Computer Sciences Commons^™

A Computational Framework For Learning From Complex Data: Formulations, Algorithms, And Applications, Wenlu Zhang

Computer Science Theses & Dissertations

Many real-world processes are dynamically changing over time. As a consequence, the observed complex data generated by these processes also evolve smoothly. For example, in computational biology, the expression data matrices are evolving, since gene expression controls are deployed sequentially during development in many biological processes. Investigations into the spatial and temporal gene expression dynamics are essential for understanding the regulatory biology governing development. In this dissertation, I mainly focus on two types of complex data: genome-wide spatial gene expression patterns in the model organism fruit fly and Allen Brain Atlas mouse brain data. I provide a framework to explore …

Defining The Competencies, Programming Languages, And Assessments For An Introductory Computer Science Course, Simon Sultana

STEMPS Theses & Dissertations

The purpose of this study was to define the competencies, programming languages, and assessments for an introductory computer science course at a small private liberal arts university. Three research questions were addressed that involved identifying the competencies, programming languages, and assessments that academic and industry experts in California’s Central Valley felt most important and appropriate for an introduction to computer science course.

The Delphi methodology was used to collect data from the two groups of experts with various backgrounds related to computing. The goal was to find consensus among the individual groups to best define aspects that would best comprise …

Principles Of Anti-Discriminatory Design, D. E. Wittkower

Philosophy Faculty Publications

Technical design can produce exclusionary and even discriminatory effects for users. A lack of discriminatory intent is insufficient to avoid discriminatory design, since implicit assumptions about users rarely include all relevant user demographics, and in some cases, designing for all relevant users is actually impossible. To minimize discriminatory effects of technical design, an actively anti-discriminatory design perspective must be adopted. This article provides examples of discriminatory user exclusion, then defining exclusionary design in terms of disaffordances and dysaffordances. Once these definitions are in place, principles of anti-discriminatory design are advanced, drawing upon a method of phenomenological variation employed in the …

Section Abstracts: Computer Science

Virginia Journal of Science

Abstracts of the Computer Science Section for the 94th Annual Virginia Academy of Science Meeting, May 18-20, 2016, at University of Mary Washington, Fredericksburg, VA.

Scripts In A Frame: A Framework For Archiving Deferred Representations, Justin F. Brunelle

Computer Science Theses & Dissertations

Web archives provide a view of the Web as seen by Web crawlers. Because of rapid advancements and adoption of client-side technologies like JavaScript and Ajax, coupled with the inability of crawlers to execute these technologies effectively, Web resources become harder to archive as they become more interactive. At Web scale, we cannot capture client-side representations using the current state-of-the art toolsets because of the migration from Web pages to Web applications. Web applications increasingly rely on JavaScript and other client-side programming languages to load embedded resources and change client-side state. We demonstrate that Web crawlers and other automatic archival …

An Optimized Multiple Right-Hand Side Dslash Kernel For Intel Xeon Phi, Aaron Walden

Computer Science Theses & Dissertations

Lattice quantum chromodynamics (LQCD) stands unique as the only computationally tractable, non-perturbative, and model-independent quantum field theory of the strong nuclear force. The computational core of LQCD is the Wilson Dslash operator, a nearest neighbor stencil operator summing matrix-vector multiplications over lattice points, whose performance is bandwidth-bound on most architectures. Reportedly, up to 90\% of LQCD running time may be spent computing Dslash. In recent years, efforts have been made by researchers to optimize LQCD calculations for floating point coprocessor cards such as GPUs and Intel Xeon Phi Knights Corner (KNC), which boast powerful vector processing units. Most of these …

Watertight And 2-Manifold Surface Meshes Using Dual Contouring With Tetrahedral Decomposition Of Grid Cubes, Tanweer Rashid, Sharmin Sultana, Michel A. Audette

Computational Modeling & Simulation Engineering Faculty Publications

The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. The advantage of DC is that it can reproduce sharp features by inserting vertices anywhere inside the grid cube, as opposed to the Marching Cubes (MC) algorithm that can insert vertices only on the grid edges. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. Our method decomposes an ambiguous grid cube into a …

