Statistical Models Commons^™

Bayesian Statistical Modeling Of Spatially Resolved Transcriptomics Data, Xi Jiang

Statistical Science Theses and Dissertations

Spatially resolved transcriptomics (SRT) quantifies expression levels at different spatial locations, providing a new and powerful tool to investigate novel biological insights. As experimental technologies enhance both in capacity and efficiency, there arises a growing demand for the development of analytical methodologies.

One question in SRT data analysis is to identify genes whose expressions exhibit spatially correlated patterns, called spatially variable (SV) genes. Most current methods to identify SV genes are built upon the geostatistical model with Gaussian process, which could limit the models' ability to identify complex spatial patterns. In order to overcome this challenge and capture more types …

Optimizing Tumor Xenograft Experiments Using Bayesian Linear And Nonlinear Mixed Modelling And Reinforcement Learning, Mary Lena Bleile

Statistical Science Theses and Dissertations

Tumor xenograft experiments are a popular tool of cancer biology research. In a typical such experiment, one implants a set of animals with an aliquot of the human tumor of interest, applies various treatments of interest, and observes the subsequent response. Efficient analysis of the data from these experiments is therefore of utmost importance. This dissertation proposes three methods for optimizing cancer treatment and data analysis in the tumor xenograft context. The first of these is applicable to tumor xenograft experiments in general, and the second two seek to optimize the combination of radiotherapy with immunotherapy in the tumor xenograft …

Applications Of Machine Learning Algorithms In Materials Science And Bioinformatics, Mohammed Quazi

Mathematics & Statistics ETDs

The piezoelectric response has been a measure of interest in density functional theory (DFT) for micro-electromechanical systems (MEMS) since the inception of MEMS technology. Piezoelectric-based MEMS devices find wide applications in automobiles, mobile phones, healthcare devices, and silicon chips for computers, to name a few. Piezoelectric properties of doped aluminum nitride (AlN) have been under investigation in materials science for piezoelectric thin films because of its wide range of device applicability. In this research using rigorous DFT calculations, high throughput ab-initio simulations for 23 AlN alloys are generated.

This research is the first to report strong enhancements of piezoelectric properties …

Statistical Theory For Specialized Linear Regression Adjustment Methods Compared To Multiple Linear Regression In The Presence And Absence Of Interaction Effects, Leon Su

Theses and Dissertations--Statistics

When building models to investigate outcomes and variables of interest, researchers often want to adjust for other variables. There is a variety of ways that these adjustments are performed. In this work, we will consider four approaches to adjustment utilized by researchers in various fields. We will compare the efficacy of these methods to what we call the ”true model method”, fitting a multiple linear regression model in which adjustment variables are model covariates. Our goal is to show that these adjustment methods have inferior performance to the true model method by comparing model parameter estimates, power, type I error, …

Finding The Best Predictors For Foot Traffic In Us Seafood Restaurants, Isabel Paige Beaulieu

Honors Theses and Capstones

COVID-19 caused state and nation-wide lockdowns, which altered human foot traffic, especially in restaurants. The seafood sector in particular suffered greatly as there was an increase in illegal fishing, it is made up of perishable goods, it is seasonal in some places, and imports and exports were slowed. Foot traffic data is useful for business owners to have to know how much to order, how many employees to schedule, etc. One issue is that the data is very expensive, hard to get, and not available until months after it is recorded. Our goal is to not only find covariates that …

Causal Inference And Prediction On Observational Data With Survival Outcomes, Xiaofei Chen

Statistical Science Theses and Dissertations

Infants with hypoplastic left heart syndrome require an initial Norwood operation, followed some months later by a stage 2 palliation (S2P). The timing of S2P is critical for the operation’s success and the infant’s survival, but the optimal timing, if one exists, is unknown. We attempt to estimate the optimal timing of S2P by analyzing data from the Single Ventricle Reconstruction Trial (SVRT), which randomized patients between two different types of Norwood procedure. In the SVRT, the timing of the S2P was chosen by the medical team; thus with respect to this exposure, the trial constitutes an observational study, and …

