Statistics and Probability Commons^™

Bayesian Models For Repeated Measures Data Using Markov Chain Monte Carlo Methods, Yuanzhi Li

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bayesian models for repeated measures data are fitted to three different data an analysis projects. Markov Chain Monte Carlo (MCMC) methodology is applied to each case with Gibbs sampling and/or an adaptive Metropolis-Hastings (MH) algorithm used to simulate the posterior distribution of parameters. We implement a Bayesian model with different variance-covariance structures to an audit fee data set. Block structures and linear models for variances are used to examine the linear trend and different behaviors before and after regulatory change during year 2004-2005. We proposed a Bayesian hierarchical model with latent teacher effects, to determine whether teacher professional development (PD) …

Bivariate Negative Binomial Hurdle With Random Spatial Effects, Robert Mcnutt

Dissertations

Count data with excess zeros widely occur in ecology, epidemiology, marketing, and many other disciplines. Mixture distributions consisting of a point mass at zero and a separate discrete distribution are often employed in regression models to account for excessive zero observations in the data. While Poisson models are very popular for count data, Negative Binomial models provide greater flexibility due to their ability to account for overdispersion.

This research focuses on developing a method for analyzing bivariate count data with excess zeros collected over a lattice. A bivariate Zero-Inflated Negative Binomial Hurdle (ZINBH) regression model with spatial random effects is …

Bayesian Rank Based Methods For Linear And Generalized Linear Models, James Kodzo Dzikunu

Dissertations

A Bayesian Rank Based Method for linear models is developed in this research. The estimation of the regression coefficients is based on the full conditional distributions utilizing a rank based initial fit. The data likelihood is based on the asymptotic distribution of the gradient function and the asymptotic linearity of this rank-based procedure. Prior distributions are put on regression coefficient(s) and scale parameter(s). The effects of different priors on this scale parameter(s) are studied. Using these full conditional distributions, the estimates are obtained by a Markov Chain Monte-Carlo (MCMC) procedure. The results of our simulation studies show that these Bayesian …

Confident Difference Criterion: A New Bayesian Differentially Expressed Gene Selection Algorithm With Applications., Fang Yu, Ming-Hui Chen, Lynn Kuo, Heather Talbott, John S. Davis

Journal Articles: Biostatistics

BACKGROUND: Recently, the Bayesian method becomes more popular for analyzing high dimensional gene expression data as it allows us to borrow information across different genes and provides powerful estimators for evaluating gene expression levels. It is crucial to develop a simple but efficient gene selection algorithm for detecting differentially expressed (DE) genes based on the Bayesian estimators.

RESULTS: In this paper, by extending the two-criterion idea of Chen et al. (Chen M-H, Ibrahim JG, Chi Y-Y. A new class of mixture models for differential gene expression in DNA microarray data. J Stat Plan Inference. 2008;138:387-404), we propose two new gene …

Germline Mutation Detection In Next Generation Sequencing Data And Tp53 Mutation Carrier Probability Estimation For Li-Fraumeni Syndrome, Gang Peng

Dissertations and Theses (Open Access)

Next generation sequencing technology has been widely used in genomic analysis, but its application has been compromised by the missing true variants, especially when these variants are rare. We proposed a family-based variant calling method, FamSeq, integrating Mendelian transmission information with de novo mutation and sequencing data to improve the variant calling accuracy. We investigated the factors impacting the improvement of family-based variant calling in simulation data and validated it in real sequencing data. In both simulation and real data, FamSeq works better than the single individual based method.

In FamSeq, we implemented four different methods for the Mendelian genetic …

Bayesian Adaptive Penalized Splines In Nonparametric Regression And In Spectral Time Series Analysis, Luis Angel Mora

Open Access Theses & Dissertations

A Bayesian approach to nonparametric regression using Penalized splines (P-splines) is presented. The approach uses the linear mixed model formulation of P-spines. The usual model assumes a single value for the smoothing parameter controlling the amount of smoothing of the fitted function. The main focus of the Thesis is on spatially adaptive smoothing where the smoothing parameter is a function of the covariate so that different amounts of smoothing are applied in different regions of the covariate. An application to spectral time series analysis will be demonstrated. Markov chain Monte Carlo methods are used to make inference based on the …

Objective Priors For Estimation Of Extended Exponential Geometric Distribution, Pedro L. Ramos, Fernando A. Moala, Jorge A. Achcar

Journal of Modern Applied Statistical Methods

A Bayesian analysis was developed with different noninformative prior distributions such as Jeffreys, Maximal Data Information, and Reference. The aim was to investigate the effects of each prior distribution on the posterior estimates of the parameters of the extended exponential geometric distribution, based on simulated data and a real application.

Exonest: Bayesian Model Selection Applied To The Detection And Characterization Of Exoplanets Via Photometric Variations, Ben Placek, Kevin H. Knuth, Daniel Angerhausen

Physics Faculty Scholarship

EXONEST is an algorithm dedicated to detecting and characterizing the photometric signatures of exoplanets, which include reflection and thermal emission, Doppler boosting, and ellipsoidal variations. Using Bayesian inference, we can test between competing models that describe the data as well as estimate model parameters. We demonstrate this approach by testing circular versus eccentric planetary orbital models, as well as testing for the presence or absence of four photometric effects. In addition to using Bayesian model selection, a unique aspect of EXONEST is the potential capability to distinguish between reflective and thermal contributions to the light curve. A case study is …

A Bayesian Analysis Of The Spatial Concentration Of Individual Wealth In The Us North During The Nineteenth Century, Alice Kasakoff, Andrew Lawson, Emily Van Meter

Biostatistics Faculty Publications

Background: Kin effects can be difficult to distinguish from those of spatial proximity, since kin tend to live close to each other. Thus, past research showing correlations between the wealth of relatives may be showing the effects of proximity and shared locations, not the effects of kin.

Objective: What are the effects of kin and of spatial proximity upon wealth? This is studied both for fathers and sons and for brothers.

Methods: Data comes from a genealogical sample that has been linked to the US census of 1860. The genealogies allow us to identify fathers, sons, and …

Markov Chain Monte Carlo Bayesian Predictive Framework For Artificial Neural Network Committee Modeling And Simulation, Michael S. Goodrich

Computational Modeling & Simulation Engineering Theses & Dissertations

A logical inference method of properly weighting the outputs of an Artificial Neural Network Committee for predictive purposes using Markov Chain Monte Carlo simulation and Bayesian probability is proposed and demonstrated on machine learning data for non-linear regression, binary classification, and 1-of-k classification. Both deterministic and stochastic models are constructed to model the properties of the data. Prediction strategies are compared based on formal Bayesian predictive distribution modeling of the network committee output data and a stochastic estimation method based on the subtraction of determinism from the given data to achieve a stochastic residual using cross validation. Performance for Bayesian …

Dynamic Bayesian Approaches To The Statistical Calibration Problem, Derick Lorenzo Rivers

Theses and Dissertations

The problem of statistical calibration of a measuring instrument can be framed both in a statistical context as well as in an engineering context. In the first, the problem is dealt with by distinguishing between the "classical" approach and the "inverse" regression approach. Both of these models are static models and are used to estimate "exact" measurements from measurements that are affected by error. In the engineering context, the variables of interest are considered to be taken at the time at which you observe the measurement. The Bayesian time series analysis method of Dynamic Linear Models (DLM) can be used …

Disk Diffusion Breakpoint Determination Using A Bayesian Nonparametric Variation Of The Errors-In-Variables Model, Glen Richard Depalma

Open Access Dissertations

Drug dilution (MIC) and disk diffusion (DIA) are the two most common antimicrobial susceptibility tests used by hospitals and clinics to determine an unknown pathogen's susceptibility to various antibiotics. Both tests use breakpoints to classify the pathogen as either susceptible, indeterminant, or resistant to each drug under consideration. While the determination of these drug-specific MIC classification breakpoints is straightforward, determination of comparable DIA breakpoints is not. It is this issue that motivates this research.

Traditionally, the error-rate bounded (ERB) method has been used to calibrate the two tests. This procedure involves determining DIA breakpoints which minimize the observed discrepancies between …

Objective Bayesian Hypothesis Testing And Estimation For The Risk Ratio In A Correlated 2x2 Table With Structural Zero, Xiaohua Bai

All Theses

We illustrate the construction of an objective Bayesian hypothesis testing and point estimation for the risk ratio in a correlated 2x2 table with structural zero. We solve the problem using Bayesian method through the reference prior, and corresponding posterior distribution of the risk ratio can be derived. Then combined the intrinsic discrepancy, an invariant inforamtion-based loss function, provides an integrated objective Bayesian solution to both hypothesis testing and point estimation problems.

Modeling A Sensor To Improve Its Efficacy, Nabin K. Malakar, Daniil Gladkov, Kevin H. Knuth

Physics Faculty Scholarship

Robots rely on sensors to provide them with information about their surroundings. However, high-quality sensors can be extremely expensive and cost-prohibitive. Thus many robotic systems must make due with lower-quality sensors. Here we demonstrate via a case study how modeling a sensor can improve its efficacy when employed within a Bayesian inferential framework. As a test bed we employ a robotic arm that is designed to autonomously take its own measurements using an inexpensive LEGO light sensor to estimate the position and radius of a white circle on a black field. The light sensor integrates the light arriving from a …

Applications Of Bayesian Statistics In Fluvial Bed Load Transport, Mark L. Schmelter

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The science of fluvial sediment transport studies the processes involved in the movement of river sediments. It is commonly understood that when rivers flood they have a great capacity to move sand, gravel, and even larger cobbles and boulders. This process is not only limited to the big floods that usually attract so much attention, but also the more common river flows play a very important role in forming a river. As engineers and scientists, we like to be able to develop equations and relationships that describe some natural phenomenon—in this case, fluvial sediment transport. While we are able to …

Objective Bayesian Inference On The Common Mean Of Normal Distributions, Shiyi Tu

All Theses

One of the oldest problems in statistical area is to make inference on a common mean of several different normal populations with unknown and probably unequal variances. There are several different ways to make inference on the common mean. The most common methods are point estimation, hypothesis testing, and interval estimation. Point estimation uses sample data to calculate a single value serving as a best guess for the unknown population mean. Hypothesis testing assumes all populations have the same mean as the null hypothesis. Interval estimation is an interval of possible values of the unknown mean.
In this paper, we …

Foundations Of Inference, Kevin H. Knuth, John Skilling

Physics Faculty Scholarship

We present a simple and clear foundation for finite inference that unites and significantly extends the approaches of Kolmogorov and Cox. Our approach is based on quantifying lattices of logical statements in a way that satisfies general lattice symmetries. With other applications such as measure theory in mind, our derivations assume minimal symmetries, relying on neither negation nor continuity nor differentiability. Each relevant symmetry corresponds to an axiom of quantification, and these axioms are used to derive a unique set of quantifying rules that form the familiar probability calculus. We also derive a unique quantification of divergence, entropy and information.

Development Of A Bayesian Joint Logistic Model To Better Study The Association Between Haplotypes And Disease, Anthony M. D'Amelio Jr

Dissertations and Theses (Open Access)

In 2011, there will be an estimated 1,596,670 new cancer cases and 571,950 cancer-related deaths in the US. With the ever-increasing applications of cancer genetics in epidemiology, there is great potential to identify genetic risk factors that would help identify individuals with increased genetic susceptibility to cancer, which could be used to develop interventions or targeted therapies that could hopefully reduce cancer risk and mortality.

In this dissertation, I propose to develop a new statistical method to evaluate the role of haplotypes in cancer susceptibility and development. This model will be flexible enough to handle not only haplotypes of any …

Hierarchical Probit Models For Ordinal Ratings Data, Allison M. Butler

Theses and Dissertations

University students often complete evaluations of their courses and instructors. The evaluation tool typically contains questions about the course and the instructor on an ordinal Likert scale. We assess instructor effectiveness while adjusting for known confounders. We present a probit regression model with a latent variable to measure the instructor effectiveness accounting for student specific covariates, such as student grade in the course, high school and university GPA, and ACT score.

Adaptive Threat Detector Testing Using Bayesian Gaussian Process Models, Bradley Thomas Ferguson

Theses and Dissertations

Detection of biological and chemical threats is an important consideration in the modern national defense policy. Much of the testing and evaluation of threat detection technologies is performed without appropriate uncertainty quantification. This paper proposes an approach to analyzing the effect of threat concentration on the probability of detecting chemical and biological threats. The approach uses a probit semi-parametric formulation between threat concentration level and the probability of instrument detection. It also utilizes a bayesian adaptive design to determine at which threat concentrations the tests should be performed. The approach offers unique advantages, namely, the flexibility to model non-monotone curves …

Development And Implementation Of A Bayesian Model For Sediment Transport In Fluvial Systems, Mark Schmelter

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Recent studies in the field of fluvial sediment transport underscore the difficulty in reliably estimating transport model parameters, collecting accurate observations, and making predictions due to measurement error and conceptual model uncertainty. There is a pressing need to develop models that can account for measurement error, conceptual model uncertainty, and natural variability while providing probability-based predictions as well as a means for conceptual model discrimination. The model presented in this research employs an excess shear sediment transport equation for a uni-size sediment bed developed in a Bayesian statistical framework. This statistical model provides a means to rigorously estimate distributions of …

Improving Accuracy Of Large-Scale Prediction Of Forest Disease Incidence Through Bayesian Data Reconciliation, Ephraim M. Hanks

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Increasing the accuracy of predictions made from ecological data typically involves replacing or replicating the data, but the cost of updating large-scale data sets can be prohibitive. Focusing resources on a small sample of locations from a large, less accurate data set can result in more reliable observations, though on a smaller scale. We present an approach for increasing the accuracy of predictions made from a large-scale eco logical data set through reconciliation with a small, highly accurate data set within a Bayesian hierarchical modeling framework. This approach is illustrated through a study of incidence of eastern spruce dwarf mistletoe …

Bayesian Nonparametric Regression With A Flexible Error Term Distribution, Courtney Marie Barnes

Open Access Theses & Dissertations

Datasets often exhibit heavy tailed behavior and standard analyses are often heavily influenced by outliers. We propose a nonparametric regression model whose error term distribution is a mixture of a normal and a Student t distribution. This results in a model that is more resistant to outliers compared to a model with a normal error term.

