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Full-Text Articles in Computer Sciences

Graph-Based Regularization In Machine Learning: Discovering Driver Modules In Biological Networks, Xi Gao Jan 2015

Graph-Based Regularization In Machine Learning: Discovering Driver Modules In Biological Networks, Xi Gao

Theses and Dissertations

Curiosity of human nature drives us to explore the origins of what makes each of us different. From ancient legends and mythology, Mendel's law, Punnett square to modern genetic research, we carry on this old but eternal question. Thanks to technological revolution, today's scientists try to answer this question using easily measurable gene expression and other profiling data. However, the exploration can easily get lost in the data of growing volume, dimension, noise and complexity. This dissertation is aimed at developing new machine learning methods that take data from different classes as input, augment them with knowledge of feature relationships, …

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Modeling Properties Of Deformation Pattern, Yuan Lin Dec 2014

Modeling Properties Of Deformation Pattern, Yuan Lin

Theses and Dissertations

The human aging process is a complicated topic in the biological sciences. It is human nature to want to keep looking young and interested in one's appearance many years into the future. Some fundamental questions related to this issue are, "How fast are we aging?" Is it a continuous process or is it a process of phases? What will I possibly look like after ten years? To provide an answer to all of these questions, it is necessary to closely monitor the changes taking places in our anatomy. Wrinkles and human face shape deformation, which are the natural signs of …

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Characterizing Fetal Sleep States Of Iugr And Low-Risk Fetuses Using Fetal Magnetocardiography, Bhargavi Sriram Dec 2014

Characterizing Fetal Sleep States Of Iugr And Low-Risk Fetuses Using Fetal Magnetocardiography, Bhargavi Sriram

Theses and Dissertations

Intrauterine growth restriction (IUGR) is a fetal condition characterized by growth-rate reduction. Afflicted fetuses tend to display abnormalities in heart rate. Hence, studying its heart rate variability (HRV) along with comparisons against normal fetal HRV might give some insight into the heart rate dynamics between the two groups. Heart rate variability (HRV) is one of the prominent markers that could help in identifying fetal distress. Four fetal heart rate patterns were previously defined based on HRV, which can provide clinicians with valuable information regarding fetus health during pregnancy. Past studies that differentiate the HRV with or without considering patterns, have …

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Replication And Knowledge Production In Empirical Software Engineering Research, Jonathan L. Krein Dec 2014

Replication And Knowledge Production In Empirical Software Engineering Research, Jonathan L. Krein

Theses and Dissertations

Although replication is considered an indispensable part of the scientific method in software engineering, few replication studies are published each year. The rate of replication, however, is not surprising given that replication theory in software engineering is immature. Not only are replication taxonomies varied and difficult to reconcile, but opinions on the role of replication contradict. In general, we have no clear sense of how to build knowledge via replication, particularly given the practical realities of our research field. Consequently, most replications in software engineering yield little useful information. In particular, the vast majority of external replications (i.e., replications performed …

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Framework To Implement Authentication, Authorization And Secure Communications In A Multiuser Collaborative Cax Environment, Francis Mensah Dec 2014

Framework To Implement Authentication, Authorization And Secure Communications In A Multiuser Collaborative Cax Environment, Francis Mensah

Theses and Dissertations

Computer Aided Design (CAD) applications have historically been based on a single user per application architecture. Although this architecture is still popular to date, it does have several drawbacks. First of all the single user CAD architecture inhibits a concurrent engineering design process where several designers can work on the same model simultaneously. This limitation introduces time inefficiency especially when a project involves geographically dispersed designers. A solution to these drawbacks could be a transition from the traditional single user CAD architecture to a multiuser collaborative architecture. Advances in computer networking technologies, especially relating to the Internet, have provided the …

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The Bioluminescence Heterozygous Genome Assembler, Jared Calvin Price Dec 2014

The Bioluminescence Heterozygous Genome Assembler, Jared Calvin Price

Theses and Dissertations

High-throughput DNA sequencing technologies are currently revolutionizing the fields of biology and medicine by elucidating the structure and function of the components of life. Modern DNA sequencing machines typically produce relatively short reads of DNA which are then assembled by software in an attempt to produce a representation of the entire genome. Due to the complex structure of all but the smallest genomes, especially the abundant presence of exact or almost exact repeats, all genome assemblers introduce errors into the final sequence and output a relatively large set of contigs instead of full-length chromosomes (a contig is a DNA sequence …

