod et al. (2008) to integrate answer set programming (ASP) and constraint logic programming. In a similar vein, Gebser et al. (2009) proposed a CLINGCON language integrating ASP and finite domain constraints. A distinguishing feature of these languages is their capacity to allow new efficient inference algorithms that combine traditional ASP procedures and other efficient methods in constraint programming. In this paper we show that a transition system introduced by Nieuwenhuis et al. (2006) can be extended to model the “hybrid” ACSOLVER algorithm, by Mellarkod et al., designed for processing a …

Asp-Based Problem Solving With Cutting-Edge Tools, Marcello Balduccini, Yuliya Lierler

Computer Science Faculty Proceedings & Presentations

In the development of practical applications of answer set programming (ASP), encodings that use well-established solvers such as CLASP and DLV are sometimes affected by scalability issues. In those situations, one can resort to more sophisticated ASP tools exploiting, for instance, incremental and constraint ASP. However, today there is no specific methodology for the selection or use of such tools. In this paper we describe how we used such cutting-edge ASP tools on challenging problems from the Third Answer Set Programming Competition, and outline the methodology we followed. We view this paper as a first step in the development of …

Trends In Phishing Attacks: Suggestions For Future Research, Ryan M. Schuetzler

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

Deception in computer-mediated communication is a widespread phenomenon. Cyber criminals are exploiting technological mediums to communicate with potential targets as these channels reduce both the deception cues and the risk of detection itself. A prevalent deception-based attack in computer-mediated communication is phishing. Prior phishing research has addressed the “bait” and “hook” components of phishing attacks, the human-computer interaction that takes place as users judge the veracity of phishing emails and websites, and the development of technologies that can aid users in identifying and rejecting these attacks. Despite the extant research on this topic, phishing attacks continue to be successful as …

Role Of Cloud Computing Interventions For Micro-Enterprise Growth: Implications For Global Development, Sajda Qureshi, Mehruz Kamal

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

While the majority of businesses around the world are micro-enterprises, they are the most vulnerable and are often run by people with limited resources, and skills to be able to avail the benefits of Information and Communication Technologies (ICTs). These are a form of small business which employs between 1-5 people and face challenges of limited resources, skills and ability to grow. When they do adopt IT their potential to survive and grow increases as they are then able to participate in the global economy. The challenge for global development lies in enabling these micro-enterprises to adopt the appropriate IT …

A Novel Correlation Networks Approach For The Identification Of Gene Targets, Kathryn Dempsey Cooper, Stephen Bonasera, Dhundy Raj Bastola, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks are emerging as a powerful tool for modeling temporal mechanisms within the cell. Particularly useful in examining coexpression within microarray data, studies have determined that correlation networks follow a power law degree distribution and thus manifest properties such as the existence of “hub” nodes and semicliques that potentially correspond to critical cellular structures. Difficulty lies in filtering coincidental relationships from causative structures in these large, noise-heavy networks. As such, computational expenses and algorithm availability limit accurate comparison, making it difficult to identify changes between networks. In this vein, we present our work identifying temporal relationships from microarray data …

Evaluation Of Essential Genes In Correlation Networks Using Measures Of Centrality, Kathryn Dempsey Cooper, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks are emerging as powerful tools for modeling relationships in high-throughput data such as gene expression. Other types of biological networks, such as protein-protein interaction networks, are popular targets of study in network theory, and previous analysis has revealed that network structures identified using graph theoretic techniques often relate to certain biological functions. Structures such as highly connected nodes and groups of nodes have been found to correspond to essential genes and protein complexes, respectively. The correlation network, which measures the level of co-variation of gene expression levels, shares some structural properties with other types of biological networks. We …

A Noise Reducing Sampling Approach For Uncovering Critical Properties In Large Scale Biological Networks, Karthik Duraisamy, Kathryn Dempsey Cooper, Hesham Ali, Sanjukta Bhowmick

Interdisciplinary Informatics Faculty Proceedings & Presentations

A correlation network is a graph-based representation of relationships among genes or gene products, such as proteins. The advent of high-throughput bioinformatics has resulted in the generation of volumes of data that require sophisticated in silico models, such as the correlation network, for in-depth analysis. Each element in our network represents expression levels of multiple samples of one gene and an edge connecting two nodes reflects the correlation level between the two corresponding genes in the network according to the Pearson correlation coefficient. Biological networks made in this manner are generally found to adhere to a scale-free structural nature, that …