Computer Sciences Commons^™

Special Issue: M&S Optimization Applications In Industry And Engineering, Part 2, Rafael Diaz, Andreas Tolk

VMASC Publications

(First paragraph) Welcome to the second part of the special issue on modeling and simulation (M&S) optimization applications in industry and engineering. This issue incorporates additional publications that reflect various applications and areas of simulation and optimization.

Employing Learning To Improve The Performance Of Meta-Raps, Fatemah Al-Duoli, Ghaith Rabadi

Engineering Management & Systems Engineering Faculty Publications

In their search for satisfactory solutions to complex combinatorial problems, metaheuristics methods are expected to intelligently explore the solution space. Various forms of memory have been used to achieve this goal and improve the performance of metaheuristics, which warranted the development of the Adaptive Memory Programming (AMP) framework [1]. This paper follows this framework by integrating Machine Learning (ML) concepts into metaheuristics as a way to guide metaheuristics while searching for solutions. The target metaheuristic method is Meta-heuristic for Randomized Priority Search (Meta-RaPS). Similar to most metaheuristics, Meta-RaPS consists of construction and improvement phases. Randomness coupled with a greedy heuristic …

Hyperspectral Image Classification Using A Spectral-Spatial Sparse Coding Model, Ender Oguslu, Guoqing Zhou, Jiang Li, Lorenzo Bruzzone (Ed.)

Electrical & Computer Engineering Faculty Publications

We present a sparse coding based spectral-spatial classification model for hyperspectral image (HSI) datasets. The proposed method consists of an efficient sparse coding method in which the l₁/l_q regularized multi-class logistic regression technique was utilized to achieve a compact representation of hyperspectral image pixels for land cover classification. We applied the proposed algorithm to a HSI dataset collected at the Kennedy Space Center and compared our algorithm to a recently proposed method, Gaussian process maximum likelihood (GP-ML) classifier. Experimental results show that the proposed method can achieve significantly better performances than the GP-ML classifier when training data …

A Method For Identifying Personalized Representations In Web Archives, Mat Kelly, Justin F. Brunelle, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

Web resources are becoming increasingly personalized — two different users clicking on the same link at the same time can see content customized for each individual user. These changes result in multiple representations of a resource that cannot be canonicalized in Web archives. We identify characteristics of this problem by presenting a potential solution to generalize personalized representations in archives. We also present our proof-of-concept prototype that analyzes WARC (Web ARChive) format files, inserts metadata establishing relationships, and provides archive users the ability to navigate on the additional dimension of environment variables in a modified Wayback Machine.

The 6th Computational Structural Bioinformatics Workshop Introduction, Jing He, Amarda Shehu, Nurit Haspel, Brian Chen

Computer Science Faculty Publications

No abstract provided.

Estimating Loop Length From Cryoem Images At Medium Resolutions, Andrew Mcknight, Dong Si, Kamal Al Nasr, Andrey Chemikov, Nikos Chrisochoides, Jing He

Computer Science Faculty Publications

Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein.

Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was …

Image-Level And Group-Level Models For Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment …

Computational Genetic Neuroanatomy Of The Developing Mouse Brain: Dimensionality Reduction, Visualization, And Clustering, Shuiwang Ji

Computer Science Faculty Publications

Background: The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development.

Results: In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in …

Dinosolve: A Protein Disulfide Bonding Prediction Server Using Context-Based Features To Enhance Prediction Accuracy, Ashraf Yaseen, Yaohang Li

Computer Science Faculty Publications

Background: Disulfide bonds play an important role in protein folding and structure stability. Accurately predicting disulfide bonds from protein sequences is important for modeling the structural and functional characteristics of many proteins.