Mining Human Activity Using Dimensionality Reduction And Pattern Recognition, Ismail El Moudden, Mounir Ouzir, Badreddine Benyacoub, Souad El Bernoussi

Research and Infrastructure Service Enterprise (RISE) Faculty Publications

Human activity recognition (HAR) is an emerging research topic in pattern recognition, especially in computer vision. The main objective of human activity recognition is to automatically detect and analyze human activities from the information acquired from different sensors. Human activity prediction using big data remains a challengingly open problem. Several approaches have recently been developed in order to find practical ways to solve high dimensionality of data problems. The aim of this study is to attempt, using data mining techniques, to deal with HAR modeling involving a significant number of variables in order to identify relevant parameters from data and …

Selective Mutation Accumulation: A Computational Model Of The Paternal Age Effect, Eoin C. Whelan, Alexander C. Nwala, Christopher Osgood, Stephan Olariu

Biological Sciences Faculty Publications

Motivation: As the mean age of parenthood grows, the effect of parental age on genetic disease and child health becomes ever more important. A number of autosomal dominant disorders show a dramatic paternal age effect due to selfish mutations: substitutions that grant spermatogonial stem cells (SSCs) a selective advantage in the testes of the father, but have a deleterious effect in offspring. In this paper we present a computational technique to model the SSC niche in order to examine the phenomenon and draw conclusions across different genes and disorders.

Results: We used a Markov chain to model the probabilities of …

A Flexible Pet-Based Wearable Sensor For Arterial Pulse Waveform Measurement, Dan Wang, Dean Krusienski, Zhili Hao

Mechanical & Aerospace Engineering Faculty Publications

In light of the need of health monitoring, the paper presents a flexible polyethylene terephthalate (PET)-based wearable sensor for arterial pulse waveform measurement. The sensor encompasses a polydimethylsiloxane (PDMS) microstructure embedded with an electrolyte-enabled 5×1 transducer array, which spans 6mm and has a spatial resolution of 1.5mm. A pulse signal exerts a deflection on the microstructure and is recorded as a resistance change by a transducer at the site of the pulse. An untrained individual can easily align the sensor on a targeted artery with a negligible margin and then acquire the arterial pulse waveform continuously and non-invasively. This sensor …

Integrating Cobots In Engineering Technology Education, Ana M. Djuric, Vukica Jovanovic, Tatiana V. Goris, Otilia Popescu

Engineering Technology Faculty Publications

Collaborative robots or CoBots, unlike traditional robots, are safe and flexible enough to work harmoniously with humans. Exploiting the efficiency of automated operations and the flexibility of manual operations in one process can improve productivity and worker job satisfaction. CoBots technology has been experiencing strong growth in different areas such as ground transportation, food-processing industry, car manufacturing, and naval or aeronautical engineering. Current CoBots education and training opportunities are rare or non-existent in university environments. In response to this need, we developed several CoBots modules which will be integrated in the current robotics and mechatronics courses. In this paper we …

High-Fidelity Simulations Of Long-Term Beam-Beam Dynamics On Gpus, B. Terzić, K. Arumugam, M. Aturban, C. Cotnoir, A. Godunov, D. Ranjan, M. Stefani, M. Zubair, F. Lin, V. Morozov, Y. Roblin, H. Zhang

Physics Faculty Publications

Future machines such as the Electron Ion Collider (MEIC), linac-ring machines (eRHIC) or LHeC are particularly sensitive to beam-beam effects. This is the limiting factor for long-term stability and high luminosity reach. The complexity of the non-linear dynamics makes it challenging to perform such simulations typically requiring millions of turns. Until recently, most of the methods have involved using linear approximations and/or tracking for a limited number of turns. We have developed a framework which exploits a massively parallel Graphical Processing Units (GPU) architecture to allow for tracking millions of turns in a sympletic way up to an arbitrary order. …

The Reconfigurable Machinery Efficient Workspace Analysis Based On The Twist Angles, Ana M. Djuric, Vukica Jovanovic, Mirjana Filipovic, Ljubinko Kevac

