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Statistical Modeling for High-Dimensional Compositional Data with Applications to the Human Microbiome.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Statistical Modeling for High-Dimensional Compositional Data with Applications to the Human Microbiome./
Author:	Dao, Thy.
Published:	Ann Arbor : ProQuest Dissertations & Theses, : 2021,
Description:	81 p.
Notes:	Source: Dissertations Abstracts International, Volume: 83-04, Section: B.
Contained By:	Dissertations Abstracts International83-04B.
Subject:	Statistics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28649733
ISBN:	9798460415458

Statistical Modeling for High-Dimensional Compositional Data with Applications to the Human Microbiome.
Dao, Thy.

Statistical Modeling for High-Dimensional Compositional Data with Applications to the Human Microbiome. - Ann Arbor : ProQuest Dissertations & Theses, 2021 - 81 p.

Source: Dissertations Abstracts International, Volume: 83-04, Section: B.

Thesis (Ph.D.)--University of Arkansas, 2021.

This item must not be sold to any third party vendors.

Compositional data refer to the data that lie on a simplex, which are common in many scientific domains such as genomics, geology, and economics. As the components in a composition must sum to one, traditional tests based on unconstrained data become inappropriate, and new statistical methods are needed to analyze this special type of data. This dissertation is motivated by some statistical problems arising in the analysis of compositional data. In particular, we focus on the high-dimensional and over-dispersed setting, where the dimensionality of compositions is greater than the sample size and the dispersion parameter is moderate or large. In this dissertation, we consider a general problem of testing for the compositional difference between K populations. We propose a new Bayesian hypothesis, together with a nonparametric and distance-based testing method. Furthermore, we utilize multiple variable-selecting models, including LASSO, elastic net, ridge regression and cumulative logit model, to identify the most important subset of variables. This dissertation is structured as follows:Chapter 1 introduces the compositional microbiome data, and then briefly review different statistical tests and model to be used in our framework, including distance correlation, LASSO, Ridge regression, elastic net, cumulative logit and adjacent-category logit model.Chapter 2 then presents our new statistical test together with two real world applications form human microbiome study. We first formulate a hypothesis from the Bayesian point of view and suggest a nonparametric test based on inter-point distance to evaluate statistical significance. Unlike most existing tests for compositional data, the distance-based method is more sensitive to the compositional difference than the mean-based method, especially when the data are over-dispersed or zero-inflated. It does not rely on any data transformation, sparsity assumption or regularity conditions on the covariance matrix, but directly analyzes the compositions. The performance of this method is evaluated using simulation studies. We apply this new procedure to two human microbiome datasets including a throat microbiome dataset and an intestinal microbiome data.In addition to the overall testing, we also want to identify a small subset of variables that distinguish different populations. Chapter 3 introduces the procedure to select most significant variables (bacteria or genus) using LASSO, Ridge regression, elastic net, cumulative logit model and adjacent-category logit models. Chapter 4 validates our findings from Chapter 3 and presents visualizations using multi-dimensional scaling (MDS).Chapter 5 discusses and concludes the dissertation with some future perspectives.

ISBN: 9798460415458Subjects--Topical Terms:

517247
Statistics.
Subjects--Index Terms:

Compositional data

Statistical Modeling for High-Dimensional Compositional Data with Applications to the Human Microbiome.
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245 1 0 $a Statistical Modeling for High-Dimensional Compositional Data with Applications to the Human Microbiome.
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300 $a 81 p.
500 $a Source: Dissertations Abstracts International, Volume: 83-04, Section: B.
500 $a Advisor: Zhang, Qingyang.
502 $a Thesis (Ph.D.)--University of Arkansas, 2021.
506 $a This item must not be sold to any third party vendors.
520 $a Compositional data refer to the data that lie on a simplex, which are common in many scientific domains such as genomics, geology, and economics. As the components in a composition must sum to one, traditional tests based on unconstrained data become inappropriate, and new statistical methods are needed to analyze this special type of data. This dissertation is motivated by some statistical problems arising in the analysis of compositional data. In particular, we focus on the high-dimensional and over-dispersed setting, where the dimensionality of compositions is greater than the sample size and the dispersion parameter is moderate or large. In this dissertation, we consider a general problem of testing for the compositional difference between K populations. We propose a new Bayesian hypothesis, together with a nonparametric and distance-based testing method. Furthermore, we utilize multiple variable-selecting models, including LASSO, elastic net, ridge regression and cumulative logit model, to identify the most important subset of variables. This dissertation is structured as follows:Chapter 1 introduces the compositional microbiome data, and then briefly review different statistical tests and model to be used in our framework, including distance correlation, LASSO, Ridge regression, elastic net, cumulative logit and adjacent-category logit model.Chapter 2 then presents our new statistical test together with two real world applications form human microbiome study. We first formulate a hypothesis from the Bayesian point of view and suggest a nonparametric test based on inter-point distance to evaluate statistical significance. Unlike most existing tests for compositional data, the distance-based method is more sensitive to the compositional difference than the mean-based method, especially when the data are over-dispersed or zero-inflated. It does not rely on any data transformation, sparsity assumption or regularity conditions on the covariance matrix, but directly analyzes the compositions. The performance of this method is evaluated using simulation studies. We apply this new procedure to two human microbiome datasets including a throat microbiome dataset and an intestinal microbiome data.In addition to the overall testing, we also want to identify a small subset of variables that distinguish different populations. Chapter 3 introduces the procedure to select most significant variables (bacteria or genus) using LASSO, Ridge regression, elastic net, cumulative logit model and adjacent-category logit models. Chapter 4 validates our findings from Chapter 3 and presents visualizations using multi-dimensional scaling (MDS).Chapter 5 discusses and concludes the dissertation with some future perspectives.
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650 4 $a Statistics. $3 517247
650 4 $a Biostatistics. $3 1002712
650 4 $a Bioinformatics. $3 553671
653 $a Compositional data
653 $a Distance-based
653 $a High dimensional compositional data
653 $a Microbiome
653 $a Statistical model
690 $a 0463
690 $a 0308
690 $a 0715
710 2 $a University of Arkansas. $b Mathematics. $3 2096727
773 0 $t Dissertations Abstracts International $g 83-04B.
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791 $a Ph.D.
792 $a 2021
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28649733