Physical Sciences and Mathematics Commons^™

Tracing And Segmentation Of Molecular Patterns In 3-Dimensional Cryo-Et/Em Density Maps Through Algorithmic Image Processing And Deep Learning-Based Techniques, Salim Sazzed

Computer Science Theses & Dissertations

Understanding the structures of biological macromolecules is highly important as they are closely associated with cellular functionalities. Comprehending the precise organization of actin filaments is crucial because they form the dynamic cytoskeleton, which offers structural support to cells and connects the cell’s interior with its surroundings. However, determining the precise organization of actin filaments is challenging due to the poor quality of cryo-electron tomography (cryo-ET) images, which suffer from low signal-to-noise (SNR) ratios and the presence of missing wedge, as well as diverse shape characteristics of actin filaments. To address these formidable challenges, the primary component of this dissertation focuses …

Towards Intelligent Runtime Framework For Distributed Heterogeneous Systems, Polykarpos Thomadakis

Computer Science Theses & Dissertations

Scientific applications strive for increased memory and computing performance, requiring massive amounts of data and time to produce results. Applications utilize large-scale, parallel computing platforms with advanced architectures to accommodate their needs. However, developing performance-portable applications for modern, heterogeneous platforms requires lots of effort and expertise in both the application and systems domains. This is more relevant for unstructured applications whose workflow is not statically predictable due to their heavily data-dependent nature. One possible solution for this problem is the introduction of an intelligent Domain-Specific Language (iDSL) that transparently helps to maintain correctness, hides the idiosyncrasies of lowlevel hardware, and …

Inverse Mappers For Qcd Global Analysis, Manal Almaeen

Computer Science Theses & Dissertations

Inverse problems – using measured observations to determine unknown parameters – are well motivated but challenging in many scientific problems. Mapping parameters to observables is a well-posed problem with unique solutions, and therefore can be solved with differential equations or linear algebra solvers. However, the inverse problem requires backward mapping from observable to parameter space, which is often nonunique. Consequently, solving inverse problems is ill-posed and a far more challenging computational problem.

Our motivated application in this dissertation is the inverse problems in nuclear physics that characterize the internal structure of the hadrons. We first present a machine learning framework …

Assessing The Prevalence And Archival Rate Of Uris To Git Hosting Platforms In Scholarly Publications, Emily Escamilla

Computer Science Theses & Dissertations

The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs). Similarly, Software Heritage is working to archive public source code, but there is value in archiving the surrounding ephemera that provide important context to the code while maintaining their original URIs. In current implementations, source code …

Supporting Account-Based Queries For Archived Instagram Posts, Himarsha R. Jayanetti

Computer Science Theses & Dissertations

Social media has become one of the primary modes of communication in recent times, with popular platforms such as Facebook, Twitter, and Instagram leading the way. Despite its popularity, Instagram has not received as much attention in academic research compared to Facebook and Twitter, and its significant role in contemporary society is often overlooked. Web archives are making efforts to preserve social media content despite the challenges posed by the dynamic nature of these sites. The goal of our research is to facilitate the easy discovery of archived copies, or mementos, of all posts belonging to a specific Instagram account …

Machine Learning-Based Event Generator, Yasir Alanazi

Computer Science Theses & Dissertations

Monte Carlo-based event generators have been the primary source for simulating particle collision experiments for the study of interesting physics scenarios. Monte Carlo generators rely on theoretical assumptions, which limit their ability to capture the full range of possible correlations between particle’s momenta. In addition, the simulations of the complete pipeline often take minutes to generate a single event even with the help of supercomputers.

