Digital Commons Network^™

Two-Sample Bi-Directional Causality Between Two Traits With Some Invalid Ivs In Both Directions Using Gwas Summary Statistics, Siyi Chen

School of Public Health Faculty Publications

Mendelian randomization (MR) is a widely used method for assessing causal relationships between risk factors and outcomes using genetic variants as instrumental variables (IVs). While traditional MR assumes uni-directional causality, bi-directional MR aims to identify the true causal direction. In uni-directional MR, invalid IVs due to pleiotropy can violate assumptions and introduce biases. In bi-directional MR, traditional MR can be performed separately for each direction, but the presence of invalid IVs poses even greater challenges. We introduce a new bi-directional MR method incorporating stepwise selection (Bidir-SW) designed to address these challenges. Our approach leverages public genome-wide association study (GWAS) datasets …

Modeling Literary Connections: Exploring Transregional Resistance In Dalit Poetry, Antara Bhattacharyay

Mathematics, Statistics, and Computer Science Honors Projects

Structuring socio-political identities, the caste system (a graded form of hierarchy) remains entrenched in contemporary Indian society. Dalits, marginalized by the caste system, have expressed their resistance through literature, envisioning substantive equality and social change. In this thesis, I draw on digital humanities methods to examine regional variation in translated Dalit poetry from Bengali, Hindi/Urdu, Marathi, and Tamil languages. I utilize topic modeling—a machine learning algorithm that detects latent semantic structures in a text—as a point of departure for poetry analysis. I observe how topic modeling enables newer readings of the poems, revealing regionally resonant and broader Dalit themes.

Contribution Of Various Factors On The Rate Of Traffic Accidents In The Us, Martin Mnatsakanyan

Undergraduate Research Symposium Lightning Talks

Background:

Until 2020, the number of traffic accidents has been steadily decreasing. After 2020, the number started increasing until 2022, then started s lowly decreasing again. Most drivers aren’t fully aware of the reason behind all of these accidents.

Variable Selection In Mixture Cure Models Using Elastic Net Penalty: Application To Covid-19 Data, Aluwani Ramalata, Akim Adekpedjou, Maseka Lesaoana

Mathematics and Statistics Faculty Research & Creative Works

In survival analysis, it is often assumed that all individuals will eventually experience the event of interest if followed long enough. However, in many real-world scenarios, a subset of individuals remains event-free indefinitely. For instance, in clinical studies, some patients never relapse and are considered cured rather than censored. Traditional survival models are inadequate for capturing this heterogeneity. Mixture cure models address this limitation by distinguishing between cured and susceptible individuals while modeling the survival of the latter. A key challenge in mixture cure modeling is selecting relevant covariates, particularly when dealing with time-varying effects. This study develops a penalized …

The Impact Of Maternal Age On The Expression Of Transgenerational Plasticity In Daphnia Pulicaria, Calvin Nguyen

2025 Spring Honors Capstone Projects - Archive

Transgenerational plasticity refers to heritable, non-genetic changes in phenotype that persist across multiple generations and can enhance offspring survivability in variable environments. In Daphnia, increasing maternal age has been associated with maladaptive plasticity. To investigate this relationship, six clones were collected from two Wisconsin lakes and acclimated to laboratory conditions through a common garden rearing process. For each clone, ten replicates were generated and evenly divided between young (clutches 2–4) and old (clutches 5–8) maternal age groups. Offspring were exposed to three dietary treatments for three experimental generations: one fed only green algae, one fed only cyanobacteria (a nutritionally …

New Bayesian Methods For Longitudinal Data Analysis With Complex Dependence Structures., Anish Mukherjee

Electronic Theses and Dissertations

Longitudinal data in real-world settings are frequently found to be heterogeneous and exhibit intricate spatio-temporal dependence structures. Analyzing such complex data to obtain reliable estimation while quantifying uncertainty necessitates using sophisticated Bayesian methodology. In this work, we present novel Bayesian methods developed to address these challenges. We often observe heterogeneity in longitudinal data, where the mean and variance for certain profiles meaningfully differs from the rest. Some profiles may also exhibit outliers at a limited number of measurements. Using a standard mixed effects model, which assumes homogeneity, can lead to overestimating the residual variance and inefficient estimation. In this work, …

