Biostatistics Commons^™

Statistical Methodologies For Count Time Series Analysis And Topological Data Analysis Of Medical Images, Yuhyeong Jang

Statistical Science Theses and Dissertations

This dissertation addresses two distinct topics related to count time series analysis and topological medical image analysis, respectively. The first part of the dissertation comprises an application of a count time series model to analysis of US monthly sex trafficking data and development of a new model for multivariate count data that exhibits serial dependence and overdispersion. By imposing a family of multivariate mixed Poisson distributions on the count random vector, the proposed model can accommodate a broad range of overdispersion as well as positive contemporaneous correlations. For maximum likelihood estimation, a computationally feasible EM-type algorithm is derived based on …

Developing A Humpback Whale Vocalization Detector Using Machine Learning Models, Lucas Kantorowski

Master's Theses

Humpback whale songs are notoriously complex. Identification of humpback whale song units requires bioacousticians to tediously listen, analyze, and annotate collected sound data. Even sparse data requires listening to the entirety of the collected acoustic data. In this study, three hours of audio containing over one-thousand humpback whale song units was collected in Monterey Bay, California.

Prior studies have seen success using convolutional neural networks by performing image classification on hundreds of hours worth of spectrograms. Our study uses traditional machine learning models, as they are less computationally demanding, and require less data.

We use time splitting and Mel-frequency cepstrum …

Efficacy Analysis In Clinical Trials: A Comprehensive Review Of Statistical And Machine Learning Approaches, Dhrubajyoti Ghosh, Samhita Pal

Faculty Articles

Efficacy testing is a cornerstone of clinical trials, ensuring that medical interventions achieve their intended therapeutic effects. Over the decades, a wide range of statistical methodologies have been developed to address the complexities of clinical trial data, including parametric, nonparametric, Bayesian, and machine learning approaches. Parametric methods, such as t-tests, ANOVA, and LMMs, have traditionally been the foundation of efficacy testing due to their efficiency under well-defined assumptions. Nonparametric techniques, including the Friedman test, Brunner-Munzel test, and modern extensions like nparLD, have emerged as robust alternatives, particularly for skewed, ordinal, or non-normal data. Bayesian methodologies have enabled the incorporation of …

Beyond The Lace Index: Benchmarking Machine Learning Architectures And Explaining 30-Day Hospital Readmission Risk With Shap Analysis, Carl E. Hughes Iii

Williams Honors College, Honors Research Projects

Unplanned 30-day hospital readmission remains a fundamental challenge in US healthcare, associated with increased risk to patient recovery and representing an estimated $52.4 billion in annual expenses (Beauvais et al., 2022). While the rigorously validated LACE index serves as the clinical standard for readmission modeling, its linear structure and four explanatory variables lack the complexity to capture the high-dimensional and interactive nature of patient risk. This study utilizes an admission granularity level cohort of the MIMIC-IV database to develop and compare machine learning architectures against the baseline LACE index. Due to the imbalanced prevalence of readmission, the penalized logistic regression, …

Advancing Periodic Time Series Analysis: Application, Bias Assessment, And Optimal Window Selection In The Variable Bandpass Periodic Block Bootstrap Method, Yanan Sun

Electronic Theses & Dissertations (2024 - present)

Time series analysis is essential for understanding long-term patterns, periodic behavior, and underlying correlations in complex datasets. The periodically correlated (PC) time series is a type of time series where the correlation structure repeats over fixed intervals. The Variable Bandpass Periodic Block Bootstrap (VBPBB) has recently been proposed as a resampling method that preserves PC structures through the use of periodogram, bandpass filters, and block bootstrap resampling. Although promising, VBPBB remains underutilized, and its limitations have not been fully examined. This dissertation advances both the application and methodological development of the VBPBB.

