Digital Commons Network^™

Exploration Of Extended Chemical Reaction Networks, Ramiro Santos

Theses and Dissertations

Chemical Reaction Networks (CRNs) is a well-established model for analyzing distributed and concurrent systems. A central problem studied across CRNs is the reachability problem, which asks whether a target configuration can be obtained from a given initial configuration through a sequence of valid transitions. Classical CRNs are highly expressive but not Turing-universal; their reachability problem is Ackermann-complete, indicating extremely high computational complexity that nevertheless falls short of full universality.

In this thesis, we study Extended Models of Chemical Reaction Networks in which the dynamics of the system are modified. We analyze these models through two fundamental questions. First, simulation, we …

Vision-Language Guided Quadruped Navigation With Reinforcement Learning Control, Chen Yuan Wang

Theses and Dissertations

Large Language Models and their multimodal variants, Vision-Language Models (VLMs), can interpret natural language instructions and visual context. Reinforcement Learning (RL) methods such as Proximal Policy Optimization (PPO) have been shown to successfully learn stable quadruped locomotion. This work investigates whether a VLM integrated with an RL controller can control a quadruped robot to perform instruction-following navigation to a predefined target using text instructions, egocentric vision, and proprioceptive state.

Most VLM-based robotics work directly target prediction of robot actions from multimodal inputs. This approach often depends on large amounts of expert demonstration data, generated by controllers such as trained RL …

Using Siamese Neural Networks To Effectively Detect Trojans In Fpgas When Trojans Manipulate Encryption Operations At The Bitstream Level, Kylie Arnett

Graduate Theses and Dissertations (2019 - present)

This research investigates security vulnerabilities in Field-Programmable Gate Arrays (FPGAs) at the bitstream level, focusing on hardware trojans (HTs) that manipulate encryption operations. This study addresses two critical questions: (1) The feasibility of exploiting FPGA bitstreams to selectively bypass encryption operations when a predefined input pattern is observed (all ones), thereby exposing sensitive data, and (2) the efficacy of Siamese Neural Networks (SNNs) in detecting such trojans with high accuracy. FPGAs are vulnerable to malicious modifications during manufacturing or deployment, posing risks to data integrity and system functionality. In this work, a trojan is inserted into a Xilinx series-7 FPGA …

Polyglot File Detection For Forensic Investigations, Chase Stevens

Graduate Theses and Dissertations (2019 - present)

As technology has become far more ubiquitous over the years, so too has the amount of digital evidence that can and needs to be collected and processed. Forensic tools are developed in response to the growing need, but are limited to what they are programmed to do. One such forensic tool is Autopsy, one of the most widely used open-source tools. Autopsy uses known file-type signatures (e.g., headers, trailers) to identify and recover files from forensic images. Polyglot files introduce a unique problem to both these forensic tools and investigators alike. In the context of the research conducted, polyglot files …

Detecting Sophisticated Cyberattacks On Public Water Infrastructure, Ayrton Purdy

Graduate Theses and Dissertations (2019 - present)

In recent years there has been an increasing number of cyberattacks on public water generation and distribution systems. Advanced persistent attackers could usurp sensors and control systems to contaminate public drinking water. In order to conceal their malicious activity, they can manipulate sensor data flows to give the appearance of normal activity. The compromised sensors would report normal chemical levels even though unsafe water is entering the distribution system. In response, this research proposes a multi-sensor, cross-comparison approach to anomaly detection. The proposed approach is designed to detect sophisticated cyberattacks which are not easily detectable using traditional cyber tools. The …

Datapeer: A Hybrid Interaction Model Web Application Integrating Llms For Human–Llm Collaboration In Data Analysis And Exploration, William I. Bumcum

Honors Theses

DataPeer is a web application that combines open-ended high agency (OHA) and structured low-agency (SLA) interaction paradigms to support human-LLM collaboration in exploratory data analysis. DataPeer integrates a large language model (LLM) with a React frontend and FastAPI backend, allowing both qualitative and quantitative analysis of user-uploaded CSV datasets through a chat-based interface. Users can attach datasets and provide natural language queries, while the LLM provides data analysis to the user. This thesis investigates the integration of LLMs into data analysis workflows and addresses gaps in interaction design and user agency in LLM-driven data tools by offering a responsive interface …

Sql Query Optimization - Human Vs. Chatgpt, Hailey Dennis

All Graduate Reports and Creative Projects, Fall 2023 to Present

Large Language Models (LLMs) such as ChatGPT have become ubiquitous tools for working professionals in the software industry. Many engineers are finding new ways to increase productivity by offloading tasks onto LLMs, while others are finding it difficult to trust code produced artificially, even after review. Taking a look at both perspectives, this study aims to compare a human’s ability to optimize SQL queries to that of an LLM and assess the experience using both methods.