Robust Predictive Inference For Multivariate Linear Models With Elliptically Contoured Distribution Using Bayesian, Classical And Structural Approaches, B. M. Golam Kibria

Journal of Modern Applied Statistical Methods

Predictive distributions of future response and future regression matrices under multivariate elliptically contoured distributions are discussed. Under the elliptically contoured response assumptions, these are identical to those obtained under matric normal or matric-t errors using structural, Bayesian with improper prior, or classical approaches. This gives inference robustness with respect to departure from the reference case of independent sampling from the matric normal or matric t to multivariate elliptically contoured distributions. The importance of the predictive distribution for skewed elliptical models is indicated; the elliptically contoured distribution, as well as matric t distribution, have significant applications in statistical practices.

An Adaptive Bayesian Approach To Bernoulli-Response Clinical Trials, Andrew W. Stacey

Theses and Dissertations

Traditional clinical trials have been inefficient in their methods of dose finding and dose allocation. In this paper a four-parameter logistic equation is used to model the outcome of Bernoulli-response clinical trials. A Bayesian adaptive design is used to fit the logistic equation to the dose-response curve of Phase II and Phase III clinical trials. Because of inherent restrictions in the logistic model, symmetric candidate densities cannot be used, thereby creating asymmetric jumping rules inside the Markov chain Monte Carlo algorithm. An order restricted Metropolis-Hastings algorithm is implemented to account for these limitations. Modeling clinical trials in a Bayesian framework …

Development Of Informative Priors In Microarray Studies, Kassandra M. Fronczyk

Theses and Dissertations

Microarrays measure the abundance of DNA transcripts for thousands of gene sequences, simultaneously facilitating genomic comparisons across tissue types or disease status. These experiments are used to understand fundamental aspects of growth and development and to explore the underlying genetic causes of many diseases. The data from most microarray studies are found in open-access online databases. Bayesian models are ideal for the analysis of microarray data because of their ability to integrate prior information; however, most current Bayesian analyses use empirical or flat priors. We present a Perl script to build an informative prior by mining online databases for similar …

Graphical And Bayesian Analysis Of Unbalanced Patient Management Data, Emily Stewart Righter

Theses and Dissertations

The International Normalizing Ratio (INR) measures the speed at which blood clots. Healthy people have an INR of about one. Some people are at greater risk of blood clots and their physician prescribes a target INR range, generally 2-3. The farther a patient is above or below their prescribed range, the more dangerous their situation. A variety of point-of-care (POC) devices has been developed to monitor patients. The purpose of this research was to develop innovative graphics to help describe a highly unbalanced dataset and to carry out Bayesian analyses to determine which of five devices best manages patients. An …

A Marginalized Diffusion Model For Estimating Age At First Endoscopy Examination From Current Status Data, Diana Miglioretti, Elizabeth Brown

UW Biostatistics Working Paper Series

We propose an approach for estimating the age at first endoscopy examination from current status data collected via two series of cross-sectional surveys. To model the national probability of ever having an endoscopy, we incorporate birth cohort effects into a mixed-influence diffusion model. We link a state-specific model to the national-level diffusion model using a marginalized modeling approach. In future research, results from our model will be used as microsimulation model inputs to estimate the contribution of endoscopy examinations to observed changes in colorectal cancer incidence and mortality.

Modeling Distributions Of Test Scores With Mixtures Of Beta Distributions, Jingyu Feng

Theses and Dissertations

Test score distributions are used to make important instructional decisions about students. The test scores usually do not follow a normal distribution. In some cases, the scores appear to follow a bimodal distribution that can be modeled with a mixture of beta distributions. This bimodality may be due different levels of students' ability. The purpose of this study was to develop and apply statistical techniques for fitting beta mixtures and detecting bimodality in test score distributions. Maximum likelihood and Bayesian methods were used to estimate the five parameters of the beta mixture distribution for scores in four quizzes in a …

On The Power Function Of Bayesian Tests With Application To Design Of Clinical Trials: The Fixed-Sample Case, Lyle Broemeling, Dongfeng Wu

Journal of Modern Applied Statistical Methods

Using a Bayesian approach to clinical trial design is becoming more common. For example, at the MD Anderson Cancer Center, Bayesian techniques are routinely employed in the design and analysis of Phase I and II trials. It is important that the operating characteristics of these procedures be determined as part of the process when establishing a stopping rule for a clinical trial. This study determines the power function for some common fixed-sample procedures in hypothesis testing, namely the one and two-sample tests involving the binomial and normal distributions. Also considered is a Bayesian test for multi-response (response and toxicity) in …