Physical Sciences and Mathematics Commons^™

Multivariate Models And Algorithms For Systems Biology, Lipi Rani Acharya

University of New Orleans Theses and Dissertations

Rapid advances in high-throughput data acquisition technologies, such as microarraysand next-generation sequencing, have enabled the scientists to interrogate the expression levels of tens of thousands of genes simultaneously. However, challenges remain in developingeffective computational methods for analyzing data generated from such platforms. In thisdissertation, we address some of these challenges. We divide our work into two parts. Inthe first part, we present a suite of multivariate approaches for a reliable discovery of geneclusters, often interpreted as pathway components, from molecular profiling data with replicated measurements. We translate our goal into learning an optimal correlation structure from replicated complete and incomplete …

Android Memory Capture And Applications For Security And Privacy, Joseph T. Sylve

University of New Orleans Theses and Dissertations

The Android operating system is quickly becoming the most popular platform for mobiledevices. As Android’s use increases, so does the need for both forensic and privacy toolsdesigned for the platform. This thesis presents the first methodology and toolset for acquiringfull physical memory images from Android devices, a proposed methodology for forensicallysecuring both volatile and non-volatile storage, and details of a vulnerability discovered by theauthor that allows the bypass of the Android security model and enables applications to acquirearbitrary permissions.

The Vulnerability Assessment And Penetration Testing Of Two Networks, Steven L. Simpson

Regis University Student Publications (comprehensive collection)

Vulnerability assessments and penetration testing are two approaches available for use by internet security practitioners to determine the security posture of information networks. By assessing network vulnerabilities and attempting to exploit found vulnerabilities through penetration testing security professionals are able to evaluate the effectiveness of their network defenses by identifying defense weaknesses, affirming the defense mechanisms in place, or some combination of the two. This project is a discussion of the methods and tools used during the vulnerability assessment and penetration testing, and the respective test results of two varied and unique networks. The assessment and testing of the first …

A General Model For Continuous Noninvasive Pulmonary Artery Pressure Estimation, Robert Anthony Smith

Theses and Dissertations

Elevated pulmonary artery pressure (PAP) is a significant healthcare risk. Continuous monitoring for patients with elevated PAP is crucial for effective treatment, yet the most accurate method is invasive and expensive, and cannot be performed repeatedly. Noninvasive methods exist but are inaccurate, expensive, and cannot be used for continuous monitoring. We present a machine learning model based on heart sounds that estimates pulmonary artery pressure with enough accuracy to exclude an invasive diagnostic operation, allowing for consistent monitoring of heart condition in suspect patients without the cost and risk of invasive monitoring. We conduct a greedy search through 38 possible …

Multiple Biolgical Sequence Alignment: Scoring Functions, Algorithms, And Evaluations, Ken D. Nguyen

Computer Science Dissertations

Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. These alignments may contain invaluable information that scientists need to predict the sequences' structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-Complete. In addition, the lack of a reliable scoring method makes it very hard to align the sequences reliably and to evaluate the alignment outcomes.

In this dissertation, we have designed a new scoring method for use in multiple sequence alignment. Our scoring method …

Syntactic And Semantic Analysis And Visualization Of Unstructured English Texts, Saurav Karmakar

Computer Science Dissertations

People have complex thoughts, and they often express their thoughts with complex sentences using natural languages. This complexity may facilitate efficient communications among the audience with the same knowledge base. But on the other hand, for a different or new audience this composition becomes cumbersome to understand and analyze. Analysis of such compositions using syntactic or semantic measures is a challenging job and defines the base step for natural language processing.

In this dissertation I explore and propose a number of new techniques to analyze and visualize the syntactic and semantic patterns of unstructured English texts.

The syntactic analysis is …

Framework To Secure Cloud-Based Medical Image Storage And Management System Communications, Timothy James Rostrom

Theses and Dissertations

Picture Archiving and Communication Systems (PACS) have been traditionally constrained to the premises of the healthcare provider. This has limited the availability of these systems in many parts of the world and mandated major costs in infrastructure for those who employ them. Public cloud services could be a solution that eases the cost of ownership and provides greater flexibility for PACS implementations. This could make it possible to bring medical imaging services to places where it was previously unavailable and reduce the costs associated with these services for those who utilize them. Moving these systems to public cloud infrastructure requires …

