Computer Sciences Commons^™

Combining Cryo-Em Density Map And Residue Contact For Protein Secondary Structure Topologies, Maytha Alshammari, Jing He

Computer Science Faculty Publications

Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. A topology of secondary structures defines the mapping between a set of sequence segments and a set of traces of secondary structures in three-dimensional space. In order to enhance accuracy in ranking secondary structure topologies, we explored a method that combines three sources of information: a set …

See-Trend: Secure Traffic-Related Event Detection In Smart Communities, Stephan Olariu, Dimitrie C. Popescu

Computer Science Faculty Publications

It has been widely recognized that one of the critical services provided by Smart Cities and Smart Communities is Smart Mobility. This paper lays the theoretical foundations of SEE-TREND, a system for Secure Early Traffic-Related EveNt Detection in Smart Cities and Smart Communities. SEE-TREND promotes Smart Mobility by implementing an anonymous, probabilistic collection of traffic-related data from passing vehicles. The collected data are then aggregated and used by its inference engine to build beliefs about the state of the traffic, to detect traffic trends, and to disseminate relevant traffic-related information along the roadway to help the driving public make informed …

Adaptive Physics-Based Non-Rigid Registration For Immersive Image-Guided Neuronavigation Systems, Fotis Drakopoulos, Christos Tsolakis, Angelos Angelopoulos, Yixun Liu, Chengjun Yao, Kyriaki Rafailia Kavazidi, Nikolaos Foroglou, Andrey Fedorov, Sarah Frisken, Ron Kikinis, Alexandra Golby, Nikos Chrisochoides

Computer Science Faculty Publications

Objective: In image-guided neurosurgery, co-registered preoperative anatomical, functional, and diffusion tensor imaging can be used to facilitate a safe resection of brain tumors in eloquent areas of the brain. However, the brain deforms during surgery, particularly in the presence of tumor resection. Non-Rigid Registration (NRR) of the preoperative image data can be used to create a registered image that captures the deformation in the intraoperative image while maintaining the quality of the preoperative image. Using clinical data, this paper reports the results of a comparison of the accuracy and performance among several non-rigid registration methods for handling brain deformation. A …

Extraction And Evaluation Of Statistical Information From Social And Behavioral Science Papers, Sree Sai Teja Lanka, Sarah Rajtmajer, Jian Wu, C. Lee Giles

Computer Science Faculty Publications

With substantial and continuing increases in the number of published papers across the scientific literature, development of reliable approaches for automated discovery and assessment of published findings is increasingly urgent. Tools which can extract critical information from scientific papers and metadata can support representation and reasoning over existing findings, and offer insights into replicability, robustness and generalizability of specific claims. In this work, we present a pipeline for the extraction of statistical information (p-values, sample size, number of hypotheses tested) from full-text scientific documents. We validate our approach on 300 papers selected from the social and behavioral science literatures, and …

A Tool For Segmentation Of Secondary Structures In 3d Cryo-Em Density Map Components Using Deep Convolutional Neural Networks, Yongcheng Mu, Salim Sazzed, Maytha Alshammari, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Although cryo-electron microscopy (cryo-EM) has been successfully used to derive atomic structures for many proteins, it is still challenging to derive atomic structures when the resolution of cryo-EM density maps is in the medium resolution range, such as 5–10 Å. Detection of protein secondary structures, such as helices and β-sheets, from cryo-EM density maps provides constraints for deriving atomic structures from such maps. As more deep learning methodologies are being developed for solving various molecular problems, effective tools are needed for users to access them. We have developed an effective software bundle, DeepSSETracer, for the detection of protein secondary structure …

Ssentiaa: A Self-Supervised Sentiment Analyzer For Classification From Unlabeled Data, Salim Sazzed, Sampath Jayarathna

Computer Science Faculty Publications

In recent years, supervised machine learning (ML) methods have realized remarkable performance gains for sentiment classification utilizing labeled data. However, labeled data are usually expensive to obtain, thus, not always achievable. When annotated data are unavailable, the unsupervised tools are exercised, which still lag behind the performance of supervised ML methods by a large margin. Therefore, in this work, we focus on improving the performance of sentiment classification from unlabeled data. We present a self-supervised hybrid methodology SSentiA (Self-supervised Sentiment Analyzer) that couples an ML classifier with a lexicon-based method for sentiment classification from unlabeled data. We first introduce LRSentiA …