The first project applies the VBPBB to a …

Spectral Analysis Of Traffic Accidents In New York's Capital Region, Michael Barr

Electronic Theses & Dissertations (2024 - present)

In this paper we estimate the spectral density of traffic accident events in the Capital Distict, NY area using a band-pass filter known as the Kolmogorov-Zurbenko Fourier Transform (KZFT). The source data is provided by Moosavi, et al. (2019) and originally captured from various public entities and sensors in the road network. Spectral density estimation with KZFT suppresses noise to reveal the constituent frequencies embedded in the noisy signal. Signal reconstruction based on KZFT produces an approximate weekly accident arrivals for this noisy signal, or in other words a pattern which is proportionate to the event expectation viewed over a …

A Comparative Study Of Classification Methods For Healthcare Analytics, Xueting Zhao

UNF Graduate Theses and Dissertations

This thesis presents a comparative study of logistic regression, Linear Discriminant Analy- sis (LDA), and Quadratic Discriminant Analysis (QDA) for binary classification in healthcare analytics, integrating theoretical derivation, simulation, and real-data application. A facto- rial simulation study crosses the covariance structure (equal vs. unequal), predictor correla- tion (ρ ∈ {0, 0.5, 0.9}), dimensionality (p ∈ {2, 5, 10}) and sample size (n ∈ {50, 100, 200}) across 54 scenarios with 1,000 Monte Carlo replicates each. Three main findings emerge. Logistic regression and LDA are nearly interchangeable when the assumption of equal-covariance holds. QDA achieves substantially better discrimi- nation when class-specific …

Correlation With Car Density In Urban Environments And Its Influence On Chronic Obstructive Pulmonary Disease (Copd) Rates In The United States, Daniel Barreiro-Torres, Kedai Cheng

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Smarter Disease Detection From Electronic Health Record Data: An End-To-End Ai-Augmented Pipeline For Computable Phenotyping, Dylan Owens

Statistical Science Theses and Dissertations

Electronic Health Records (EHR) contain a wealth of structured and unstructured patient data that can be leveraged for computable phenotyping, the process of algorithmically identifying patient cohorts with specific diseases or conditions. Traditional rule-based phenotyping approaches, while interpretable, often struggle with scalability, portability across institutions, and effective use of unstructured clinical narratives. Recent advances in large language models (LLMs) present new opportunities for synthesizing complex free-text information into concise, clinically meaningful representations. However, integrating LLMs into phenotyping workflows requires careful design to maintain transparency, interpretability, and measurable uncertainty—features essential for clinical adoption and downstream applications such as decision support.

We …

Spatiotemporal Modeling Of Maternal Mortality In South Carolina 2018-2023, Leah Wood, Ray Bai, Emily Mann

Senior Theses

Maternal death serves as a public health indicator due to fact that it is considered preventable with the availability of modern biomedicine, however, it persists broadly throughout the United States. Current literature outlines national trends in maternal mortality with complicating, preexisting conditions, and structural upstream factors often cited as being the largest contributors to increased risk. This study utilizes publicly available, county-level data for maternal death in addition to demographic and descriptive data in order to estimate maternal mortality rates in each of South Carolina’s 46 counties from 2018 to 2023. In order to address sparsity in the outcome variable …

Statistical Methods For Joint Outcome Modeling And Dynamic Assessment Of Recurrent Events, Zifang Kong

Statistical Science Theses and Dissertations

Recurrent event data frequently arise in clinical studies where individuals experience repeated, possibly related, events over time. These data are often accompanied by sparse and irregular longitudinal measurements, creating challenges for traditional joint modeling approaches that struggle to account for time-dependent associations and within-subject correlations. We propose FRAILTY (Functional Regression with AutoRegressIve fraiLTY), a novel two-step framework that integrates functional principal component analysis (PACE) with a dynamic frailty model featuring autoregressive structure. FRAILTY accommodates both scalar and functional predictors and captures within-subject dependence across recurrent events. To further extend its utility, we develop a multivariate joint modeling framework that simultaneously …

Evaluating Alpha Spending Functions Applied To Observational Time-To-Event Analysis, Moses Torgbenu

Electronic Theses and Dissertations

This thesis explores the theoretical foundation of the alpha spending approach and extends its application beyond the conventional setting of randomized controlled trials (RCTs) to observational studies with time to event analyses. In these less structured environments, key design parameters such as the total number of events are often unknown, posing challenges for the standard implementation of sequential analysis methods.

