Biostatistics Commons^™

Bayesian Variable Selection Strategies In Longitudinal Mixture Models And Categorical Regression Problems., Md Nazir Uddin

Electronic Theses and Dissertations

In this work, we seek to develop a variable screening and selection method for Bayesian mixture models with longitudinal data. To develop this method, we consider data from the Health and Retirement Survey (HRS) conducted by University of Michigan. Considering yearly out-of-pocket expenditures as the longitudinal response variable, we consider a Bayesian mixture model with $K$ components. The data consist of a large collection of demographic, financial, and health-related baseline characteristics, and we wish to find a subset of these that impact cluster membership. An initial mixture model without any cluster-level predictors is fit to the data through an MCMC …

Identification And Characterization Of De Novo Germline Tp53 Mutation Carriers In Families With Li-Fraumeni Syndrome, Carlos C. Vera Recio

Dissertations and Theses (Open Access)

Li-Fraumeni syndrome (LFS) is an inherited cancer syndrome caused by a deleterious mutation in TP53. An estimated 48% of LFS patients present due to a de novo mutation (DNM) in TP53. The knowledge of DNM status, DNM or familial mutation (FM), of an LFS patient requires genetic testing of both parents which is often inaccessible, making de novo LFS patients difficult to study. Famdenovo.TP53 is a Mendelian Risk prediction model used to predict DNM status of TP53 mutation carriers based on the cancer-family history and several input genetic parameters, including disease-gene penetrance. The good predictive performance of Famdenovo.TP53 was demonstrated …

Sars-Cov-2 Pandemic Analytical Overview With Machine Learning Predictability, Anthony Tanaydin, Jingchen Liang, Daniel W. Engels

SMU Data Science Review

Understanding diagnostic tests and examining important features of novel coronavirus (COVID-19) infection are essential steps for controlling the current pandemic of 2020. In this paper, we study the relationship between clinical diagnosis and analytical features of patient blood panels from the US, Mexico, and Brazil. Our analysis confirms that among adults, the risk of severe illness from COVID-19 increases with pre-existing conditions such as diabetes and immunosuppression. Although more than eight months into pandemic, more data have become available to indicate that more young adults were getting infected. In addition, we expand on the definition of COVID-19 test and discuss …

Statistical Approaches For Estimation And Comparison Of Brain Functional Connectivity, Jifang Zhao

Theses and Dissertations

Drug addiction can lead to many health-related problems and social concerns. Functional connectivity obtained from functional magnetic resonance imaging (fMRI) data promotes a variety of fundamental understandings in such association. Due to its complex correlation structure and large dimensionality, the modeling and analysis of the functional connectivity from neuroimage are challenging. By proposing a spatio-temporal model for multi-subject neuroimage data, we incorporate voxel-level spatio-temporal dependencies of whole-brain measurements to improve the accuracy of statistical inference. To tackle large-scale spatio-temporal neuroimage data, we develop a computationally efficient algorithm to estimate the parameters. Our method is used to identify functional connectivity and …

Investigations Into The Genetics Of Mixed Pathologies In Dementia, Adam Dugan

Theses and Dissertations--Epidemiology and Biostatistics

Alzheimer’s disease (AD) is an irreversible, progressive brain disorder that leads to a loss of memory and thinking skills. While tremendous progress has been made in our understanding of the genetics underlying AD, currently known genetic variants explain only approximately 30% of the heritable risk of developing AD. One hurdle to AD research is that it can only be definitively diagnosed at autopsy, making cruder, clinic-based diagnoses more common. In recent years, several brain pathologies that mimic AD’s clinical presentation have been identified including brain arteriolosclerosis, hippocampal sclerosis (HS), and, most recently, limbic-predominant age-related TDP-43 encephalopathy (LATE). It has become …