Understanding And Predicting Retractions Of Published Work, Sai Ajay Modukuri, Sarah Rajtmajer, Anna Cinzia Squicciarini, Jian Wu, C. Lee Giles

Computer Science Faculty Publications

Recent increases in the number of retractions of published papers reflect heightened attention and increased scrutiny in the scientific process motivated, in part, by the replication crisis. These trends motivate computational tools for understanding and assessment of the scholarly record. Here, we sketch the landscape of retracted papers in the Retraction Watch database, a collection of 19k records of published scholarly articles that have been retracted for various reasons (e.g., plagiarism, data error). Using metadata as well as features derived from full-text for a subset of retracted papers in the social and behavioral sciences, we develop a random forest classifier …

Recognizing Figure Labels In Patents, Ming Gong, Xin Wei, Diane Oyen, Jian Wu, Martin Gryder

Computer Science Faculty Publications

Scientific documents often contain significant information in figures. The United States Patent and Trademark Office (USPTO) awards thousands of patents each week, with each patent containing on the order of a dozen figures. The information conveyed by these figures typically include a drawing or diagram, a label, caption and reference text within the document. Yet associating the short bits of text to the figure is challenging when labels are embedded within the figure, as they typically are in patents. Using patents as a testbench, this paper highlights an open challenge in analyzing all of the information presented in scientific/technical documents …

Analysis Of Subtelomeric Rextal Assemblies Using Quast, Tunazzina Islam, Desh Ranjan, Mohammad Zubair, Eleanor Young, Ming Xiao, Harold Riethman

Computer Science Faculty Publications

Genomic regions of high segmental duplication content and/or structural variation have led to gaps and misassemblies in the human reference sequence, and are refractory to assembly from whole-genome short-read datasets. Human subtelomere regions are highly enriched in both segmental duplication content and structural variations, and as a consequence are both impossible to assemble accurately and highly variable from individual to individual. Recently, we developed a pipeline for improved region-specific assembly called Regional Extension of Assemblies Using Linked-Reads (REXTAL). In this study, we evaluate REXTAL and genome-wide assembly (Supernova) approaches on 10X Genomics linked-reads data sets partitioned and barcoded using the …

Extractive Research Slide Generation Using Windowed Labeling Ranking, Athar Sefid, Prasenjit Mitra, Jian Wu, C. Lee Giles

Computer Science Faculty Publications

Presentation slides generated from original research papers provide an efficient form to present research innovations. Manually generating presentation slides is labor-intensive. We propose a method to automatically generates slides for scientific articles based on a corpus of 5000 paper-slide pairs compiled from conference proceedings websites. The sentence labeling module of our method is based on SummaRuNNer, a neural sequence model for extractive summarization. Instead of ranking sentences based on semantic similarities in the whole document, our algorithm measures the importance and novelty of sentences by combining semantic and lexical features within a sentence window. Our method outperforms several baseline methods …

Systematizing Confidence In Open Research And Evidence (Score), Nazanin Alipourfard, Beatrix Arendt, Daniel M. Benjamin, Noam Benkler, Michael Bishop, Mark Burstein, Martin Bush, James Caverlee, Yiling Chen, Chae Clark, Anna Dreber Almenberg, Timothy M. Errington, Fiona Fidler, Nicholas Fox, Aaron Frank, Hannah Fraser, Scott Friedman, Ben Gelman, James Gentile, Jian Wu, Et Al., Score Collaboration

Computer Science Faculty Publications

Assessing the credibility of research claims is a central, continuous, and laborious part of the scientific process. Credibility assessment strategies range from expert judgment to aggregating existing evidence to systematic replication efforts. Such assessments can require substantial time and effort. Research progress could be accelerated if there were rapid, scalable, accurate credibility indicators to guide attention and resource allocation for further assessment. The SCORE program is creating and validating algorithms to provide confidence scores for research claims at scale. To investigate the viability of scalable tools, teams are creating: a database of claims from papers in the social and behavioral …

Automatic Metadata Extraction Incorporating Visual Features From Scanned Electronic Theses And Dissertations, Muntabir Hasan Choudhury, Himarsha R. Jayanetti, Jian Wu, William A. Ingram, Edward A. Fox