Methods: In this work, we introduce an approach of enhancing disulfide bonding prediction accuracy by taking advantage of context-based features. We firstly derive the first-order and second-order mean-force potentials according to the amino acid environment around the cysteine residues from large number of cysteine samples. The mean-force potentials are integrated as context-based scores to estimate the favorability of a cysteine residue in disulfide bonding state as well as …

A Mesh Generation And Machine Learning Framework For Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, Shuiwang Ji

Computer Science Faculty Publications

Background: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide …

Convergence Analysis Of Markov Chain Monte Carlo Linear Solvers Using Ulam--Von Neumann Algorithm, Hao Ji, Michael Mascagni, Yaohang Li

Computer Science Faculty Publications

The convergence of Markov chain--based Monte Carlo linear solvers using the Ulam--von Neumann algorithm for a linear system of the form x = Hx + b is investigated in this paper. We analyze the convergence of the Monte Carlo solver based on the original Ulam--von Neumann algorithm under the conditions that ||H|| < 1 as well as ρ(H) < 1, where ρ(H) is the spectral radius of H. We find that although the Monte Carlo solver is based on sampling the Neumann series, the convergence of Neumann series is not a sufficient condition for the convergence of the Monte Carlo solver. Actually, properties of H are not the only factors determining the convergence of the Monte Carlo solver; the underlying transition probability matrix plays an important role. An improper selection of the transition matrix may result in divergence even though the condition ||H|| <1 holds. However, if the condition ||H|| < 1 is satisfied, we show that there always exist certain transition matrices that guarantee convergence of the Monte Carlo solver. On the other hand, if ρ(H) <1 but ||H|| ≥ 1, the Monte Carlo linear solver may or may not converge. In particular, if the row sum ∑ n/j= 1|H_ij > 1 for every row in H or, more generally, ρ(H⁺) >1, where H⁺ is the nonnegative matrix where H+_ij = |H_ij|, we show that transition matrices leading to convergence of the Monte Carlo solver do not exist. Finally, given …

Conformational Sampling In Template Free Protein Loop Structure Modeling: An Overview, Yaohang Li

Computer Science Faculty Publications

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the …

Intensity-Based Skeletonization Of Cryoem Gray-Scale Images Using A True Segmentation-Free Algorithm, Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the …

Gpu-Optimized Code For Long-Term Simulations Of Beam-Beam Effects In Colliders, Y. Roblin, V. Morozov, B. Terzić, M. Aturban, D. Ranjan, M. Zubair

Computer Science Faculty Publications

We report on the development of the new code for long-term simulation of beam-beam effects in particle colliders. The underlying physical model relies on a matrix-based arbitrary-order symplectic particle tracking for beam transport and the Bassetti-Erskine approximation for beam-beam interaction. The computations are accelerated through a parallel implementation on a hybrid GPU/CPU platform. With the new code, a previously computationally prohibitive long-term simulations become tractable. We use the new code to model the proposed medium-energy electron-ion collider (MEIC) at Jefferson Lab.

A Technical Framework For Resource Synchronization, Martin Klein, Robert Sanderson, Herbert Van De Sompel, Simeon Warner, Bernhard Haslhofer, Carl Lagoze, Michael L. Nelson

Computer Science Faculty Publications

This is the second paper in D-Lib Magazine about the ResourceSync effort conducted by the National Information Standards Organization (NISO) and the Open Archives Initiative (OAI). The first part provided a perspective on the resource synchronization problem and introduced a template that organized possible components of a resource synchronization framework in a modular manner. This paper details a technical framework devised using that template.

Warcreate And Wail: Warc, Wayback, And Heritrix Made Easy, Mat Kelly, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

[First slide]

The Problem

Institutional Tools, Personal Archivists

• ON YOUR MACHINE

-Complex to Operate

-Require Infrastructure

• DELEGATED TO INSTITUTIONS

-$$$

-Lose original perspective

• Locale content tailoring (DC vs. San Francisco)
• Observation Medium (PC web browser vs. Crawler)

Visualizing Digital Collections At Archive-It, Michele C. Weigle, Michael L. Nelson

Computer Science Presentations

PDF of a powerpoint presentation from a Archive-It Partners Meeting in Annapolis, Maryland, December 3, 2012. Also available on Slideshare.