Manual query optimization is a tedious task that relies heavily on statistics, heuristics, and good intuition. The SQL developer must search for the optimal …

Provenance Analysis Of Advanced Persistent Threats In Operational Technology Environments, Laura Aminta Guevara

Open Access Theses & Dissertations

Live vulnerability testing and penetration assessments of critical infrastructure are costly, complex operationally and, in many cases, unsafe to conduct directly against live systems, whether these are commissioned in-house and through third-party providers. For Operational Technology environments specifically, these constraints are further aggravated by the limited vendor support and inconsistent security patching available that characterize many industrial communication protocols. This significantly restricts the scope and feasibility of conventional penetration testing. At the same time, the increasing overlapping of OT systems with enterprise networks and the internet has expanded the attack surface of ICS infrastructure, making more pressing the need for …

Numerical Methods For Modeling Darcy-Forchheimer Flow In Heterogeneous Porous Media, Nate Mcnair

Open Access Theses & Dissertations

Classic approaches to modeling fluid flow in porous media rely on Darcy's Law, which assumes a linear relationship between volumetric flow rate and the pressure gradient. However, in recent years, applications such as enhanced geothermal systems have highlighted the need to model nonlinear flow behavior, since experimental and observational data show that, once flow velocity exceeds a certain threshold, the relationship between velocity and macroscopic pressure gradient becomes nonlinear. This requires alternative models that more accurately capture the physical behavior of these systems.The Darcy-Forchheimer model provides one such alternative by introducing a nonlinear velocity-pressure relationship. However, this nonlinearity creates additional …

Zero-Knowledge Proofs For Verifiable Machine Unlearning, Bidur Niroula

Open Access Theses & Dissertations

Machine unlearning aims to remove the influence of deleted data from a trained machine learning model. This is important because privacy regulations such as GDPR, CCPA, and PIPEDA give individuals the right to request the deletion of their personal data. Since unlearning can be expensive, a dishonest server may skip it or return an incorrect model and this motivates verifiable machine unlearning. Existing cryptographic approaches prove that the server executed a specific training or unlearning algorithm on the committed dataset, so the proof is tied to the algorithm's trajectory. Empirical verifiers avoid this cost but are known to be circumventable …

Penalty Approach To Constrained Optimization Problems In Water Reservoir And Energy Generation Management, Edwin Horacio Trejo

Open Access Theses & Dissertations

The growing demand for resilient and sustainable energy generation has driven interest in Hybrid Floating Photovoltaic-Hydropower (HFPVH) systems. Operating these systems effectively requires making water release decisions that satisfy physical and regulatory constraints while maximizing energy production. Prior work by Vega (2024) developed a Dynamic Outlier Filter Long Short-Term Memory (DOF-LSTM) architecture for forecasting reservoir release patterns. That predictive work is valid and addresses an important component of the HFPVH decision pipeline. However, the constraint system in that work operates externally to the learning process, and the behavior of penalty-based constraint enforcement had not been studied independently in this context. …

Automated Arctic Coastal Boundary Extraction From Multispectral Satellite Imagery, Harshavardhini Bagavathyraj

Open Access Theses & Dissertations

Arctic coastlines are changing rapidly as permafrost thaw and coastal erosion accelerate under a warming climate, creating a need for accurate and scalable methods to monitor landscape change. Two geomorphically important indicators of this change are the shoreline, which represents the land--water boundary, and the bluff edge, which marks the transition from vegetated tundra to the coastal slope or cliff. However, delineating these features from high-resolution imagery remains challenging because Arctic scenes are spatially extensive and visually complex. In this study, we address these challenges by developing deep learning methods for automated shoreline and bluff-edge extraction from high-resolution satellite imagery …

