Statistics and Probability Commons^™

Artificial Intelligence In Biomedical Team Science: Perceptions, Practices, And Training Needs, Emily Slade, Kelsey N. Karnik, Caitline Phan, Megan E. Hall, Yana Feygin, Kristen J. Mcquerry

Biostatistics Faculty Publications

Introduction: Artificial intelligence (AI) is increasingly used in biomedical research, yet limited empirical work has described how researchers use AI tools on collaborative research teams and how they view their role within team-based research. This study examines researchers’ experience with and attitudes toward AI use in collaborative research environments.

Methods: A cross-sectional survey was administered to 178 investigators engaged in collaborative research at the University of Kentucky. Questions assessed AI use across research and communication tasks, team-related decision-making practices, perceived benefits and concerns, and preferences for training and frameworks.

Results: Thirty-nine participants responded (22%). AI use was heterogeneous: 26% had …

Flavor, Transverse Momentum, And Azimuthal Dependence Of Charged Pion Multiplicities In Semi-Inclusive Deep-Inelastic Scattering With 10.6 Gev Electrons, P. Bosted, H. Bhatt, S. Jia, W. Armstrong, D. Dutta, R. Ent, D. Gaskell, E. Kinney, H. Mkrtchyan, S. Ali, R. Ambrose, D. Androic, C. Ayerbe Gayoso, A. Bandari, V. Berdnikov, D. Bhetuwal, D. Biswas, M. Boer, E. Brash, A. Camsonne, M. Cardonna, J. P. Chen, J. Chen, M. Chen, E. M. Christy, S. Covrig, S. Danagoulian, M. Diefenthaler, B. Duran, C. Elliot, H. Fenker, E. Fuchey, J. O. Hansen, F. Hauenstein, T. Horn, G. M. Huber, M. K. Jones, M. L. Kabir, A. Karki, B. Karki, S. J. D. Kay, C. Keppel, V. Kumar, N. Lashley-Colthirst, W. B. Li, D. Mack, S. Malace, P. Markowitz, M. Mccaughan, E. Mcclellan, D. Meekins, R. Michaels, A. Mkrtchyan, C. Morean, G. Niculescu, I. Niculescu, B. Pandey, S. Park, E. Pooser, B. Sawatzky, G. R. Smith, H. Szumila-Vance, A. S. Tadepalli, V. Tadevosyan, R. Trotta, H. Voskanyan, S. A. Wood, Z. Ye, C. Yero, X. Zheng, Hall C Sidis Collaboration

Physics Faculty Publications

Measurements of semi-inclusive deep-inelastic scattering multiplicities for 𝜋⁺ and 𝜋⁻ from proton and deuteron targets are reported on a grid of hadron kinematic variables 𝑧, 𝑃𝑇, and 𝜙* for leptonic kinematic variables in the range 0.3< 𝑥< 0.6 and 3< 𝑄²< 5GeV². Data were acquired in 2018 and 2019 at Jefferson Lab Hall C with a 10.6 GeV electron beam impinging on 10-cm-long liquid hydrogen and deuterium targets. Scattered electrons and charged pions were detected in the High Momentum Spectrometer and Super High Momentum Spectrometer, respectively. The multiplicities were fitted for each bin in (𝑥,𝑄²,𝑧,𝑃_𝑡) to extract the 𝜙*—independent 𝑀₀ and the azimuthal modulations ⟨cos⁡(𝜙*)⟩ and ⟨cos⁡(2⁢𝜙*)⟩. The 𝑃_𝑡 dependence of the 𝑀₀ results was found to be remarkably consistent for the four cases studied: 𝑒⁢𝑝→𝑒⁢𝜋⁺⁢𝑋, 𝑒⁢𝑝→𝑒⁢𝜋^−⁢𝑋, 𝑒⁢𝑑→𝑒⁢𝜋⁺⁢𝑋, 𝑒⁢𝑑→𝑒⁢𝜋^−⁢𝑋 over the range 0GeV< 𝑃_𝑡< 0.4GeV, as were the multiplicities evaluated near 𝜙*=180∘ over the extended range 0GeV< 𝑃_𝑡< 0.7GeV. The Gaussian widths of the 𝑃𝑡 dependence exhibit a quadratic increase with 𝑧. The cos⁡(𝜙*) modulations were found to be consistent with zero for 𝜋⁺, in agreement with previous world data, while the 𝜋⁻ moments were, in many cases, significantly greater than zero. The cos⁡(2⁢𝜙*) modulations …

Cross-Temporal Statistical Approaches For Evaluating Predictor-Outcome Relationships, Jeff Joseph

Dartmouth College Ph.D Dissertations

Central auditory function is linked with cognitive deficits, but few research projects use existing statistical approaches or develop new ones to forecast cognitive deficits using the results of central auditory tests. To address this limitation, we use a series of statistical learning frameworks for predicting a child’s cognitive abilities based on his/her central auditory performances and demographic factors. Two key challenges exist. First, children may start the study at a time when they are unable to perform the central auditory tests or cognitive tests. Second, cognitive performance is age-dependent, particularly in the early formative years of childhood and adolescence. To …

The Excess Path Length Distribution: A Stochastic Model For Sample-Based Path Planners, Chaz B. Cornwall

Dissertations, Master's Theses and Master's Reports

Through random sampling, sample-based path planners enable autonomous agents to quickly find paths without human intervention. However, due to the paths' randomness, sample-based path planners currently require additional verification, partially nullifying agents' ability to act autonomously. I set out to characterize this uncertainty so humans know what to expect from these path planners and know how to alter the path planner to desired specifications. To ensure the results are theoretical as well as practical, I first create a stochastic model of path length uncertainty using the trade-off between sampling time and optimality. By leveraging this model, my proposed algorithm reduces …

Computational And Ai Frameworks For Identifying Key Regulatory Genes And Their Target Genes In Plants And Humans, Md Khairul Islam

Dissertations, Master's Theses and Master's Reports

This dissertation presents computational and AI-driven frameworks for identifying key regulatory genes and their downstream targets across plant and human biological systems. Three studies address distinct challenges in genomic regulation using advanced machine learning and bioinformatics approaches.

The first study introduces DyGAF (Dynamic Gene Attention Focus), a dual-attention transformer framework that identifies and ranks disease-relevant biomarker genes by simultaneously modeling independent molecular responses and interdependent regulatory network behavior. Two attention models provide complementary perspectives on gene importance and are fused through a novel combination metric. Applied to COVID-19 nasopharyngeal swab profiles, the attention-weighted representations achieved 94.23% classification accuracy, high sensitivity, …

Designing A Research Study: Controlling For A Variable And Using Chatgpt, Fritz Umbach

Open Educational Resources

This assignment uses a hypothetical society to help students understand the idea of “controlling for a variable” and practice applying it to a real-world research question. Students design a research approach to examine whether income differences are better explained by family background or by systemic prejudice, working within clear data limits. ChatGPT is used as a research guide to help students brainstorm, test, and revise their methods, while encouraging them to critically evaluate the usefulness and limits of AI-generated suggestions. The assignment emphasizes careful reasoning, clear research design, and thoughtful use of AI as a support for learning rather than …

Body Mass Index Has No Impact On Complications And Mortality For Patients With Stage Iv Pancreatic Ductal Adenocarcinoma, Ren Bryant, Hannah Darnell, Megan Hall, Kelsey N. Karnik, Kristen J. Mcquerry, Ruben R. Plentz

Biostatistics Faculty Publications

Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of United States (USA) cancer death. Overweight and obesity developing into a growing global medical and socio-economic problem, affecting approximately 42% of adults in the USA population. The aim of our analysis was to evaluate the influence of overweight and obesity on complications and clinical outcome in patients with stage IV PDAC.

Methods: We retrospectively reviewed electronic health records of patients diagnosed with stage IV PDAC (n=162) who followed with the University of Kentucky from January 2017–October 2024. Comparisons were based on the body mass index (BMI): low BMI …

Enhancing Team Science By Training Collaborative Biostatisticians To Have A Strong Statistical Voice, Gina-Maria Pomann, Steven C. Grambow, Marissa C. Ashner, Bibhas Chakraborty, Nan Liu, Megan L. Neely, Sarah Peskoe, Lacey Rende, Emily Slade, Tracy Truong, Lexie Zidanyue Yang, Greg P. Samsa, Jesse D. Troy

Biostatistics Faculty Publications

Strong statistical voice is defined as the ability to advocate and negotiate for good and ethical statistical practices, including integrating and resolving differing scientific approaches. This skill is crucial for biostatisticians who work on biomedical research teams, as it ensures the integrity and accuracy of statistical analyses and fosters productive collaborations with non-statisticians. Despite its importance, new graduates often lack targeted training opportunities. This manuscript presents a scalable training approach through the development of online videos. Preliminary didactic materials focused on two key applications: providing written comments on manuscripts and engaging in study design discussions. To evaluate this training approach, …

Variational Autoencoder Inverse Mapper For Extraction Of Compton Form Factors: Benchmarks And Conditional Learning, Douglas Adams, Md Fayaz Bin Hossen, Joshua Bautista, Gia-Wei Chern, Simonetta Liuti, Marie Boër, Marija Čuić, Michael Engelhardt, Gary R. Goldstein, Huey-Wen Lin, Yaohang Li

Computer Science Faculty Publications

Deeply virtual exclusive scattering processes (DVES) serve as precise probes of nucleon quark and gluon distributions in coordinate space. These distributions are derived from generalized parton distributions (GPDs) via Fourier transform relative to proton momentum transfer. QCD factorization theorems enable DVES to be parameterized by Compton form factors (CFFs), which are convolutions of GPDs with perturbatively calculable kernels. Accurate extraction of CFFs from DVCS, benefiting from interference with the Bethe–Heitler (BH) process and a simpler final state structure, is essential for inferring GPDs. This paper focuses on extracting CFFs from DVCS data using a variational autoencoder inverse mapper (VAIM) and …

Modeling Rank Distribution And The Relative Importance Factor Index In Discrete Power-Law Models: Application To Social Resilience Using The Scopus Database, Brian Llinas, Jose Padilla, Humberto Llinas, Erika Frydenlund, Katherine Palacio

VMASC Publications

Prior research on power-law distributions has primarily focused on modeling frequency patterns, with less attention given to rank distributions and how ranked positions reflect relative importance among elements. In discrete power-law distributions, frequency-based metrics often provide limited discrimination in the tail, where elements may exhibit similar counts but differ in relative dominance. These patterns are especially evident, for instance, in academic publishing, where keywords, affiliations, and citations commonly exhibit power-law behavior. To address this limitation, we introduce the Relative Importance Factor (RIF) Index, a statistical measure derived from the estimated discrete power-law rank distribution rather than an additional independent parameter. …

High Algal Biomass Is Decoupled From Metabolism In The Gallatin River, Cora Mae Steinbach

Graduate Student Theses, Dissertations, & Professional Papers

Assessing eutrophication in rivers is difficult compared to lakes and coastal waters, because most algal biomass occurs on the riverbed and flows interact and co-vary with production (Biggs and Close, 1989; Bernhardt et al., 2018). Riverine eutrophication is typically assessed using algal biomass and water column nutrients (U.S. Environmental Protection Agency, 2000), but biomass is highly variable and labor-intensive to measure, while nutrient concentrations often underestimate enrichment due to rapid biological uptake (Dodds and Smith, 2016). Reach-scale river metabolism can help evaluate long-term functional change in rivers recovering from nutrient enrichment (Arroita et al., 2019; Jankowski et al., 2021; Diamond …

Multiple Changepoint Detection For Non-Gaussian Time Series, Robert Lund, Thomas J. Fisher, Norou Diawara, Michael Wehner

Mathematics & Statistics Faculty Publications

This article combines methods from existing techniques to identify multiple changepoints in non‐Gaussian autocorrelated time series. A transformation is used to convert a Gaussian series into a non‐Gaussian series, enabling penalized likelihood methods to handle non‐Gaussian scenarios. When the marginal distribution of the data is continuous, the methods essentially reduce to the change of variables formula for probability densities. When the marginal distribution is count‐oriented, Hermite expansions and particle filtering techniques are used to quantify the scenario. Simulations demonstrating the efficacy of the methods are given and two data sets are analyzed: 1) the proportion of home runs hit by …

An Ensemble Classifier For Ordinal Outcomes In High-Dimensional Genomics Data, Heranga K. Rathnasekara, Sinjini Sikdar

Mathematics & Statistics Faculty Publications

Analysis of genomics data for predicting disease outcomes is a fast-growing field in medical research. There often exist categorical, specifically, ordinal outcomes that need to be predicted based on genomic profiles. This has led to recent development of some high-dimensional ordinal classification methods that can address the large dimensionality of the genomic covariate set. These high-dimensional ordinal models tend to vary widely in their performance depending on the data they are applied to and the evaluation criteria used. In this article, we outline an ensemble ordinal classifier that integrates different ordinal modeling approaches through bootstrap-based model evaluation, multi-metric performance assessment, …

Differential Impact Of Admission Type And Clinical Complexity On Diabetes Hospitalization Costs Among African American And Hispanic Patients In Southeastern Virginia, Ismail El Moudden, Asra Amidi, Reem Sharaf-Alddin, Michael C. Bittner, Qi Zhang

Department of Obstetrics & Gynecology Faculty Publications

Background

Diabetes mellitus (DM) imposes substantial healthcare costs with documented disparities among African Americans and Hispanic patients. To inform care delivery and resource allocation, this study identified hospitalization cost predictors among African American and Hispanic patients with diabetes in Southeastern Virginia.

Methods

We analyzed 6,011 hospital discharges from the Virginia Health Information database (2016-2020) for adults aged 18-85 with diabetes. Discharges were classified by Medicare Severity Diagnosis-Related Groups: DM with complications/comorbidities (DCC, n = 3,328), DM with major complications/comorbidities (DMCC, n = 1,518), and DM without major complications/comorbidities (DWO, n = 1,165). Because cost distributions were right-skewed (skewness 3.5-8.24), we …

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, …

Modeling Housing Prices: Which Features Matter Most?, Alex Ruvolo

Williams Honors College, Honors Research Projects

This paper attempts to find the biggest factors and traits that influence the cost of housing. This will include the lot size, type of street, utilities, neighborhood, year built, heating, electrical, yard size, number of different rooms, age, condition, and others. I will attempt to answer the question of whether the prices of houses have changed within the last 5 to 10 years, and obviously this is an easy question to answer. However, the bigger question beyond this is are the main factors affecting housing prices all important in explaining this relationship? Is one factor more important than the rest …

Infimum Dimension Nash Embeddings For 2d Projective Shape Analysis, Robert L. Paige, Vic Patrangenaru

Mathematics and Statistics Faculty Research & Creative Works

Vector embeddings make complicated data extracted from networks, words and images, more amendable to data science applications. At the present time, the Veronese-Whitney (VW) matrix embedding of the real projective space is the state of the art for making inference about digital images from an uncalibrated camera, such as a cell phone or security camera. In this work we consider vector embeddings for the projective shape data and in particular determine the minimum dimension isometric (distance-preserving or Nash) vector embedding for a projective space. We determine such an embedding for the projective plane in closed-form. From this embedding we determine …

From Lap To Map: How Musical Scale, Place, And Play Drive The Interconnected Mario Kart World, Cameron Cummins

Honors Undergraduate Theses

With their deserts, castles, and ghost houses, the environments of Super Mario games are colorful, whimsical, and charming, but why are they so compelling, and what happens when our analysis of these environments extends beyond individual levels to expansive game worlds? Drawing on Cresswell’s theory of place (2014) and recent work on musical place-building in Mario Kart 8 (Heazlewood-Dale, 2024), I propose a spectrum between localized and globalized scale in games. As game environments become increasingly globalized, the music may be similarly altered to account for this shift in scale. Consequently, players may then encounter a broader, less musically congruent …

Hybrid Patchtst And Physics-Based Framework For Predicting Lithium-Ion Battery State Of Health, Pavan Ravuri

Honors Undergraduate Theses

Accurately forecasting the state of health of lithium-ion batteries is critical for improving performance, reliability and lifetime in energy storage applications. Battery capacity degrades into a nonlinear pattern over cycling due to electrochemical processes where neither purely data driven nor physics-based models can capture alone. This study looks at a hybrid framework combining that PatchTST patch-based transformer architecture with physics-based features derived from the solid electrolyte interphase and pseudo two-dimensional models. Physics inspired proxy features were computed from cycling data and concatenated with electrochemical measurements as added input channels before patch segmentation. There are five model configurations that were evaluated …

Integer-Valued Time Series Model Via Copula-Based Bivariate Skellam Distribution, Mohammed Alqawba, Norou Diawara, Mame Mor Sene

Mathematics & Statistics Faculty Publications

Time series analysis is crucial for modeling and forecasting diverse real-world phenomena. Traditional models typically assume continuous-valued data; however, many applications involve integer-valued series, often including negative integers. This paper introduces an approach that combines copula theory with the bivariate Skellam distribution to handle such integer-valued data effectively. Copulas are widely recognized for capturing complex dependencies among variables. By integrating copulas, our proposed method respects integer constraints while modeling positive, negative, and temporal dependencies accurately. Through simulation and an empirical study on a real-life example, we demonstrate that our class of models performs well. This approach has broad applicability in …