Statistical Designs For Learning User Preference And Experience, William S. Fisher

All Dissertations

For any organization, designing a new product or planning the features of a new service is a complex decision-making process which depends on understanding its users' preferences and the experiences they have with prototypes of the new product or service. Design of experiments (DOE) offers a framework to aid in the modeling and collection of data to learn user preferences and experiences to facilitate this decision-making process. Questions such as ``which of our newly proposed products is preferred most by our customers" and ``which version of our new service results in the highest monthly revenue" can be readily addressed by …

Deleting Values May Either Increase Or Decrease Variance, David L. Farnsworth

Articles

The impact upon variance when a value is deleted is addressed. It is shown that the cutoff for the deleted value yielding an increase or a decrease in variance is approximately one standard deviation from the mean for a univariate random variable with equally distributed probability on a finite set of elements and for a univariate set of observations. The influence of truncation of the domain for such a discrete random variable and for observations is considered.

Impacts Of Cognitive Workload On Veteran Driver Reaction Time: Predictive Modeling Using Bayesian And Machine Learning Methods, Kenneth Ofosu-Kwabe

All Theses

In high-demand environments, the ability to manage cognitive workload can mean the difference between optimal or safe performance and critical failure or accidents. Veterans face an elevated risk of fatal motor vehicle accidents due to post-deployment stress, combat-related injuries, and challenges readjusting to civilian driving. This study explores how cognitive workload affects reaction time performance using a driving simulator by collecting and analyzing subjective workload ratings (using the NASA-TLX survey), physiological signals from eye-tracking and performance data from a sample of 28 Veterans.

We examined how task difficulty, cognitive indicators and personal attributes influence reaction times across an interactive driving …

Computer Vision In Soccer: Yolov11 Analytics Engine For Quantifying Game Strategy, Connor S. Maurer

Data Science Undergraduate Honors Theses

Single-shot object detection capabilities significantly reduce computational overhead for real-time computer vision in sports analytics at 60 FPS. YOLO11’s lightweight CNN gives promising accuracy while meeting the low-latency demand of dynamic soccer matches. As data-driven approaches take over the sport of soccer, efficient player tracking systems become critical for informing coach’s strategies. I prototype the ETL (Extract, Transform, Load) process of data collected from a single- shot detection program and evaluate its viability for estimating player fatigue. YOLO11 detects players, the ball, and other characteristics, with the output transformed by homography to estimate the positions in the real world. These …

Reinforcement Learning, Modeling Markets, And Professional Basketball Free Agency, Jacob Cohn

Computational and Data Sciences (PhD) Dissertations

This dissertation presents a reinforcement learning-based approach to modeling and optimizing decision-making in professional basketball free agency and related economic environments. A Markov Decision Process (MDP) framework is introduced to capture the strategic interactions of NBA teams bidding for free agents under budgetary and roster constraints. To address computational scalability challenges, a reinforcement learning (RL) environment is developed, leveraging Proximal Policy Optimization (PPO) to approximate optimal policies for team decision-making.

Empirical results demonstrate that the RL agent successfully learns strategic bidding behavior that aligns with dynamic programming benchmarks in simplified settings while scaling effectively to larger, intractable environments. The study …

Multimodal Benchmarking For Ncaa Basketball, Brendan Barnett

Honors Scholar Theses

We present the first multimodal, multitask benchmark for NCAA basketball, synthesizing structured statistical features with large language model (LLM)-generated game summaries across 19,739 games spanning four NCAA Division I seasons (2021--2025). We evaluate three model families---XGBoost, deep neural networks, and Transformers---under tabular-only and early-fusion settings to measure the impact of LLM-derived textual embeddings. To assess practical utility, we simulate fixed-stake and Kelly criterion-based betting strategies using historical bookmaker odds, analyzing both profitability and downside risk via Monte Carlo simulation. Our results show that XGBoost with early-fusion achieves the highest return on investment and the lowest risk of loss. This work …

Leveraging Historical Data For Estimating Genetic Gain And Implementing Genomic Selection In A Student Led Barley Breeding Program, Sydney Graham

Department of Statistics: Dissertations, Theses, and Student Research

In Nebraska, winter feed barley presents an emerging market for producers and an opportunity to diversify cropping systems. The University of Nebraska Barley Breeding Program aims to develop high-yielding, winter-hardy varieties. A unique aspect of this program is that doctoral students serve as barley breeders and are responsible for crossing, data collection, and advancement decisions. While this provides hands-on experience for the students, the impact of student leadership has not been examined.