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 …

Bayesian Hierarchical Meta-Analysis Of Asymptomatic Ebola Seroprevalence, Peter Brody-Moore

CMC Senior Theses

The continued study of asymptomatic Ebolavirus infection is necessary to develop a more complete understanding of Ebola transmission dynamics. This paper conducts a meta-analysis of eight studies that measure seroprevalence (the number of subjects that test positive for anti-Ebolavirus antibodies in their blood) in subjects with household exposure or known case-contact with Ebola, but that have shown no symptoms. In our two random effects Bayesian hierarchical models, we find estimated seroprevalences of 8.76% and 9.72%, significantly higher than the 3.3% found by a previous meta-analysis of these eight studies. We also produce a variation of this meta-analysis where we exclude …

Association Tests For Genetic Effect And Its Interaction With Environmental Factors, Zhengyang Zhou

Statistical Science Theses and Dissertations

My research is in the area of statistical genetics, and it contains three projects: (1) Differentiating the Cochran-Armitage (CA) trend test and Pearson’s chi-square test: location and dispersion; (2) Decomposing Pearson’s chi-square test: a linear regression and its departure from linearity; (3) Testing nonlinear gene-environment (GxE) interaction through varying coefficient and linear mixed models.

(1) In genetic case-control association studies, a standard practice is to perform the CA trend test with 1 degree-of-freedom (df) under the assumption of an additive model. However, when the true genetic model is recessive or near recessive, it is outperformed by Pearson’s chi-square test with …

Developing Statistical Methods For Data From Platforms Measuring Gene Expression, Gaoxiang Jia

Statistical Science Theses and Dissertations

This research contains two topics: (1) PBNPA: a permutation-based non-parametric analysis of CRISPR screen data; (2) RCRnorm: an integrated system of random-coefficient hierarchical regression models for normalizing NanoString nCounter data from FFPE samples.

Clustered regularly-interspaced short palindromic repeats (CRISPR) screens are usually implemented in cultured cells to identify genes with critical functions. Although several methods have been developed or adapted to analyze CRISPR screening data, no single spe- cific algorithm has gained popularity. Thus, rigorous procedures are needed to overcome the shortcomings of existing algorithms. We developed a Permutation-Based Non-Parametric Analysis (PBNPA) algorithm, which computes p-values at the gene level …

The Battle Against Malaria: A Teachable Moment, Randy K. Schwartz

Journal of Humanistic Mathematics

Malaria has been humanity’s worst public health problem throughout recorded history. Mathematical methods are needed to understand which factors are relevant to the disease and to develop counter-measures against it. This article and the accompanying exercises provide examples of those methods for use in lower- or upper-level courses dealing with probability, statistics, or population modeling. These can be used to illustrate such concepts as correlation, causation, conditional probability, and independence. The article explains how the apparent link between sickle cell trait and resistance to malaria was first verified in Uganda using the chi-squared probability distribution. It goes on to explain …

Preparedness Of Hospitals In The Republic Of Ireland For An Influenza Pandemic, An Infection Control Perspective, Mary Reidy, Fiona Ryan, Dervla Hogan, Seán Lacey, Claire Buckley

Department of Mathematics Publications

When an influenza pandemic occurs most of the population is susceptible and attack rates can range as high as 40–50 %. The most important failure in pandemic planning is the lack of standards or guidelines regarding what it means to be ‘prepared’. The aim of this study was to assess the preparedness of acute hospitals in the Republic of Ireland for an influenza pandemic from an infection control perspective.

An Analysis Of Risk Reduction Choices In Dcis Breast Cancer Patients, Lauren Soltesz

Statistics

The main focus of this paper was to evaluate possible demographic and clinical characteristics associated with a woman’s choice of breast conserving surgery (BCS), unilateral mastectomy (ULM), or bilateral risk reduction mastectomy (BRRM). The cohort consisted of patients presenting to the City of Hope National Medical Center with ductal carcinoma in situ breast cancer who elected to have cancer directed surgery (N=305). Analyses to examine associations of patient characteristics with type of surgery were conducted using a multinomial logistic regression. Results showed that older women were more likely to choose breast conserving surgery over bilateral risk reduction mastectomy than younger …