Through simulation studies, this research delivers several important contributions. First, it presents a modified approach that uses calendar time to define the timing of interim analyses while relying on event-based information to estimate the correlation among test statistics. This adjustment …

Sequential Data Modeling Of Influenza A Via Traditional, Dwt-Gpr Hybrid, And Deep Learning Architectures, Edmund Fosu Agyemang

Theses and Dissertations

Influenza A is responsible for 290,000 to 650,000 respiratory deaths a year, though this estimate is an improvement from years past due to improved sanitation, healthcare practices, and vaccination programs. In this study, we perform a comparative analysis of traditional, deep-learning and discrete wavelet (DWT)-Gaussian Process (GP) hybrid models to predict Influenza A outbreaks. Using historical data from January 2009 to December 2023, we compared the performance of traditional ARIMA and ETS models, four variants of DWT-GPR models and six distinct deep learning architectures: Simple RNN, LSTM, GRU, BiLSTM, BiGRU and Transformer. The results reveal a clear superiority of all …

Predicting Capture And Survival Probabilities Of The Arizona Tiger Salamander: A Comparison Of Capture-Recapture Models, Brittney Nelson

Scholars Week

Capture-recapture models are essential tools for estimating population dynamics in ecological studies. A fundamental component of these models is the capture history matrix, which records individual detection over time and serves as the basis for estimating survival and capture probabilities. This presentation explores three statistical approaches to these estimations: the Cormack-Jolly-Seber (CJS) model, the Hidden Markov Model (HMM) for CJS, and the Bayesian CJS model. The CJS model provides a likelihood-based framework for estimation, and the HMM CJS incorporates latent states into the model to account for uncertainty in detection. The Bayesian CJS extends this same analysis by integrating prior …

Linking Water Quality And Climate Change To Long-Term Trends In Species Abundance In Norwalk Harbor, Viktoria Savatorova, Aidan Kieft, Nicole C. Spiller, Kasey Burns

Spora: A Journal of Biomathematics

This study examines the effects of environmental changes on fish populations in Norwalk Harbor, focusing on winter flounder (Pseudopleuronectes americanus), cunner (Tautogolabrus adspersus), northern pipefish (Syngnathus fuscus), and naked goby (Gobiosoma bosci) as examples of species responding to climate-related shifts. We analyze how water temperature, salinity, and dissolved oxygen correlate with fish abundance. To assess statistically significant differences in catch per unit effort (CPUE) across harbor regions, we applied the Kruskal-Wallis test followed by Dunn's post-hoc test. Seasonal variations in CPUE were examined by comparing monthly catch data for each species. K-means …

Discounting Effect Size When Borrowing External Data In Clinical Studies, Zhuanzhuan Ma, Chul Ahn, Bin Wang, Xuefeng Li

Research Symposium

Background: When borrowing information from external data to augment a current trial, many available methods discount the sample size but retain the effect size from previous studies. Discounting the sample size is just one way to discount the prior information. It may not be appropriate if the underlying assumption of unbiased treatment effect does not hold, for example, when the treatment effect in the historical study is likely higher than the one expected in the current trial.

Methods: To tackle this potential issue, we study some methods to shrink the effect size from previous studies assuming that the prior effect …

Sparse Bayesian Variable Selection Using Global-Local Shrinkage Priors For The Analysis Of Cancer Datasets, Zhuanzhuan Ma

Research Symposium

Background: With a rapid development of data collection technology, high dimensional data, whose model dimension k may be growing or much larger than the sample size n, is becoming increasingly prevalent in different fields of study, such as ecology, genetics, among others. This data deluge is introducing new challenges to traditional statistical procedures and theories and is thus generating a renewed interest in the problems of variable selection and classification in high dimensional regression models. In large k, small n settings, variable selection is usually the first step for dimension reduction to uncover significant covariates, which contribute to …

Methods In Statistics, Machine Learning, And Deep Learning For Combining Multi-Omics Dataset, Md Mutasim Billah

Dissertations, Master's Theses and Master's Reports

Transcriptome-wide association studies (TWAS) have emerged as a powerful strategy to bridge genome-wide association studies (GWAS) with gene regulatory mechanisms by integrating genotypic data with gene expression data. While early TWAS methods typically rely on linear models and single-tissue expression references, recent advances underscore the need for flexible, multi-tissue approaches that can capture heterogeneous regulatory architectures and tissue-specific expression patterns. This dissertation introduces a three‑part research project that advances multi‑tissue transcriptome‑wide association studies (TWAS) along complementary axes of methodology, statistical power, and modelling flexibility.

