Exact Stiefel Optimization for Probabilistic PLS: Closed-Form Updates, Error Bounds, and Calibrated Uncertainty

TL;DR

This paper introduces an exact Stiefel manifold optimization approach for probabilistic PLS, improving parameter estimation, uncertainty calibration, and prediction accuracy in high-noise and multi-omics data settings.

Contribution

It replaces previous noise averaging with noise-subspace estimation and uses exact Stiefel optimization, enhancing robustness and theoretical guarantees in probabilistic PLS.

Findings

Achieves near-nominal coverage without recalibration.

Reaches Ridge-level accuracy on TCGA-BRCA at rank 3.

Improves stability of parameter recovery in benchmarks.

Abstract

Probabilistic partial least squares (PPLS) is a central likelihood-based model for two-view learning when one needs both interpretable latent factors and calibrated uncertainty. Building on the identifiable parameterization of Bouhaddani et al.\ (2018), existing fitting pipelines still face two practical bottlenecks: noise--signal coupling under joint EM/ECM updates and nontrivial handling of orthogonality constraints. Following the fixed-noise scalar-likelihood line of Hu et al.\ (2025), we develop an end-to-end framework that combines noise pre-estimation, constrained likelihood optimization, and prediction calibration in one pipeline. Relative to Hu et al.\ (2025), we replace full-spectrum noise averaging with noise-subspace estimation and replace interior-point penalty handling with exact Stiefel-manifold optimization. The noise-subspace estimator attains a signal-strength-independent leading finite-sample rate and matches a minimax lower bound, while the full-spectrum estimator is shown to be inconsistent under the same model. We further extend the framework to sub-Gaussian settings via optional Gaussianization and provide closed-form standard errors through a block-structured Fisher analysis. Across synthetic high-noise settings and two multi-omics benchmarks (TCGA-BRCA and PBMC CITE-seq), the method achieves near-nominal coverage without post-hoc recalibration, reaches Ridge-level point accuracy on TCGA-BRCA at rank $r=3$, matches or exceeds PO2PLS on cross-view prediction while providing native calibrated uncertainty, and improves stability of parameter recovery.