Adversarial Heterogeneous Agent Learning For Robotic Systems: A Framework For Coordinated Competitive Behaviors, Christopher T. Allred

All Graduate Theses and Dissertations, Fall 2023 to Present

Autonomous robot teams must move reliably, explain their actions, and work together—even in changing or adversarial settings. We present a structured, three-stage pathway that builds coordinated team behavior from strong single-robot skills. First, we develop robust legged-robot locomotion and interpretability using only internal actuator signals. From these proprioceptive cues, robots learn to classify terrain and predict short-term power use, enabling energy-aware movement without external sensors. We further analyze learned behaviors with motif discovery to reveal recurring sensor–action patterns, which clarify how agility emerges and guide reward design. Second, we compose these skills into heterogeneous teamwork using centralized training with decentralized …

Advancing Context-Aware Detection Of Socially Harmful Discourse Using Transformer-Based Models, Santosh Chapagain

All Graduate Theses and Dissertations, Fall 2023 to Present

Social media platforms are a central part of modern communication, shaping how people share ideas, build communities, and discuss social issues. While these spaces can support connection and self expression, they also enable the spread of harmful language such as hate speech. At the same time, social media is an important place where members of marginalized communities, including sexual and gender minorities, express stress, discrimination, and emotional challenges in ways that are often indirect and context dependent.

This research examines whether modern artificial intelligence systems can better identify harmful language and expressions of minority stress in online posts. The study …

How Novices Write Code: Discovering Best Practices, Matt Rau

All Graduate Theses and Dissertations, Fall 2023 to Present

Learning to program is a difficult endeavor, leading to chronically high failure rates in introductory programming courses. One thing that makes teaching programming difficult is that we don’t fully understand what problem solving habits and writing strategies separate successful programmers from struggling ones. Knowing how to teach these habits to a new programmer is an equally difficult challenge,

Studying the way people write code has proved difficult. Until recently, there was very little relevant publicly available data, and no good ways to analyze student programming behavior at a large scale. In this thesis, I address both issues. I publish a …

Large Language Models For Introductory Computer Science Education: Content Generation, Intelligent Tutoring, And Learner Modeling, Muhammad Fawad Akbar Khan

All Graduate Theses and Dissertations, Fall 2023 to Present

This dissertation studies how artificial intelligence, especially large language models such as GPT, can help students learn introductory computer programming when the models are used inside a carefully designed learning system. Instead of focusing on AI as a standalone tool, the dissertation follows a connected story: generating learning resources, building a tutoring platform, running a user study, and then analyzing how students behave while they program.

The work first uses prompt engineering to create a large collection of 11,700 Python exercises aligned with introductory computer science topics. Students and instructors then evaluate these exercises to check whether they are clear, …

A Survey On Digital Reading Materials And Personal Study Of Christian Religious Texts, Teancum Price

All Graduate Theses and Dissertations, Fall 2023 to Present

Religion, including reading from religious texts such as scriptures, are a part of the daily lives of many people. Modern technology has influenced the way that this religious reading takes place, but its effects have not yet been studied. Existing research of the effects of technology on reading focus on topics such as reading comprehension, but the study of religious texts is often focused on achieving a religious experience, so the existing research does not capture the whole scope of these changes. In our study, we surveyed two universities (Utah State University and Abilene Christian University) to ask individuals how …

An Alternative Representation For Temporal Json, Bishal Sarkar

All Graduate Theses and Dissertations, Fall 2023 to Present

JavaScript Object Notation (JSON) is a common format for representing and exchanging data on the web. Most systems only keep the current version of a JSON document, even though, in many situations, it is also important to know how that document changed over time. For example, an application might need to answer questions such as “What did this record look like last week?” or “How has this list grown over the past year?” A simple way to keep this history is to store a full copy of the document every time it changes, but this quickly becomes wasteful, most of …

Singularity-Enriched Neural Networks For Elliptic Problems In Polygonal Domains, Harshini Reddy Kodiganti

Open Access Theses & Dissertations

This thesis develops and analyzes neural-network-based solvers for the Poisson equation on polygonal domains, where re-entrant corners induce reduced solution regularity and challenge standard numerical methods.

