Numerical Analysis and Scientific Computing Commons^™

Pyspqr: A Python Package For Density Estimation Using Deep Learning, Cameron Eddy, Reetam Majumder

Electrical Engineering and Computer Science Undergraduate Honors Theses

Splines are used for representing complex functions. In statistics, splines can be used for distributional shapes that are difficult to model by traditional parametric approaches. Ramsay (1) uses M-Spline bases to estimate continuous distributions. Semi-Parametric Quantile Regression (SPQR), developed by Xu and Reich (2), models conditional distributions where a neural network is used to estimate the basis function weights that depend on covariates. (3) implements a package for SPQR in R. We build on this by implementing a version of SPQR in Python with PyTorch. By using PyTorch, we can use more sophisticated deep learning architectures than those available in …

Using Gaussian Process Regression To Learn Thermodynamic Equations Of State With Uncertainty Quantification, Austen T. Lee

Chemical Engineering Undergraduate Honors Theses

This study investigates the use of derivative-informed Gaussian Process (GP) models to estimate thermodynamic behavior across temperature and density by building a Helmholtz-based equation of state. Argon, a stable monatomic gas, was chosen as a case study within the vapor region. The GP model was trained using values of experimentally measurable properties found by taking first and second derivatives of the original potential function. Results show that while the GP model offered uncertainty quantification and informed thermodynamic behavior, it predicted values that deviated from the ground truth depending on the property. The model exhibited high confidence in regions with substantial …

Geochemical Analysis And Numerical Modeling Of Central And East Tennessee Mississippi Valley-Type Ore Districts: Constraints On Ore Genesis, Jackson Price Copeland

Geosciences Undergraduate Honors Theses

A simple two-way stochastic mixing model is presented for analysis of the lead (Pb) isotope compositions of the North American Mississippi Valley-Type (MVT) districts of East Tennessee, Central Tennessee, and Central Kentucky. Four distinct mixing scenarios were run to critically evaluate the stochastic model and examine different hypotheses regarding the genesis of Central Tennessee and Central Kentucky MVT deposits. Additionally, Pb isotope analysis was conducted on sphalerite samples from the Central and East Tennessee MVT districts. Model and sampling results suggest that Central Tennessee and Central Kentucky ores likely formed by mixing of three fluids. In contrast to conclusions from …

Data-Driven Deep Learning-Based Analysis On Thz Imaging, Haoyan Liu

Graduate Theses and Dissertations

Breast cancer affects about 12.5% of women population in the United States. Surgical operations are often needed post diagnosis. Breast conserving surgery can help remove malignant tumors while maximizing the remaining healthy tissues. Due to lacking effective real-time tumor analysis tools and a unified operation standard, re-excision rate could be higher than 30% among breast conserving surgery patients. This results in significant physical, physiological, and financial burdens to those patients. This work designs deep learning-based segmentation algorithms that detect tissue type in excised tissues using pulsed THz technology. This work evaluates the algorithms for tissue type classification task among freshly …

The Effects Of Side-Channel Attacks On Post-Quantum Cryptography: Influencing Frodokem Key Generation Using The Rowhammer Exploit, Michael Jacob Fahr

Graduate Theses and Dissertations

Modern cryptographic algorithms such as AES and RSA are effectively used for securing data transmission. However, advancements in quantum computing pose a threat to modern cryptography algorithms due to the potential of solving hard mathematical problems faster than conventional computers. Thus, to prepare for quantum computing, NIST has started a competition to standardize quantum-resistant public-key cryptography algorithms. These algorithms are evaluated for strong theoretical security and run-time performance. NIST is in the third round of the competition, and the focus has shifted to analyzing the vulnerabilities to side-channel attacks. One algorithm that has gained notice is the Round 3 alternate …

Gauging The State-Of-The-Art For Foresight Weight Pruning On Neural Networks, Noah James

