Data Science Commons^™

Semi-Supervised Learning For Annotation And Representation Of Single-Cell Rna Sequencing And Spatial Transcriptomics Data, Haoran Liu

Dissertations

Semi-supervised learning has emerged as a powerful paradigm for analyzing single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data, where full annotation is often costly or impractical. scRNA-seq technologies measure the expression of thousands of genes across tens of thousands of cells, whereas ST additionally captures the spatial coordinates of gene expression within intact tissue sections. Annotation is a key step in both scRNA-seq and ST analysis pipelines, aiming to identify cell types, spatial domains, and latent biological structures. However, most existing annotation approaches rely on separate clustering methods that are typically fully unsupervised and fail to leverage side information …

Beyond Words: A Systematic Multimodal Framework For Text, Images, And Extreme Helpfulness In Online Reviews, Alvaro J. Aguado Marin

Dissertations

Online product reviews have become increasingly multimodal, combining text with media-rich elements such as images. However, academic research has largely examined textual features in isolation, overlooking how visual content and its interaction with text shape perceived helpfulness. This dissertation addresses that gap by developing and empirically validating a comprehensive framework capturing how textual, visual, and contextual features collectively influence review evaluation. Grounded in the Elaboration Likelihood Model (ELM) and extended through the Text-Image Elaboration Likelihood Model (TI-ELM), the framework advances understanding of how consumers process content from both user- and business-generated sources. It also lays the foundation for examining emerging …

Real-Time Deep Learning Detection Of Toraja Carving Motifs Using Yolo11m For Cultural Heritage Preservation, Herman Herman, Farid Wajdi Mufti, Abdul Rachman Manga, Haidawati Nasir

Knowledge Engineering and Data Science

Toraja carvings are an important part of Indonesia’s cultural heritage, rich in symbolic, aesthetic, and philosophical meaning. However, the identification and preservation of carving motifs still rely on subjective, time-consuming manual processes, limiting scalability and inconsistent knowledge transmission. From a Knowledge Engineering and Cognitive Data Science perspective, this challenge highlights the need for mechanisms that can transform visual cultural artifacts into structured, machine-interpretable knowledge. This study investigates the use of the YOLO11m model as a data-driven approach for modeling cultural knowledge through automated detection of three Toraja carving motifs: pa_tedong, pa_kapu_baka, and pa_manu_londongan using original images collected directly from traditional …

Construction And Data-Driven Analysis Of A Stochastic, Individual-Based Opioid Epidemiology Network Model, Leigh Bennett Pearcy, Owen Queen, Vincent Jodoin, Suzanne Lenhart, Christopher Strickland

Mathematical Modelling and Numerical Simulation with Applications

While substance use epidemiology has been an active area of mathematical research in recent years, the social and mental processes that are involved in the development of substance use disorders have presented challenges to advancing the epidemiological theory and how they differ from the contraction of pathogenic disease. Such distinction is especially pertinent in the context of the current United States opioid epidemic and its intersection with the recent COVID-19 pandemic, as both prescription drugs and social influence play major roles in the development of opioid use disorder. In this paper, we construct a stochastic network model capturing how individual …

Panda-Plus: Improved Dataset Of Prostate Whole Slide Images From Panda Challenge With Pixel-Level Expert Annotations, Spencer Hopson, Carson Mildon, Corbyn Kubalek, Joshua L. Ebbert, Ryan Vance, Lauren Laverty, Paul Urie, Dennis Della Corte

Faculty Publications

Artificial intelligence (AI)-based prostate cancer detection through whole slide images (WSIs) offers promising potential to address the global pathologist shortage while improving clinical consistency. Digital slides and improving image analysis methods encourage the creation of tools to aid in WSI classification. Despite promising advances, these tools are still limited by available training data. Current publicly available datasets, such as Kaggle's PANDA Challenge, while large in scale, rely on slide-level labels that may introduce noise and limit model reliability. Others contain detailed annotations, but are smaller in size due to manual processing efforts. In this work, we introduce PANDA-PLUS, a 546-image …

Enhancing Education Through Virtual Reality: A Comparative Study Of Vr And Traditional Learning Environments, Shrivardhan Atluri

The Journal of Purdue Undergraduate Research

No abstract provided.