Communications And Energy-Harvesting In Nanosensor Networks, Michele C. Weigle

Computer Science Presentations

PDF of a powerpoint presentation from the National Science Foundation (NSF) Workshop on Biological Computations and Communications in Boston, Massachusetts, November 9, 2012. Also available on Slideshare.

Semi-Automatic Simulation Initialization By Mining Structured And Unstructured Data Formats From Local And Web Data Sources, Olcay Sahin

Computational Modeling & Simulation Engineering Theses & Dissertations

Initialization is one of the most important processes for obtaining successful results from a simulation. However, initialization is a challenge when 1) a simulation requires hundreds or even thousands of input parameters or 2) re-initializing the simulation due to different initial conditions or runtime errors. These challenges lead to the modeler spending more time initializing a simulation and may lead to errors due to poor input data.

This thesis proposes two semi-automatic simulation initialization approaches that provide initialization using data mining from structured and unstructured data formats from local and web data sources. First, the System Initialization with Retrieval (SIR) …

Modification And Application Of A Turbulence Response Analysis Method For Flexible Aircraft Configurations, Christie Jeanne Funk

Mechanical & Aerospace Engineering Theses & Dissertations

A software program and associated methodology to study gust loading on aircraft exists for a classification of geometrically simplified flexible configurations. This program consists of a simple aircraft response model with two rigid and three flexible symmetric degrees of freedom and allows for the calculation of various airplane responses due to a discrete one-minus-cosine gust as well as continuous turbulence. Simplifications, assumptions, and opportunities for potential improvements pertaining to the existing software program are first identified, then a revised version of the original software tool is developed with improved methodology to include more complex geometries, additional excitation cases, and output …

The Factors Behind A Successful Implementation Of Electronic Health Records Systems, Anjee Gorkhali

Engineering Management & Systems Engineering Theses & Dissertations

This research explores the role that budget for Information System (IS) and technical expertise of healthcare service provider staff play on the successful leap from a partial to exhaustive implementation of Electronic Health Records (EHR) Systems. Technical expertise in Information Systems might not be easily measurable directly, but there are a number of indicators that could be used as a proxy, such as: Information System (IS) Department Budget, number of IS staff and the extent of technical trainings provided by the IS department to the clinical staff. This research study hypothesizes that quality technical trainings conducted by an IS department …

A Multi-Paradigm Modeling Framework For Modeling And Simulating Problem Situations, Christopher James Lynch

Computational Modeling & Simulation Engineering Theses & Dissertations

Problem situations are problems whose specifications are not universally agreed upon making them a challenge to be modeled and simulated. Models of problem situations depart from the premise of well-defined problems, problems where stakeholders disagree, but also modelers' interpretations play a role in their design and computer implementation.

This thesis proposes a multi-paradigm modeling framework for modeling and simulating problem situations in order to explore the problem space of the problem situations and answer specific modeling questions.

The proposed framework implements the Modeling and Simulation (M&S) System Development Framework (MS-SDF), which is a methodology for modeling a problem situation while …

Friend: A Cyber-Physical System For Traffic Flow Related Information Aggregation And Dissemination, Samy S. El-Tawab

Computer Science Theses & Dissertations

The major contribution of this thesis is to lay the theoretical foundations of FRIEND — A cyber-physical system for traffic Flow-Related Information aggrEgatioN and Dissemination. By integrating resources and capabilities at the nexus between the cyber and physical worlds, FRIEND will contribute to aggregating traffic flow data collected by the huge fleet of vehicles on our roads into a comprehensive, near real-time synopsis of traffic flow conditions. We anticipate providing drivers with a meaningful, color-coded, at-a-glance view of flow conditions ahead, alerting them to congested traffic.

