Bayesian Simultaneous Factorization and Prediction Using Multi-Omic Data

TL;DR

This paper introduces Bayesian Simultaneous Factorization and Prediction (BSFP), a novel framework for multi-omic data analysis that enables latent pattern discovery, prediction of clinical outcomes, and handling of missing data with uncertainty quantification.

Contribution

The paper develops BSF and BSFP, Bayesian methods that unify factorization, prediction, and imputation for multi-omic data, with theoretical and practical advantages over existing approaches.

Findings

BSFP effectively recovers latent structures in simulated data.

BSFP accurately predicts lung function in HIV-associated OLD.

The methods handle complex missing data scenarios with uncertainty quantification.

Abstract

Understanding of the pathophysiology of obstructive lung disease (OLD) is limited by available methods to examine the relationship between multi-omic molecular phenomena and clinical outcomes. Integrative factorization methods for multi-omic data can reveal latent patterns of variation describing important biological signal. However, most methods do not provide a framework for inference on the estimated factorization, simultaneously predict important disease phenotypes or clinical outcomes, nor accommodate multiple imputation. To address these gaps, we propose Bayesian Simultaneous Factorization (BSF). We use conjugate normal priors and show that the posterior mode of this model can be estimated by solving a structured nuclear norm-penalized objective that also achieves rank selection and motivates the choice of hyperparameters. We then extend BSF to simultaneously predict a continuous or binary response, termed Bayesian Simultaneous Factorization and Prediction (BSFP). BSF and BSFP accommodate concurrent imputation and full posterior inference for missing data, including "blockwise" missingness, and BSFP offers prediction of unobserved outcomes. We show via simulation that BSFP is competitive in recovering latent variation structure, as well as the importance of propagating uncertainty from the estimated factorization to prediction. We also study the imputation performance of BSF via simulation under missing-at-random and missing-not-at-random assumptions. Lastly, we use BSFP to predict lung function based on the bronchoalveolar lavage metabolome and proteome from a study of HIV-associated OLD. Our analysis reveals a distinct cluster of patients with OLD driven by shared metabolomic and proteomic expression patterns, as well as multi-omic patterns related to lung function decline. Software is freely available at https://github.com/sarahsamorodnitsky/BSFP .