Statistics and Probability Commons^™

Robust Statistical Methods For Microbiome Abundance Data, Yiming Shi

WUSM Theses and Dissertations – All Programs

Differential abundance analysis in microbiome studies aims to identify taxa whose abundance differs across biological or clinical conditions. The observed data are typically taxon-specific sequencing read counts, representing reads assigned to different taxa within each sample. These counts are indirect measurements of the underlying microbial abundance profile and are constrained by sample-specific library sizes. Microbiome count data are also typically sparse, overdispersed, and heteroscedastic. Together, these characteristics create substantial challenges for differential abundance analysis and make the results highly sensitive to normalization procedures, model specification, and the statistical methods used for inference.

Normalization defines the scale on which samples are …

Rethinking Road Racing Standards: Comparing New York Road Runners Race Results To Running Industry Standards, Jennie Coughlin

Dissertations, Theses, and Capstone Projects

Running has undergone a third boom in participation since 2020, driven largely by people seeking fitness options that were outside and socially distanced during the COVID-19 pandemic. Social media has also allowed runners from groups that did not traditionally participate to find community. As the road racing population has expanded to include more people, some road racing industry standards have not kept up. This project assesses what the road racing community looks like and measures industry standards against the community of participants to see what changes in those standards would be needed to make them inclusive for all participants.

To …

Mapping The Water Quality Of Jamaica Bay, New York (1996-2024): Principal Component Analysis And K-Means Clustering, Sneha Srivastava

Dissertations, Theses, and Capstone Projects

Jamaica Bay, located along the southeastern coast of New York City, acts as a biodiverse estuary of wetlands, meadows, and salt marsh islands. The purpose of this study is to analyze the water quality conditions of the region over time, comparing locations around the bay to identify hyperlocal features that influence larger trends in the hydrological system. Ten variables were used as water quality indicators, including total Kjeldahl nitrogen, salinity, pH, Secchi disk depth, and total phosphorus, among others, across five stations in the bay, between 1994 and 2024. After data cleaning and standardization methods were applied, principal component analysis …

Geometric Convergence And State-Space Decompositions For Stochastic Gradient Descent Markov Chains, Philip Zaleski

Dissertations

No abstract provided.

Motor Imagery Eeg Decoding For Brain-Computer Interfaces: Structured Representation, Transfer, And Drift, Yiming Shen

Graduate Doctoral Dissertations

Motor imagery EEG decoding is often summarized by the accuracy of a final classifier, but the classifier is only the last stage of the pipeline. Before classification, the signal has already been shaped by preprocessing, feature extraction, source-session organization, and adaptation. This dissertation studies how feature representation, source-session transfer, and drift shape reliable MI-EEG decoding for brain-computer interfaces.

It first studies within-session decoding on public MI-EEG datasets using nested validation that keeps preprocessing, feature fitting, and model selection inside the training folds. This analysis separates gains from feature representation from gains due to nonlinear classification, and relates both comparisons to …

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 …

Algebraic And Topological Methods In Computational Neuroscience, Trong-Thuc Trang

Electronic Theses and Dissertations

Neural data is incredibly rich in combinatorial, topological, and geometrical information, reflecting the intricate shape and connectivity of neural firing patterns. To decipher these structures, neuroscience increasingly relies on advanced mathematical tools to analyze neural activity. Here we study (1) neural codes within the poset P_Code of neural codes and (2) the connectivity of neural population activity within the insular cortex when responding to interoceptive information. In (1), we establish combinatorial constructions for all upward covering relations based on what we call “isolated subsets” with supporting theorems and give a slight modification of the existing downward covering relations. We …

Criticality In A Heterogeneous Neutron Transport Rod Model, Samuel Kaleb Crowford

All Graduate Reports and Creative Projects, Fall 2023 to Present

This work studies the stochastic behavior of neutron populations in a one-dimensional rod model using Monte Carlo simulation. The first part of this project reproduces the computational results of Dumonteil, Horton, Kyprianou, and Zoia (2025) by independently implementing the Monte Carlo algorithm described in their article, with the asymptotic behavior of the first moment analyzed in relation to the dominant eigenvalue and adjoint eigenfunction of the neutron transport operator. The model is then extended to a heterogeneous setting by introducing a central region where fission is suppressed. A global expectation over initial positions and directions is used to estimate the …

Mapler: An R Package For Estimating The Impact Of Climate Change On Maple Syrup Production, Matthew T. White