What Does Graptolite Origination And Extinction Reveal About The Cause Of The Late Ordovician Mass Extinction?, Charles E. Mitchell, H. David Sheets, Michael J. Melchin, Chris Holmden

Computer and Data Science Faculty Publications

Assesses the macroevolutionary turnover of paleotropical planktic graptolites during the Late Ordovician Mass Extinction (LOME) via automated sequencing and capture-mark-recapture modeling. Graptolites exhibited a succession of turnover pulses (sensu Elizabeth Vrba) that were coincident with the main phases of the Hirnantian glaciation and during which the Diplograptina experienced declining metapopulation size, elevated extinction, zero species originations, and ultimately, complete extermination. Concurrently, the Neograptina (latest Katian temperate zone immigrants) exhibit pulses of both extinction and adaptive radiation. Thus, the LOME involved intense species selection and the wholesale alteration of the clade diversity structure of a major element of the zooplankton. The …

Visualizing And Evaluating Binary Classifier Performance With Contingency Space, Colin D. Kehoe, Azim Ahmadzadeh

Undergraduate Research Symposium

Traditional metrics for evaluating binary classifiers, such as Accuracy, F1 Score, and True Skill Statistic (TSS), often obscure the underlying tradeoffs between true positive and true negative performance—particularly in imbalanced or high-stakes domains. This poster introduces the Contingency Space, a two-dimensional representation of classifier behavior defined by true positive rate (TPR) and true negative rate (TNR). Within this space, scalar performance metrics become geometric surfaces, revealing how scores vary across the entire landscape of possible classifier outputs.

We present a Python package that implements this framework, enabling users to map model predictions into the Contingency Space, visualize metric surfaces …

Face Value: A Computational Approach To Subjective Impressions Of Faces, Kevin Kpankou

Undergraduate Research Symposium

Various computational models of first impressions have been developed to uncover the mechanisms driving these judgments. However, the implicit notion of a singular ``human'' often overlooks meaningful individual differences in beliefs, attitudes, and associations, as well as culturally grounded group-level constructs. In this paper, we extend Cultural Consensus Theory (CCT) to estimate culturally shared beliefs about faces by incorporating latent constructs structured around interpretable facial features extracted via computer vision algorithms. We apply our model to a large-scale dataset of people’s first impressions of faces. Our approach reveals a robust mapping between facial features and culturally constructed impressions, allowing us …

A Bump Hunting Approach To Finding Interpretable Data Pockets, Tushar Ojha

Electrical and Computer Engineering ETDs

This dissertation approaches the problem of extracting simple interpretations from local regions of data. This is sometimes called bump hunting because the local regions of interest have a high concentration of a particular output value. This work develops a bump hunting method for discrete-valued tabular data where each bump is modeled by a rectangular region of the input data space so its rule-based description admits a simple logical interpretation that can inform decisions. This method is designed for labeled data where each input feature has a distinct meaning that may or may not be related to the output, and the …

Parameter Informed Reinforcement Learning For Vehicle System Identification, Nathan Schaff

Doctoral Dissertations and Master's Theses

Accurate system identification is essential for modeling and controlling vehicle dynamics. This dissertation explores the application of Parameter Informed Reinforcement Learning (PIRL) as a novel approach to system identification (SYSID). PIRL integrates prior system knowledge, such as physical parameters, into reinforcement learning (RL) frameworks to improve estimation accuracy. The study begins with an overview of traditional SYSID methods and then introduces PIRL as a modification of standard RL. The research applies PIRL to short-period aircraft dynamics, demonstrating its effectiveness in both offline and online learning frameworks. The dissertation then further explores PIRL’s utility in an indirect model reference adaptive control …

Modeling Private Debt Using U.S. Consumer Expenditure Data, Stsiapan Dziamentsyeu

Honors Capstones

This project models private household debt among U.S. consumers using data from the Consumer Expenditure Survey (CES) between 2013 and 2023. The analysis focuses on identifying how demographic and economic characteristics, such as income, housing expenditures, education, and occupation, relate to non-mortgage “other” loan balances. After initial model development produced poor residual behavior due to zero-inflation from imputed debt values, the analysis was refined to include only households reporting verifiable debt. Multiple modeling techniques, including AIC-based variable selection and Lasso regularization, were compared under a five-fold cross-validation framework. The Lasso model achieved superior predictive accuracy (RMSE = 1.55, MAE = …

Is Hockey Still Canada’S Game? How Usa Teams Have Won Every Stanley Cup Since 1994, Aaron Montgomery, Long Doan, Joe Demaio, Michael Frankel