In chapter One, TWAS‑CTL introduces a two‑stage cross‑tissue learner that trains any user‑chosen single‑tissue imputers (STLs) …

Theoretical Foundations And Applied Performance Of Periodicity-Aware Imputation: Variable Bandpass Block Bootstrap Methods For Incomplete Time Series, Asmaa Ahmad

Electronic Theses & Dissertations (2024 - present)

Time series data are prevalent across a wide range of disciplines, including health surveillance, public policy, and environmental monitoring. In the presence of underlying cyclical patterns, the integrity of time series analysis depends critically on the ability to detect, model, and impute structured missing data without compromising the temporal structure. This dissertation introduces and validates a novel imputation framework that integrates the Variable Bandpass Periodic Block Bootstrap (VBPBB) into multiple imputation procedures, improving the accuracy, robustness, and interpretability of time series models under high rates of missingness and noise. The overarching goal of this dissertation was to develop and evaluate …

Predictive Modeling For Healthcare Data Using Nonlinear Bayesian Methods, Prince Kofi Asare

Theses and Dissertations

Unplanned hospital readmissions represent a significant challenge for healthcare systems, contributing to substantial financial burdens and highlighting gaps in patient care coordination. In the U.S., approximately 20% of Medicare beneficiaries are readmitted within 30 days, costing billions annually. Social determinants of health, such as income, housing stability, and social support, account for up to 80% of health outcomes, yet their integration into predictive models remains underexplored. This study introduces a novel Bayesian framework for predicting 30-day readmission risk, combining Gaussian Process models with spike-and-slab priors and Bayesian Lasso regression with Laplace priors. Utilizing Markov Chain Monte Carlo methods, the approach …

Hybrid Mixtures Of Factor Analyzers For High Dimensional Data, Kazeem Abiodun Kareem

Dissertations, Master's Theses and Master's Reports

Factor analysis is a powerful tool for modeling latent structures in high-dimensional data, traditional approaches assume a single global structure, limiting their ability to capture heterogeneity. The Mixture of Factor Analyzers (MFA) extends classical factor analysis by modeling data as a mixture of Gaussian-distributed local subspaces, effectively uncovering cluster-specific latent structures. However, MFA relies on Gaussian mixtures, making it sensitive to outliers and ill-suited for heavy-tailed data. The Mixture of $t$-Factor Analyzers (M$t$FA) addresses these limitations by incorporating multivariate $t$-distributions, improving robustness. Despite their advantages, both MFA and M$t$FA face significant computational challenges in high-dimensional settings, particularly due to costly …

Mean From Median Estimation In Longitudinal Meta-Analysis Of Quality Of Life In Radiation Oncology Patients, Harlan R. Sayles

Theses & Dissertations

Meta-analysis of longitudinal data, where some of the studies report results with means and standard errors while others use medians and ranges, is a complex analytical problem with several challenges which must be overcome. Existing methods for estimating means from medians and either ranges, interquartile ranges, or both have not previously been evaluated in a longitudinal setting. In this work, a simulation study was used to estimate mean bias, between studies variance bias, and coverage of confidence intervals in a longitudinal setting. A second simulation study estimated the variance of meta-analysis results from a given set of studies that may …

The Impact Of “Multiple Looks” When Performing Survival Analysis, Quentin Eloise

Electronic Theses and Dissertations

Survival analysis is a critical statistical method in healthcare to assess patient treatment effects and disease progression. Another critical area of statistical methodology in health care is the practice of adaptive designs. Adaptive designs allow for interim analyses to take place during a study and various decisions and actions can take place more ethically. This is beneficial for studies that take multiple years to complete and allows administrators and healthcare providers to make sound decisions as early as possible. A challenging aspect of adaptive designs is that the number of interim analyses is known in advance which is applicable in …