In recent years, much attention has been devoted to the development of machine learning event generators. They demonstrate attractive advantages, including fast simulations, data compression, and being agnostic of theoretical assumptions. However, most of the …

A Relevance Model For Threat-Centric Ranking Of Cybersecurity Vulnerabilities, Corren G. Mccoy

Computer Science Theses & Dissertations

The relentless and often haphazard process of tracking and remediating vulnerabilities is a top concern for cybersecurity professionals. The key challenge they face is trying to identify a remediation scheme specific to in-house, organizational objectives. Without a strategy, the result is a patchwork of fixes applied to a tide of vulnerabilities, any one of which could be the single point of failure in an otherwise formidable defense. This means one of the biggest challenges in vulnerability management relates to prioritization. Given that so few vulnerabilities are a focus of real-world attacks, a practical remediation strategy is to identify vulnerabilities likely …

Towards Privacy And Security Concerns Of Adversarial Examples In Deep Hashing Image Retrieval, Yanru Xiao

Computer Science Theses & Dissertations

With the explosive growth of images on the internet, image retrieval based on deep hashing attracts spotlights from both research and industry communities. Empowered by deep neural networks (DNNs), deep hashing enables fast and accurate image retrieval on large-scale data. However, inheriting from deep learning, deep hashing remains vulnerable to specifically designed input, called adversarial examples. By adding imperceptible perturbations on inputs, adversarial examples fool DNNs to make wrong decisions. The existence of adversarial examples not only raises security concerns for real-world deep learning applications, but also provides us with a technique to confront malicious applications.

In this dissertation, we …

Evaluation Of Generative Models For Predicting Microstructure Geometries In Laser Powder Bed Fusion Additive Manufacturing, Andy Ramlatchan

Computer Science Theses & Dissertations

In-situ process monitoring for metals additive manufacturing is paramount to the successful build of an object for application in extreme or high stress environments. In selective laser melting additive manufacturing, the process by which a laser melts metal powder during the build will dictate the internal microstructure of that object once the metal cools and solidifies. The difficulty lies in that obtaining enough variety of data to quantify the internal microstructures for the evaluation of its physical properties is problematic, as the laser passes at high speeds over powder grains at a micrometer scale. Imaging the process in-situ is complex …

Using Ensemble Learning Techniques To Solve The Blind Drift Calibration Problem, Devin Scott Drake

Computer Science Theses & Dissertations

Large sets of sensors deployed in nearly every practical environment are prone to drifting out of calibration. This drift can be sensor-based, with one or several sensors falling out of calibration, or system-wide, with changes to the physical system causing sensor-reading issues. Recalibrating sensors in either case can be both time and cost prohibitive. Ideally, some technique could be employed between the sensors and the final reading that recovers the drift-free sensor readings. This paper covers the employment of two ensemble learning techniques — stacking and bootstrap aggregation (or bagging) — to recover drift-free sensor readings from a suite of …

Transparscit: A Transformer-Based Citation Parser Trained On Large-Scale Synthesized Data, Md Sami Uddin

Computer Science Theses & Dissertations

Accurately parsing citation strings is key to automatically building large-scale citation graphs, so a robust citation parser is an essential module in academic search engines. One limitation of the state-of-the-art models (such as ParsCit and Neural-ParsCit) is the lack of a large-scale training corpus. Manually annotating hundreds of thousands of citation strings is laborious and time-consuming. This thesis presents a novel transformer-based citation parser by leveraging the GIANT dataset, consisting of 1 billion synthesized citation strings covering over 1500 citation styles. As opposed to handcrafted features, our model benefits from word embeddings and character-based embeddings by combining the bidirectional long …

Move: Mobile Observers Variants And Extensions, Ryan Florin

Computer Science Theses & Dissertations

Traffic state estimation is a fundamental task of Intelligent Transportation Systems. Recent advances in sensor technology and emerging computer and vehicular communications paradigms have brought the task of estimating traffic state parameters in real-time within reach.

This has led to the main research question of this thesis: Can a vehicle accurately estimate traffic parameters using onboard resources shared through CV technology in a lightweight manner without utilizing centralized or roadside infrastructure?

