Computer Sciences Commons^™

Evaluation Of Microarray-Based Dna Methylation Measurement Using Technical Replicates: The Atherosclerosis Risk In Communities (Aric) Study, Maitreyee Bose, Chong Wu, James S. Pankow, Ellen W. Demerath, Jan Bressler, Myriam Fornage, Megan L. Grove, Thomas H. Mosley, Chindo Hicks, Kari North, Wen Hong Kao, Yu Zhang, Eric Boerwinkle, Weihua Guan

Computer Science Faculty Publications

Background: DNA methylation is a widely studied epigenetic phenomenon; alterations in methylation patterns influence human phenotypes and risk of disease. As part of the Atherosclerosis Risk in Communities (ARIC) study, the Illumina Infinium HumanMethylation450 (HM450) BeadChip was used to measure DNA methylation in peripheral blood obtained from ~3000 African American study participants. Over 480,000 cytosine-guanine (CpG) dinucleotide sites were surveyed on the HM450 BeadChip. To evaluate the impact of technical variation, 265 technical replicates from 130 participants were included in the study.

Results: For each CpG site, we calculated the intraclass correlation coefficient (ICC) to compare variation of methylation levels …

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 …

Quantification Of Information Flow In A Smart Grid, Li Feng, Bruce Mcmillin

Computer Science Faculty Research & Creative Works

The key to computer security is the notion of information flow. Information flow occurs either explicitly or implicitly in a system. In cyber-physical systems (CPSs), complicated interactions occur frequently between computational components and physical components. Thus, detecting and quantifying information flow in these systems is more difficult than it is in purely cyber systems. In CPSs, failures and attacks are either from the physical infrastructure, or from cyber part of data management and communication protocol, or a combination of both. As the physical infrastructure is inherently observable, aggregated physical observations can lead to unintended cyber information leakage. The computational portion …

On The Approximability Of The Exemplar Adjacency Number Problem For Genomes With Gene Repetitions, Zhinxiag Chen, Bin Fu, Randy Goebel, Guohui Lin, Weitian Tong, Jinhui Xu, Boting Yang, Zhiyu Zhao, Binhai Zhu

Computer Science Faculty Publications

In this paper, we apply a measure, exemplar adjacency number, which complements and extends the well-studied breakpoint distance between two permutations, to measure the similarity between two genomes (or in general, between any two sequences drawn from the same alphabet). For two genomes and drawn from the same set of n gene families and containing gene repetitions, we consider the corresponding Exemplar Adjacency Number problem (EAN), in which we delete duplicated genes from and such that the resultant exemplar genomes (permutations) G and H have the maximum adjacency number. We obtain the following results. First, we prove that the one-sided …

High Performance Computing Markov Models Using Hadoop Mapreduce, Matthew Shaffer

e-Research: A Journal of Undergraduate Work

In this paper, I will explain how I used the probability modeling tool, Markov Models, in combination with Hadoop MapReduce parallel programming platform in order to quickly and efficiently analyses documents and create a probability model of them. I will explain what Markov Models are, give a brief overview of what MapReduce is, explain why Markov models can be used for document analysis, explain my code of the modeling program, and examine the performance of various MapReduce platforms and techniques in analyzing documents.

Assistive Technologies Used By Students With Asperger’S Syndrome To Improve Performance In The General Education Classroom, Sara (Beth) Cardwell Foreman

CCAC Theses and Dissertations

The No Child Left Behind Act requires all students; regardless of poverty level, learning disability, limited English proficiency, or racial/ethnic origins; to be in general education classrooms meeting high standards of proficiency in reading/language arts and mathematics by 2013-14. Meeting high standards of proficiency in a general education classroom is particularly challenging for students diagnosed with pervasive developmental disorders, such as Asperger's syndrome. Limited interests, inflexible language, and social skills deficits without a history of cognitive or language delays before the age of three characterize the disorder. Other symptoms, such as clumsiness, unusual sensory reactions, and talk in unusual ways …

Analysis And Acceleration Of Ntru Lattice-Based Cryptographic System, Tianyu Bai

Student Theses and Dissertations

Lattice based cryptography is attractive for its quantum computing resistance and efficient encryption/decryption process. . However, the big data problem has perplexed lattice based cryptographic systems with the slow processing speed. This paper intends to analyze one of the major lattice-based cryptographic systems, Nth-degree truncated polynomial ring (NTRU), and accelerate its execution with Graphic Processing Unit (GPU) for acceptable processing performance. Three strategies, including single GPU with zero copy, single GPU with data transfer, and multi-GPU versions are proposed. GPU computing techniques such as stream and zero copy are applied to overlap the computation and communication for possible speedup. Experimental …

Computational Methods For Historical Research On Wikipedia’S Archives, Jonathan Cohen

e-Research: A Journal of Undergraduate Work

This paper presents a novel study of geographic information implicit in the English Wikipedia archive. This project demonstrates a method to extract data from the archive with data mining, map the global distribution of Wikipedia editors through geocoding in GIS, and proceed with a spatial analysis of Wikipedia use in metropolitan cities.

