arXiv subjects

Hee Cheol Chung

Publications and source records attributed to Hee Cheol Chung.

5 recordsLinked to original sources

arXiv2024

A Comparison of Zero-Inflated Models for Modern Biomedical Data

Many data sets cannot be accurately described by standard probability distributions due to the excess number of zero values present. For example, zero-inflation is prevalent in microbiome data and single-cell RNA sequencing data, which serve as our real data examples. Several models have been proposed to address zero-inflated datasets including the zero-inflated negative binomial, hurdle negative binomial model, and the truncated latent Gaussian copula model. This study aims to compare various models and determine which one performs optimally under different conditions using both simulation studies and real data analyses. We are particularly interested in investigating how dependence among the variables, level of zero-inflation or deflation, and variance of the data affects model selection.

stat.ME↗

arXiv2024

Unsupervised Outlier Detection using Random Subspace and Subsampling Ensembles of Dirichlet Process Mixtures

Probabilistic mixture models are recognized as effective tools for unsupervised outlier detection owing to their interpretability and global characteristics. Among these, Dirichlet process mixture models stand out as a strong alternative to conventional finite mixture models for both clustering and outlier detection tasks. Unlike finite mixture models, Dirichlet process mixtures are infinite mixture models that automatically determine the number of mixture components based on the data. Despite their advantages, the adoption of Dirichlet process mixture models for unsupervised outlier detection has been limited by challenges related to computational inefficiency and sensitivity to outliers in the construction of outlier detectors. Additionally, Dirichlet process Gaussian mixtures struggle to effectively model non-Gaussian data with discrete or binary features. To address these challenges, we propose a novel outlier detection method that utilizes ensembles of Dirichlet process Gaussian mixtures. This unsupervised algorithm employs random subspace and subsampling ensembles to ensure efficient computation and improve the robustness of the outlier detector. The ensemble approach further improves the suitability of the proposed method for detecting outliers in non-Gaussian data. Furthermore, our method uses variational inference for Dirichlet process mixtures, which ensures both efficient and rapid computation. Empirical analyses using benchmark datasets demonstrate that our method outperforms existing approaches in unsupervised outlier detection.

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arXiv2024

Bayesian segmented Gaussian copula factor model for single-cell sequencing data

Single-cell sequencing technologies have significantly advanced molecular and cellular biology, offering unprecedented insights into cellular heterogeneity by allowing for the measurement of gene expression at an individual cell level. However, the analysis of such data is challenged by the prevalence of low counts due to dropout events and the skewed nature of the data distribution, which conventional Gaussian factor models struggle to handle effectively. To address these challenges, we propose a novel Bayesian segmented Gaussian copula model to explicitly account for inflation of zero and near-zero counts, and to address the high skewness in the data. By employing a Dirichlet-Laplace prior for each column of the factor loadings matrix, we shrink the loadings of unnecessary factors towards zero, which leads to a simple approach to automatically determine the number of latent factors, and resolve the identifiability issue inherent in factor models due to the rotational invariance of the factor loadings matrix. Through simulation studies, we demonstrate the superior performance of our method over existing approaches in conducting factor analysis on data exhibiting the characteristics of single-cell data, such as excessive low counts and high skewness. Furthermore, we apply the proposed method to a real single-cell RNA-sequencing dataset from a lymphoblastoid cell line, successfully identifying biologically meaningful latent factors and detecting previously uncharacterized cell subtypes.

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arXiv2022

Sparse semiparametric discriminant analysis for high-dimensional zero-inflated data

Sequencing-based technologies provide an abundance of high-dimensional biological datasets with skewed and zero-inflated measurements. Classification of such data with linear discriminant analysis leads to poor performance due to the violation of the Gaussian distribution assumption. To address this limitation, we propose a new semiparametric discriminant analysis framework based on the truncated latent Gaussian copula model that accommodates both skewness and zero inflation. By applying sparsity regularization, we demonstrate that the proposed method leads to the consistent estimation of classification direction in high-dimensional settings. On simulated data, the proposed method shows superior performance compared to the existing method. We apply the method to discriminate healthy controls from patients with Crohn's disease based on microbiome data and to identify genera with the most influence on the classification rule.

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arXiv2021

Phylogenetically informed Bayesian truncated copula graphical models for microbial association networks

Microorganisms play a critical role in host health. The advancement of high-throughput sequencing technology provides opportunities for a deeper understanding of microbial interactions. However, due to the limitations of 16S ribosomal RNA sequencing, microbiome data are zero-inflated, and a quantitative comparison of microbial abundances cannot be made across subjects. By leveraging a recent microbiome profiling technique that quantifies 16S ribosomal RNA microbial counts, we propose a novel Bayesian graphical model that incorporates microorganisms' evolutionary history through a phylogenetic tree prior and explicitly accounts for zero-inflation using the truncated Gaussian copula. Our simulation study reveals that the evolutionary information substantially improves the network estimation accuracy. We apply the proposed model to the quantitative gut microbiome data of 106 healthy subjects, and identify three distinct microbial communities that are not determined by existing microbial network estimation models. We further find that these communities are discriminated based on microorganisms' ability to utilize oxygen as an energy source.

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