Computer Science and Computer Engineering Undergraduate Honors Theses

The state-of-the-art for pruning neural networks is ambiguous due to poor experimental practices in the field. Newly developed approaches rarely compare to each other, and when they do, their comparisons are lackluster or contain errors. In the interest of stabilizing the field of pruning, this paper initiates a dive into reproducing prominent pruning algorithms across several architectures and datasets. As a first step towards this goal, this paper shows results for foresight weight pruning across 6 baseline pruning strategies, 5 modern pruning strategies, random pruning, and one legacy method (Optimal Brain Damage). All strategies are evaluated on 3 different architectures …

A Versatile Python Package For Simulating Dna Nanostructures With Oxdna, Kira Threlfall

Computer Science and Computer Engineering Undergraduate Honors Theses

The ability to synthesize custom DNA molecules has led to the feasibility of DNA nanotechnology. Synthesis is time-consuming and expensive, so simulations of proposed DNA designs are necessary. Open-source simulators, such as oxDNA, are available but often difficult to configure and interface with. Packages such as oxdna-tile-binding pro- vide an interface for oxDNA which allows for the ability to create scripts that automate the configuration process. This project works to improve the scripts in oxdna-tile-binding to improve integration with job scheduling systems commonly used in high-performance computing environments, improve ease-of-use and consistency within the scripts compos- ing oxdna-tile-binding, and move …

An Investigation Into, And The Construction Of, An Operable Windows Notifier, Grey Hixson

Computer Science and Computer Engineering Undergraduate Honors Theses

The Office of Sustainability at the University of Arkansas identified that building occupants that have control over operable windows may open them at inappropriate times. Windows opened in a building with a temperature and air differential leads to increased HVAC operating costs and building occupant discomfort. This led the Associate Vice Chancellor of Facilities at the University of Arkansas to propose the construction of a mobile application that a building occupant can use to make an informed decision before opening their window. I have formulated a series of research objectives in conjunction with the Director of the Office of Sustainability …

Side-Channel Analysis On Post-Quantum Cryptography Algorithms, Tristen Teague

Computer Science and Computer Engineering Undergraduate Honors Theses

The advancements of quantum computers brings us closer to the threat of our current asymmetric cryptography algorithms being broken by Shor's Algorithm. NIST proposed a standardization effort in creating a new class of asymmetric cryptography named Post-Quantum Cryptography (PQC). These new algorithms will be resistant against both classical computers and sufficiently powerful quantum computers. Although the new algorithms seem mathematically secure, they can possibly be broken by a class of attacks known as side-channels attacks (SCA). Side-channel attacks involve exploiting the hardware that the algorithm runs on to figure out secret values that could break the security of the system. …

Using Bluetooth Low Energy And E-Ink Displays For Inventory Tracking, David Whelan

Computer Science and Computer Engineering Undergraduate Honors Theses

The combination of Bluetooth Low energy and E-Ink displays allow for a low energy wire-less display. The application of this technology is far reaching especially given how the Bluetooth Low Energy specification can be extended. This paper proposes an extension to this specification specifically for inventory tracking. This extension combined with the low energy E-Ink display results in a smart label that can keep track of additional meta data and inventory counts for physical inventory. This label helps track the physical inventory and can help mitigate any errors in the logical organization of inventory.

Component Damage Source Identification For Critical Infrastructure Systems, Nathan Davis

Graduate Theses and Dissertations

Cyber-Physical Systems (CPS) are becoming increasingly prevalent for both Critical Infrastructure and the Industry 4.0 initiative. Bad values within components of the software portion of CPS, or the computer systems, have the potential to cause major damage if left unchecked, and so detection and locating of where these occur is vital. We further define features of these computer systems and create a use-based system topology. We then introduce a function to monitor system integrity and the presence of bad values as well as an algorithm to locate them. We then show an improved version, taking advantage of several system properties …