Bayesian And Deep Generative Modeling In Immunology, Yuqiu Yang

Statistical Science Theses and Dissertations

Due to the accumulation of a large volume of data of different natures such as sequencing data, proteomics data, and clinical data, statistical methods and deep learning algorithms have become increasingly important in the field of immunology. By leveraging the diverse datasets as well as interdisciplinary knowledge from areas like biology and public health, these quantitative methods have revolutionized this field by providing powerful tools for data analysis, modeling, and prediction. This has led to a deeper understanding of the immune system, accelerated the development of novel therapies, and paved the way for personalized and precision medicine approaches in immunology. …

Visualization Of Species Tree Likelihood Under The Multispecies Coalescent Model, Jaimasan Sutton

Mathematics & Statistics ETDs

A commonly used tool for evolutionary biologists is a phylogenetic tree that represents the ancestry of a set of species and the evolution of traits. Statistical models can be used to predict the probabilities of gene trees which represent ancestral relationships of genes sampled from species. Because of this, we are able to represent the likelihood of a species tree, which represents the evolutionary history of a set of species, as a function of the counts of gene tree topologies, where each gene tree represents the ancestry of a specific genetic locus for multiple species. Because we can represent these …

Examining The Interaction Between Calcium Supplement Use, Demographics, And Lifestyle Factors On Bone Health In Women, Vix Talbot

University Honors Theses

Osteoporosis is a condition which poses a significant health threat, particularly among women during the menopause transition, where accelerated bone loss increases fracture risk. Calcium supplementation has been shown to be an important intervention to mitigate bone mineral density (BMD) decline during this and other periods of life. However, the efficacy of calcium supplementation is influenced by various individual factors, including demographics and lifestyle habits. This study investigates the interaction between calcium supplement use, and several interaction terms on bone health in women. Multiple linear regression analysis is employed to assess the impact of these factors on BMD. Data from …

An Improved Bayesian Pick-The-Winner (Ibpw) Design For Randomized Phase Ii Clinical Trials, Wanni Lei, Maosen Peng, Xi K. Zhou

COBRA Preprint Series

Phase II clinical trials play a pivotal role in drug development by screening a large number of drug candidates to identify those with promising preliminary efficacy for phase III testing. Trial designs that enable efficient decision-making with small sample sizes and early futility stopping while controlling for type I and II errors in hypothesis testing, such as Simon’s two-stage design, are preferred. Randomized multi-arm trials are increasingly used in phase II settings to overcome the limitations associated with using historical controls as the reference. However, how to effectively balance efficiency and accurate decision-making continues to be an important research topic. …

Variable Selection For High-Dimensional Data With Interaction Effects: Methods, Applications, And Inferences, Leiyue Li

Theses and Dissertations--Statistics

For high-dimensional data where the number of variables greatly exceeds the number of observations, selecting important variables while maintaining the required heredity conditions can be challenging. This dissertation is structured into three interconnected parts. In the first part, we propose a variable selection method by implementing a well-known optimization technique, the Genetic Algorithm. An R package was developed to simplify the implementation and usage of the proposed method. We then propose another variable selection method by extending the study from the Genetic Algorithm to a different but related optimization technique, Simulated Annealing. We consider three different hierarchical structures in both …

Multiscale Modelling Of Brain Networks And The Analysis Of Dynamic Processes In Neurodegenerative Disorders, Hina Shaheen

Theses and Dissertations (Comprehensive)

The complex nature of the human brain, with its intricate organic structure and multiscale spatio-temporal characteristics ranging from synapses to the entire brain, presents a major obstacle in brain modelling. Capturing this complexity poses a significant challenge for researchers. The complex interplay of coupled multiphysics and biochemical activities within this intricate system shapes the brain's capacity, functioning within a structure-function relationship that necessitates a specific mathematical framework. Advanced mathematical modelling approaches that incorporate the coupling of brain networks and the analysis of dynamic processes are essential for advancing therapeutic strategies aimed at treating neurodegenerative diseases (NDDs), which afflict millions of …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …