Tree-aggregated compositional regression under measurement error

Abstract

Compositional covariates in microbiome studies are often measured with error and organized by a biological hierarchy. Tree aggregation can improve multiresolution interpretation, but it also combines leaf-level errors into correlated contamination whose scale varies across the hierarchy. Existing tree aggregation and compositional measurement-error correction do not combine directly in redundant tree coordinates because a generic positive semidefinite projection can make the corrected criterion depend on the chosen representation. TARCO resolves this mismatch by normalizing tree coordinates by descendant leaf counts and applying a kernel-preserving positive semidefinite projection to the corrected tree-space Gram matrix. The resulting criterion is constant across equivalent tree representations, and the tree-coordinate estimator is exactly equivalent to an estimator on the identifiable coefficient space. For this estimator, we establish finite-sample prediction and coefficient-estimation bounds and, under sufficient separation and an appropriate grouping threshold, exact recovery of the maximal constant subtrees of the identifiable coefficient. These guarantees extend, with additional covariance-estimation terms, when the measurement-error covariance is estimated from independent auxiliary technical replicates. In a longitudinal gut microbiome analysis, correction changes the displayed taxonomic resolution of some associations with body mass index while preserving their directions, illustrating why the hierarchy should guide both signal aggregation and error correction.