Statistical Methodology Commons^™

Group Testing Regression Models, Boan Zhang

Department of Statistics: Dissertations, Theses, and Student Work

Group testing, where groups of individual specimens are composited to test for the presence or absence of a disease (or some other binary characteristic), is a procedure commonly used to reduce the costs of screening a large number of individuals. Statistical research in group testing has traditionally focused on a homogeneous population, where individuals are assumed to have the same probability of having a disease. However, individuals often have different risks of positivity, so recent research has examined regression models that allow for heterogeneity among individuals within the population. This dissertation focuses on two problems involving group testing regression models. …

Big Data And The Future, Sherri Rose

Sherri Rose

No abstract provided.

Targeted Maximum Likelihood Estimation For Dynamic Treatment Regimes In Sequential Randomized Controlled Trials, Paul Chaffee, Mark J. Van Der Laan

Paul H. Chaffee

Sequential Randomized Controlled Trials (SRCTs) are rapidly becoming essential tools in the search for optimized treatment regimes in ongoing treatment settings. Analyzing data for multiple time-point treatments with a view toward optimal treatment regimes is of interest in many types of afflictions: HIV infection, Attention Deficit Hyperactivity Disorder in children, leukemia, prostate cancer, renal failure, and many others. Methods for analyzing data from SRCTs exist but they are either inefficient or suffer from the drawbacks of estimating equation methodology. We describe an estimation procedure, targeted maximum likelihood estimation (TMLE), which has been fully developed and implemented in point treatment settings, …

Differential Patterns Of Interaction And Gaussian Graphical Models, Masanao Yajima, Donatello Telesca, Yuan Ji, Peter Muller

COBRA Preprint Series

We propose a methodological framework to assess heterogeneous patterns of association amongst components of a random vector expressed as a Gaussian directed acyclic graph. The proposed framework is likely to be useful when primary interest focuses on potential contrasts characterizing the association structure between known subgroups of a given sample. We provide inferential frameworks as well as an efficient computational algorithm to fit such a model and illustrate its validity through a simulation. We apply the model to Reverse Phase Protein Array data on Acute Myeloid Leukemia patients to show the contrast of association structure between refractory patients and relapsed …

Targeted Maximum Likelihood Estimation Of Natural Direct Effects, Wenjing Zheng, Mark Van Der Laan

Wenjing Zheng

In many causal inference problems, one is interested in the direct causal effect of an exposure on an outcome of interest that is not mediated by certain intermediate variables. Robins and Greenland (1992) and Pearl (2001) formalized the definition of two types of direct effects (natural and controlled) under the counterfactual framework. The efficient scores (under a nonparametric model) for the various natural effect parameters and their general robustness conditions, as well as an estimating equation based estimator using the efficient score, are provided in Tchetgen Tchetgen and Shpitser (2011b). In this article, we apply the targeted maximum likelihood framework …

Statistical Methods For Proteomic Biomarker Discovery Based On Feature Extraction Or Functional Modeling Approaches, Jeffrey S. Morris

Jeffrey S. Morris

In recent years, developments in molecular biotechnology have led to the increased promise of detecting and validating biomarkers, or molecular markers that relate to various biological or medical outcomes. Proteomics, the direct study of proteins in biological samples, plays an important role in the biomarker discovery process. These technologies produce complex, high dimensional functional and image data that present many analytical challenges that must be addressed properly for effective comparative proteomics studies that can yield potential biomarkers. Specific challenges include experimental design, preprocessing, feature extraction, and statistical analysis accounting for the inherent multiple testing issues. This paper reviews various computational …

Integrative Bayesian Analysis Of High-Dimensional Multi-Platform Genomics Data, Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju C. Manyam, Kim-Anh Do

Jeffrey S. Morris

Motivation: Analyzing data from multi-platform genomics experiments combined with patients’ clinical outcomes helps us understand the complex biological processes that characterize a disease, as well as how these processes relate to the development of the disease. Current integration approaches that treat the data are limited in that they do not consider the fundamental biological relationships that exist among the data from platforms.

Statistical Model: We propose an integrative Bayesian analysis of genomics data (iBAG) framework for identifying important genes/biomarkers that are associated with clinical outcome. This framework uses a hierarchical modeling technique to combine the data obtained from multiple platforms …

R Code: A Non-Iterative Implementation Of Tango's Score Confidence Interval For A Paired Difference Of Proportions, Zhao Yang

Zhao (Tony) Yang, Ph.D.

For matched-pair binary data, a variety of approaches have been proposed for the construction of a confidence interval (CI) for the difference of marginal probabilities between two procedures. The score-based approximate CI has been shown to outperform other asymptotic CIs. Tango’s method provides a score CI by inverting a score test statistic using an iterative procedure. In the developed R code, we propose an efficient non-iterative method with closed-form expression to calculate Tango’s CIs. Examples illustrate the practical application of the new approach.

Proportional Mean Residual Life Model For Right-Censored Length-Biased Data, Gary Kwun Chuen Chan, Ying Qing Chen, Chongzhi Di

Chongzhi Di

To study disease association with risk factors in epidemiologic studies, cross-sectional sampling is often more focused and less costly for recruiting study subjects who have already experienced initiating events. For time-to-event outcome, however, such a sampling strategy may be length-biased. Coupled with censoring, analysis of length-biased data can be quite challenging, due to the so-called “induced informative censoring” in which the survival time and censoring time are correlated through a common backward recurrence time. We propose to use the proportional mean residual life model of Oakes and Dasu (1990) for analysis of censored length-biased survival data. Several nonstandard data structures, …

Incorporating Network Structure In Integrative Analysis Of Cancer Prognosis Data, Shuangge Ma

Shuangge Ma

In high-throughput cancer genomic studies, markers identified from the analysis of single datasets may have unsatisfactory properties because of low sample sizes. Integrative analysis pools and analyzes raw data from multiple studies, and can effectively increase sample size and lead to improved marker identification results. In this study, we consider the integrative analysis of multiple high-throughput cancer prognosis studies. In the existing integrative analysis studies, the interplay among genes, which can be described using the network structure, has not been effectively accounted for. In network analysis, tightly-connected nodes (genes) are more likely to have related biological functions and similar regression …

Risk Factors Of Follicular Lymphoma, Shuangge Ma

Shuangge Ma

No abstract provided.

Health Insurance Coverage And Impact: A Survey In Three Cities In China, Shuangge Ma

Shuangge Ma

No abstract provided.

Integrative Analysis Of Multiple Cancer Genomic Datasets Under The Heterogeneity Model, Shuangge Ma

Shuangge Ma

No abstract provided.

Health Insurance Coverage, Medical Expenditure And Coping Strategy: Evidence From Taiwan, Shuangge Ma

Shuangge Ma

No abstract provided.

Impact Of Illness And Medical Expenditure On Household Consumptions: A Survey In Western China, Shuangge Ma

Shuangge Ma

No abstract provided.

Identification Of Gene-Environment Interactions In Cancer Prognosis Studies Using Penalization, Shuangge Ma

Shuangge Ma

High-throughput cancer studies have been extensively conducted, searching for genetic risk factors independently associated with prognosis beyond clinical and environmental risk factors. Many studies have shown that the gene-environment interactions may have important implications. Some of the existing methods, such as the commonly adopted single-marker analysis, may be limited in that they cannot accommodate the joint effects of a large number of genetic markers or use ineffective marker identification techniques. In this study, we analyze cancer prognosis studies, and adopt the AFT (accelerated failure time) model to describe survival. A weighted least squares approach, which has the lowest computational cost, …