Engineering Technology Faculty Publications

A novel methodology for the calculation, visualisation and analysis of the Reconfigurable Machinery Efficient Workspace (RMEW), based on the twist angles, is presented in this paper. The machinery's kinematic parameters are used for calculating the workspace, while the efficient workspace is associated with the machinery's path and includes the end-effector position and orientation. To analyse and visualise many different machinery efficient workspaces at the same time, the calculation is based on the previously developed and validated complex reconfigurable machinery's kinematic structure named n-DOF Global Kinematic Model (n-GKM). An industrial robot is used as an example to demonstrate …

Development Of The Electron Cooling Simulation Program For Jleic, H. Zhang, J. Chen, R. Li, Y. Zhang, H. Huang, L. Luo

Mathematics & Statistics Faculty Publications

In the JLab Electron Ion Collider (JLEIC) project the traditional electron cooling technique is used to reduce the ion beam emittance at the booster ring, and to compensate the intrabeam scattering effect and maintain the ion beam emittance during collision at the collider ring. A new electron cooling process simulation program has been developed to fulfill the requirements of the JLEIC electron cooler design. The new program allows the users to calculate the electron cooling rate and simulate the cooling process with either DC or bunched electron beam to cool either coasting or bunched ion beam. It has been benchmarked …

An Efficient Solution To The Mixed Shop Scheduling Problem Using A Modified Genetic Algorithm, V. Nguyen, H. P. Bao

Mechanical & Aerospace Engineering Faculty Publications

The mixed job shop scheduling problem is one in which some jobs have fixed machine orders and other jobs may be processed in arbitrary orders. In past literature, optimal solutions have been proposed based on adaptations of classical solutions such as by Johnson, Thompson and Giffler among many others, by pseudopolynomial algorithms, by simulation, and by Genetic Algorithms (GA). GA based solutions have been proposed for flexible Job shops. This paper proposes a GA algorithm for the mixed job shop scheduling problem. The paper starts with an analysis of the characteristics of the so-called mixed shop problem. Based on those …

Probing The Landscape: Toward A Systematic Taxonomy Of Online Peer Assessment Systems In Education, Dymytro Babik, Edward F. Gehringer, Jennifer Kidd, Ferry Pramudianto, David Tinapple

Teaching & Learning Faculty Publications

We present the research framework for a taxonomy of online educational peer-assessment systems. This framework enables researchers in technology-supported peer assessment to understand the current landscape of technologies supporting student peer review and assessment, specifically, its affordances and constraints. The framework helps identify the major themes in existing and potential research and formulate an agenda for future studies. It also informs educators and system design practitioners about use cases and design options.

An Efficient Method For Optimizing Segmentation Parameters, Jacob D' Avy, Wei-Wen Hsu, Chung-Hao Chen, Andreas F. Koschan, Mongi Abidi

Electrical & Computer Engineering Faculty Publications

Segmenting an image into meaningful regions is an important step in many computer vision applications such as facial recognition, target tracking and medical image analysis. Because image segmentation is an ill-posed problem, parameters are needed to constrain the solution to one that is suitable for a given application. For a user, setting parameter values is often unintuitive. We present a method for automating segmentation parameter selection using an efficient search method to optimize a segmentation objective function. Efficiency is improved by utilizing prior knowledge about the relationship between a segmentation parameter and the objective function terms. An adaptive sampling of …

Java Based Visualization And Animation For Teaching The Dijkstra Shortest Path Algorithm In Transportation Networks, Ivan Makohon, Duc T. Nguyen, Masha Sosonkina, Yuzhong Shen, Manwo Ng

Civil & Environmental Engineering Faculty Publications

Shortest path (SP) algorithms, such as the popular Dijkstra algorithm has been considered as the "basic building blocks" for many advanced transportation network models. Dijkstra algorithm will find the shortest time (ST) and the corresponding SP to travel from a source node to a destination node. Applications of SP algorithms include real-time GPS and the Frank-Wolfe network equilibrium.