Computer Science Faculty Publications

Electronic Theses and Dissertations (ETDs) contain domain knowledge that can be used for many digital library tasks, such as analyzing citation networks and predicting research trends. Automatic metadata extraction is important to build scalable digital library search engines. Most existing methods are designed for born-digital documents, so they often fail to extract metadata from scanned documents such as ETDs. Traditional sequence tagging methods mainly rely on text-based features. In this paper, we propose a conditional random field (CRF) model that combines text-based and visual features. To verify the robustness of our model, we extended an existing corpus and created a …

Fundamentals Of Human-Centric Artificial Intelligence (A.I.): Comparative Analysis Of Europe And The U. S. Landscape, Torré A. Williams

Cybersecurity Undergraduate Research Showcase

This research is a comparative analysis of human-centric Artificial Intelligence (A.I.) in Europe and the U.S. This research establishes fundamentals that are critical to what makes A.I. human-centric. This research contains eight phases: 1) Lawful A.I.; 2) Robust A.I.; 3) Ethical A.I.; 4) Human-centric A.I.; 5) Current State of A.I.; 6) A.I. in Europe; 7) A.I. in the U.S.; 9) Importance of Human-centric A.I. This research shows that there are still ongoing changes with having a human-centric A.I. and why it is very important to society. This research is the beginning of the making of a successful and reliable human-centric …

Internet Of Things (Iot): Cybersecurity Risks In Healthcare, Ruhi Patel

Cybersecurity Undergraduate Research Showcase

The rapid growth and investment in the Internet of Things (IoT) has significantly impacted how individuals and industries operate. The Internet of Things (IoT) refers to a network of physical, technology-embedded objects that communicate, detect, and interact with their external environment or internal state (Hung, 2017). According to Tankovska (2020), IoT devices are estimated to reach 21.5 billion units by 2025. This technological boom is leading various industrial sectors to notice a quick increase in cybersecurity risks and threats. One industrial sector has been particularly vulnerable to numerous cyber threats across the globe: healthcare. Oliver Noble (2020), a data encryption …

Parallelization Of The Advancing Front Local Reconnection Mesh Generation Software Using A Pseudo-Constrained Parallel Data Refinement Method, Kevin Mark Garner Jr.

Computer Science Theses & Dissertations

Preliminary results of a long-term project entailing the parallelization of an industrial strength sequential mesh generator, called Advancing Front Local Reconnection (AFLR), are presented. AFLR has been under development for the last 25 years at the NSF/ERC center at Mississippi State University. The parallel procedure that is presented is called Pseudo-constrained (PsC) Parallel Data Refinement (PDR) and consists of the following steps: (i) use an octree data-decomposition scheme to divide the original geometry into subdomains (octree leaves), (ii) refine each subdomain with the proper adjustments of its neighbors using the given refinement code, and (iii) combine all subdomain data into …

The Effects Of Security Framing, Time Pressure, And Brand Familiarity On Risky Mobile Application Downloads, Cody Parker

Psychology Theses & Dissertations

The current study examined the effects of security system framing, time pressure, and brand familiarity on mobile application download behaviors, with an emphasis on risk taking. According to the Prospect Theory, people tend to engage in irrational decision making, and make qualitatively different decisions when information is framed in terms of gains and losses (i.e., the framing effect). Past research has used this framing effect to guide the design of a risk display for mobile applications (apps), with the purpose of communicating the potential risks and minimizing insecure app selections. Time pressure has been shown to influence the framing effect …

Mementomap: A Web Archive Profiling Framework For Efficient Memento Routing, Sawood Alam

Computer Science Theses & Dissertations

With the proliferation of public web archives, it is becoming more important to better profile their contents, both to understand their immense holdings as well as to support routing of requests in Memento aggregators. A memento is a past version of a web page and a Memento aggregator is a tool or service that aggregates mementos from many different web archives. To save resources, the Memento aggregator should only poll the archives that are likely to have a copy of the requested Uniform Resource Identifier (URI). Using the Crawler Index (CDX), we generate profiles of the archives that summarize their …

Enhanced Traffic Incident Analysis With Advanced Machine Learning Algorithms, Zhenyu Wang