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Classifying And Cataloging Cyber-Security Incidents Within Cyber-Physical Systems, William B. Miller Dec 2014

Classifying And Cataloging Cyber-Security Incidents Within Cyber-Physical Systems, William B. Miller

Theses and Dissertations

In the past, there were perceived delineations between the cyber world and the physical world. We are becoming increasingly aware of the overlap between these two worlds, and the overlap itself is increasing. The overlap between these two worlds is known as cyber-physical systems. There have been several incidents involving cyber-physical systems and the number of these incidents is increasing dramatically. In the past there has been no effort to identify methods for describing these incidents in the unique context of cyber-physical systems. This research provides a taxonomy for classifying these incidents that focuses on cross domain, impact oriented analysis. …

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Using Random Forest In The Field Of Metabolomics, Curtis White Nov 2014

Using Random Forest In The Field Of Metabolomics, Curtis White

Theses and Dissertations

Metabolomics is the science of comprehensive evaluation of changes in the metabolome with a goal to elucidate underlying biological mechanisms of a living system. There is an opinion in the field of metabolomics, the study of the set of metabolites present within an organism, cell, or tissue, that the future development of the field is contingent upon two factors. One of the factors is the advancement of analytical instrumentation, and the other is developing data mining methodologies for extracting meaningful and interpretable experimental results. There are many different types of data mining methodologies, but the undertaking of selecting a particular …

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Using Variations Of Shape And Appearance In Alignment Methods For Classifying Human Actions, Sultan Mohammad Almotairi Nov 2014

Using Variations Of Shape And Appearance In Alignment Methods For Classifying Human Actions, Sultan Mohammad Almotairi

Theses and Dissertations

In this dissertation, we address the problem of recognizing human-action from videos. The recognition aims at recovering action information from the image sequences using different features such as variations of the human shape. Approaches based on such features often use sequence-alignment methods. We propose two novel methods for human-action recognition. We also propose an elliptical-shaped band for the Dynamic Time Warping (DTW) that provides a good compromise between alignment accuracy and computational speed. First, we study the applicability of the pairwise shape-similarity measurements for human-action recognition. Since action can be seen as a sequence of shapes of silhouette poses, there …

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A Privacy Risk Scoring Framework For Mobile, Jedidiah Spencer Montgomery Nov 2014

A Privacy Risk Scoring Framework For Mobile, Jedidiah Spencer Montgomery

Theses and Dissertations

Protecting personal privacy has become an increasingly important issue as computers become a more integral part of everyday life. As people begin to trust more personal information to be contained in computers they will question if that information is safe from unwanted intrusion and access. With the rise of mobile devices (e.g., smartphones, tablets, wearable technology) users have enjoyed the convenience and availability of stored personal information in mobile devices, both in the operating system and within applications.For a mobile application to function correctly it needs permission or privileges to access and control various resources and controls on the mobile …

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The Information Value Methodology: How Users Assess The Quality Of Web Information, Marilou Haines Oct 2014

The Information Value Methodology: How Users Assess The Quality Of Web Information, Marilou Haines

Theses and Dissertations

The Internet is a self-regulating complex system in which users decide what is relevant through their actions. Since the burden of locating and evaluating information depends on knowledge, experience, and skill, this study rigorously and holistically investigates the Web users' experience. The study began with a multidisciplinary literature review to determine how academics assess IQ on the Web. While individual models are narrowly focused, in aggregate, they delineate the boundaries of IQ needs, and identify the dimensions that are significant to the Web community. These dimensions, categorized into six knowledge domains, are the core of the information value methodology (IVM). …

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Scalable Detection And Extraction Of Data In Lists In Ocred Text For Ontology Population Using Semi-Supervised And Unsupervised Active Wrapper Induction, Thomas L. Packer Oct 2014

Scalable Detection And Extraction Of Data In Lists In Ocred Text For Ontology Population Using Semi-Supervised And Unsupervised Active Wrapper Induction, Thomas L. Packer

Theses and Dissertations

Lists of records in machine-printed documents contain much useful information. As one example, the thousands of family history books scanned, OCRed, and placed on-line by FamilySearch.org probably contain hundreds of millions of fact assertions about people, places, family relationships, and life events. Data like this cannot be fully utilized until a person or process locates the data in the document text, extracts it, and structures it with respect to an ontology or database schema. Yet, in the family history industry and other industries, data in lists goes largely unused because no known approach adequately addresses all of the costs, challenges, …