Three neural formulations are investigated: Physics-Informed Neural Networks (PINNs), Physics-Informed Extreme Learning Machines (PIELMs), and Rank-Inspired Neural Networks (RINNs). PINNs rely on gradient-based optimization with automatic differentiation, while PIELMs employ randomly initialized hidden features with least-squares training, achieving significantly lower computational cost. RINNs extend this framework through covariance-driven orthogonalization to improve numerical conditioning and stability.

On convex polygonal domains, all three methods are benchmarked against analytical solutions. Both PIELM and RINN consistently achieve higher …

Three Essays On Workplace Ethics And Ai: Conceptualizing, Scale Development, And Validation Of Self-Value Actualization, And Ai-Enabled High-Performance Work Systems, Mansura Nusrat

Open Access Theses & Dissertations

This dissertation advances understanding of workplace ethics and responsible AI integration across three interconnected essays unified by social cognitive theory. My first essay introduces self-value actualization (SVA), a novel construct defined as the dynamic, integrated psychological process through which individuals continually strive to align and fulfill their core moral values through observable professional behavior. Drawing on social cognitive theory and emotional intelligence theory, I conceptualize SVA as a higher-order self-regulatory orientation comprising three mutually reinforcing processes: value congruence, moral reflection, and adaptive morality. I developed and validated a 9-item SVA scale across four studies using expert panels, exploratory factor analysis, …

Efficient Solvers For Phase Field Models, Raymond Obeng

Open Access Theses & Dissertations

Phase field models provide a versatile framework for describing phase transitions and pattern formation in materials, enabling the study of complex phenomena such as crystallization, grain growth, and defect dynamics. Among these models, the Phase Field Crystal (PFC) equation has gained significant attention due to its ability to capture atomic-scale structures while evolving on diffusive time scales. However, the numerical solution of the PFC equation presents substantial challenges arising from its high-order nature and the large-scale, coupled linear systems generated by discretization.

In particular, standard formulations of the discretized PFC system lead to non-symmetric and often ill-conditioned linear systems, which …

Understanding Machine Learning Model Behavior Under Fairness And Privacy Constraints, David Anthony Sanchez

Open Access Theses & Dissertations

Machine learning systems deployed in high-stakes domains are increasingly expected to satisfy demands beyond predictive accuracy-including fairness across demographic groups, protection of sensitive information, and explanations that human stakeholders can inspect and trust. This thesis investigates how those demands can be met through learning frameworks that explicitly govern the relationship between data and models, arguing that trustworthiness is a design problem rather than a post hoc correction. The thesis is organized around three studies, each targeting a distinct point of data-facing control. The first develops CondFairGen, a fairness-aware conditional generator for tabular data that improves subgroup equity by dynamically reweighting …

Bayesian Deep Learning For Photovoltaic Power Forecasting: A Probabilistic Framework For Uncertainty Quantification And Grid Reliability Optimization, Pablo Abraham Bustamante

Open Access Theses & Dissertations

The global energy landscape is undergoing a profound transformation, driven by the urgent need to decarbonize power systems, enhance energy security, and meet growing electricity demands. Solar photovoltaic (PV) power has emerged as a critical component of future energy infrastructure due to its abundance, scalability, and cost-effectiveness. However, PV generation is inherently variable and weather-dependent, introducing significant uncertainty into grid operations and complicating the task of balancing supply and demand. Accurate forecasting of PV power generation-particularly on day-ahead and hour-ahead horizons-has become a strategic necessity for grid stability, economic efficiency, and environmental sustainability. PV output is influenced by numerous factors, …

Timing And Synchronization: Software And Hardware Approaches For Precision Maximizing, Christina Alicia Alejandra Carreon Jimenez

Open Access Theses & Dissertations

This thesis explores the design of synchronization mechanisms that allow multiple FPGA boards to operate as if they were a single coherent timing domain. The solutions span three layers: a software PLL for E1 telecommunication links, a PCIe-based timestamp exchange protocol, and a hardware-level multi-FPGA mesh architecture. Across these layers, the work demonstrates that practical, low-cost synchronization can achieve sub-microsecond accuracy without the burden of specialized hardware such as GPSDOs or White Rabbit infrastructure. Experiments show stable alignment within the nanosecond-microsecond range, validating the feasibility of the proposed methods for SDR and telecom applications.

