Multi-sample Estimation of Bacterial Composition Matrix in Metagenomics Data

Abstract

Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many rare bacterial taxa might not be captured in the final sequencing reads, which results in many zero counts. Naive composition estimation using count normalization leads to many zero proportions, which tend to result in inaccurate estimates of bacterial abundance and diversity. This paper takes a multi-sample approach to the estimation of bacterial abundances in order to borrow information across samples and across species. Empirical results from real data sets suggest that the composition matrix over multiple samples is approximately low rank, which motivates a regularized maximum likelihood estimation with a nuclear norm penalty. An efficient optimization algorithm using the generalized accelerated proximal gradient and Euclidean projection onto simplex space is developed. The theoretical upper bounds and the minimax lower bounds of the estimation errors, measured by the Kullback-Leibler divergence and the Frobenius norm, are established. Simulation studies demonstrate that the proposed estimator outperforms the naive estimators. The method is applied to an analysis of a human gut microbiome dataset.

References in corpus (12)

• Guaranteed Minimum-Rank Solutions of Linear Matrix Equations via Nuclear Norm Minimization
• Templates for Convex Cone Problems with Applications to Sparse Signal Recovery
• A Differential Equation for Modeling Nesterov's Accelerated Gradient Method: Theory and Insights
• Matrix estimation by Universal Singular Value Thresholding
• Robust estimation of microbial diversity in theory and in practice
• Restricted strong convexity and weighted matrix completion: Optimal bounds with noise
• Unbiased Risk Estimates for Singular Value Thresholding and Spectral Estimators
• Minimax risk of matrix denoising by singular value thresholding
• Does Dirichlet Prior Smoothing Solve the Shannon Entropy Estimation Problem?
• Maximum Likelihood Estimation of Functionals of Discrete Distributions
• Poisson Matrix Recovery and Completion
• Inference of High-dimensional Autoregressive Generalized Linear Models

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