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 …

A Comparison Of Confidence Intervals In State Space Models, Jinyu Du

Statistical Science Theses and Dissertations

This thesis develops general procedures for constructing confidence intervals (CIs) of the error disturbance parameters (standard deviations) and transformations of the error disturbance parameters in time-invariant state space models (ssm). With only a set of observations, estimating individual error disturbance parameters accurately in the presence of other unknown parameters in ssm is a very challenging problem. We attempted to construct four different types of confidence intervals, Wald, likelihood ratio, score, and higher-order asymptotic intervals for both the simple local level model and the general time-invariant state space models (ssm). We show that for a simple local level model, both the …

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 …

Dynamic Prediction For Alternating Recurrent Events Using A Semiparametric Joint Frailty Model, Jaehyeon Yun

Statistical Science Theses and Dissertations

Alternating recurrent events data arise commonly in health research; examples include hospital admissions and discharges of diabetes patients; exacerbations and remissions of chronic bronchitis; and quitting and restarting smoking. Recent work has involved formulating and estimating joint models for the recurrent event times considering non-negligible event durations. However, prediction models for transition between recurrent events are lacking. We consider the development and evaluation of methods for predicting future events within these models. Specifically, we propose a tool for dynamically predicting transition between alternating recurrent events in real time. Under a flexible joint frailty model, we derive the predictive probability of …

Modeling Stochastically Intransitive Relationships In Paired Comparison Data, Ryan Patrick Alexander Mcshane

Statistical Science Theses and Dissertations

If the Warriors beat the Rockets and the Rockets beat the Spurs, does that mean that the Warriors are better than the Spurs? Sophisticated fans would argue that the Warriors are better by the transitive property, but could Spurs fans make a legitimate argument that their team is better despite this chain of evidence?

We first explore the nature of intransitive (rock-scissors-paper) relationships with a graph theoretic approach to the method of paired comparisons framework popularized by Kendall and Smith (1940). Then, we focus on the setting where all pairs of items, teams, players, or objects have been compared to …

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 …