FRIEND can be used to provide accurate information about traffic flow and can be …

Kinematic Analysis Of Gesture In Aphasia, Haroon Osmanzada

Mechanical & Aerospace Engineering Theses & Dissertations

Individuals who have experienced a left hemispheric stroke often develop aphasia, which results in a loss of effective verbal communication and reliance on gesturing to communicate. In this study we combined these two aspects of aphasic word retrieval difficulties and gesturing with three-dimensional kinematics. The purposes of this study were: 1) to develop a preliminary database of upper extremity movements for two common gestures used in gestural facilitation of naming (GES) training, slicing and hammering, in participants who experienced a left-hemisphere stroke and compare them to age-matched healthy controls, and 2) to perform a case study consisting of a single …

De Novo Protein Structure Modeling From Cryoem Data Through A Dynamic Programming Algorithm In The Secondary Structure Topology Graph, Kamal H. Al Nasr

Computer Science Theses & Dissertations

Proteins are the molecules carry out the vital functions and make more than the half of dry weight in every cell. Protein in nature folds into a unique and energetically favorable 3-Dimensional (3-D) structure which is critical and unique to its biological function. In contrast to other methods for protein structure determination, Electron Cryorricroscopy (CryoEM) is able to produce volumetric maps of proteins that are poorly soluble, large and hard to crystallize. Furthermore, it studies the proteins in their native environment. Unfortunately, the volumetric maps generated by current advances in CryoEM technique produces protein maps at medium resolution about (~5 …

An Extensible Framework For Creating Personal Archives Of Web Resources Requiring Authentication, Matthew Ryan Kelly

Computer Science Theses & Dissertations

The key factors for the success of the World Wide Web are its large size and the lack of a centralized control over its contents. In recent years, many advances have been made in preserving web content but much of this content (namely, social media content) was not archived, or still to this day is not being archived,for various reasons. Tools built to accomplish this frequently break because of the dynamic structure of social media websites. Because many social media websites exhibit a commonality in hierarchy of the content, it would be worthwhile to setup a means to reference this …

Serious Game Design Principles: The Impact Of Game Design On Learning Outcomes, Michael W. Martin

Computational Modeling & Simulation Engineering Theses & Dissertations

This dissertation examines the research question "How do video game design principles affect learning outcomes in serious games?" This research first develops a theoretical foundation concerning the meaning of the terms "game" and "serious game". This conceptual clarification is broken down into analytic propositions, which state that games have participants, rules, goals and challenges, and synthetic propositions, which state that the games should be intrinsically compelling, provide meaningful choices, and be self encapsulated. Based on these synthetic propositions, three hypotheses were developed. The hypotheses are that games with an enhanced aesthetic presentation, more meaningful choices, or provide player competition will …

Incorporating Memory And Learning Mechanisms Into Meta-Raps, Arif Arin

Engineering Management & Systems Engineering Theses & Dissertations

Due to the rapid increase of dimensions and complexity of real life problems, it has become more difficult to find optimal solutions using only exact mathematical methods. The need to find near-optimal solutions in an acceptable amount of time is a challenge when developing more sophisticated approaches. A proper answer to this challenge can be through the implementation of metaheuristic approaches. However, a more powerful answer might be reached by incorporating intelligence into metaheuristics.

Meta-RaPS (Metaheuristic for Randomized Priority Search) is a metaheuristic that creates high quality solutions for discrete optimization problems. It is proposed that incorporating memory and learning …

Visualizing Digital Collections At Archive-It, Kalpesh Padia

Computer Science Theses & Dissertations

Archive-It, a subscription service from the Internet Archive, allows users to create,maintain, and view digital collections of web resources. The current interface of Archive-It is largely text-based, supporting drill-down navigation using lists of URIs.While this interface provides good searching capabilities, it is not efficient for browsing. In the absence of keywords, a user has to spend large amount of time trying to locate a web page of interest. In order to provide a better visual experience to the user, we have studied the underlying characteristics of Archive-It collections and implemented six different visualizations (treemap, time cloud, bubble chart, image plot, …

Section Abstracts: Computer Science

Virginia Journal of Science

Abstracts of the Computer Science Section for the 90th Annual Meeting of the Virginia Academy of Science, May 23-25, 2012, Norfolk State University, Norfolk, Virginia.