All Graduate Theses and Dissertations, Fall 2023 to Present

Successful maple sap tapping depends on the freeze/thaw cycle (i.e., temperatures fluctuating above/below freezing) during the winter and spring. Climate change threatens to alter the timing and duration of the tapping season. This necessitates research into how maple sap tapping will be impacted by climate change in order to help maple syrup producers prepare for the future. We define a sap day as a day where the freeze/thaw cycle occurred. Using information climate scientists use to predict future temperatures, we calculate how many sap days could occur each year. We develop software to analyze these sap day calculations to determine …

Modeling Mean And Variability Of Anxiety In Ecological Momentary Assessment Data Using Mixed-Effects Location–Scale Models, Trenzy Odero

Electronic Theses and Dissertations

Ecological Momentary Assessment is a method of collecting repeated measures of people in real time within natural environments. This results in hierarchical data that has a significant amount of variation at the person level. The traditional linear mixedeffects models assume that the residual variance is constant, which might not be true when the residual variance varies among individuals as well as in time. This thesis uses mixed-effects location-scale (MELS) models to model the mean and variance of an EMA outcome together. By introducing the possibility of variability in residual variance within and across individuals and with covariates, the MELS framework …

Machine Learning For Predictive Energy And Emissions Modeling Of Vehicles And Power Grids In The United States, S M Tanvir Faysal Alam Chowdhoury

Dissertations

The environmental benefits of electric vehicle (EV) adoption depend on more than replacing internal combustion engine vehicles with electric powertrains. EV adoption reshapes electricity demand, interacts with regional generation mixes, and influences travel behavior and congestion, creating a coupled transportation-energy system in which vehicle and power-plant emissions must be evaluated together. This dissertation develops machine-learning frameworks for predicting energy consumption and emissions from vehicles and power grids under rising EV adoption. The first component forecasts grid emissions from EV charging. Using simulation data from NREL's Cambium database, a Prophet-based time-series framework predicts carbon dioxide, nitrous oxide, and methane emission rates …

Learning Latent Structure In High-Dimensional Data Via Geometry And Graphs, Haozhe Chen

All Graduate Theses and Dissertations, Fall 2023 to Present

Modern datasets often contain many measured variables for each observation, such as gene-expression levels, brain activity signals, or features in tabular data. These data are also often noisy, meaning that useful patterns are mixed with measurement error or irrelevant variation. Although such datasets can appear complex, they are frequently represented by simpler hidden structures, such as trajectories, clusters, or relationships between observations. This dissertation develops methods for uncovering these hidden structures by learning geometric and graph-based representations directly from data. The first part introduces Functional Information Geometry, which represents local patterns in high-dimensional data using functional features and constructs a …

Unifying And Expanding Global And Local Variable Importance Methods For Explainable Machine Learning, Kelvyn K. Bladen

All Graduate Theses and Dissertations, Fall 2023 to Present

Machine learning methods are powerful analytical tools used across all scientific disciplines and many other fields of investigation for prediction and inference from diverse data sources. Despite their broad applicability, machine learning methods are often highly complex and difficult to interpret. Developing a greater understanding of which variables most influence a response is essential for increasing the interpretability of these models and supporting informed decision-making. This research focuses on improving how we evaluate the importance of these variables.

One common approach is to shuffle the values of a variable and see how much the model accuracy gets worse. Another approach …

Spatial Prediction Under Uncertainty: Methodological And Computational Advances In Bayesian Maximum Entropy, Kinspride K. Duah

All Graduate Theses and Dissertations, Fall 2023 to Present

Environmental decisions such as infrastructure design, water management, and snow load estimation depend on spatial data that are often incomplete or uncertain. In many cases, measurements are not exact values but ranges, reflecting limitations in data collection methods. Traditional mapping techniques typically simplify these uncertain measurements, which can lead to less accurate predictions. This dissertation introduces improved statistical tools for making spatial predictions when data are uncertain or partially known. By utilizing a framework called Bayesian Maximum Entropy (BME), this research demonstrates how exact measurements and range-based data can be combined in a mathematically consistent way. The work demonstrates that …

Community Detection In Bipartite Networks Using Bipartite Stochastic Block Models With Node-Level Covariates, Geraldine Elaine Percival

Dissertations

In this age, monumental webs of data demands for perpetual cultivation of ways to untangle these webs of information. One of the many curiosities is how to systematically group entities. When clustering, one avenue to take is ascertaining the interconnectedness between the data points, and gauging their influence to each other. This perspective is programmed to model the relationships between the data presented as a network. Many of the methods being used today are algorithm-based, which may pose limitations in understanding and explaining the uncertainty revolving around the data. Hence, it is proposed to steer towards a model-based approach that …