Analysis Of Titan's Fluvial Features Using Numerical Modeling, Jeshurun Horton

Mechanical Engineering Undergraduate Honors Theses

River channels have been observed near the Huygens probe landing site on the surface of Titan, along with evidence of rounded water ice boulders transported through fluid flow. Evidence near the landing site suggests active flow of liquid methane, which has motivated the study of the effects of sediment load and channel sizes on Titan’s fluvial features. A numerical model is used to determine the viscosity, flow velocity, and critical boulder transport diameter based on channel size, slope, and a range of sediment concentrations. This model achieves two ends: first, observed boulder diameters are used to determine the ideal channel …

An Automated Method To Enrich Consumer Health Vocabularies Using Glove Word Embeddings And An Auxiliary Lexical Resource, Mohammed Ibrahim, Susan Gauch, Omar Salman, Mohammed Alqahtani

Computer Science and Computer Engineering Faculty Publications and Presentations

Background

Clear language makes communication easier between any two parties. A layman may have difficulty communicating with a professional due to not understanding the specialized terms common to the domain. In healthcare, it is rare to find a layman knowledgeable in medical terminology which can lead to poor understanding of their condition and/or treatment. To bridge this gap, several professional vocabularies and ontologies have been created to map laymen medical terms to professional medical terms and vice versa.

Objective

Many of the presented vocabularies are built manually or semi-automatically requiring large investments of time and human effort and consequently the …

Design And Development Of Techniques To Ensure Integrity In Fog Computing Based Databases, Abdulwahab Fahad S. Alazeb

Graduate Theses and Dissertations

The advancement of information technology in coming years will bring significant changes to the way sensitive data is processed. But the volume of generated data is rapidly growing worldwide. Technologies such as cloud computing, fog computing, and the Internet of things (IoT) will offer business service providers and consumers opportunities to obtain effective and efficient services as well as enhance their experiences and services; increased availability and higher-quality services via real-time data processing augment the potential for technology to add value to everyday experiences. This improves human life quality and easiness. As promising as these technological innovations, they are prone …

A Machine Learning Approach To Understanding Emerging Markets, Namita Balani

Graduate Theses and Dissertations

Logistic providers have learned to efficiently serve their existing customer bases with optimized routes and transportation resource allocation. The problem arises when there is potential for logistics growth in an emerging market with no previous data. The purpose of this work is to use industry data for previously known and well-documented markets to apply data analytic techniques such as machine learning to investigate the uncertainty in a new market. The thesis looks into machine learning techniques to predict miles per stop given historical data. It mainly focuses on Random Forest Regression Analysis, but concludes that additional techniques, such as Polynomial …

Using Deep Learning For Children Brain Image Analysis, Rafael Toche Pizano

Computer Science and Computer Engineering Undergraduate Honors Theses

Analyzing the correlation between brain volumetric/morphometry features and cognition/behavior in children is important in the field of pediatrics as identifying such relationships can help identify children who may be at risk for illnesses. Understanding these relationships can not only help identify children who may be at risk of illnesses, but it can also help evaluate strategies that promote brain development in children. Currently, one way to do this is to use traditional statistical methods such as a correlation analysis, but such an approach does not make it easy to generalize and predict how brain volumetric/morphometry will impact cognition/behavior. One of …

A Comparison Of Word Embedding Techniques For Similarity Analysis, Tyler Gerth

Computer Science and Computer Engineering Undergraduate Honors Theses

There have been a multitude of word embedding techniques developed that allow a computer to process natural language and compare the relationships between different words programmatically. In this paper, similarity analysis, or the testing of words for synonymic relations, is used to compare several of these techniques to see which performs the best. The techniques being compared all utilize the method of creating word vectors, reducing words down into a single vector of numerical values that denote how the word relates to other words that appear around it. In order to get a holistic comparison, multiple analyses were made, with …

Improving Bayesian Graph Convolutional Networks Using Markov Chain Monte Carlo Graph Sampling, Aneesh Komanduri

