Reference-Invariant Inverse Covariance Estimation with Application to Microbial Network Recovery

TL;DR

This paper introduces a novel reference-invariant method for inverse covariance estimation in microbiome data, addressing issues with existing transformations and ensuring consistent network inference regardless of reference choice.

Contribution

It establishes the reference-invariance property for subnetworks and proposes a modified compositional graphical lasso that maintains invariance under ALR transformation.

Findings

The method is validated through simulations.

Application to oceanic microbiome data demonstrates effectiveness.

Ensures consistent network estimation regardless of reference choice.

Abstract

The interactions between microbial taxa in microbiome data has been under great research interest in the science community. In particular, several methods such as SPIEC-EASI, gCoda, and CD-trace have been proposed to model the conditional dependency between microbial taxa, in order to eliminate the detection of spurious correlations. However, all those methods are built upon the central log-ratio (CLR) transformation, which results in a degenerate covariance matrix and thus an undefined inverse covariance matrix as the estimation of the underlying network. Jiang et al. (2021) and Tian et al. (2022) proposed bias-corrected graphical lasso and compositional graphical lasso based on the additive log-ratio (ALR) transformation, which first selects a reference taxon and then computes the log ratios of the abundances of all the other taxa with respect to that of the reference. One concern of the ALR transformation would be the invariance of the estimated network with respect to the choice of reference. In this paper, we first establish the reference-invariance property of a subnetwork of interest based on the ALR transformed data. Then, we propose a reference-invariant version of the compositional graphical lasso by modifying the penalty in its objective function, penalizing only the invariant subnetwork. We validate the reference-invariance property of the proposed method under a variety of simulation scenarios as well as through the application to an oceanic microbiome data set.