Evaluating Machine Learning Models On Classification Of Novel Cyber Attacks In The Healthcare Domain, Promise Ehimen

Dissertations, Theses, and Projects

The increasing adoption of the Internet of Medical Things (IoMT) has improved healthcare delivery through connected medical devices while simultaneously expanding the cybersecurity risks facing healthcare organizations. Although machine learning based intrusion detection systems have demonstrated high detection accuracy, their ability to respond reliably to previously unseen cyberattacks remains uncertain. This study investigated how a Neural Network model and a Logistic Regression model classified novel cyberattacks within the IoMT environment. The Neural Network and Logistic Regression models were both trained and tested using a subset of the CICIoMT2024 benchmark dataset. The Neural Network achieved 99.82% test accuracy and a 0.94 …

Interpretable Case-Control Inference Through Log-Linear General Location Models, Zacharia Stuart

Mathematics & Statistics ETDs

This dissertation analyzes one of the few publicly available NFL injury datasets to study field type and non-contact lower-limb injuries. Field type is studied jointly with other risk factors to understand how these factors interact to affect injury risk. The data were gathered through a case-control sampling scheme, which limits direct inference on absolute injury probabilities. While not the most common approach for case-control data, this dissertation models the retrospective distribution directly through Log-Linear General Location Models (Log-Linear GLOMs). Through a log-linear structure placed on a log-odds-ratio reparameterization, the model provides directly interpretable marginal and interaction contributions to injury log-odds …

The Uncertainty Principles, Lee Michael Felicetti

Mathematics & Statistics ETDs

The Heisenberg uncertainty principle is a central aspect of quantum mechanics, but also illustrates an essential quality of the Fourier transform. After Heisenberg, a variety of uncertainty inequalities emerged in the fields of physics and mathematics. In this thesis we will analyze the Heisenberg uncertainty principle in both the setting of quantum mechanics and Fourier analysis. We will then look at how the work of Heisenberg has been expanded upon in both physics and mathematics. Particularity, we will see how uncertainty principles can be applied to signal recovery and explore current research in this field.

Mapping And Modeling Threat-Evoked Brain States After Early Life Adversity, Taylor W. Uselman

Biomedical Sciences ETDs

Early life adversity (ELA) increases lifelong neuropsychiatric vulnerability. Yet how ELA reorganizes brain-wide activity and circuit coordination across later experience remains unclear. This dissertation tests the hypothesis that ELA alters adult brain-wide activity and responses to threat through disrupted coordination among neural systems that regulate emotional experience, including prefrontal-limbic and monoaminergic systems. Longitudinal manganese-enhanced MRI of adult mice exposed to standard or fragmented early care, combined with computational processing and statistical modeling, quantified brain states before, during, and long after innate predator threat. These studies established that acute threat evokes large-scale, distributed brain activity that evolves over time. ELA potentiates …

Statistical Evaluation Of A New Orleans Historic Rainfall Dataset (1840–1893), Arielle C. Filostrat

LSU Master's Theses

This study evaluates the climatic credibility of a newly identified historical rainfall dataset for New Orleans, Louisiana, spanning 1840–1893. The New Orleans Historical Dataset (NOHD) is compared to a modern observational record from the Audubon rain gauge (1893–2024) to determine whether nineteenth-century rainfall observations are consistent with known precipitation behavior in the region. Establishing the reliability of early records is critical for extending climatological baselines and improving understanding of long-term rainfall variability.

Historical rainfall observations were first evaluated through archival review using the New Orleans Medical and Surgical Journal and other nineteenth-century meteorological records to verify notable rainfall events. Daily …

Statistical Methods For Mendelian Randomization Under Nonlinearity And Non-Normality, Mary Appah

ETDs from 2020-2029

Instrumental variable (IV) methods are widely used for estimating causal effects in observational studies where unmeasured confounding may bias traditional regression estimates. The core idea is to use a variable referred to as an instrument that is associated with the exposure of interest, independent of unmeasured confounders, and influences the outcome only through the exposure. While originally developed in econometrics, IV methods have been increasingly adopted in epidemiology and genetic research under the framework of Mendelian Randomization (MR), where genetic variants, most commonly single nucleotide polymorphisms (SNPs), serve as instruments. MR provides a powerful tool for investigating causal relationships between …

Mycelial Modeling: Teaching Biology Students Statistical Modeling With Mushrooms, Colette Wolf

