Computer Sciences Commons^™

Long-Term Simulations Of Beam-Beam Dynamics On Gpus, B. Terzić, K. Arumugam, R. Majeti, C. Cotnoir, M. Stefani, D. Ranjan, A. Godunov, V. Morozov, H. Zhang, F. Lin, Y. Roblin, E. Nissen, T. Satogata

Physics Faculty Publications

Future machines such as the electron-ion colliders (JLEIC), 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 which require millions of turns. Until recently, most of the methods used 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 and colliding them …

Simulations Of Coherent Synchrotron Radiation On Parallel Hybrid Gpu/Cpu Platform, B. Terzić, K. Arumugam, D. Duffin, A. Godunov, T. Islam, D. Ranjan, S. Sangam, Mohammad Zubair

Physics Faculty Publications

Coherent synchrotron radiation (CSR) is an effect of self-interaction of an electron bunch as it traverses a curved path. It can cause a significant emittance degradation, as well as fragmentation and microbunching. Numerical simulations of the 2D/3D CSR effects have been extremely challenging due to computational bottlenecks associated with calculating retarded potentials via integrating over the history of the bunch. We present a new high-performance 2D, particle-in-cell code which uses massively parallel multicore GPU/GPU platforms to alleviate computational bottlenecks. The code formulates the CSR problem from first principles by using the retarded scalar and vector potentials to compute the self-interaction …

Human-Intelligence/Machine-Intelligence Decision Governance: An Analysis From Ontological Point Of View, Faisal Mahmud, Teddy Steven Cotter

Engineering Management & Systems Engineering Faculty Publications

The increasing CPU power and memory capacity of computers, and now computing appliances, in the 21st century has allowed accelerated integration of artificial intelligence (AI) into organizational processes and everyday life. Artificial intelligence can now be found in a wide range of organizational processes including medical diagnosis, automated stock trading, integrated robotic production systems, telecommunications routing systems, and automobile fuzzy logic controllers. Self-driving automobiles are just the latest extension of AI. This thrust of AI into organizations and everyday life rests on the AI community’s unstated assumption that “…every aspect of human learning and intelligence could be so precisely described …

Preparing Teacher Candidates For Virtual Field Placements Via An Exposure To K-12 Online Teaching, Tian Luo, Laura Hibbard, Teresa Franklin, David R. Moore

STEMPS Faculty Publications

Aim/Purpose The goal of this project was to determine what effects exposure to online K-12 teaching and learning activities had on teacher candidates’ perceptions of K-12 online learning, how the exposure allowed teacher candidates to reach greater understanding of online pedagogy, and what effect such exposure had on teacher candidates’ aspirations to complete virtual field experiences.

Background With an increasing number of K-12 students learning online within full-time online schools and in blended learning environments, universities must prepare future educators to teach in virtual environments including clinical practice. Before engaging in online field placement, preservice teachers must be oriented to …

Error Aggregation In The Reengineering Process From 3d Scanning To Printing, Jennifer G. Michaeli, Matthew C. Degroff, Roman C. Roxas

Engineering Technology Faculty Publications

This work aims to study the aggregation of dimensional errors in the reengineering processes using 3D scanning and printing without initial design drawings. A 57-tooth spur gear is used as an example to facilitate the discussion. Two approaches are investigated. The first one builds the gear model based upon measurement taken from a caliper, and the second approach uses a 3D scanner to collect geometry data. Dimensional errors in each stage of these two approaches are investigated. Particular attention is paid to the geometry data flow in the reengineering process from data acquisition and editing to model construction. Recommendations are …

Advances On Software Defined Wireless Networking, D. B. Rawat, M. Song, C. Xin

Electrical & Computer Engineering Faculty Publications

Software defined wireless networking is regarded as an emerging technology to enhance spectrum efficiency and improve the overall network performance. In this paper, we summarise the special issue on recent advances in software defined wireless networking. Specifically, this special issue publishes following findings: i) a novel context aware medium access control scheme for multichannel buffer-aided cognitive networks to reduce the delay by exploiting the packets’ contexts; ii) a utility-based uplink scheduling algorithm that accommodates different performance metrics and adapts its decisions based on user-specified profiles by incorporating an intermediary layer between the MAC and network layer; iii) an opportunistic spectrum …