This study used a historical data set to evaluate the realized genetic gain of the breeding program, and as a training population for genomic selection. The dataset consisted …

Maximal Independent Set Algorithms Within Procedural Planar Maps: A Large-Scale Evaluation, Chaucer Ihrig

Honors College Theses

Analysis of a childhood game has led us to the problem of maximum independent sets in planar graphs. We wrote a graph creation utility using R to generate a random planar map and its dual graph. This utility then finds a graph’s maximal independent set using a variety of six algorithms. We investigate statistical connections between graph structure, colorability, and the maximal independent sets found using these algorithms over an incredibly large and procedurally generated dataset. We find one can always win the coloring game if the resultant graph is two-colorable. The algorithms perform statistically and practically significantly better on …

A Study Of End-Cut Preference In Tree-Based Modeling, Xiangya Wang

Open Access Theses & Dissertations

Decision trees, particularly those built using the Classification and Regression Trees (CART) algorithm, are widely used for their interpretability and flexibility. However, the greedy nature of the CART splitting procedure gives rise to the end-cut preference (ECP) phenomenon, wherein split points near the extremes of predictor ranges are favored. This study offers a comprehensive investigation of ECP, exploring its theoretical underpinnings, practical manifestations, and implications for both single decision trees and ensemble methods such as Random Forests. Through theoretical analysis and simulation studies, we examine how ECP affects tree structure, variable selection, and predictive accuracy across tree-structured, linear, and nonlinear …

Designing Accessible And Dependable Tools For Vocational Rehabilitation Data Analysis, Ruth E. Taylor

All Graduate Theses and Dissertations, Fall 2023 to Present

Since 1973, the U.S. Rehabilitation Services Administration (RSA) has partnered with state vocational rehabilitation (VR) agencies to help individuals with disabilities achieve meaningful employment and independence. RSA-911 datasets play a crucial role in this effort by capturing detailed participant data, but their complexity can hinder effective analysis.

To simplify this process, we present an R software package to streamline the cleaning and analysis of RSA-911 and Transition Readiness Toolkit (TRT) data, a new measure of program effectiveness. We also deliver a user-friendly dashboard, empowering both VR researchers and counselors with the opportunity to conduct analyses. Using our developed tools, we …

A Comparative Analysis Of Nf-Κb1 Gene Regulatory Sequence Methylation In Normotensive And Hypertensive Kenyans, Aaryan Barlas Piracha

Honors Theses

Accounting for the majority of deaths worldwide, non-communicable diseases (NCDs) present the greatest health challenge of the twenty-first century. Specifically, cardiovascular diseases (CVDs) exceed all other NCDs in annual deaths and especially affect low- and middle-income countries (LMICs). Hypertension, being the primary risk factor for CVD, affects over 75% of adults in LMICs due to inadequate health care and preventative measures. Additionally, epigenetic modifications of DNA are important mechanisms that regulate gene expression; DNA methylation, in particular, affects cytosine residues in cytosine-phosphate-guanine (CpG) islands on regulatory sequences. Previous research in our laboratory analyzed percent methylation at 8 different CpG islands …

Analysing Bell Experiments Through Test Factors: Applications To Randomness And Strength Of Nonlocality, Soumyadip Patra

LSU New Orleans Theses and Dissertations

This work presents practical tools to analyse Bell experiments---experiments demonstrating correlations that defy classical explanations and proving that nature violates local realism. We begin by showing that in the Bell scenario specified by n parties with each party having a choice of m binary-outcome measurements---the (n,m,2) scenario---projecting weakly-signalling settings-conditional outcome distributions onto the smallest-dimensional affine subspace (containing the no-signalling set) via an L^2-distance-minimising map preserves correlators. This result ensures that Bell inequalities written in terms of correlators remain invariant under such projections, and we provide an efficient construction method for the projection operator that avoids computationally costly steps such as …