Computer Science and Computer Engineering Undergraduate Honors Theses

In the modern age of social media and networks, graph representations of real-world phenomena have become incredibly crucial. Often, we are interested in understanding how entities in a graph are interconnected. Graph Neural Networks (GNNs) have proven to be a very useful tool in a variety of graph learning tasks including node classification, link prediction, and edge classification. However, in most of these tasks, the graph data we are working with may be noisy and may contain spurious edges. That is, there is a lot of uncertainty associated with the underlying graph structure. Recent approaches to modeling uncertainty have been …

Trunctrimmer: A First Step Towards Automating Standard Bioinformatic Analysis, Z. Gunner Lawless, Dana Dittoe, Dale R. Thompson, Steven C. Ricke

Computer Science and Computer Engineering Undergraduate Honors Theses

Bioinformatic analysis is a time-consuming process for labs performing research on various microbiomes. Researchers use tools like Qiime2 to help standardize the bioinformatic analysis methods, but even large, extensible platforms like Qiime2 have drawbacks due to the attention required by researchers. In this project, we propose to automate additional standard lab bioinformatic procedures by eliminating the existing manual process of determining the trim and truncate locations for paired end 2 sequences. We introduce a new Qiime2 plugin called TruncTrimmer to automate the process that usually requires the researcher to make a decision on where to trim and truncate manually after …

Using Large Pre-Trained Language Models To Track Emotions Of Cancer Patients On Twitter, Will Baker

Computer Science and Computer Engineering Undergraduate Honors Theses

Twitter is a microblogging website where any user can publicly release a message, called a tweet, expressing their feelings about current events or their own lives. This candid, unfiltered feedback is valuable in the spaces of healthcare and public health communications, where it may be difficult for cancer patients to divulge personal information to healthcare teams, and randomly selected patients may decline participation in surveys about their experiences. In this thesis, BERTweet, a state-of-the-art natural language processing (NLP) model, was used to predict sentiment and emotion labels for cancer-related tweets collected in 2019 and 2020. In longitudinal plots, trends in …

Achieving Differential Privacy And Fairness In Machine Learning, Depeng Xu

Graduate Theses and Dissertations

Machine learning algorithms are used to make decisions in various applications, such as recruiting, lending and policing. These algorithms rely on large amounts of sensitive individual information to work properly. Hence, there are sociological concerns about machine learning algorithms on matters like privacy and fairness. Currently, many studies only focus on protecting individual privacy or ensuring fairness of algorithms separately without taking consideration of their connection. However, there are new challenges arising in privacy preserving and fairness-aware machine learning. On one hand, there is fairness within the private model, i.e., how to meet both privacy and fairness requirements simultaneously in …

Prediction, Recommendation And Group Analytics Models In The Domain Of Mashup Services And Cyber-Argumentation Platform, Md Mahfuzer Rahman

Graduate Theses and Dissertations

Mashup application development is becoming a widespread software development practice due to its appeal for a shorter application development period. Application developers usually use web APIs from different sources to create a new streamlined service and provide various features to end-users. This kind of practice saves time, ensures reliability, accuracy, and security in the developed applications. Mashup application developers integrate these available APIs into their applications. Still, they have to go through thousands of available web APIs and chose only a few appropriate ones for their application. Recommending relevant web APIs might help application developers in this situation. However, very …

Lecture 08: Partial Eigen Decomposition Of Large Symmetric Matrices Via Thick-Restart Lanczos With Explicit External Deflation And Its Communication-Avoiding Variant, Zhaojun Bai

Mathematical Sciences Spring Lecture Series

There are continual and compelling needs for computing many eigenpairs of very large Hermitian matrix in physical simulations and data analysis. Though the Lanczos method is effective for computing a few eigenvalues, it can be expensive for computing a large number of eigenvalues. To improve the performance of the Lanczos method, in this talk, we will present a combination of explicit external deflation (EED) with an s-step variant of thick-restart Lanczos (s-step TRLan). The s-step Lanczos method can achieve an order of s reduction in data movement while the EED enables to compute eigenpairs in batches along with a number …

Lecture 00: Opening Remarks: 46th Spring Lecture Series, Tulin Kaman

Mathematical Sciences Spring Lecture Series

Opening remarks for the 46th Annual Mathematical Sciences Spring Lecture Series at the University of Arkansas, Fayetteville.