A Hierarchical Image Processing Approach For Diagnostic Analysis Of Microcirculation Videos, Nazanin Mirshahi

Theses and Dissertations

Knowledge of the microcirculatory system has added significant value to the analysis of tissue oxygenation and perfusion. While developments in videomicroscopy technology have enabled medical researchers and physicians to observe the microvascular system, the available software tools are limited in their capabilities to determine quantitative features of microcirculation, either automatically or accurately. In particular, microvessel density has been a critical diagnostic measure in evaluating disease progression and a prognostic indicator in various clinical conditions. As a result, automated analysis of the microcirculatory system can be substantially beneficial in various real-time and off-line therapeutic medical applications, such as optimization of resuscitation. …

Quality Selection For Dynamic Adaptive Streaming Over Http With Scalable Video Coding, Travis L. Andelin

Theses and Dissertations

Video streaming on the Internet is increasingly using Dynamic Adaptive Streaming over HTTP (DASH), in which the video is converted into various quality levels and divided into two-second segments. A client can then adjust its video quality over time by choosing to download the appropriate quality level for a given segment using standard HTTP. Scalable Video Coding (SVC) is a promising enhancement to the DASH protocol. With SVC, segments are divided into subset bitstream blocks. At playback, blocks received for a given segment are combined to additively increase the current quality. Unlike traditional DASH, which downloads segments serially, this encoding …

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 …

A Scalable Architecture For Simplifying Full-Range Scientific Data Analysis, Wesley James Kendall

Doctoral Dissertations

According to a recent exascale roadmap report, analysis will be the limiting factor in gaining insight from exascale data. Analysis problems that must operate on the full range of a dataset are among the most difficult. Some of the primary challenges in this regard come from disk access, data managment, and programmability of analysis tasks on exascale architectures. In this dissertation, I have provided an architectural approach that simplifies and scales data analysis on supercomputing architectures while masking parallel intricacies to the user. My architecture has three primary general contributions: 1) a novel design pattern and implmentation for reading multi-file …

Energy Functional For Nuclear Masses, Michael Giovanni Bertolli

Doctoral Dissertations

An energy functional is formulated for mass calculations of nuclei across the nuclear chart with major-shell occupations as the relevant degrees of freedom. The functional is based on Hohenberg-Kohn theory. Motivation for its form comes from both phenomenology and relevant microscopic systems, such as the three-level Lipkin Model. A global fit of the 17-parameter functional to nuclear masses yields a root- mean-square deviation of χ[chi] = 1.31 MeV, on the order of other mass models. The construction of the energy functional includes the development of a systematic method for selecting and testing possible functional terms. Nuclear radii are computed within …

Quantification Of Stochastic Uncertainty Propagation For Monte Carlo Depletion Methods In Reactor Analysis, Quentin Thomas Newell

UNLV Theses, Dissertations, Professional Papers, and Capstones

The Monte Carlo method provides powerful geometric modeling capabilities for large problem domains in 3-D; therefore, the Monte Carlo method is becoming popular for 3-D fuel depletion analyses to compute quantities of interest in spent nuclear fuel including isotopic compositions. The Monte Carlo approach has not been fully embraced due to unresolved issues concerning the effect of Monte Carlo uncertainties on the predicted results.

Use of the Monte Carlo method to solve the neutron transport equation introduces stochastic uncertainty in the computed fluxes. These fluxes are used to collapse cross sections, estimate power distributions, and deplete the fuel within depletion …

A Distributed Approach For Fault Mitigation In Large Scale Distributed Systems, Mina Jung

Electrical Engineering and Computer Science - Dissertations

In a large scale real-time distributed system, a large number of components and the time criticality of tasks can contribute to complex situations. Providing predictable and reliable service is a paramount interest in such a system. For example, a single point failure in an electric grid system may lead to a widespread power outage like the Northeast Blackout of 2003. System design and implementation address fault avoidance and mitigation. However, not all faults and failures can be removed during these phases, and therefore run-time fault avoidance and mitigation are needed during the operation. Timing constraints and predictability of the system …

Report On Advances In The Field Of Artificial Intelligence Attributed To Captcha, Craig M. Schow

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

A CAPTCHA is a specialized human interaction proof that exploits gaps between human and computer recognition abilities. By design, the hardness of a CAPTCHA is based on the difficulty of advancing the underlying artificial intelligence [AI] technology to a level that eliminates any exploitable gap. Due to this fact computer scientists have concluded that the widespread use of CAPTCHA would accelerate research in the underlying fields of AI eventually leading to near-­‐human capabilities in certain AI systems. Despite these predictions no attempt has been made to identify advances in AI which can be attributed to the use of CAPTCHA.