Nonparametric Methods For Bayesian Community Detection In Complex Networks, Kedran Young

Graduate Theses and Dissertations

Network analysis is becoming an increasingly popular interdisciplinary area of study, with emerging interest in fields like sociology, biology, economics, and ecology. Within the niche of network analysis, capturing the community structure of a network is one important achievement that many statisticians have been working toward over recent decades. The most popular modeling technique for latent community detection is the Stochastic Block Model (SBM), which falls into the category of latent variable models and will serve as the baseline model throughout this thesis. SBM is widely regarded as the most effective community detection method as it detects latent community membership …

Application Of Ordinal Regression Models To Acquired Stress Resistance In Wild Strains Of Saccharomyces Cerevisiae, Carson Stacy

Graduate Theses and Dissertations

This thesis explores the application of ordinal regression to the analysis of semi-quantitative growth assays often used when comparing fitness for different strains of the model yeast Saccharomyces cerevisiae. For stress survival assays, yeast stress resistance is measured using an ordered survival score that ranges from 0 (no growth) to 4 (confluent growth). Traditional approaches to analyze this type of data either treats data as a nominal categorical variable or as a continuous numerical variable. These approaches risk loss of information or violation of testing assumptions. In contrast, cumulative logit ordinal regression uses the information contained in the order …

Nonlinear Power Function Model Changepoint Detection., Jacob Steven Townson

Electronic Theses and Dissertations

Most work surrounding changepoint analysis focuses on linear models. This dissertation explores changepoint detection in nonlinear power function models, specifically focusing on models where the constant multiplier and power are the parameters to be estimated in addition to the changepoint parameter. The study assumes an asymptotic framework as the number of observations approaches infinity. The study explores various model fitting algorithms, and decides to employ the Newton-Raphson method for parameter estimation, with a custom implementation developed to optimize the process. The research first establishes the strong consistency of estimators for the model without a changepoint. Building on this result, consistency …

Joint Modelling Of Longitudinal Egfr Trajectory And Time To Acute Kidney Injury In Lung Transplant Patients, Samiha Zakir

Theses and Dissertations

Progressive declines in estimated glomerular filtration rate (eGFR) often precede acute kidney injury (AKI), yet the relationship between eGFR trends and AKI risk remains unclear. This study investigates longitudinal eGFR changes and their association with AKI in 459 lung transplant patients followed for up to 7 years (n = 6419). We applied a piecewise linear mixed-effects model to evaluate eGFR trajectories and a Cox proportional hazards model to assess time to AKI. A joint model was used to explore the interplay between longitudinal and survival processes. Key covariates included gender, age at transplantation, antibody-mediated rejection (AMR), and pre-transplant eGFR. Males …

Decoding The Algorithm: The Mathematics Behind Tiktok’S Short-Form Content Success, Ashley N. Lynch

Honors Scholar Theses

Within the realm of social networks, TikTok has become the central hub for short-form video content. The network’s unique ability to capture individual preferences using predictive analytics has greatly contributed to its massive success, allowing the company to optimize its performance and content personalization. In an age where digital media have such a significant influence on society, it is essential that users develop an understanding of how social network algorithms function to make more informed online decisions. Although TikTok’s technological system is primarily undisclosed, the platform certifiably leverages several key mathematical principles within its algorithm to achieve its core goals …

Car Price Prediction Using Machine Learning: Analyzing The Dvm-Car Dataset, Yaman Abu Ghareebaih

Electronic Theses and Dissertations

The objective of this study is to predict car prices using machine learning models and the DVM-CAR dataset, which includes over 1.4 million images and car specifi- cations from 899 car models. Key factors such as mileage, engine power, and year of registration were analyzed for their correlation with car prices. Extensive data cleaning was performed, including filling missing values, identifying outliers, and normalizing numerical variables. Discrete variables like car make and body type were encoded using one-hot encoding. Linear relationships were analyzed with Multiple Logistic Regression, and Random Forest models were used for nonlinear patterns. Model performance was evaluated …

