Optimal Estimation of Bacterial Growth Rates Based on Permuted Monotone Matrix

Abstract

Motivated by the problem of estimating the bacterial growth rates for genome assemblies from shotgun metagenomic data, we consider the permuted monotone matrix model $Y=\Theta\Pi+Z$, where $Y\in \mathbb{R}^{n\times p}$ is observed, $\Theta\in \mathbb{R}^{n\times p}$ is an unknown approximately rank-one signal matrix with monotone rows, $\Pi \in \mathbb{R}^{p\times p}$ is an unknown permutation matrix, and $Z\in \mathbb{R}^{n\times p}$ is the noise matrix. This paper studies the estimation of the extreme values associated to the signal matrix $\Theta$, including its first and last columns, as well as their difference. Treating these estimation problems as compound decision problems, minimax rate-optimal estimators are constructed using the spectral column sorting method. Numerical experiments through simulated and synthetic microbiome metagenomic data are presented, showing the superiority of the proposed methods over the alternatives. The methods are illustrated by comparing the growth rates of gut bacteria between inflammatory bowel disease patients and normal controls.