Modeling Causal Interactions Across Brain Functional Systems For Population-Specific Disease Analysis, Alissen Moreno

Theses and Dissertations

Functional brain connectivity provides critical insight into neural mechanisms underlying neurodegenerative and affective disorders. Traditional neuroimaging studies rely on undirected or region-specific connectivity measures developed predominantly using racially homogeneous cohorts, limiting fairness and generalizability across diverse populations.

We propose a population-aware framework modeling directed causal interactions across large-scale brain functional subnetworks. Resting-state fMRI data from the HABS-HD cohort were used to construct subject-level causal connectivity matrices via ICA-LiNGAM, aggregated into interpretable system-level hyper-connectomes representing interactions among eleven canonical brain subsystems. These features trained nonlinear models for Alzheimer’s disease stage classification and trait worry prediction.

Results demonstrate that MLP models outperform …

Agentcite: Trustworthy Ai Agents For Information Verification Across Referenced Documents, Eymen Yigit

Master's Theses

This thesis presents AgentCite, a multi-agent framework for automated verification of referenced numerical data in research documents. The framework employs a hybrid design in which LLM-based agents handle document understanding and evidence retrieval, while deterministic components manage structured parsing and value comparison, improving consistency and reproducibility while reducing token consumption and execution time compared to fully agentic approaches.

AgentCite consists of three autonomous agents: a Negotiator, a Main Document Agent, and a Source Documents Agent, coordinated through a fixed tool-call pipeline. The Negotiator orchestrates verification by extracting tabular data from the main document, retrieving evidence from per-source vector stores, and …

Probing Representational Emergence In Large Language Models, Shawn Ismail

Master's Theses

This thesis investigates whether abrupt behavioral gains in large language models under scaling are accompanied by systematic changes in internal representations. It combines a behavioral screen of 65 tasks per family with targeted layerwise probing across eight decoder-only, open-weight model families. Behavioral emergence is defined for each family-task trajectory using an empirical jump detector, with segmented regression retained only as a diagnostic. The representational follow-up analyzes 27 selected MMLU subtasks shared across all families, spanning 37 checkpoints and 216 family-task units.

For each follow-up checkpoint, frozen linear probes are trained on every layer's hidden states to measure how much task-relevant …

Towards Generalizable Representation Learning Across Domains, Hossein Kashiani

All Dissertations

Despite remarkable progress in deep learning, a major challenge remains: machine learning models often struggle to generalize to unseen domains under distribution shift. In real-world settings, data often differ from training conditions due to changes in lighting, sensor type, image resolution, and style. These differences can significantly degrade performance, highlighting the need for representations that are both robust and generalizable. This thesis addresses this challenge by developing a set of frameworks for generalization across domains in anomaly detection, deepfake detection, and vision-language image recognition. For anomaly detection, this thesis introduces ROADS, a robust prompt-driven framework for multi-class unified anomaly detection. …

Conditioning Hierarchical Diffusion Transformers On Rf Circuit Parameters, Ethan Morton

McKelvey School of Engineering Graduate Student Theses & Dissertations

As modern ML techniques have become increasingly advanced, they have begun to be integrated into wireless RF systems for classification, identification, and spectrum management. Deep Neural Networks (DNNs) enable RF system operators and designers to design more flexible systems with greater robustness to errors and attacks. However, neural networks require significant amounts of properly annotated data to train. Current data labeling methods lack the ability to obtain reliable true labels for circuit properties such as carrier frequency offset (CFO), power amplifier (PA) non-linearity, and in-phase/quadrature (IQ) imbalance. This thesis investigates the efficacy of a novel architecture, RF-Diffusion, for generating high-quality …

Enhancing Control Charting Schemes And Exploring New Assessment Metrics To Advance Quality Control And Cyber-Attack Detection In Manufacturing, Ahmad Al Majali

Dissertations

The increasing integration of digital technologies and industrial control systems in modern manufacturing has introduced new cybersecurity vulnerabilities within cyber–physical production environments. Malicious actors can exploit these vulnerabilities to induce subtle process deviations that degrade product quality while remaining undetected by conventional statistical monitoring tools. Such attacks can be deliberately engineered to manipulate process behavior through transient shifts that vary in magnitude, duration, and frequency. Despite extensive research on transient shifts caused by assignable causes in Statistical Process Control (SPC), limited attention has been given to intelligently designed cyber–physical attacks that exploit the structural characteristics and limitations of control charting …