"Archive What I See Now" Bringing Institutional Web Archiving Tools To The Individual Researcher, Michele C. Weigle, Michael L. Nelson, Liza Potts

Computer Science Presentations

PDF of a powerpoint presentation from the 2014 National Endowment for the Humanities (NEH) Office of Digital Humanities (ODH) Project Directors' Meeting in Washington D. C., September 15, 2014. Also available form Slideshare.

Efficient Caching And Incrementalization Of Object Queries On Collections In Programming Codes, Venkata Krishna Suhas Nerella, Sanjay Madria, Thomas Weigert

Computer Science Faculty Research & Creative Works

Object oriented programming languages raised the level of abstraction by incorporating first class query constructs explicitly into program codes. These query constructs allow programmers to express operations over collections as object queries. They also provide optimal query execution, utilizing query optimization strategies from the database domain. However, when a query is repeated in the program, it is executed as a new query. Existing approaches, however, such as Java Query Language (JQL), which caches such query constructs on collections have high run time overhead. Therefore, this paper presents an approach to reduce the run time execution of programs involving explicit queries …

Visualization And Manipulation Of Stereophonic Audio Signals By Means Of Iid And Ipd, Giorgio Presti, Goffredo Haus, Davide Andrea Mauro

Computer Sciences and Electrical Engineering Faculty Research

In this paper we will discuss a model aimed at improving the spectral data representation of stereophonic audio in a way that allows efficient stereophonic data visualization and linear manipulation of arbitrary parts of the stereo image. The stereo pair is here interpreted as a single spectrum with additional dimensions, expressing the Interaural Intensity Difference (IID) and Interaural Phase Difference (IPD) for each FFT bin. These dimensions are evaluated assuming that the stereo signal is an instantaneous mixture with a residual amount of convolutive phenomena. Even if this assumption is not generally true for the majority of music signals it …

A Keyword Sense Disambiguation Based Approach For Noise Filtering In Twitter, Sanjaya Wijeratne, Bahareh R. Heravi

Kno.e.sis Publications

In this paper, we describe an approach to filter out noisy data generated by keywords-based tweet filtering methods by performing Word Sense Disambiguation on those keywords used to collect tweets. We present the noise filtering problem as a binary classification problem and discuss our evaluation strategy which is to be carried out in future.

An Investigation Of The Key Factors That Affect The Adoption Of Smartphones In Global Midmarket Professional Service Firms, Mark S. Kocour

CCAC Theses and Dissertations

The evolution and proliferation of mobile devices (m-devices) in the workplace have been rapid. In comparison to conventional services provided by mobile phones (m-phones), smartphones feature sophisticated functionality, such as Internet access, video/audio streaming, and business productivity applications. As a consequence of increased demand for smartphones in the workplace, an understanding of the factors that determine the decision to adopt smartphones in business settings is necessary. The goal of this investigation was to identify the key factors that have an impact on the adoption of smartphones.

This dissertation investigation provided an understanding of the key factors that affect the adoption …

We Can Hear You With Wifi!, Guanhua Wang, Yongpan Zou, Zimu Zhou, Kaishun Wu, Lionel M. Ni

Research Collection School Of Computing and Information Systems

Recent literature advances Wi-Fi signals to “see” people’s motions and locations. This paper asks the following question: Can Wi-Fi “hear” our talks? We present WiHear, which enables Wi-Fi signals to “hear” our talks without deploying any devices. To achieve this, WiHear needs to detect and analyze fine-grained radio reflections from mouth movements. WiHear solves this micro-movement detection problem by introducing Mouth Motion Profile that leverages partial multipath effects and wavelet packet transformation. Since Wi-Fi signals do not require line-of-sight, WiHear can “hear” people talks within the radio range. Further, WiHear can simultaneously “hear” multiple people’s talks leveraging MIMO technology. We …

Piecing The Puzzle Together: A Revisit To Transcript Reconstruction Problem In Rna-Seq, Yan Huang, Yin Hu, Jinze Liu

Computer Science Faculty Publications

The advancement of RNA sequencing (RNA-seq) has provided an unprecedented opportunity to assess both the diversity and quantity of transcript isoforms in an mRNA transcriptome. In this paper, we revisit the computational problem of transcript reconstruction and quantification. Unlike existing methods which focus on how to explain the exons and splice variants detected by the reads with a set of isoforms, we aim at reconstructing transcripts by piecing the reads into individual effective transcript copies. Simultaneously, the quantity of each isoform is explicitly measured by the number of assembled effective copies, instead of estimated solely based on the collective read …