Teaching Hands-On Cyber Defense Labs To Middle School And High School Students: Our Experience From Gencyber Camps, Peng Jiang, Xin Tian, Chunsheng Xin, Wu He

Electrical & Computer Engineering Faculty Publications

With the high demand of the nation for next generation cybersecurity experts, it is important to design and provide hands-on labs for students at the K-12 level in order to increase their interest in cybersecurity and enhance their confidence in learning cybersecurity skills at the young age. This poster reports some preliminary analysis results from the 2016 GenCyber summer camp held at Old Dominion University (ODU), which is part of a nationwide grant program funded by the National Security Agency (NSA) and the National Science Foundation (NSF). This poster also demonstrates the design of three hands-on labs which have been …

Deep Models For Engagement Assessment With Scarce Label Information, Feng Li, Guangfan Zhang, Wei Wang, Roger Xu, Tom Schnell, Jonathan Wen, Frederic Mckenzie, Jiang Li

Electrical & Computer Engineering Faculty Publications

Task engagement is defined as loadings on energetic arousal (affect), task motivation, and concentration (cognition) [1]. It is usually challenging and expensive to label cognitive state data, and traditional computational models trained with limited label information for engagement assessment do not perform well because of overfitting. In this paper, we proposed two deep models (i.e., a deep classifier and a deep autoencoder) for engagement assessment with scarce label information. We recruited 15 pilots to conduct a 4-h flight simulation from Seattle to Chicago and recorded their electroencephalograph (EEG) signals during the simulation. Experts carefully examined the EEG signals and labeled …

Impact Of Uri Canonicalization On Memento Count, Mat Kelly, Lulwah M. Alkwai, Michael L. Nelson, Michele C. Weigle, Herbert Van De Sompel

Computer Science Faculty Publications

Quantifying the captures of a URI over time is useful for researchers to identify the extent to which a Web page has been archived. Memento TimeMaps provide a format to list mementos (URI-Ms) for captures along with brief metadata, like Memento-Datetime, for each URI-M. However, when some URI-Ms are dereferenced, they simply provide a redirect to a different URI-M (instead of a unique representation at the datetime), often also present in the TimeMap. This infers that confidently obtaining an accurate count quantifying the number of non-forwarding captures for a URI-R is not possible using a TimeMap alone and that the …

Modeling Beta-Traces For Beta-Barrels From Cryo-Em Density Maps, Dong Si, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although ά-helices can be detected from density maps at 5-8 angstrom resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 angstrom-8.25 angstrom resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands …

Homeomorphic Tetrahedralization Of Multi-Material Images With Quality And Fidelity Guarantees, Jing Xu, Andrey N. Chernikov

Computer Science Faculty Publications

We present a novel algorithm for generating three-dimensional unstructured tetrahedral meshes of multi-material images. The algorithm produces meshes with high quality since it provides a guaranteed dihedral angle bound of up to 19.47° for the output tetrahedra. In addition, it allows for user-specified guaranteed bounds on the two-sided Hausdorff distance between the boundaries of the mesh and the boundaries of the materials. Moreover, the mesh boundary is proved to be homeomorphic to the object surface. The algorithm is fast and robust, it produces a sufficiently small number of mesh elements that comply with these guarantees, as compared to other software. …

An Effective Computational Method Incorporating Multiple Secondary Structure Predictions In Topology Determination For Cryo-Em Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, Jing He

Computer Science Faculty Publications

A key idea in de novo modeling of a medium-resolution density image obtained from cryo-electron microscopy is to compute the optimal mapping between the secondary structure traces observed in the density image and those predicted on the protein sequence. When secondary structures are not determined precisely, either from the image or from the amino acid sequence of the protein, the computational problem becomes more complex. We present an efficient method that addresses the secondary structure placement problem in presence of multiple secondary structure predictions and computes the optimal mapping. We tested the method using 12 simulated images from alpha-proteins and …

Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He

Computer Science Faculty Publications

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM …

Efficient Core Utilization In A Hybrid Parallel Delaunay Meshing Algorithm On Distributed-Memory Cluster, Daming Feng, Andrey N. Chernikov, Nikos P. Chrisochoides

Computer Science Faculty Publications

Most of the current supercomputer architectures consist of clusters of nodes that are used by many clients (users). A user wants his/her job submitted in the job queue to be scheduled promptly. However, the resource sharing and job scheduling policies that are used in the scheduling system to manage the jobs are usually beyond the control of users. Therefore, in order to reduce the waiting time of their jobs, it is becoming more and more crucial for the users to consider how to implement the algorithms that are suitable to the system scheduling policies and are able to effectively and …

Homeomorphic Tetrahedral Tessellation For Biomedical Images, Jing Xu, Andrey N. Chernikov

Computer Science Faculty Publications

We present a novel algorithm for generating three-dimensional unstructured tetrahedral meshes for biomedical images. The method uses an octree as the background grid from which to build the final graded conforming meshes. The algorithm is fast and robust. It produces meshes with high quality since it provides dihedral angle lower bound for the output tetrahedra. Moreover, the mesh boundary is a geometrically and topologically accurate approximation of the object surface in the sense that it allows for guaranteed bounds on the two-sided Hausdorff distance and the homeomorphism between the boundaries of the mesh and the boundaries of the materials. The …

An Iterative Bézier Method For Fitting Beta-Sheet Component Of A Cryo-Em Density Map, Michael Poteat, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy (Cryo-EM) is a powerful technique to produce 3-dimensional density maps for large molecular complexes. Although many atomic structures have been solved from cryo-EM density maps, it is challenging to derive atomic structures when the resolution of density maps is not sufficiently high. Geometrical shape representation of secondary structural components in a medium-resolution density map enhances modeling of atomic structures. We compare two methods in producing surface representation of the β-sheet component of a density map. Given a 3-dimensional volume of β-sheet that is segmented from a density map, the performance of a polynomial fitting was compared with that …

Ansi/Niso Z39.99-2017 Resourcesync Framework Specification, Kevin Ruthen, Jill Emery, Mark Doyle, Mark Needleman, Sue Baughman, Evan Owens, Oliver Pesch, Mike Dicus, Nassib Nassar, Tim Auger, Amy Kirchhoff, Sally Mccallum, Diana Magnoni, Paul Swanson, Gregory Grazevich, Nara Newcomer, Gregory Grazevich, Juha Hakala, Barbara Rapp, Beverly Geckle, Carol Brent, Gary Van Overborg, Rick Burke, Kristin Antelman, Scott Bernier, Pascal Calarco, John Dove, Lucy Harrison, Peter Murray, Christine Stohn, Julie Zhu, Todd Carpenter, Bernhard Haslhofer, Richard Jones, Martin Klein, Graham Klyne, Carl Lagoze, Stuart Lewis, Peter Murray, Michael Nelson, Shlomo Sanders, Robert Sanderson, Herbert Van De Sompel, Paul Walk, Simeon Warner, Zhiwu Xie, Jeff Young

Computer Science Faculty Publications

This ResourceSync specification describes a synchronization framework for the web consisting of various capabilities that allow third-party systems to remain synchronized with a server’s evolving resources. The capabilities may be combined in a modular manner to meet local or community requirements. This specification also describes how a server should advertise the synchronization capabilities it supports and how third-party systems may discover this information. The specification repurposes the document formats defined by the Sitemap protocol and introduces extensions for them.