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Arimaa: Developing A Higher Ranked Fall Back Move Generator Using A Relational Database, Patrick Mckee Sep 2014

Arimaa: Developing A Higher Ranked Fall Back Move Generator Using A Relational Database, Patrick Mckee

Theses and Dissertations

Our approach to playing the game of Arimaa understands that the game was created to showcase the limits of brute force computing power. Using a relational database, we will be able to view similar situations that have already been played out, inventory a number of suitable reactions and make the best move given a number of attributes. This results in us making a decision that can theoretically result in a win, and hopefully will. Measurable positive results have been procured specifically from the area of concentration component of the research. In the area of concentration component we target a specific …

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Measuring Human Workload In Unmanned Aerial Vehicles, Timothy J. Gledhill Sep 2014

Measuring Human Workload In Unmanned Aerial Vehicles, Timothy J. Gledhill

Theses and Dissertations

Unmanned aerial systems (UASs) often require multiple human operators fulfilling diverse roles for safe and correct operation. Reliably designing the human interaction, autonomy, and decision making aspects of these systems requires the use of modeling. We propose a conceptual model that models human machine interaction systems as a group of actors connected by a network of communication channels. We present a simulation framework implemented in Java, with an optional XML model parser that can be analyzed using the Java Pathfinder (JPF) model checker. We propose two human workload metrics based on a taxonomy extracted from the relevant literature. Using the …

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Intelligent Indexing: A Semi-Automated, Trainable System For Field Labeling, Robert T. Clawson Sep 2014

Intelligent Indexing: A Semi-Automated, Trainable System For Field Labeling, Robert T. Clawson

Theses and Dissertations

We present Intelligent Indexing: a general, scalable, collaborative approach to indexing and transcription of non-machine-readable documents that exploits visual consensus and group labeling while harnessing human recognition and domain expertise. In our system, indexers work directly on the page, and with minimal context switching can navigate the page, enter labels, and interact with the recognition engine. Interaction with the recognition engine occurs through preview windows that allow the indexer to quickly verify and correct recommendations. This interaction is far superior to conventional, tedious, inefficient post-correction and editing. Intelligent Indexing is a trainable system that improves over time and can provide …

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A Method To Develop Neck Injury Criteria To Aid Design And Test Of Escape Systems Incorporating Helmet Mounted Displays, Jeffrey C. Parr Sep 2014

A Method To Develop Neck Injury Criteria To Aid Design And Test Of Escape Systems Incorporating Helmet Mounted Displays, Jeffrey C. Parr

Theses and Dissertations

HMDs are becoming common human-machine interface equipment in manned military flight, but introducing this equipment into the overall aircraft escape system poses new and significant system design, development, and test concerns. Although HMDs add capabilities, which improve operator performance, the increased capability is often accompanied by increased head supported mass. The increased mass can amplify the risk of pilot neck injury during ejection when compared to lighter legacy helmets. Currently no adequate USAF neck injury criteria exist to effectively guide the requirements, design, and test of escape systems for pilots with HMDs. This research effort presents a novel method to …

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Browser-Based Manual Encryption, Yuanzheng Song Aug 2014

Browser-Based Manual Encryption, Yuanzheng Song

Theses and Dissertations

Billions of web-based email and chat messages are sent over the Internet every day. However, very few service providers support end-to-end privacy protection. While providing security for these messages is technically feasible, usability remains a challenge in this field. Recent research attempts to hide security details like key management and encryption in order to make the system more usable. However usability studies demonstrated that hiding these details may confuse the user and contribute to mistakes (e.g., sending out an email in plaintext when the user thought it would be encrypted). In an effort to increase trust and eliminate mistakes, this …

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An Adaptive Educational Game To Help Students Learn How To Solve Systems Of Linear Equations, Wang Zhang Aug 2014

An Adaptive Educational Game To Help Students Learn How To Solve Systems Of Linear Equations, Wang Zhang

Theses and Dissertations

Educational games have been proven to be effective in developing problem solving skills in well-defined domain, such as Math and Physics. In this thesis, an educational game called Matrix was developed to foster problem solving skills in the domain of linear algebra, particularly solving a system of linear equations. Matrix is an adaptive educational game that uses intelligent tutoring modules to guide the student's learning process and provide feedback based on the student's performance. These modules are domain module, student module, pedagogical module and presentation module. The domain module contains all the concepts the student needs to learn and an …

