Biostatistics Commons^™

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 …

Supplemental Bibliographic Details. From 2001 Mars Odyssey To Earth’S Climate Crisis: Integrating Gamma Spectroscopy, Martian Soil Simulants, And Plant Genomes For Agroecology, Anchored In Sri Lanka’S Mars-Context Serpentinites, Suniti Karunatillake, Maheshi Dassanayake, Carlos Gary Bicas

Planetary Science Lab

Bibliographic details follow to supplement hyperlinked citations in the multinational GANGOTRI-supporting project conceived by Karunatillake, Dassanayake, and Gary-Bicas

Two-Stage Response-Adaptive Randomization Designs For Multi-Arm Trials With Normal Outcome, Tanjin Tamanna Happy

UNF Graduate Theses and Dissertations

This study focuses on improving how clinical trials compare new treatments with a standard treatment, when the response is quantitative (normally distributed). In a common two-stage design, several new treatments are first evaluated, and the best-performing one is selected if it appears better than the standard. In the second stage, this selected treatment is compared again with the standard using additional data to confirm its effectiveness. This approach is known to be efficient in terms of accuracy and sample size savings. We extend this design by introducing an adaptive method for assigning patients to treatments in the second stage. Instead …

A Comparative Evaluation Of Data Imbalance Handling Techniques In Machine Learning Models For One-Year Mortality Prediction In Liver Cirrhosis, Sumiya Hasan Trisha

UNF Graduate Theses and Dissertations

Liver cirrhosis is associated with substantial morbidity and mortality, making one-year mortality prediction a clinically relevant problem. Using a liver cirrhosis dataset as the motivating application, this thesis evaluates five machine learning classifiers—Logistic Regression, Random Forest, XGBoost, LightGBM, and CatBoost—under five class-imbalance handling strategies: Baseline learning, Random Oversampling, SMOTE-NC, ADASYN, and Cost-Sensitive Learning. Hyperparameter tuning was conducted using randomized search, and predictive performance was assessed over 200 iterations of Monte Carlo Cross-Validation using Accuracy, Precision, Recall, Fl-score, and ROC-AUC.

The results suggest that imbalance-handling strategies can materially affect predictive performance, particularly recall. Because the outcome of interest is death within …

Ridit-Based Adaptive Allocation In Two-Stage Clinical Trials With Binary Outcomes, Dewan Fahim

UNF Graduate Theses and Dissertations

This study explores better ways to assign patients to treatments in clinical trials with binary outcomes, such as success or failure. Adaptive methods are used to learn from early results and adjust treatment assignments during the trial, helping more patients receive better performing treatments while maintaining reliable conclusions. We focus on trials comparing multiple treatments using a two-stage design. In the first stage, several treatments are tested to identify the most promising one; in the second stage, that treatment is compared with a control. Unlike traditional equal assignment, we use adaptive allocation in the second stage to make better use …

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 …

Flexible Spatial Priors In Bayesian Neuroimaging: Gmrf, Nngp, And Deep Gmrf, Boyoung Hur

All Dissertations

Structural neuroimaging is essential for understanding neurological disorders such as Alzheimer’s disease, enabling accurate delineation of brain regions through image segmentation. Among various segmentation methods, multi-atlas-based approaches like label fusion have become leading techniques. In statistics, Bayesian hierarchical models for label fusion are increasingly favored for their ability to incorporate uncertainty and prior knowledge. Also, a key challenge in modeling neuroimaging data is spatial dependence among image voxels, making the choice of spatial prior critical—particularly in high-resolution settings where segmentation accuracy and computational efficiency are both essential.

This dissertation proposes fully Bayesian spatial hierarchical models that explore two flex- ible …

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 …

Towards Reliable Clinical Applications Of Ai Models In Radiotherapy, Biling Wang

Statistical Science Theses and Dissertations

Over the past decade, artificial intelligence (AI), particularly through deep learning (DL) techniques, has made significant strides in fields like computer vision (CV) and natural language processing (NLP), leading to transformative advancements across numerous applications. This progress has sparked considerable enthusiasm within the medical field, where DL-related research has grown exponentially since 2015. However, despite these promising developments, the real-world deployment of DL models in healthcare remains limited, especially in safety-critical domains such as radiotherapy (RT), where reliability, safety, and sustained performance are critical. This thesis addresses three core challenges associated with the clinical application of DL models: (1) post-deployment …

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 …

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 …

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 …

Beyond Homogeneity: Exploring Causal Heterogeneity In Psychopathology, Philip B. Vinh

Theses and Dissertations

Traditional models in psychiatric research often impose assumptions of causal homogeneity, treating population-level associations as reflective of uniform underlying mechanisms. This dissertation challenges that assumption by introducing statistical and machine learning frameworks designed to detect and model causal heterogeneity in the development of psychopathology. Central to this approach is the advancement of finite mixture structural equation modeling (FM-SEM) to identify latent subgroups characterized by distinct, and sometimes opposing, causal pathways.