Addressing The Ecological Fallacy With Lagrangian Inference, Michael Schwob

Calvert Undergraduate Research Awards

Most epidemiologists elect to use statistical models that use population-level data to make inference on the spread of some virus or disease. This has become commonplace in the fields of epidemiology and biostatistics since most data used to construct and verify epidemic models are recorded at the population-level. Obtaining inference from a population-level model may be beneficial in studying the spread of disease in a homogeneous population, but the use of such models to describe a heterogeneous population results in inadequate inference. The inaccuracy of these models is further amplified when one tries to make individual-level inference from these population-level …

Ensemble Protein Inference Evaluation, Kyle Lee Lucke

Graduate Student Theses, Dissertations, & Professional Papers

The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …

Bayesian Techniques For Relating Genetic Polymorphisms To Diffusion Tensor Images Of Cocaine Users, Tmader Alballa

Theses and Dissertations

Past investigations utilizing Diffusion Tensor Imaging (DTI) have demonstrated that cocaine use disorder (CUD) yields white matter changes. We proposed three Bayesian techniques in order to explore the relationship between Fractional Anisotropy (FA), genetic data, and years of cocaine use (YCU). CUD participants exhibit abnormality in different areas of the brain versus non-drug using controls, which is measured by DTI. This dissertation is motivated by a neuroimaging genetic study in cocaine dependence, which found that there were relationships between several genes such as GAD and 5-HT₂R and CUD subjects.

In the first chapter, there is background on the …

Statistical Methods In Genetic Studies, Cheng Gao

Dissertations, Master's Theses and Master's Reports

This dissertation includes three Chapters. A brief description of each chapter is organized as follows.

In Chapter 1, we proposed a new method, called MF-TOWmuT, for genome-wide association studies with multiple genetic variants and multiple phenotypes using family samples. MF-TOWmuT uses kinship matrix to account for sample relatedness. It is worth mentioning that in simulations, we considered hidden polygenic effects and varied the proportion of variance contributed by it to generate phenotypes. Simulation studies show that MF-TOWmuT can preserve the type I error rates and is more powerful than several existing methods in different simulation scenarios, MFTOWmuT is also quite …

Bayesian Semi-Supervised Keyphrase Extraction And Jackknife Empirical Likelihood For Assessing Heterogeneity In Meta-Analysis, Guanshen Wang

Statistical Science Theses and Dissertations

This dissertation investigates: (1) A Bayesian Semi-supervised Approach to Keyphrase Extraction with Only Positive and Unlabeled Data, (2) Jackknife Empirical Likelihood Confidence Intervals for Assessing Heterogeneity in Meta-analysis of Rare Binary Events.

In the big data era, people are blessed with a huge amount of information. However, the availability of information may also pose great challenges. One big challenge is how to extract useful yet succinct information in an automated fashion. As one of the first few efforts, keyphrase extraction methods summarize an article by identifying a list of keyphrases. Many existing keyphrase extraction methods focus on the unsupervised setting, …

Statistical Approaches Of Gene Set Analysis With Quantitative Trait Loci For High-Throughput Genomic Studies., Samarendra Das

Electronic Theses and Dissertations

Recently, gene set analysis has become the first choice for gaining insights into the underlying complex biology of diseases through high-throughput genomic studies, such as Microarrays, bulk RNA-Sequencing, single cell RNA-Sequencing, etc. It also reduces the complexity of statistical analysis and enhances the explanatory power of the obtained results. Further, the statistical structure and steps common to these approaches have not yet been comprehensively discussed, which limits their utility. Hence, a comprehensive overview of the available gene set analysis approaches used for different high-throughput genomic studies is provided. The analysis of gene sets is usually carried out based on …

Aspects Of Causal Inference., John A. Craycroft

Electronic Theses and Dissertations

Observational studies differ from experimental studies in that assignment of subjects to treatments is not randomized but rather occurs due to natural mechanisms, which are usually hidden from researchers. Yet objectives of the two studies are frequently the same: identify the causal – rather than merely associational – relationship between some treatment or exposure and an outcome. The statistical issues that arise in properly analyzing observational data for this goal are numerous and fascinating, and these issues are encompassed in the domain of causal inference. The research presented in this dissertation explores several distinct aspects of causal inference. This dissertation …