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Communicating Affective Meaning From Software To Wetware Through The Medium Of Digital Art, R David Norton Aug 2014

Communicating Affective Meaning From Software To Wetware Through The Medium Of Digital Art, R David Norton

Theses and Dissertations

Computational creativity is a new and developing field of artificial intelligence concerned with computational systems that either autonomously produce original and functional products, or that augment the ability of humans to do so. As the role of computers in our daily lives is continuing to expand, the need for such systems is becoming increasingly important. We introduce and document the development of a new “creative” system, called DARCI (Digital ARtist Communicating Intention), that is designed to autonomously create novel artistic images that convey linguistic concepts to the viewer. Within the scope of this work, the system becomes capable of creating …

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Using A Model Of Temporal Latency To Improve Supervisory Control Of Human-Robot Teams, Kyle Lee Blatter Jul 2014

Using A Model Of Temporal Latency To Improve Supervisory Control Of Human-Robot Teams, Kyle Lee Blatter

Theses and Dissertations

When humans and remote robots work together on a team, the robots always interact with a human supervisor, even if the interaction is limited to occasional reports. Distracting a human with robotic interactions doesn't pose a problem so long as the inclusion of robots increases the team's overall effectiveness. Unfortunately, increasing the supervisor's cognitive load may decrease the team's sustainable performance to the point where robotic agents are more a liability than an asset. Present approaches resolve this problem with adaptive autonomy, where a robot changes its level of autonomy based on the supervisor's cognitive load. This thesis proposes to …

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Nderlidhja Mes Rrjetit Fiks Dhe Rrjetit Mobil, Saranda Xhokli Jul 2014

Nderlidhja Mes Rrjetit Fiks Dhe Rrjetit Mobil, Saranda Xhokli

Theses and Dissertations

Qëllimi i punimit tim është paraqitja e ndërlidhjes të rrjetit fiks dhe rrjetit mobil të telekomit të Kosovës, teknologji të cilat bashkjetojnë për mëse 5 vite dhe I japin shërbime abonentëve, duke përfshirë organizimit të shtyllës kurrizore të rrjetit transmetues të Kosovës i cili zhvillohet nëpërmjet kabllit optik, sistemti transmetues PDH/SDH në skaje të të cilave janë të lidhura paisjet komutuese të paketëve IP të quajtura SOFT SWICH i cili është i vendosur në qendër dhe paraqet boshtin kurrizor të telekomit si dhe nderlidhjen me rrjetin e telefonisë mobile GSM 2.75 dhe në parim paraqet shpirtin komunikues i ndërlidhur në …

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Slice—N—Dice Algorithm Implementation In Jpf, Eric S. Noonan Jul 2014

Slice—N—Dice Algorithm Implementation In Jpf, Eric S. Noonan

Theses and Dissertations

This work deals with evaluating the effectiveness of a new verification algorithm called slice--n--dice. In order to evaluate the effectiveness of slice--n--dice, a vector clock POR was implemented to compare it against. The first paper contained in this work was published in ACM SIGSOFT Software Engineering Notes and discusses the implementation of the vector clock POR. The results of this paper show the vector clock POR performing better than the POR in Java Pathfinder by at least a factor of two. The second paper discusses the implementation of slice--n--dice and compares it against other verification techniques. The results show that …

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Autocompletion Without Static Typing, Nicholas Mckay Shelley Jun 2014

Autocompletion Without Static Typing, Nicholas Mckay Shelley

Theses and Dissertations

Code completion systems act both as a way to decrease typing and as a way to easily access documentation, both implicit and explicit. The former is typically done by completing known variable or function names, while the latter is done by providing a list of possible completions or by providing convenient views of or access to documentation. Because static type information makes these goals possible and feasible for qualifying languages, many improvements to completion systems are focused on improving the order of results or trimming less-valuable results. It follows that almost all validation techniques for this work have focused on …

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Improved Computer-Generated Simulation Using Motion Capture Data, Seth A. Brunner Jun 2014

Improved Computer-Generated Simulation Using Motion Capture Data, Seth A. Brunner

Theses and Dissertations

Ever since the first use of crowds in films and videogames there has been an interest in larger, more efficient and more realistic simulations of crowds. Most crowd simulation algorithms are able to satisfy the viewer from a distance but when inspected from close up the flaws in the individual agent's movements become noticeable. One of the bigger challenges faced in crowd simulation is finding a solution that models the actual movement of an individual in a crowd. This paper simulates a more realistic crowd by using individual motion capture data as well as traditional crowd control techniques to reach …

