Interpretable dimension reduction for compositional data

Abstract: High-dimensional compositional data, such as those from human microbiome studies, pose unique statistical challenges due to the simplex constraint and excess zeros. While dimension reduction is indispensable for analyzing such data, conventional approaches often rely on log-ratio transformations that compromise interpretability and distort the data through ad hoc zero replacements. We introduce a novel framework for interpretable dimension reduction of compositional data that avoids extra transformations and zero imputations. Our approach generalizes the concept of amalgamation by softening its operation, mapping high-dimensional compositions directly to a lower-dimensional simplex, which can be visualized in ternary plots. The framework further provides joint visualization of the reduction matrix, enabling intuitive, at-a-glance interpretation. To achieve optimal reduction within our framework, we incorporate sufficient dimension reduction, which defines a new identifiable objective: the central compositional subspace. For estimation, we propose a compositional kernel dimension reduction (CKDR) method. The estimator is provably consistent, exhibits sparsity that reveals underlying amalgamation structures, and comes with an intrinsic predictive model for downstream analyses. Applications to real microbiome datasets demonstrate that our approach provides a powerful graphical exploration tool for uncovering meaningful biological patterns, opening a new pathway for analyzing high-dimensional compositional data.