The …

Enhancing Inettest By Improving The Programming Question And Group Grading, Sushil Dosi

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

This report describes an improvement to the Utah State University iNetTest testing system. The iNetTest system allows instructors and/or students to: • Create/take tests with rich sets of question types (multiple choice, essay, true/false, computational programming question, etc.); • Monitor the test takers for cheating; • Auto-grade for many types of questions, as well as group grade for all question types; and • Send scores to students via either email or SMS. Specifically, this report discusses the design and development of an improved computational programming question for the iNetTest system. For programming questions, iNetTest allows for the use of various …

Mechanical And Modular Verification Condition Generation For Object-Based Software, Heather Harton

All Dissertations

The foundational goal of this work is the development of mechanizable proof rules and a verification condition generator based on those rules for modern software. The verification system will be modular so that it is possible to verify the implementation of a component relying upon only the specifications of underlying components that are reused. The system must enable full behavioral verification. The proof rules used to generate verification conditions (VCs) of correctness must be amenable to automation. While automation requires software developers to annotate implementations with assertions, it should not require assistance in the proofs. This research has led to …

The Design & Implementation Of An Abstract Semantic Graph For Statement-Level Dynamic Analysis Of C++ Applications, Edward Duffy

All Dissertations

In this thesis, we describe our system, Hylian, for statement-level analysis,
both static and dynamic, of a C++ application. We begin by extending the
GNU gcc parser to generate parse trees in XML format for each of the
compilation units in a C++ application. We then provide verification that the
generated parse trees are structurally equivalent to the code in the
original C++
application. We use the generated parse trees, together with an augmented
version of the gcc test suite, to recover a grammar for the C++ dialect that
we parse. We use the recovered grammar to generate a schema …

A Web-Integrated Environment For Component-Based Software Reasoning, Charles Cook

All Theses

This thesis presents the Web IDE, a web-integrated environment for component-based software reasoning. The Web IDE is specifically tailored to emphasize the relationships among various components in component-based software engineering (CBSE) and to facilitate reasoning. It allows students to use RESOLVE, a component-based, integrated specification and programming language, to build components and systems, providing real-time feedback that can be used to reason about the correctness of their component implementations. Real-time interaction and relationship focused component presentation reinforces CBSE and reasoning principles in a way not possible with traditional programming exercises and file management systems.
The Web IDE has gone through …

Data-Intensive Computing For Bioinformatics Using Virtualization Technologies And Hpc Infrastructures, Pengfei Xuan

All Theses

The bioinformatics applications often involve many computational components and massive data sets, which are very difficult to be deployed on a single computing machine. In this thesis, we designed a data-intensive computing platform for bioinformatics applications using virtualization technologies and high performance computing (HPC) infrastructures with the concept of multi-tier architecture, which can seamlessly integrate the web user interface (presentation tier), scientific workflow (logic tier) and computing infrastructure (data/computing tier). We demonstrated our platform on two bioinformatics projects. First, we redesigned and deployed the cotton marker database (CMD) (http://www.cottonmarker.org), a centralized web portal in the cotton research community, using the …

Object Recognition Based On Shape And Function, Akihiro Eguchi

Computer Science and Computer Engineering Undergraduate Honors Theses

This thesis explores a new approach to computational object recognition by borrowing an idea from child language acquisition studies in developmental psychology. Whereas previous image recognition research used shape to recognize and label a target object, the model proposed in this thesis also uses the function of the object resulting in a more accurate recognition. This thesis makes use of new gaming technology, Microsoft’s Kinect, in implementing the proposed new object recognition model. A demonstration of the model developed in this project properly infers different names for similarly shaped objects and the same name for differently shaped objects.