Avoiding Zombies In Archival Replay Using Serviceworker, Sawood Alam, Mat Kelly, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

[First paragraph] A Composite Memento is an archived representation of a web page with all the page requisites such as images and stylesheets. All embedded resources have their own URIs, hence, they are archived independently. For a meaningful archival replay, it is important to load all the page requisites from the archive within the temporal neighborhood of the base HTML page. To achieve this goal, archival replay systems try to rewrite all the resource references to appropriate archived versions before serving HTML, CSS, or JS. However, an effective server-side URL rewriting is difficult when URLs are generated dynamically using JavaScript. …

Multiple Imputation Of Missing Data In Structural Equation Models With Mediators And Moderators Using Gradient Boosted Machine Learning, Robert J. Milletich Ii

Psychology Theses & Dissertations

Mediation and moderated mediation models are two commonly used models for indirect effects analysis. In practice, missing data is a pervasive problem in structural equation modeling with psychological data. Multiple imputation (MI) is one method used to estimate model parameters in the presence of missing data, while accounting for uncertainty due to the missing data. Unfortunately, commonly used MI methods are not equipped to handle categorical variables or nonlinear variables such as interactions. In this study, we introduce a general MI framework that uses the Bayesian bootstrap (BB) method to generate posterior inferences for indirect effects and gradient boosted machine …

Robust Algorithms For Estimating Vehicle Movement From Motion Sensors Within Smartphones, Ilyas Ustun

Computational Modeling & Simulation Engineering Theses & Dissertations

Building sustainable traffic control solutions for urban streets (e.g., eco-friendly signal control) and highways requires effective and reliable sensing capabilities for monitoring traffic flow conditions so that both the temporal and spatial extents of congestion are observed. This would enable optimal control strategies to be implemented for maximizing efficiency and for minimizing the environmental impacts of traffic. Various types of traffic detection systems, such as inductive loops, radar, and cameras have been used for these purposes. However, these systems are limited, both in scope and in time. Using GPS as an alternative method is not always viable because of problems …

Machine Learning Methods For Brain Image Analysis, Ahmed Fakhry

Computer Science Theses & Dissertations

Understanding how the brain functions and quantifying compound interactions between complex synaptic networks inside the brain remain some of the most challenging problems in neuroscience. Lack or abundance of data, shortage of manpower along with heterogeneity of data following from various species all served as an added complexity to the already perplexing problem. The ability to process vast amount of brain data need to be performed automatically, yet with an accuracy close to manual human-level performance. These automated methods essentially need to generalize well to be able to accommodate data from different species. Also, novel approaches and techniques are becoming …

Novel Monte Carlo Methods For Large-Scale Linear Algebra Operations, Hao Ji

Computer Science Theses & Dissertations

Linear algebra operations play an important role in scientific computing and data analysis. With increasing data volume and complexity in the "Big Data" era, linear algebra operations are important tools to process massive datasets. On one hand, the advent of modern high-performance computing architectures with increasing computing power has greatly enhanced our capability to deal with a large volume of data. One the other hand, many classical, deterministic numerical linear algebra algorithms have difficulty to scale to handle large data sets.

Monte Carlo methods, which are based on statistical sampling, exhibit many attractive properties in dealing with large volume of …

Toward Open And Programmable Wireless Network Edge, Mostafa Uddin

Computer Science Theses & Dissertations

Increasingly, the last hop connecting users to their enterprise and home networks is wireless. Wireless is becoming ubiquitous not only in homes and enterprises but in public venues such as coffee shops, hospitals, and airports. However, most of the publicly and privately available wireless networks are proprietary and closed in operation. Also, there is little effort from industries to move forward on a path to greater openness for the requirement of innovation. Therefore, we believe it is the domain of university researchers to enable innovation through openness. In this thesis work, we introduce and defines the importance of open framework …

Towards Aggregating Time-Discounted Information In Sensor Networks, Xianping Wang

Computer Science Theses & Dissertations

Sensor networks are deployed to monitor a seemingly endless list of events in a multitude of application domains. Through data collection and aggregation enhanced with data mining and machine learning techniques, many static and dynamic patterns can be found by sensor networks. The aggregation problem is complicated by the fact that the perceived value of the data collected by the sensors is affected by many factors such as time, location and user valuation. In addition, the value of information deteriorates often dramatically over time. Through our research, we already achieved some results:

A formal algebraic analysis of information discounting, especially …

Magnopark, Smart Parking Detection Based On Cellphone Magnetic Sensor, Maryam Arab

Computer Science Theses & Dissertations

We introduce a solution that uses the availability of heavy crowds and their smart devices, to gain more result as to where potential parking is possible. By leveraging the raw magnetometer, gyroscope, and accelerometer data, we are able to detect parking spots through the natural movement exerted by the walking pedestrians on the sidewalks beside the streets. Dating back as far as 2013, a very large portion of pedestrians composing the crowds on the sidewalk, possessed at least one smart device in their hand or pocket14]. It is this statistic that fuels our application, in which we depend on crowds …

A Hybrid Tabu/Scatter Search Algorithm For Simulation-Based Optimization Of Multi-Objective Runway Operations Scheduling, Bulent Soykan

Engineering Management & Systems Engineering Theses & Dissertations

As air traffic continues to increase, air traffic flow management is becoming more challenging to effectively and efficiently utilize airport capacity without compromising safety, environmental and economic requirements. Since runways are often the primary limiting factor in airport capacity, runway operations scheduling emerge as an important problem to be solved to alleviate flight delays and air traffic congestion while reducing unnecessary fuel consumption and negative environmental impacts. However, even a moderately sized real-life runway operations scheduling problem tends to be too complex to be solved by analytical methods, where all mathematical models for this problem belong to the complexity class …

Using Web Archives To Enrich The Live Web Experience Through Storytelling, Yasmin Alnoamany

Computer Science Theses & Dissertations

Much of our cultural discourse occurs primarily on the Web. Thus, Web preservation is a fundamental precondition for multiple disciplines. Archiving Web pages into themed collections is a method for ensuring these resources are available for posterity. Services such as Archive-It exists to allow institutions to develop, curate, and preserve collections of Web resources. Understanding the contents and boundaries of these archived collections is a challenge for most people, resulting in the paradox of the larger the collection, the harder it is to understand. Meanwhile, as the sheer volume of data grows on the Web, "storytelling" is becoming a popular …

Machine Learning Methods For Medical And Biological Image Computing, Rongjian Li

Computer Science Theses & Dissertations

Medical and biological imaging technologies provide valuable visualization information of structure and function for an organ from the level of individual molecules to the whole object. Brain is the most complex organ in body, and it increasingly attracts intense research attentions with the rapid development of medical and bio-logical imaging technologies. A massive amount of high-dimensional brain imaging data being generated makes the design of computational methods for efficient analysis on those images highly demanded. The current study of computational methods using hand-crafted features does not scale with the increasing number of brain images, hindering the pace of scientific discoveries …

Development Of Visualization-Animation Software For Learning Transportation Algorithms, Ivan P. Makohon

Computational Modeling & Simulation Engineering Theses & Dissertations

Recognizing the steady decline in US Science Technology Engineering Mathematics (STEM) interests and enrollments, the National Science Foundation (NSF) and the White House have developed national strategies and provided significant budget resources to STEM education research [1-2] in the past years, with the ultimate goals being to improve both the quality and number of highly trained US educators, student workforce in STEM topics, in today’s highly competitive global markets. With the explosion of the internet’s capability and availability, it is even more critical to effectively train this future USA-STEM work-force and/or to develop effective STEM related teaching tools to reach …

A Simulation-Based Layered Framework Framework For The Development Of Collaborative Autonomous Systems, Ioannis Sakiotis

Computational Modeling & Simulation Engineering Theses & Dissertations

The purpose of this thesis is to introduce a simulation-based software framework that facilitates the development of collaborative autonomous systems. Significant commonalities exist in the design approaches of both collaborative and autonomous systems, mirroring the sense, plan, act paradigm, and mostly adopting layered architectures. Unfortunately, the development of such systems is intricate and requires low-level interfacing which significantly detracts from development time. Frameworks for the development of collaborative and autonomous systems have been developed but are not flexible and center on narrow ranges of applications and platforms. The proposed framework utilizes an expandable layered structure that allows developers to define …