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Towards An Automated System For Evaluation Of Visualizations, Douglas Taggart Jun 2014

Towards An Automated System For Evaluation Of Visualizations, Douglas Taggart

Theses and Dissertations

The Information Visualization field focuses on the visualization of abstract data, and with the growing interest in big data analysis, the need for analyzing complex datasets is nowadays highly relevant. With the growing amount and diversity of these datasets new and exciting ways to visualize them are being developed. However, being able to thoroughly test and evaluate the effectiveness of these new visualization techniques is an arduous manual process. Moreover, different researchers hold different opinions on how to thoroughly evaluate a new visualization method. A step towards automating the process of evaluation of visualizations, called the Framework for the Evaluation …

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Necessary And Sufficient Conditions For State-Space Network Realization, Philip E. Paré Jr. Jun 2014

Necessary And Sufficient Conditions For State-Space Network Realization, Philip E. Paré Jr.

Theses and Dissertations

This thesis presents the formulation and solution of a new problem in systems and control theory, called the Network Realization Problem. Its relationship to other problems, such as State Realization and Structural Identifiability, is shown. The motivation for this work is the desire to completely quantify the conditions for transitioning between different mathematical representations of linear time-invariant systems. The solution to this problem is useful for theorists because it lays a foundation for quantifying the information cost of identifying a system's complete network structure from the transfer function.

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Trustworthy, Useful Languages For Probabilistic Modeling And Inference, Neil B. Toronto Jun 2014

Trustworthy, Useful Languages For Probabilistic Modeling And Inference, Neil B. Toronto

Theses and Dissertations

The ideals of exact modeling, and of putting off approximations as long as possible, make Bayesian practice both successful and difficult. Languages for modeling probabilistic processes, whose implementations answer questions about them under asserted conditions, promise to ease much of the difficulty. Unfortunately, very few of these languages have mathematical specifications. This makes them difficult to trust: there is no way to distinguish between an implementation error and a feature, and there is no standard by which to prove optimizations correct. Further, because the languages are based on the incomplete theories of probability typically used in Bayesian practice, they place …

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Application Sharing From Mobile Devices With A Collaborative Shared Display, Richard S. Shurtz Jun 2014

Application Sharing From Mobile Devices With A Collaborative Shared Display, Richard S. Shurtz

Theses and Dissertations

With the increasing ubiquity of smartphones, tablets, and large pixel-rich displays, there are many exciting new possibilities for using these devices for collaborative work. While there already exist hardware and software that support communication and interaction between mobile devices and shared displays, application sharing in these scenarios is still limited and inflexible. We present a new method of application sharing which allows collaborators to download clips or snapshots of each other's applications. These snapshots can be used to re-launch and resume the shared application back to the state it was in when it was shared. We have built a system …

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Musical Motif Discovery In Non-Musical Media, Daniel S. Johnson Jun 2014

Musical Motif Discovery In Non-Musical Media, Daniel S. Johnson

Theses and Dissertations

Many music composition algorithms attempt to compose music in a particular style. The resulting music is often impressive and indistinguishable from the style of the training data, but it tends to lack significant innovation. In an effort to increase innovation in the selection of pitches and rhythms, we present a system that discovers musical motifs by coupling machine learning techniques with an inspirational component. The inspirational component allows for the discovery of musical motifs that are unlikely to be produced by a generative model, while the machine learning component harnesses innovation. Candidate motifs are extracted from non-musical media such as …

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Toward Automating Web Protocol Configuration For A Programmable Logic Controller Emulator, Deanna R. Fink Jun 2014

Toward Automating Web Protocol Configuration For A Programmable Logic Controller Emulator, Deanna R. Fink

Theses and Dissertations

Industrial Control Systems (ICS) remain vulnerable through attack vectors that exist within programmable logic controllers (PLC). PLC emulators used as honeypots can provide insight into these vulnerabilities. Honeypots can sometimes deter attackers from real devices and log activity. A variety of PLC emulators exist, but require manual figuration to change their PLC pro le. This limits their flexibility for deployment. An automated process for configuring PLC emulators can open the door for emulation of many types of PLCs. This study investigates the feasibility of creating such a process. The research creates an automated process for figuring the web protocols of …

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