University Honors Theses

This paper summarizes and describes the development of a set of learning materials that were created to educate students and professionals from other fields in statistical modeling techniques. These materials are primarily aimed at biology students, but are still intended to be useful for anyone who is interested in incorporating decision trees and random forest models into their personal research in the future. By directing the reader towards the JMP software, these materials navigate around the statistical knowledge base and coding implementation practices that otherwise would serve as a barrier to learning statistical modeling techniques, and instead focus on the …

Bias, Structure, And Inference In Applied Network Analysis, Anna Vasenina

Dartmouth College Ph.D Dissertations

This dissertation develops mathematical and statistical methods for extracting reliable information from network data across biological applications, with an emphasis on understanding what observed network structure can and cannot resolve. The first study leverages protein–protein interaction network topology in the c-di-GMP signaling system of Pseudomonas fluorescens, showing that node centrality measures accurately classify protein domain types and that physical interaction structure contributes statistically significant predictive power for biofilm formation phenotypes across nearly 200 environments, while gene expression does not. The second study examines sampling bias in lemur-plant trophic interaction networks in Madagascar, demonstrating that differential detection of diurnal versus …

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 …

Muon Lifetime: Theory, Experiment, And Simulation, Soren Agustin Munoz

Physics

This senior project investigates the muon lifetime through three complementary approaches: theoretical calculation, laboratory measurement, and computational simulation. The theoretical component develops the necessary background from relativistic field theory to the effective weak interaction, culminating in the leading-order Fermi-theory prediction of τ ≈ 2.2 μs, which explains why the muon lifetime lies on the microsecond scale.

The experimental component measures the lifetime of stopped cosmic-ray muons using a plastic scintillator, photomultiplier tube, and analog timing electronics. A binned Poisson likelihood fit to the primary 15-day acquisition run τ = 2.17^+0.03_-0.09 μs, consistent with the accepted value within the …

Reexamining The Croton Aqueduct: A Ward-Level Microhistorical Analysis Of Infrastructure And Cholera Mortality In 1849 New York City, Alexandria R. Toothman

Dissertations, Theses, and Capstone Projects

This work reexamines the Croton Aqueduct’s role in public health by shifting analysis from the citywide level to the ward level, revealing that infrastructure expansion did not produce uniform benefits across New York City. When the Croton Aqueduct opened in 1842, it was celebrated as an achievement that would deliver pure water and eliminate disease. However, only seven years after its opening, in 1849, cholera returned with greater force in the Sixth Ward. This work shows that the uneven distribution of Croton infrastructure corresponded with uneven cholera mortality rates, challenging narratives that present Croton as a singular triumph of urban …

Scaling Limits Of Critical Observables Through The High Dimensional Incipient Infinite Cluster, Pranav Chinmay

Dissertations, Theses, and Capstone Projects

We give a general construction of the incipient infinite cluster in high dimensional percolation, and use it as a decoupling tool to rigorize geometric heuristics for analyzing the asymptotics of observables at criticality. Examples include demonstrating the limiting distribution of the chemical distance and full-strength asymptotics for k-point functions, which constitute foundational inputs for scaling limit results associated to critical clusters.

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

A Predictive Coding Account Of Spatial Working Memory Following Prophylactic Levetiracetam Administration Prior To Traumatic Brain Injury, Omeima Mutwali

Dissertations, Theses, and Capstone Projects

Traumatic brain injury (TBI) symptom prevention and remediation is an important area of research that would benefit vulnerable groups, including active-duty and veteran soldiers. These patients can sustain penetrative forces in fields of combat or in training, which result in focal lesions that trigger inflammatory and degenerative processes in the brain. Both primary and secondary injuries are associated with changes to cognition, behavior and affective state. This disease poses increased risk of epileptogenesis, as well. Given these outcomes, prior research has evaluated levetiracetam (LEV) as a prophylactic treatment for seizures, cognitive deficits and negative emotionality. LEV acts as a presynaptic …

Crab: A Novel Clustering Score Using Clustering With Rivals And Buddies For Unsupervised Learning, Allen Choi

Master's Theses

Unsupervised clustering algorithms today are used across a wide variety of fields such as biology, engineering, and industry in order to classify observations into groups where labels are not provided. This can provide important latent information regarding the observations within groups, as well as insight regarding the groups themselves. In order to judge the optimal number of clusters for an unsupervised clustering algorithm, many methods exist such as the Elbow Method and Silhouette Score; however, these methods come with drawbacks and are not necessarily flexible across many unsupervised methods. We present a novel clustering score framework relying on a resampling-based …