Direct Questioning Of Sensitive Topics In Public Health Studies: A Simulation Study, Jessica K. Fox, Evrim Oral

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Novel Correction For The Adjusted Box-Pierce Test — New Risk Factors For Emergency Department Return Visits Within 72 Hours For Children With Respiratory Conditions — General Pediatric Model For Understanding And Predicting Prolonged Length Of Stay, Sidy Danioko

Computational and Data Sciences (PhD) Dissertations

This thesis represents the results of three research projects that underline the breadth and depth of my interests.

Firstly, I devoted some efforts to the well-known Box-Pierce goodness-of-fit tests for time series models which has been an important research topic over the last few decades. All previously proposed tests are focused on changes of the test statistics. Instead, I adopted a different approach that takes the best performing test and modifying the rejection region. Thus, I developed a semiparametric correction of the Adjusted Box-Pierce test that attains the best I error rates for all sample sizes and lags and outperforms …

Linear Methods For Regression With Small Sample Sizes Relative To The Number Of Variables., Rajesh Sikder

Electronic Theses and Dissertations

In data sets where there are a small number of observations but a large number of variables observed for each observation, ordinary least squares estimation cannot be used for regression models. There are many alternative including stepwise regression, penalized methods such as ridge regression and the LASSO, and methods based on derived inputs such as principal components regression and partial least squares regression. In this thesis, these five methods are described. K-fold cross validation is also discussed as a way for determining regularization parameters for each method. The performance of these methods in estimation and prediction is also examined through …

Maximum Likelihood Estimation Of Species Trees And Anomaly Zone Detection Using Ranked Gene Trees, Anastasiia Kim

Mathematics & Statistics ETDs

A phylogenetic tree represents the evolutionary relationships among a set of organisms. Gene trees can be used to reconstruct phylogenetic trees. The methods in this dissertation focus on the gene tree topologies with emphasis on ranked gene tree topologies. A ranked tree depicts the order in which nodes appear in the tree together with topological relationships among gene lineages. One challenge that arises during phylogenetic inference is the existence of the anomaly zones, the regions of branch-length space in the species tree that can produce gene trees that have topologies differing from the species tree topology but are more probable …

Improving The Quality And Design Of Retrospective Clinical Outcome Studies That Utilize Electronic Health Records, Oliwier Dziadkowiec, Jeffery Durbin, Vignesh Jayaraman Muralidharan, Megan Novak, Brendon Cornett

HCA Healthcare Journal of Medicine

Electronic health records (EHRs) are an excellent source for secondary data analysis. Studies based on EHR-derived data, if designed properly, can answer previously unanswerable clinical research questions. In this paper we will highlight the benefits of large retrospective studies from secondary sources such as EHRs, examine retrospective cohort and case-control study design challenges, as well as methodological and statistical adjustment that can be made to overcome some of the inherent design limitations, in order to increase the generalizability, validity and reliability of the results obtained from these studies.

Novel Inference Methods For Generalized Linear Models Using Shrinkage Priors And Data Augmentation., Arinjita Bhattacharyya

Electronic Theses and Dissertations

Generalized linear models have broad applications in biostatistics and sociology. In a regression setup, the main target is to find a relevant set of predictors out of a large collection of covariates. Sparsity is the assumption that only a few of these covariates in a regression setup have a meaningful correlation with an outcome variate of interest. Sparsity is incorporated by regularizing the irrelevant slopes towards zero without changing the relevant predictors and keeping the resulting inferences intact. Frequentist variable selection and sparsity are addressed by popular techniques like Lasso, Elastic Net. Bayesian penalized regression can tackle the curse of …

Introduction To Research Statistical Analysis: An Overview Of The Basics, Christian Vandever

HCA Healthcare Journal of Medicine

This article covers many statistical ideas essential to research statistical analysis. Sample size is explained through the concepts of statistical significance level and power. Variable types and definitions are included to clarify necessities for how the analysis will be interpreted. Categorical and quantitative variable types are defined, as well as response and predictor variables. Statistical tests described include t-tests, ANOVA and chi-square tests. Multiple regression is also explored for both logistic and linear regression. Finally, the most common statistics produced by these methods are explored.

Predicting Diabetes Diagnoses, Sarah Netchert

Student Research Poster Presentations 2020

This study explored the traits and health state of African Americans in central Virginia in order to determine what traits put people at a higher probability of being diagnosed with diabetes. We also want to know which traits will generate the highest probability a person will be diagnosed with diabetes. Traits that were included and used in this study were cholesterol, stabilized glucose, high density lipoprotein levels, age(years), gender, height(inches), weight(pounds), systolic blood pressure, diastolic blood pressure, waist size(inches), and hip size(inches). There were 403 individuals included in study since they were only ones screened for diabetes out of 1,046 …

Zero-Inflated Longitudinal Mixture Model For Stochastic Radiographic Lung Compositional Change Following Radiotherapy Of Lung Cancer, Viviana A. Rodríguez Romero

Theses and Dissertations

Compositional data (CD) is mostly analyzed as relative data, using ratios of components, and log-ratio transformations to be able to use known multivariable statistical methods. Therefore, CD where some components equal zero represent a problem. Furthermore, when the data is measured longitudinally, observations are spatially related and appear to come from a mixture population, the analysis becomes highly complex. For this matter, a two-part model was proposed to deal with structural zeros in longitudinal CD using a mixed-effects model. Furthermore, the model has been extended to the case where the non-zero components of the vector might a two component mixture …

Semiparametric And Nonparametric Methods For Comparing Biomarker Levels Between Groups, Yuntong Li

Theses and Dissertations--Statistics

Comparing the distribution of biomarker measurements between two groups under either an unpaired or paired design is a common goal in many biomarker studies. However, analyzing biomarker data is sometimes challenging because the data may not be normally distributed and contain a large fraction of zero values or missing values. Although several statistical methods have been proposed, they either require data normality assumption, or are inefficient. We proposed a novel two-part semiparametric method for data under an unpaired setting and a nonparametric method for data under a paired setting. The semiparametric method considers a two-part model, a logistic regression for …

Bayesian Kinetic Modeling For Tracer-Based Metabolomic Data, Xu Zhang

Theses and Dissertations--Statistics

Kinetic modeling of the time dependence of metabolite concentrations including the unstable isotope labeled species is an important approach to simulate metabolic pathway dynamics. It is also essential for quantitative metabolic flux analysis using tracer data. However, as the metabolic networks are complex including extensive compartmentation and interconnections, the parameter estimation for enzymes that catalyze individual reactions needed for kinetic modeling is challenging. As the pa- rameter space is large and multi-dimensional while kinetic data are comparatively sparse, the estimation procedure (especially the point estimation methods) often en- counters multiple local maximum such that standard maximum likelihood methods may yield …

Measuring Change: Prediction Of Early Onset Sepsis, Aric Schadler

Theses and Dissertations--Statistics

Sepsis occurs in a patient when an infection enters into the blood stream and spreads throughout the body causing a cascading response from the immune system. Sepsis is one of the leading causes of morbidity and mortality in today’s hospitals. This is despite published and accepted guidelines for timely and appropriate interventions for septic patients. The largest barrier to applying these interventions is the early identification of septic patients. Early identification and treatment leads to better outcomes, shorter lengths of stay, and financial savings for healthcare institutions. In order to increase the lead time in recognizing patients trending towards septicemia …

Generalization Of Kullback-Leibler Divergence For Multi-Stage Diseases: Application To Diagnostic Test Accuracy And Optimal Cut-Points Selection Criterion, Chen Mo

College of Graduate Studies: Theses & Dissertations

The Kullback-Leibler divergence (KL), which captures the disparity between two distributions, has been considered as a measure for determining the diagnostic performance of an ordinal diagnostic test. This study applies KL and further generalizes it to comprehensively measure the diagnostic accuracy test for multi-stage (K > 2) diseases, named generalized total Kullback-Leibler divergence (GTKL). Also, GTKL is proposed as an optimal cut-points selection criterion for discriminating subjects among different disease stages. Moreover, the study investigates a variety of applications of GTKL on measuring the rule-in/out potentials in the single-stage and multi-stage levels. Intensive simulation studies are conducted to compare the performance …

Distribution Of Human Exposure To Ozone During Commuting Hours In Connecticut Using The Cellular Device Network, Owais Gilani, Simon Urbanek, Michael J. Kane

Faculty Journal Articles

Epidemiologic studies have established associations between various air pollutants and adverse health outcomes for adults and children. Due to high costs of monitoring air pollutant concentrations for subjects enrolled in a study, statisticians predict exposure concentrations from spatial models that are developed using concentrations monitored at a few sites. In the absence of detailed information on when and where subjects move during the study window, researchers typically assume that the subjects spend their entire day at home, school, or work. This assumption can potentially lead to large exposure assignment bias. In this study, we aim to determine the distribution of …

Estimating Response Status In Sequential Multiple Assignment (Smar)-Like Trials, Keighly Bradbrook

Theses and Dissertations

Sequential, multiple assignment, randomized trials (SMARTs) allow investigators to develop and compare experimental treatment regimens in which individuals are successively randomized to different treatments based on some set of predetermined rules. The rules used to make decisions on when and how to switch treatments are based on a chosen set of tailoring variables. Although not always true, intermediate response is commonly used as the primary tailoring variable as it is often predictive of future treatment success. As such, successful implementation depends on identifying patients who respond to treatment, though in some situations such mechanisms may not exist. Further, patient-level covariates …

The Analysis Of Neural Heterogeneity Through Mathematical And Statistical Methods, Kyle Wendling

Theses and Dissertations

Diversity of intrinsic neural attributes and network connections is known to exist in many areas of the brain and is thought to significantly affect neural coding. Recent theoretical and experimental work has argued that in uncoupled networks, coding is most accurate at intermediate levels of heterogeneity. I explore this phenomenon through two distinct approaches: a theoretical mathematical modeling approach and a data-driven statistical modeling approach.

Through the mathematical approach, I examine firing rate heterogeneity in a feedforward network of stochastic neural oscillators utilizing a high-dimensional model. The firing rate heterogeneity stems from two sources: intrinsic (different individual cells) and network …

Sex And Age Differences In Prevalence And Risk Factors For Prediabetes In Mexican-Americans, Kristina Vatcheva, Belinda M. Reininger, Susan P. Fisher-Hoch, Joseph B. Mccormick

School of Mathematical & Statistical Sciences Faculty Publications

AIMS:

Over 1/3 of Americans have prediabetes, while 9.4% have type 2 diabetes. The aim of our study was to estimate the prevalence of prediabetes in Mexican Americans, with known 28.2% prevalence of type 2 diabetes, by age and sex and to identify critical socio-demographic and clinical factors associated with prediabetes.

METHODS:

Data were collected between 2004 and 2017 from the Cameron County Hispanic Cohort in Texas. Weighted crude and sex- and age- stratified prevalences were calculated. Survey weighted logistic regression analyses were conducted to identify risk factors for prediabetes.

RESULTS:

The prevalence of prediabetes (32%) was slightly higher than …

Classification Of Coronary Artery Disease In Non-Diabetic Patients Using Artificial Neural Networks, Demond Handley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.