For transportation engineering students, the Dijkstra algorithm is not easily understood. This paper discusses the design and development of a software that will help the students to fully understand the key components involved in the Dijkstra SP algorithm. The software presents an …

An Improved Smote Algorithm Based On Genetic Algorithm For Imbalanced Data Collection, Qiong Gu, Xian-Ming Wang, Zhao Wu, Bing Ning, Chun-Sheng Xin

Electrical & Computer Engineering Faculty Publications

Classification of imbalanced data has been recognized as a crucial problem in machine learning and data mining. In an imbalanced dataset, minority class instances are likely to be misclassified. When the synthetic minority over-sampling technique (SMOTE) is applied in imbalanced dataset classification, the same sampling rate is set for all samples of the minority class in the process of synthesizing new samples, this scenario involves blindness. To overcome this problem, an improved SMOTE algorithm based on genetic algorithm (GA), namely, GASMOTE was proposed. First, GASMOTE set different sampling rates for different minority class samples. A combination of the sampling rates …

Leveraging Heritrix And The Wayback Machine On A Corporate Intranet: A Case Study On Improving Corporate Archives, Justin F. Brunelle, Krista Ferrante, Eliot Wilczek, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

In this work, we present a case study in which we investigate using open-source, web-scale web archiving tools (i.e., Heritrix and the Wayback Machine installed on the MITRE Intranet) to automatically archive a corporate Intranet. We use this case study to outline the challenges of Intranet web archiving, identify situations in which the open source tools are not well suited for the needs of the corporate archivists, and make recommendations for future corporate archivists wishing to use such tools. We performed a crawl of 143,268 URIs (125 GB and 25 hours) to demonstrate that the crawlers are easy to set …

Rcd+: Fast Loop Modeling Server, José R. López-Blanco, Alejandro J. Canosa-Valis, Yaohang Li, Pablo Chacón

Computer Science Faculty Publications

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop …

A Hybrid Algorithm Based On Optimal Quadratic Spline Collocation And Parareal Deferred Correction For Parabolic Pdes, Jun Liu, Yan Wang, Rongjian Li

Computer Science Faculty Publications

Parareal is a kind of time parallel numerical methods for time-dependent systems. In this paper, we consider a general linear parabolic PDE, use optimal quadratic spline collocation (QSC) method for the space discretization, and proceed with the parareal technique on the time domain. Meanwhile, deferred correction technique is also used to improve the accuracy during the iterations. In fact, the optimal QSC method is a correction of general QSC method. Along the temporal direction we embed the iterations of deferred correction into parareal to construct a hybrid method, parareal deferred correction (PDC) method. The error estimation is presented and the …

A Hybrid Parallel Delaunay Image-To-Mesh Conversion Algorithm Scalable On Distributed-Memory Clusters, Daming Feng, Andrey N. Chernikov, Nikos Chrisochoides

Computer Science Faculty Publications

In this paper, we present a scalable three dimensional hybrid MPI+Threads parallel Delaunay image-to-mesh conversion algorithm. A nested master-worker communication model for parallel mesh generation is implemented which simultaneously explores process-level parallelization and thread-level parallelization: inter-node communication using MPI and inter-core communication inside one node using threads. In order to overlap the communication (task request and data movement) and computation (parallel mesh refinement), the inter-node MPI communication and intra-node local mesh refinement is separated. The master thread that initializes the MPI environment is in charge of the inter-node MPI communication while the worker threads of each process are only responsible …

Big Data-Enabled Multiscale Serviceability Analysis For Aging Bridges, Yu Liang, Dalei Wu, Guirong Liu, Yaohang Li, Cuilan Gao, Zhongguo John Ma, Weidong Wu