Static And Dynamical Properties Of Multiferroics, Sayed Omid Sayedaghaee

Graduate Theses and Dissertations

Since the silicon industrial revolution in the 1950s, a lot of effort was dedicated to the research and development activities focused on material and solid-state sciences. As a result, several cutting-edge technologies are emerging including the applications of functional materials in the design and enhancement of novel devices such as sensors, highly capable data storage media, actuators, transducers, and several other types of electronic tools. In the last two decades, a class of functional materials known as multiferroics has captured significant attention because of providing a huge potential for new designs due to possessing multiple ferroic order parameters at the …

An Update On The Computational Theory Of Hamiltonian Period Functions, Bradley Joseph Klee

Graduate Theses and Dissertations

Lately, state-of-the-art calculation in both physics and mathematics has expanded to include the field of symbolic computing. The technical content of this dissertation centers on a few Creative Telescoping algorithms of our own design (Mathematica implementations are given as a supplement). These algorithms automate analysis of integral period functions at a level of difficulty and detail far beyond what is possible using only pencil and paper (unless, perhaps, you happen to have savant-level mental acuity). We can then optimize analysis in classical physics by using the algorithms to calculate Hamiltonian period functions as solutions to ordinary differential equations. The simple …

Shakespeare In The Eighteenth Century: Algorithm For Quotation Identification, Marion Pauline Chiariglione

Graduate Theses and Dissertations

Quoting a borrowed excerpt of text within another literary work was infrequently done prior to the beginning of the eighteenth century. However, quoting other texts, particularly Shakespeare, became quite common after that. Our work develops automatic approaches to identify that trend. Initial work focuses on identifying exact and modified sections of texts taken from works of Shakespeare in novels spanning the eighteenth century. We then introduce a novel approach to identifying modified quotes by adapting the Edit Distance metric, which is character based, to a word based approach. This paper offers an introduction to previous uses of this metric within …

An Fpga-Based Hardware Accelerator For The Digital Image Correlation Engine, Keaten Stokke

Graduate Theses and Dissertations

The work presented in this thesis was aimed at the development of a hardware accelerator for the Digital Image Correlation engine (DICe) and compare two methods of data access, USB and Ethernet. The original DICe software package was created by Sandia National Laboratories and is written in C++. The software runs on any typical workstation PC and performs image correlation on available frame data produced by a camera. When DICe is introduced to a high volume of frames, the correlation time is on the order of days. The time to process and analyze data with DICe becomes a concern when …

Incorporating Word Order Explicitly In Glove Word Embedding, Brandon Cox

Computer Science and Computer Engineering Undergraduate Honors Theses

Word embedding is the process of representing words from a corpus of text as real number vectors. These vectors are often derived from frequency statistics from the source corpus. In the GloVe model as proposed by Pennington et al., these vectors are generated using a word-word cooccurrence matrix. However, the GloVe model fails to explicitly take into account the order in which words appear within the contexts of other words. In this paper, multiple methods of incorporating word order in GloVe word embeddings are proposed. The most successful method involves directly concatenating several word vector matrices for each position in …

Sentiment Analysis, Quantification, And Shift Detection, Kevin Labille

Graduate Theses and Dissertations

This dissertation focuses on event detection within streams of Tweets based on sentiment quantification. Sentiment quantification extends sentiment analysis, the analysis of the sentiment of individual documents, to analyze the sentiment of an aggregated collection of documents. Although the former has been widely researched, the latter has drawn less attention but offers greater potential to enhance current business intelligence systems. Indeed, knowing the proportion of positive and negative Tweets is much more valuable than knowing which individual Tweets are positive or negative. We also extend our sentiment quantification research to analyze the evolution of sentiment over time to automatically detect …