Computational Modeling & Simulation Engineering Theses & Dissertations

Traffic incident analysis is a crucial task in traffic management centers (TMCs) that typically manage many highways with limited staff and resources. An effective automatic incident analysis approach that can report abnormal events timely and accurately will benefit TMCs in optimizing the use of limited incident response and management resources. During the past decades, significant efforts have been made by researchers towards the development of data-driven approaches for incident analysis. Nevertheless, many developed approaches have shown limited success in the field. This is largely attributed to the long detection time (i.e., waiting for overwhelmed upstream detection stations; meanwhile, downstream stations …

Autonomous Vehicles And The Ethical Tension Between Occupant And Non-Occupant Safety, Jason Borenstein, Joseph Herkert, Keith Miller

The Journal of Sociotechnical Critique

Given that the creation and deployment of autonomous vehicles is likely to continue, it is important to explore the ethical responsibilities of designers, manufacturers, operators, and regulators of the technology. We specifically focus on the ethical responsibilities surrounding autonomous vehicles that these stakeholders have to protect the safety of non-occupants, meaning individuals who are around the vehicles while they are operating. The term “non-occupants” includes, but is not limited to, pedestrians and cyclists. We are particularly interested in how to assign moral responsibility for the safety of non-occupants when autonomous vehicles are deployed in a complex, land-based transportation system.

Deepfrag-K: A Fragment-Based Deep Learning Approach For Protein Fold Recognition, Wessam Elhefnawy, Min Li, Jianxin Wang, Yaohang Li

Computer Science Faculty Publications

Background: One of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminative features at fragment level to improve the accuracy of protein fold recognition. DeepFrag-k is composed of two stages: the first stage employs a multi-modal Deep Belief Network (DBN) to predict the potential structural fragments given a sequence, represented as a fragment vector, and then the second stage uses a deep convolutional neural network (CNN) to classify the fragment vector into the corresponding fold.

Results: Our results show that DeepFrag-k yields …

A Survey On Securing Personally Identifiable Information On Smartphones, Dar’Rell Pope, Yen-Hung (Frank) Hu, Mary Ann Hoppa

Virginia Journal of Science

With an ever-increasing footprint, already topping 3 billion devices, smartphones have become a huge cybersecurity concern. The portability of smartphones makes them convenient for users to access and store personally identifiable information (PII); this also makes them a popular target for hackers. This survey shares practical insights derived from analyzing 16 real-life case studies that exemplify: the vulnerabilities that leave smartphones open to cybersecurity attacks; the mechanisms and attack vectors typically used to steal PII from smartphones; the potential impact of PII breaches upon all parties involved; and recommended defenses to help prevent future PII losses. The contribution of this …

The Hidden Advantage Among Digital Natives Within Bug Bounty Programs, James (Jimmy) Allah-Mensah

Cybersecurity Undergraduate Research Showcase

Bug bounty programs are a great way for companies and organizations to help keep their systems and information secure; however, there are only a limited number of white hat hacking participant spots. With only so many seats available at the table, being able to determine the most qualified group of individuals is critical to the efficiency of the program at large. Digital natives, people born into the digital age, provide an instinctive approach when dealing with technology. On the other hand, digital immigrants, people who grew up before the digital age and had to adapt to new technology, evidently utilize …

Agent-Based Modelling Of Values: The Case Of Value Sensitive Design For Refugee Logistics, Christine Boshuijzen-Van Burken, Ross J. Gore, Frank Dignum, Lamber Royakkers, Phillip Wozny, F. Leron Shults

VMASC Publications

We have used value sensitive design as a method to develop an agent-based model of values in humanitarian logistics for refugees. Schwartz’s theory of universal values is implemented in the model in such a way that agents can make value trade-offs, which are operationalized into a measure of refugee wellbeing and a measure of public opinion about how the refugee logistics is being handled. By trying out different ‘value scenarios’, stakeholders who are responsible for, or involved in refugee logistics can have insights into the effects of various value choices. The model is visualized and made usable as a platform …

Gaining Insight Into Solar Photovoltaic Power Generation Forecasting Utilizing Explainable Artificial Intelligence Tools, Murat Kuzlu, Umit Cali, Vinayak Sharma, Özgür Güler

Engineering Technology Faculty Publications

Over the last two decades, Artificial Intelligence (AI) approaches have been applied to various applications of the smart grid, such as demand response, predictive maintenance, and load forecasting. However, AI is still considered to be a ‘‘black-box’’ due to its lack of explainability and transparency, especially for something like solar photovoltaic (PV) forecasts that involves many parameters. Explainable Artificial Intelligence (XAI) has become an emerging research field in the smart grid domain since it addresses this gap and helps understand why the AI system made a forecast decision. This article presents several use cases of solar PV energy forecasting using …