Symposium of Student Scholars

The last Canadian team to win Lord Stanley’s cup in the National Hockey League was the Montreal Canadiens in 1993. Since then, each championship has been claimed by a team geographically located in the United States. Is this streak unusual? Perhaps it is particularly unusual in light of the fact that Hockey is known as Canada’s game. Is Hockey in its modern incarnation still Canada’s game? Given the long history of the NHL should we expect such a streak to occur at some point in time? Are we too fixated on the geographic location of the teams in question? Perhaps …

Prism (Proxy Recognition And Inclusion Scoring Method), Destiny Raburnel, Crystal Tubbs, Md Abdullah Al Hafiz Khan

Symposium of Student Scholars

AI-driven automated hiring tools are reshaping how companies find talent, but they often reproduce the hidden biases embedded in their training data. Our project, PRISM (Proxy Recognition and Inclusion Scoring Method), investigates how subtle demographic signals, specifically first names associated with gender and race, influence AI resume screening even when candidates have identical qualifications. We built a controlled dataset of resumes that are identical in every way except for the applicant's first name, with each resume using a racially neutral surname to isolate how first names alone affect scoring. We tested these resumes against job postings in technology, healthcare, and …

Examining The Intersectional And Structural Issues Of Routine Healthcare Utilization And Access Inequities For Lgb People With Chronic Diseases, Shiya Cao, Mehreen Mirza, Sophia Silovsky, Nicole Tresvalles, Lucia Qin, Sarah Susnea

Statistical and Data Sciences: Faculty Publications

In the United States, although the gaps in health insurance coverage by sexual orientation have been closing since the implementation of the Affordable Care Act and legalization of same-sex marriage, the LGB group (i.e., lesbian, gay, bisexual) continues to report healthcare utilization and access inequities such as more delayed or unmet care. The extant research has often examined healthcare utilization and access inequities due to affordability (e.g., out-of-pocket costs). However, healthcare utilization and access inequities are only partially explained by cost reasons; there are non-cost reasons that have not been adequately empirically examined. The present study innovatively includes discrimination structural …

A Predictive Model For Multi- Week Respiratory Risk From Red Tide On Florida’S Gulf Coast., Elmer S. Ochaeta

Computer Science and Engineering Faculty Publications

Florida’s Gulf Coast red tide (Karenia brevis) can put toxins into the air, making people cough, irritating the throat, and worsening asthma or other breathing problems especially when winds blow from the ocean toward the beach. Right now, most public updates don’t really help with the question people actually ask when planning a weekend or vacation: “Will going to or close to the beach be risky in the next few weeks?”.

In this project, I build a weekly early warning system that estimates respiratory risk for specific beaches and predicts that risk 2 to 4 weeks ahead. The study covers …

Bridging Machine Learning And Islamic Scholarship: A Study In Hadith Translation And Similarity Analysis, Asiyah R. Speight

Student Scholar Symposium Abstracts and Posters

Translation of Islamic religious texts poses unique challenges requiring both linguistic and theological expertise. This study explores the application of neural machine translation (NMT) models to Arabic-English hadith translation while analyzing semantic similarity patterns across different human translations. Using the complete Sahih Bukhari corpus (7,550 hadiths) as the primary dataset, we adopt a dual approach combining transfer learning and comprehensive neural network analysis to demonstrate the critical impact of corpus size on model performance.

First, we fine-tune a pre-trained MarianMT Arabic-English translation model on the full Sahih Bukhari corpus, comparing models trained on 40 hadiths versus 7,550 hadiths. Performance is …

Explainable Ai For Liver Transplant Survival Prediction: Integrating Immunological Mismatch Features, Sourab Shaik

Honors Projects

Liver Transplantations are crucial treatment for end-stage liver disease. However, a persistent deficit of donor organs necessitates maximizing the utility of each available graft to minimize failure rates. We evaluated whether donor–recipient molecular immunogenicity metrics - Electrostatic and Hydrophobic Mismatch Scores (HMS/EMS) and eplet-based counts - improve post–liver-transplant survival prediction. The analytic cohort comprised adult, first time, single-organ deceased-donor transplants drawn from Scientific Registry of Transplant Recipients; follow-up was truncated at five years, and the endpoint was all-cause graft failure (earliest of graft failure or death; otherwise, censored). HLA variables were derived via high- resolution conversion and molecular mismatch computations …