Investigating The Determinants Of Disaster Recovery Technology Investment Choice In Small And Medium-Sized Enterprises, Faranak Afshar

CCAC Theses and Dissertations

Due to the importance of small and medium-sized enterprises (SMEs) as drivers of economic growth, it is essential to explore the security issues impacting SMEs' success and failure. One of the main security risks that could significantly impair the operability of the organizations is the permanent loss of data due to man-made and/or natural disasters and interruptions. Research has shown that SMEs are not taking disaster preparedness for their computer and networking systems as seriously as they should. This dissertation is an attempt to explain the process of a risky choice, specifically the decision maker's choice of not investing in …

Employee And Organization Security Value Alignment Through Value Sensitive Security Policy Design, Dianne Blitstein Solomon

CCAC Theses and Dissertations

Every member of the organization must be involved in proactively and consistently preventing data loss. Implementing a culture of security has proven to be a reliable method of enfranchising employees to embrace security behavior. However, it takes more than education and awareness of policies and directives to effect a culture of security. Research into organizational culture has shown that programs to promote organizational culture - and thus security behavior - are most successful when the organization's values are congruent with employee values. What has not been clear is how to integrate the security values of the organization and its employees …

Build Emotion Lexicon From Microblogs By Combining Effects Of Seed Words And Emoticons In A Heterogeneous Graph, Kaisong Song, Shi Feng, Wei Gao, Daling Wang, Ling Chen, Chengqi Zhang

Research Collection School Of Computing and Information Systems

As an indispensable resource for emotion analysis, emotion lexicons have attracted increasing attention in recent years. Most existing methods focus on capturing the single emotional effect of words rather than the emotion distributions which are helpful to model multiple complex emotions in a subjective text. Meanwhile, automatic lexicon building methods are overly dependent on seed words but neglect the effect of emoticons which are natural graphical labels of fine-grained emotion. In this paper, we propose a novel emotion lexicon building framework that leverages both seed words and emoticons simultaneously to capture emotion distributions of candidate words more accurately. Our method …

Near Optimal Event-Based Control Of Nonlinear Discrete Time Systems In Affine Form With Measured Input And Output Data, Avimanyu Sahoo, Hao Xu, S. Jagannathan

Electrical and Computer Engineering Faculty Research & Creative Works

In this paper, an event-based near optimal control of uncertain nonlinear discrete time systems is presented by using input-output data and approximate dynamic programming (ADP). The nonlinear system dynamics in affine form are transformed into an input-output form. Then, three neural networks (NN) with event sampled input-output vector are used, namely, the identifier NN to relax the knowledge of the system dynamics, a critic NN to approximate the value function which is the solution to the Hamilton-Jacobi Bellman (HJB) equation, and an actor NN to approximate the optimal control policy, in an online manner without utilizing value or policy iterations. …

Finite Horizon Stochastic Optimal Control Of Nonlinear Two-Player Zero-Sum Games Under Communication Constraint, Hao Xu, S. Jagannathan

Electrical and Computer Engineering Faculty Research & Creative Works

In this paper, the finite horizon stochastic optimal control of nonlinear two-player zero-sum games, referred to as Nonlinear Networked Control Systems (NNCS) two-player zero-sum game, between control and disturbance input players in the presence of unknown system dynamics and a communication network with delays and packet losses is addressed by using neuro dynamic programming (NDP). The overall objective being to find the optimal control input while maximizing the disturbance attenuation. First, a novel online neural network (NN) identifier is introduced to estimate the unknown control and disturbance coefficient matrices which are needed in the generation of optimal control input. Then, …

Fall 2014

In The Loop

Building on success; Creating community: Meet the dynamic women of HerCDM; CIM and Theatre School collaboration connects top talent; Alumna finds success at nexus of technology and business; School of Computing colloquiums showcase leading research; Around the college; Accolades

Fuzzy Intervals As Foundation Of Metrological Support For Computations With Inaccurate Data, Konstantin K. Semenov, Gennady N. Solopchenko, Vladik Kreinovich

Departmental Technical Reports (CS)

In this paper, we discuss the possibility of using the formalism of fuzzy intervals as a basis for computational metrology. We consider advantages of using fuzzy intervals instead of the traditional intervals as a characteristic of uncertainty of the results of computations with inaccurate data.