Community Voices, Climate Action Choices: Working Towards A Resilient Monterey County, Lesley A. Solano Alonso

Capstone Projects and Master's Theses

Vulnerable communities in Monterey County face disproportionate environmental and health impacts due to climate change, yet many residents remain unaware of the tools and resources available to support local action. This capstone project was implemented in partnership with Ecology Action (EA) and the Resilient Central Coast (RCC) campaign to increase awareness and engagement with the RCC platform. Serving diverse communities across Monterey County, the project included bilingual outreach efforts, community tabling, educational presentations, and a climate action survey. Over 650 residents were engaged directly, resulting in 99 new household sign-ups on the RCC website, a major milestone for the agency. …

Expressive And Interpretable User Engagement Prediction Using Multivariate Survival Processes, Akshay Aravamudan

Theses and Dissertations

The ability to characterize how information diffuses online is of paramount importance to stakeholders that are interested in tasks such as proposing solutions for mitigating and countering dis/misinformation, predicting user engagement of content in social media, planning marketing campaigns to roll-out products and planning dissemination of political campaign messaging among others. One such facet of learning the dynamics of information diffusion is the ability to predict user engagement or the popularity of a single piece of information as it spreads through an online medium. Existing works in this regard mainly either obfuscate user level information or utilize frameworks that are …

Investigating Students’ Proficiency Across Statistical Software And Preferences Of Statistical Software Design, Sabrina White

Honors College Theses

This paper investigated students’ perceptions of their proficiency with statistical software applications and their preferences regarding software features. Results indicated that students’ statistical and coding experience, as well as the specific application used, did not significantly influence their self-perceived proficiency. This suggests that it may be more effective to focus on building student skills within a chosen application, rather than tailoring the application to match existing student capabilities. While students showed clear preferences for certain features, favoring clarity over depth, flexibility over safeguards, and built-in checks over unrestricted freedom, these preferences generally leaned toward balanced design rather than extremes. This …

Application Of Deep Learning On Gage R&R For Anomaly Detection, Oluwatope Richard Ojo

Electronic Theses and Dissertations

This thesis explores the application of deep learning techniques, specifically autoencoder based models, to enhance anomaly detection within Gage Repeatability and Reproducibility (Gage R&R) studies—an essential component of Measurement System Analysis (MSA) in quality engineering. Traditional Gage R&R methodologies, while effective for linear and low-dimensional data, exhibit limitations in detecting subtle, nonlinear variations in complex measurement systems. To address this challenge, an unsupervised autoencoder was developed and trained on a synthetically generated dataset comprising 2,500 voltage measurements (5V and 33V) derived using Generative Adversarial Networks (GANs) based on real-world manufacturing data measurements.

The proposed autoencoder model achieved a 95th percentile-based …

Innovative Methods For The Design And Analysis Of Phase Ii Clinical Trials, Feng Tian

Dissertations and Theses (Open Access)

Drug development has become increasingly time-consuming, costly, and risky in recent years. There is significant potential for improving clinical trial designs, particularly for phase II trials, which play a critical role in the drug development process. Innovative methods are especially necessary for addressing key challenges in phase II trials in terms of dose-ranging study, patient population selection, and decentralized clinical trials (DCTs). This dissertation presents a comprehensive set of methodologies that address these critical issues with three projects. The first project introduces a Bayesian adaptive dose-ranging design that integrates both efficacy and toxicity data to evaluate each dose comprehensively. The …

Dual-Criterion Dose Finding Designs For Phase I Clinical Trials, Yunlong Yang

Dissertations and Theses (Open Access)

The primary objective of Phase I oncology trials is to assess the safety and tolerability of novel therapeutics. Conventional dose escalation methods identify the maximum tolerated dose (MTD) based on dose-limiting toxicity (DLT). However, as cancer therapies have evolved from chemotherapy to targeted therapies, these traditional methods have become problematic. Many targeted therapies rarely produce DLT and are administered over multiple cycles, potentially resulting in the accumulation of lower-grade toxicities, which can lead to intolerance, such as dose reduction or interruption. To address this issue, we proposed dual-criterion designs that find the MTD based on both DLT and non-DLT-caused intolerance. …