Global-Local Method For Poroelasticity Problems With Localized Pressure Effects, Hemantha Kunwar

Math Department Colloquium Series

In many poroelasticity applications, pressure effects are confined to a small region, making it inefficient and possibly unnecessary to solve the full system across the entire domain. Instead, we propose to solve the poroelasticity problem locally, where pressure effects are significant, and use a simpler linear elasticity model elsewhere. This creates a coupled elasticity–poroelasticity problem with transmission conditions. To solve this coupled problem, we propose a new non-intrusive global–local algorithm that iteratively solves the elasticity problem in the entire (global) domain and the poroelasticity problem only in a local domain, ensuring proper transmission conditions across the interface. This approach, which …

Iso-Detr: A Novel Detection Transformer For Industrial Small Object Detection, Faisal Saeed, Anand Paul

School of Public Health Faculty Publications

Effectively detecting and assessing real-time structural and ecological parameters in contemporary manufacturing environments poses significant challenges, particularly in identifying minute objects within product images. The swift evolution of the industrial sector underscores the necessity for intelligent manufacturing environments to uphold stringent product quality standards. However, accelerating production processes at high speeds heightens the risk of defective product outcomes. This research addresses the challenges inherent in small object detection within industrial contexts, proposing an innovative detection transformer model tailored to modern manufacturing environments. The proposed model integrates a feature-enhanced multi-head self-attention block (FEMSA), merging cross-channel communication network and multiple multi-head self-attention …

Generating Predictive Gene Expression Signatures For Alzheimer's Disease Using Postmortem Brain Tissue, Ashley Duche

Pharmaceutical Sciences (PhD) Dissertations

Background: Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of amyloid-beta (Aβ) plaques and tau protein aggregates. These pathological features develop in specific brain regions, but why some areas are more vulnerable to early AD-related changes remains unclear. To address this, predictive gene expression signatures were developed to explore the molecular mechanisms underlying regional susceptibility to AD pathology.

Methods: This was performed using postmortem brain (PMB) tissue from participants in the Religious Orders Study and Memory and Aging Project (ROSMAP), Mayo Clinic, and Mount Sinai Brain Bank (MSBB) to generate gene expression signatures from six brain …

Privacy Preserving-Based Artificial Intelligence For Precision Agriculture, Partha P. Sengupta

Dissertations

The research work finds a solution to precision agriculture of cotton cultivation using artificial intelligence (AI) models. Two sets of model performance based on the application are selected namely a low resource and a high resource setting. This is because using drone surveys to capture images identifying the classes of stressed and unstressed cotton plantation requires limited model architecture and CPU based computation. Thus, traditional AI models were selected for low resource settings. Again, for high computation intensive models like transfer learning-convolution neural network (CNN) based architectures were grouped into high resource settings. There was another issue of class imbalance …

Generalized Detection Of Animal Behavior Using Accelerometers, Alexander J. Arrieta

Master's Theses

Animal mounted sensors are becoming increasingly used to passively monitor both domestic and wild animals. Advances in lightweight accelerometer and GPS technology have allowed many animals to be fitted with high accuracy sensors for extended periods of time. This leads to new opportunities to study animal behavior without direct observation. However, interpreting the raw data is difficult due to the high volume and missing context of the information. Machine learning techniques excel at extracting information from raw data streams and are excellent candidates for processing the sensor data. However, due to large variance in how different animals execute the same …

Proverag: Provenance-Driven Vulnerability Analysis With Automated Retrieval-Augmented Llms, Reza Fayyazi, Stella Hoyos Trueba, Michael Zuzak, Jay Yang

Institute for Informatics and Applied Technology Scholarship

In cybersecurity, security analysts constantly face the challenge of mitigating newly discovered vulnerabilities in real-time, with over 300,000 vulnerabilities identified since 1999. The sheer volume of known vulnerabilities complicates the detection of patterns for unknown threats. While LLMs can assist, they often hallucinate and lack alignment with recent threats. Over 40,000 vulnerabilities have been identified in 2024 alone, which are introduced after most popular LLMs’ (e.g., GPT-5) training data cutoff. This raises a major challenge of leveraging LLMs in cybersecurity, where accuracy and up-to-date information are paramount. Therefore, we aim to improve the adaptation of LLMs in vulnerability analysis by …

Coupled Machine Learning Models: Combining Observations And Numerical Analysis In A Physics-Regularized Approach, Austin B. Schmidt