Defining, Executing And Visualizing Representative Workflows In A Retail Domain, May Zeineldin

Graduate Theses and Dissertations

Our lives are filled with routine activities that we do more or less on auto-pilot such as driving to work and cooking. This thesis explores a workflow representation as a way to represent such activities of daily living. The domain of a retail store environment is used. Workflows are initially expressed in a structured English representation, then translated into a Petri net notation and implemented in mix of Petri nets, Lua, and C so that the resulting workflows can be displayed as the actions of collections of avatarbots (avatars controlled by programs) in a 3D virtual world, Second Life. One …

Webtailor: Internet Service For Salient And Automatic User Interest Profiles, John Anderson

Computer Science and Computer Engineering Undergraduate Honors Theses

Website personalization systems seek to give users unique, tailored content and experiences on the Internet. A key feature of these systems is a user profile that represents each user in a way that distinguishes them from others. In current personalization systems, the data used to create these profiles is extremely limited, which leads to a host of problems and ineffectual personalization. The main goal of this thesis is to improve these personalization systems by addressing their lack of data and its poor quality, breadth, and depth. This is accomplished by analyzing and classifying the content of each user's Internet browsing …

Continuous Analysis Of Photocatalytic Activity In Thin-Films And Coatings, Steven Michael Allee

Master's Theses

Materials that undergo photocatalytic reactions create evolved gases due to ultraviolet light decomposition. Current methods of measuring these gases typically result in destruction of the sample. A test fixture was developed to measure evolved gases in a nondestructive manner through the utilization of a flow-through sensor array system. Preliminary testing indicates responsive measurements down to parts-per-billion sensitivity for some gases and will be compared with mass spectrometry measurements. Further development of this process could lead to the ability to measure photocatalytic reaction gases on a continuous basis without interruption of the process or destruction of materials introduced to the system.

Rigging And Texturing Considerations For The Short Film Spider Fight, Casey Johnson

All Theses

This paper delves into two separate production areas of the short film, Spider Fight: the approach used to solve the problem of rigging eyelids for 3d characters, and the pipelines that were implemented for texturing 3d assets. Typically, problems exist in the rigging of eyelids for 3d characters. Productions rely on a series of blend shapes, or a combination of joints and blend shapes, to produce satisfactory eyelid movement. Spider Fight, however, used a series of curves and joints to control the movement of the eyelids, which allowed a high degree of control over eyelid movement, and also fast editing …

Network Covert Channels On The Android Platform, Wade Chester Gasior

Masters Theses and Doctoral Dissertations

Network covert channels are used to exfiltrate information from a secured environment in a way that is extremely difficult to detect or prevent. These secret channels have been identified as an important security threat to governments and the private sector, and several research efforts have focused on the design, detection, and prevention of such channels in enterprise-type environments. Mobile devices have become a ubiquitous computing platform, and are storing or have access to an increasingly large amount of sensitive information. As such, these devices have become prime targets of attackers who desire access to this information. In this work, we …

Pedestrian Leadership And Egress Assistance Simulation Environment (Please), Kyle D. Feuz

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Pedestrian simulation models are used in many different applications including, the design of safer buildings, the validation of fire codes, and automatic video surveillance and tracking. By improving the simulation model used, each of the application areas can experience similar improvements in accuracy. Current simulation models fail to address key concerns in representing pedestrian knowledge and in accurately modeling group formation. This project has at its core the goal of bringing attention these areas of concern and providing an initial look at ways to solve these problems.

The Pedestrian Leadership and Egress Assistance Simulation Environment (PLEASE) is developed specifically to …

Making An Impact On The Obesity Epidemic By Deploying A Mobile Fitness Suite On The Android Market, Chad Richards

Computer Science and Computer Engineering Undergraduate Honors Theses

The Mobile Fitness Suite aims to make an impact on the obesity epidemic by deploying a set of mobile fitness applications on the Android Market. The thesis details the health and financial issues with the obesity epidemic, along with its causes, and how a set of fitness applications can aid with the obesity epidemic. It also explains the reasons for releasing the program on the Android Market and details each step in the process of deploying a mobile application to the Android Market. Further, it discusses the design and architecture that went into the development of the Mobile Fitness Suite …

High Performance Geospatial Analysis On Emerging Parallel Architectures, Seth Warn

Graduate Theses and Dissertations

Geographic information systems (GIS) are performing increasingly sophisticated analyses on growing data sets. These analyses demand high performance. At the same time, modern computing platforms increasingly derive their performance from several forms of parallelism. This dissertation explores the available parallelism in several GIS-applied algorithms: viewshed calculation, image feature transform, and feature analysis. It presents implementations of these algorithms that exploit parallel processing to reduce execution time, and analyzes the effectiveness of the implementations in their use of parallel processing.