A Catalog Of While Loop Specification Patterns, Aditi Barua, Yoonsik Cheon

Departmental Technical Reports (CS)

This document provides a catalog of while loop patterns along with their skeletal specifications. The specifications are written in a functional form known as intended functions. The catalog can be used to derive specifications of while loops by first matching the loops to the cataloged patterns and then instantiating the skeletal specifications of the matched patterns. Once their specifications are formulated and written, the correctness of while loops can be proved rigorously or formally using the functional program verification technique in which a program is viewed as a mathematical function from one program state to another.

Rasp-Qs: Efficient And Confidential Query Services In The Cloud, Zohreh S. Alavi, Lu Zhou, James L. Powers, Keke Chen

Kno.e.sis Publications

Hosting data query services in public clouds is an attractive solution for its great scalability and significant cost savings. However, data owners also have concerns on data privacy due to the lost control of the infrastructure. This demonstration shows a prototype for efficient and confidential range/kNN query services built on top of the random space perturbation (RASP) method. The RASP approach provides a privacy guarantee practical to the setting of cloudbased computing, while enabling much faster query processing compared to the encryption-based approach. This demonstration will allow users to more intuitively understand the technical merits of the RASP approach via …

A Design Exploration On The Effectiveness Of Vocal Imitations, Stefano Delle Monache, Stefano Baldan, Davide A. Mauro

Computer Sciences and Electrical Engineering Faculty Research

Among sonic interaction design practices a rising interest is given to the use of the voice as a tool for producing fast and rough sketches. Goal of the EU project SkAT-VG (Sketching Audio Technologies using Vocalization and Gestures, 2014-2016) is to develop vocal sketching as a reference practice for sound design by (i) improving our understanding on how sounds are communicated through vocalizations and gestures, (ii) looking for physical relations between vocal sounds and sound-producing phenomena, (iii) designing tools for converting vocalizations and gestures into parametrized sound models. We present the preliminary outcomes of a vocal sketching workshop held at …

Metabolomics Characterization Of U.S. And Japanese F-15 And C-130 Flight Line Crews Exposed To Jet Fuel Volatile Organic Compounds And Aerosols, Nicholas J. Delraso, David Mattie, Asao Kobayashi, Stephen W. Mitchell, Scott Dillard, Michael L. Raymer, Isaie Sibomana, Nicholas V. Reo

Computer Science and Engineering Faculty Publications

Air and ground crews transfer a significant amount of jet fuel, and as a result of transfers, breathe its volatile emission from residues. Working on the flight line also exposes maintainers to exhaust from the jet fuel as engines are tested or run before and after flight. Since little is known concerning level of exposure and the corresponding biological response associated with human jet fuel exposure, nuclear magnetic resonance (NMR)-based metabolomics analysis of human urine was utilized for characterization of metabolite profiles of flight line personnel for potential biomarker discovery. This project was a collaborative research effort between the US …

Personality Profiles Of Software Engineers And Their Software Quality Preferences, Arif Raza, Luiz Fernando Capretz, Zaka Ul-Mustafa

Electrical and Computer Engineering Publications

Studies related to human aspects in software engineering (SE) have been performed from different perspectives. These perspectives include the study of human factors in different phases of software life cycle, effect of team performance in software development, how can a personality trait suit a particular task, and about some other miscellaneous issues. This research work aims to establish personality profiles of Pakistani software engineers using the Myers-Briggs Type Indicator (MBTI) instrument. In this survey, we have collected personality profiles of 110 software engineers. Moreover, their preferences of software quality attributes have also been collected. Analysis of the study shows that …

The Role Of Emotion And Facial Expression In Synthesised Sign Language Avatars, Robert G Smith

Other Resources

This thesis explores the role that underlying emotional facial expressions might have in regards to understandability in sign language avatars. Focusing specifically on Irish Sign Language (ISL), we examine the Deaf community’s requirement for a visual-gestural language as well as some linguistic attributes of ISL which we consider fundamental to this research. Unlike spoken language, visual-gestural languages such as ISL have no standard written representation. Given this, we compare current methods of written representation for signed languages as we consider: which, if any, is the most suitable transcription method for the medical receptionist dialogue corpus. A growing body of work …

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 …

Phase Transitions On Random Lattices: How Random Is Topological Disorder?, Hatem Barghathi, Thomas Vojta

Physics Faculty Research & Creative Works

We study the effects of topological (connectivity) disorder on phase transitions. We identify a broad class of random lattices whose disorder fluctuations decay much faster with increasing length scale than those of generic random systems, yielding a wandering exponent of ω = (d−1)/(2d) in d dimensions. The stability of clean critical points is thus governed by the criterion (d+1)ν > 2 rather than the usual Harris criterion dν > 2, making topological disorder less relevant than generic randomness. The Imry-Ma criterion is also modified, allowing first-order transitions to survive in all dimensions d > 1. These results explain a host of puzzling violations …