LSU New Orleans Theses and Dissertations

This dissertation investigates surrogate modeling for fixed-location environmental forecasting using novel data-combination techniques. The work surveys the landscape of observational measurements and numerically generated data, identifying similar research and gaps in current methodologies. The ratio-coupled training framework is introduced to combine two data sources per predicted feature through a tunable parameter that weights training signal strength. An optimization scheme is developed to simultaneously tune surrogate weights and the coupled signal ratio, allowing relative influence between signals to act as an explicit regularizer. Three case studies demonstrate the methodology and approach in a variety of contexts. The first study is based …

Topic Modeling And Culturomic Analysis Of 30,000 Books Over 100 Years Using Gensim, Michael A. Freeman

Electronic Theses and Dissertations

This thesis explores the cultural influence of historical events on English-language fiction published between 1820 and 1929. Using a corpus of 30,256 digitized books from Project Gutenberg, Latent Dirichlet Allocation (LDA) topic modeling was applied to identify recurring themes across eleven decades. The study sought to determine whether historically significant events could be detected within fictional narratives. One clear instance emerged: Napoleon Bonaparte and the Napoleonic Wars appeared explicitly in the 1820s corpus. Beyond this, several thematic patterns were observed—such as maritime language in the 1840s, national identity in the 1880s, and youth-oriented dialogue in the early 20th century—that plausibly …

Stochastic Functional Data-Driven Models For Real-Time Battery Health Forecasting Under Dynamic Operating Conditions, Joshua Owusu

Electronic Theses and Dissertations

This thesis provides an effective statistical model to predict the real-time state of lithium-ion batteries for reliable Battery Management Systems (BMS). It highlights battery data (voltage, current, temperature) as smooth functional curves. The principal method demonstrates diminishing trends to health outcomes like State of Health (SoH) and Remaining Useful Life (RUL) by employing Functional Principal Component Analysis (FPCA) and Bayesian Functional Linear Models (FLMs). The primary objective is to figure out how uncertain forecasts are. Simulations demonstrate that the highest accuracy (lowest MSE) is achieved through low noise levels along with large sample sizes. The final system provides a highly …

Postprocessing Gan-Generated Synthetic Time Series Using Dynamic Time Warping, Md Raisul Islam Roni

Electronic Theses and Dissertations

Generative Adversarial Networks (GANs) are a class of deep learning models capable of producing realistic synthetic data that preserve the statistical and temporal characteristics of real datasets. The DoppelGANger (DGAN) framework extends this approach to time series data by jointly modeling temporal dependencies and contextual metadata. However, synthetic sequences generated by GAN may show temporal misalignment, resulting in inconsistencies when compared with real data. This study presents a postprocessing framework based on Dynamic Time Warping (DTW) and its differentiable extension Soft-DTW to improve the temporal alignment of synthetic time series. The framework is evaluated using quantitative measures of alignment and …

A Leslie System For A Demographic Simulation: From An Actuarial Point Of View, David Kings

Electronic Theses and Dissertations

This thesis develops a discrete stochastic linear systems interpretation of age–stage demographic evolution grounded in Leslie operators and realized in a discrete-event simulation implemented with salabim. The central claim is that one annual cycle of the simulation constitutes a cone-preserving, stochastic affine transformation on a high- dimensional population state vector indexed by age, sex, marital status, household type, employment, and education, and that the composition of yearly operators yields a random matrix product whose top Lyapunov exponent is the stochastic counterpart of the Perron–Frobenius growth rate (Caswell, 2001; Tuljapurkar, 1997)[1, 2]. The actuarial bridge is constructed by mapping simulated survival …

A Persistent Homology Framework For Scrna-Seq: Assessing Clustering Robustness And Quantifying Preprocessing And Integration Effects On Topological Features., Jonah Daneshmand

Electronic Theses and Dissertations

As single-cell RNA sequencing (scRNA-seq) data expands, robust methods for integrating diverse datasets are critical. This dissertation applies Persistent Homology (PH), a technique from Topological Data Analysis (TDA), to a collection of scRNA-seq datasets spanning eight tissue types to quantify how data integration affects topological features and biological interpretability. We assessed global topological structure using Betti curves, Euler characteristics, and persistence landscapes across raw, normalized, and integrated data representations. Our analysis revealed a performance inversion: while conventional methods excelled on unintegrated data, high-granularity topological methods, particularly those sensitive to global data structure, became superior after integration. This suggests a synergy …