In 1954 Wardrop and Charlesworth proposed the Moving Observer method to measure traffic parameters based on an observed number of vehicle passes. We start by proposing methods for detecting …

Improving Collection Understanding For Web Archives With Storytelling: Shining Light Into Dark And Stormy Archives, Shawn M. Jones

Computer Science Theses & Dissertations

Collections are the tools that people use to make sense of an ever-increasing number of archived web pages. As collections themselves grow, we need tools to make sense of them. Tools that work on the general web, like search engines, are not a good fit for these collections because search engines do not currently represent multiple document versions well. Web archive collections are vast, some containing hundreds of thousands of documents. Thousands of collections exist, many of which cover the same topic. Few collections include standardized metadata. Too many documents from too many collections with insufficient metadata makes collection understanding …

A Unified Framework For Parallel Anisotropic Mesh Adaptation, Christos Tsolakis

Computer Science Theses & Dissertations

Finite-element methods are a critical component of the design and analysis procedures of many (bio-)engineering applications. Mesh adaptation is one of the most crucial components since it discretizes the physics of the application at a relatively low cost to the solver. Highly scalable parallel mesh adaptation methods for High-Performance Computing (HPC) are essential to meet the ever-growing demand for higher fidelity simulations. Moreover, the continuous growth of the complexity of the HPC systems requires a systematic approach to exploit their full potential. Anisotropic mesh adaptation captures features of the solution at multiple scales while, minimizing the required number of elements. …

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 …

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 …

Towards Dynamic Vehicular Clouds, Aida Ghazizadeh

Computer Science Theses & Dissertations

Motivated by the success of the conventional cloud computing, Vehicular Clouds were introduced as a group of vehicles whose corporate computing, sensing, communication, and physical resources can be coordinated and dynamically allocated to authorized users. One of the attributes that set Vehicular Clouds apart from conventional clouds is resource volatility. As vehicles enter and leave the cloud, new computing resources become available while others depart, creating a volatile environment where the task of reasoning about fundamental performance metrics becomes very challenging. The goal of this thesis is to design an architecture and model for a dynamic Vehicular Cloud built on …

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. …

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 …

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 …

Novel Use Of Neural Networks To Identify And Detect Electrical Infrastructure Performance, Evan Pierre Savaria

Computer Science Theses & Dissertations

Electrical grid maintenance and repairs are crucial services that keep America’s lights on. Electrical service providers make it their priority to uphold minimal interruptions to this service. Electricity is essential for modern technology within the home, such as cooking, refrigeration, and hot water. Organizations, such as schools, hospitals, and military bases, cannot properly function or operate without power. When analyzing the current electrical infrastructure, it is evident that considerable components of the power grid are aging and in need of replacement. Additionally, threats and damage continue to occur. These damages occur not only due to simple, single power line failure …

Scalable Parallel Delaunay Image-To-Mesh Conversion For Shared And Distributed Memory Architectures, Daming Feng

Computer Science Theses & Dissertations

Mesh generation is an essential component for many engineering applications. The ability to generate meshes in parallel is critical for the scalability of the entire Finite Element Method (FEM) pipeline. However, parallel mesh generation applications belong to the broader class of adaptive and irregular problems, and are among the most complex, challenging, and labor intensive to develop and maintain. In this thesis, we summarize several years of the progress that we made in a novel framework for highly scalable and guaranteed quality mesh generation for finite element analysis in three dimensions. We studied and developed parallel mesh generation algorithms on …

Aggregating Private And Public Web Archives Using The Mementity Framework, Matthew R. Kelly

Computer Science Theses & Dissertations

Web archives preserve the live Web for posterity, but the content on the Web one cares about may not be preserved. The ability to access this content in the future requires the assurance that those sites will continue to exist on the Web until the content is requested and that the content will remain accessible. It is ultimately the responsibility of the individual to preserve this content, but attempting to replay personally preserved pages segregates archived pages by individuals and organizations of personal, private, and public Web content. This is misrepresentative of the Web as it was. While the Memento …

Enhancing Portability In High Performance Computing: Designing Fast Scientific Code With Longevity, Jason Orender