Computer Science Faculty Publications

This work is dedicated to constructing a multi-scale structural health monitoring system to monitor and evaluate the serviceability of bridges based on the Hadoop Ecosystem (MS-SHM-Hadoop). By taking the advantages of the fault-tolerant distributed file system called the Hadoop Distributed File System (HDFS) and high-performance parallel data processing engine called MapReduce programming paradigm, MS-SHM-Hadoop features include high scalability and robustness in data ingestion, fusion, processing, retrieval, and analytics. MS-SHM-Hadoop is a multi-scale reliability analysis framework, which ranges from nationwide bridge-surveys, global structural integrity analysis, and structural component reliability analysis. This Nationwide bridge survey uses deep-learning techniques to evaluate the bridge …

Flexc: Protein Flexibility Prediction Using Context-Based Statistics, Predicted Structural Features, And Sequence Information, Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang, Yaohang Li

Computer Science Faculty Publications

The fluctuation of atoms around their average positions in protein structures provides important information regarding protein dynamics. This flexibility of protein structures is associated with various biological processes. Predicting flexibility of residues from protein sequences is significant for analyzing the dynamic properties of proteins which will be helpful in predicting their functions.

Deep Models For Brain Em Image Segmentation: Novel Insights And Improved Performance, Ahmed Fakhry, Hanchuan Peng, Shuiwang Ji

Computer Science Faculty Publications

Motivation: Accurate segmentation of brain electron microscopy (EM) images is a critical step in dense circuit reconstruction. Although deep neural networks (DNNs) have been widely used in a number of applications in computer vision, most of these models that proved to be effective on image classification tasks cannot be applied directly to EM image segmentation, due to the different objectives of these tasks. As a result, it is desirable to develop an optimized architecture that uses the full power of DNNs and tailored specifically for EM image segmentation.

Results: In this work, we proposed a novel design of DNNs for …

Results And Challenges In Visualizing Analytic Provenance Of Text Analysis Tasks Using Interaction Logs, Rhema Linder, Alyssa M. Peña, Sampath Jayarathna, Eric D. Ragan

Computer Science Faculty Publications

After data analysis, recalling and communicating the steps and rationale followed during the analysis can be difficult. This paper explores the use of interaction logs to generate summaries of an analyst's interest based on interactions with specific data items in a text analysis scenario. Our approach uses data-interaction events as a proxy for user interest in and experience of information. Logging can produce verbose logs that detail all available readable content, so the discussed approach uses topic modeling (LDA) over different time segments to summarize the verbose information and generate visualizations of the history of user interest. Our preliminary results …

Interactively Cutting And Constraining Vertices In Meshes Using Augmented Matrices, Yu-Hong Yeung, Jessica Crouch, Alex Pothen

Computer Science Faculty Publications

We present a finite-element solution method that is well suited for interactive simulations of cutting meshes in the regime of linear elastic models. Our approach features fast updates to the solution of the stiffness system of equations to account for real-time changes in mesh connectivity and boundary conditions. Updates are accomplished by augmenting the stiffness matrix to keep it consistent with changes to the underlying model, without refactoring the matrix at each step of cutting. The initial stiffness matrix and its Cholesky factors are used to implicitly form and solve a Schur complement system using an iterative solver. As changes …

Using Eye And Head Movements As A Control Mechanism For Tele-Operating A Ground-Based Robot And Its Payload, Kathryn C. Hicks

Computational Modeling & Simulation Engineering Theses & Dissertations

To date, eye and head tracking has been used to indicate users' attention patterns while performing a task or as an aid for disabled persons, to allow hands-free interaction with a computer. The increasing accuracy and the reduced cost of eye- and head-tracking equipment make utilizing this technology feasible for explicit control tasks, especially in cases where there is confluence between the visual task and control.

The goal of this research was to investigate the use of eye-tracking as a more natural interface for the control of a camera-equipped, remotely operated robot in tasks that require the operator to simultaneously …

Efficient Algorithms For Prokaryotic Whole Genome Assembly And Finishing, Abhishek Biswas

Computer Science Theses & Dissertations

De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) using both overlapping reads and linked reads until the assembly runs into an ambiguous repeat region. These contigs are further bridged into scaffolds using linked read information. However, errors can be made in both phases of assembly due to high error threshold of overlap acceptance and linking based on too few mate reads. Identical as well as similar repeat regions can …