Snitch Application: Addressing Cyber Trust In Future Living Spaces, Russell Moore

Cybersecurity Undergraduate Research Showcase

The future of smart homes is filled with excitement and ample opportunity to live in an environment that features extraordinary convenience and energy efficiency. Devices such as Amazon Alexa and Roku Smart TV’s feature voice interaction options that provide the user with enhanced functionality. While voice-activated devices are accommodating, it is imperative to acknowledge how they work on the backend. The problem is that these devices collect and share a large amount of data from users who are oftentimes unaware that it’s even happening. The Snitch App is being developed in order to inform the user of what exactly is …

A Framework For Verifying The Fixity Of Archived Web Resources, Mohamed Aturban

Computer Science Theses & Dissertations

The number of public and private web archives has increased, and we implicitly trust content delivered by these archives. Fixity is checked to ensure that an archived resource has remained unaltered (i.e., fixed) since the time it was captured. Currently, end users do not have the ability to easily verify the fixity of content preserved in web archives. For instance, if a web page is archived in 1999 and replayed in 2019, how do we know that it has not been tampered with during those 20 years? In order for the users of web archives to verify that archived web …

Secure Mobile Computing By Using Convolutional And Capsule Deep Neural Networks, Rui Ning

Electrical & Computer Engineering Theses & Dissertations

Mobile devices are becoming smarter to satisfy modern user's increasing needs better, which is achieved by equipping divers of sensors and integrating the most cutting-edge Deep Learning (DL) techniques. As a sophisticated system, it is often vulnerable to multiple attacks (side-channel attacks, neural backdoor, etc.). This dissertation proposes solutions to maintain the cyber-hygiene of the DL-Based smartphone system by exploring possible vulnerabilities and developing countermeasures.

First, I actively explore possible vulnerabilities on the DL-Based smartphone system to develop proactive defense mechanisms. I discover a new side-channel attack on smartphones using the unrestricted magnetic sensor data. I demonstrate that attackers can …

Automatic Linear And Curvilinear Mesh Generation Driven By Validity Fidelity And Topological Guarantees, Jing Xu

Computer Science Theses & Dissertations

Image-based geometric modeling and mesh generation play a critical role in computational biology and medicine. In this dissertation, a comprehensive computational framework for both guaranteed quality linear and high-order automatic mesh generation is presented. Starting from segmented images, a quality 2D/3D linear mesh is constructed. The boundary of the constructed mesh is proved to be homeomorphic to the object surface. In addition, a guaranteed dihedral angle bound of up to 19:47^o for the output tetrahedra is provided. Moreover, user-specified guaranteed bounds on the distance between the boundaries of the mesh and the boundaries of the materials are allowed. The …

Cyber-Assets At Risk (Car): Monetary Impact Of Personally Identifiable Information Data Breaches On Companies, Omer Ilker Poyraz

Engineering Management & Systems Engineering Theses & Dissertations

Cyber-systems provide convenience, ubiquity, economic advantage, and higher efficiency to both individuals and organizations. However, vulnerabilities of the cyber domain also offer malicious actors with the opportunities to compromise the most sensitive information. Recent cybersecurity incidents show that a group of hackers can cause a massive data breach, resulting in companies losing competitive advantage, reputation, and money. Governments have since taken some actions in protecting individuals and companies from such crime by authorizing federal agencies and developing regulations. To protect the public from losing their most sensitive records, governments have also been compelling companies to follow cybersecurity regulations. If companies …

Bootstrapping Web Archive Collections From Micro-Collections In Social Media, Alexander C. Nwala

Computer Science Theses & Dissertations

In a Web plagued by disappearing resources, Web archive collections provide a valuable means of preserving Web resources important to the study of past events. These archived collections start with seed URIs (Uniform Resource Identifiers) hand-selected by curators. Curators produce high quality seeds by removing non-relevant URIs and adding URIs from credible and authoritative sources, but this ability comes at a cost: it is time consuming to collect these seeds. The result of this is a shortage of curators, a lack of Web archive collections for various important news events, and a need for an automatic system for generating seeds. …