Computer Science Theses & Dissertations

Portability, an oftentimes sought-after goal in scientific applications, confers a number of possible advantages onto computer code. Portable code will often have greater longevity, enjoy a broader ecosystem, appeal to a wider variety of application developers, and by definition will run on more systems than its pigeonholed counterpart. These advantages come at a cost, however, and a rational approach to balancing costs and benefits requires a systemic evaluation. While the benefits for each application are likely situation-dependent, the costs in terms of resources, including but not limited to time, money, computational power, and memory requirements, are quantifiable. This document will …

Expanding The Usage Of Web Archives By Recommending Archived Webpages Using Only The Uri, Lulwah M. Alkwai

Computer Science Theses & Dissertations

Web archives are a window to view past versions of webpages. When a user requests a webpage on the live Web, such as http://tripadvisor.com/where_to_t ravel/, the webpage may not be found, which results in an HyperText Transfer Protocol (HTTP) 404 response. The user then may search for the webpage in a Web archive, such as the Internet Archive. Unfortunately, if this page had never been archived, the user will not be able to view the page, nor will the user gain any information on other webpages that have similar content in the archive, such as the archived webpage http://classy-travel.net. Similarly, …

Highly Accurate Fragment Library For Protein Fold Recognition, Wessam Elhefnawy

Computer Science Theses & Dissertations

Proteins play a crucial role in living organisms as they perform many vital tasks in every living cell. Knowledge of protein folding has a deep impact on understanding the heterogeneity and molecular functions of proteins. Such information leads to crucial advances in drug design and disease understanding. Fold recognition is a key step in the protein structure discovery process, especially when traditional computational methods fail to yield convincing structural homologies. In this work, we present a new protein fold recognition approach using machine learning and data mining methodologies.

First, we identify a protein structural fragment library (Frag-K) composed of a …

New Methods To Improve Protein Structure Modeling, Maha Abdelrasoul

Computer Science Theses & Dissertations

Proteins are considered the central compound necessary for life, as they play a crucial role in governing several life processes by performing the most essential biological and chemical functions in every living cell. Understanding protein structures and functions will lead to a significant advance in life science and biology. Such knowledge is vital for various fields such as drug development and synthetic biofuels production.

Most proteins have definite shapes that they fold into, which are the most stable state they can adopt. Due to the fact that the protein structure information provides important insight into its functions, many research efforts …

Novel Technique For Gait Analysis Using Two Waist Mounted Gyroscopes, Ahmed Nasr

Computer Science Theses & Dissertations

Analysis of the human gait is used in many applications such as medicine, sports, and person identification. Several research studies focused on the use of MEMS inertial sensors for gait analysis and showed promising results. The miniaturization of these sensors and their wearability allowed the analysis of gait on a long term outside of the laboratory environment which can reveal more information about the person and introduced the use of gait analysis in new applications such as indoor localization.

Step detection and step length estimation are two basic and important gait analysis tasks. In fact, step detection is a prerequisite …

Deep Learning For Segmentation Of 3d Cryo-Em Images, Devin Reid Haslam

Computer Science Theses & Dissertations

Cryo-electron microscopy (cryo-EM) is an emerging biophysical technique for structural determination of protein complexes. However, accurate detection of secondary structures is still challenging when cryo-EM density maps are at medium resolutions (5-10 Å). Most existing methods are image processing methods that do not fully utilize available images in the cryo-EM database. In this paper, we present a deep learning approach to segment secondary structure elements as helices and β-sheets from medium- resolution density maps. The proposed 3D convolutional neural network is shown to detect secondary structure locations with an F1 score between 0.79 and 0.88 for six simulated test cases. …

Leveraging Resources On Anonymous Mobile Edge Nodes, Ahmed Salem

Computer Science Theses & Dissertations

Smart devices have become an essential component in the life of mankind. The quick rise of smartphones, IoTs, and wearable devices enabled applications that were not possible few years ago, e.g., health monitoring and online banking. Meanwhile, smart sensing laid the infrastructure for smart homes and smart cities. The intrusive nature of smart devices granted access to huge amounts of raw data. Researchers seized the moment with complex algorithms and data models to process the data over the cloud and extract as much information as possible. However, the pace and amount of data generation, in addition to, networking protocols transmitting …