The dissertation comprises three integrated empirical studies. The first introduces mixDoC, a finite mixture extension of the classical Direction of Causation (DoC) model applied to twin data, enabling the detection …

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 …

Complex Missing Data Problems In Education Surveys, Thomas Wesley Robertson

Electronic Theses & Dissertations (2024 - present)

Missing data are a nearly universal problem in human subjects research, including in education. However, reporting and addressing missing data is an issue, despite guidelines from the APA style guide and the What Works Clearinghouse, as well as guidance from prominent statisticians on the best methods to use. Prior research conducted in 2004 and 2014 found that in the field of education, most studies do not report or address missing data. In addition, no study has looked specifically at how missing data are reported and addressed in complex surveys. The current study has two main objectives: first, to determine if …

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 …

Improvement And Evaluation Of Multiple Imputation By Heckman's One-Step Mle For Binary Mnar Outcomes And Various Types Of Mar Covariates, Xin W. Shore

Mathematics & Statistics ETDs

Missing data is inevitable in clinical epidemiology. It becomes one of the major challenges in the analyses and can potentially undermine the validity of results and conclusions. Although methods for handling missing data with mechanisms of missing completely at random (MCAR) or missing at random (MAR) have been widely researched, methods adapted for the missing not at random (MNAR) mechanism are less studied. Galimard et al. (2018) have derived a method to use multiple imputation by Heckman's One-Step ML Estimation for binary MNAR outcome and continuous MAR covariates (MIHEml). This dissertation focuses on updating MIHEml in terms of …

Bayesian Approaches In Multi-State Markov Models And High Dimensional Time-To-Event Data., Yuchen Han

Electronic Theses and Dissertations

This dissertation consists of two projects. The first one involves nonparametric methods on Continuous Time Markov Chains (CTMCs). The second one is centered around Bayesian shrinkage models for detecting prognostic and predictive biomarkers in high-dimensional clinical data. Both these projects build on methods from across the frequentist and Bayesian paradigm to offer novel solutions. In the first project, we aim to model the nonlinear effects of continuous variables within multistate framework in a non-parametrically by appealing to the rich mathematical framework of Reproducing Kernel Hilbert Spaces (RKHS). Then we adapted the classical Representer Theorem to penalized (squared norm) log-likelihood which …

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. …

A Computerized Mastitis Classification Aid Using A Dairy Herd-Based Records: Multi-Layer Perceptron (Mlp) Neural Network With Backpropagation Approach, Ahmed M. Gad Prof, Dina Faris De, Sherif Ramadan Prof, Ghada Afifi Dr, Eman Manaa Prof, Mahmoud El-Tarabany Prof

Business Administration

The main objective of this study is to develop an efficient machine learning-based model for the early prediction of clinical mastitis in Holstein Friesian dairy cattle where automatic milking system (AMS) data is used. The model aims to offer a costless opportunity for mastitis control and reduce its negative impact on livestock production. Different forward multilayer perceptron (MLP) neural networks with backpropagation (BP) learning algorithms using various numbers of hidden neurons and epochs have been introduced. The results of the established models are evaluated based on different metrics such as the accuracy, the F1 core, the precision, the recall, and …

The Performance Of Marginal Modeling Methods For Rare Events With Application To Opioid Overdose Mortality And Morbidity, Shawn Nigam

Theses and Dissertations--Epidemiology and Biostatistics

Opioid misuse is a nationwide epidemic, with Kentucky having one of the highest opioid overdose-related fatality rates across all US states. These rates have increased significantly over the past decade, with particularly large increases during the COVID-19 pandemic. This dissertation aims to study the behavior of these increases and the methods for the marginal modeling of count outcomes related to opioid overdose.

Opioid overdose-related fatality rates in Kentucky increased significantly during the COVID-19 pandemic. In this chapter, we characterize the changes in opioid overdose fatality rates in Kentucky and identify associations between potential factors and fatality rates. County-level opioid overdose …

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 …

Bayesian Strategies For Propensity Score Estimation In Causal Inference., Uthpala I. Wanigasekara

Electronic Theses and Dissertations

Causal inference is a method used in various fields to draw causal conclusions based on data. It involves using assumptions, study designs, and estimation strategies to minimize the impact of confounding variables. Propensity scores are used to estimate outcome effects, through matching methods, stratification, weighting methods, and the Covariate Balancing Propensity Score method. However, they can be sensitive to estimation techniques and can lead to unstable findings. Researchers have proposed integrating weighing with regression adjustment in parametric models to improve causal inference validity. The first project focuses on Bayesian joint and two-stage methods for propensity score analysis. Propensity score modeling …

Statistical And Machine Learning Approaches To Describe Factors Affecting Preweaning Mortality Of Piglets, Md Towfiqur Rahman, Tami M. Brown-Brandl, Gary A. Rohrer, Sudhendu R. Sharma, Vamsi Manthena, Yeyin Shi

Department of Agricultural and Biological Systems Engineering: Faculty Publications

High preweaning mortality (PWM) rates for piglets are a significant concern for the worldwide pork industries, causing economic loss and well-being issues. This study focused on identifying the factors affecting PWM, overlays, and predicting PWM using historical production data with statistical and machine learning models. Data were collected from 1,982 litters from the United States Meat Animal Research Center, Nebraska, over the years 2016 to 2021. Sows were housed in a farrowing building with three rooms, each with 20 farrowing crates, and taken care of by well-trained animal caretakers. A generalized linear model was used to analyze the various sow, …