Bayesian Robust Learning in Chain Graph Models for Integrative Pharmacogenomics

TL;DR

This paper introduces a Bayesian robust chain graph model that effectively captures dependencies in multi-level non-normal pharmacogenomic data, improving inference accuracy over traditional Gaussian models.

Contribution

The paper develops a Bayesian robust chain graph model using Gaussian scale mixtures to handle non-normal data, enhancing dependency inference in multi-omics analysis.

Findings

RCGM outperforms Gaussian chain graph methods in simulations

Identifies key signaling pathway dependencies in lung cancer data

Reveals molecular mechanisms behind drug responses

Abstract

Integrative analysis of multi-level pharmacogenomic data for modeling dependencies across various biological domains is crucial for developing genomic-testing based treatments. Chain graphs characterize conditional dependence structures of such multi-level data where variables are naturally partitioned into multiple ordered layers, consisting of both directed and undirected edges. Existing literature mostly focus on Gaussian chain graphs, which are ill-suited for non-normal distributions with heavy-tailed marginals, potentially leading to inaccurate inferences. We propose a Bayesian robust chain graph model (RCGM) based on random transformations of marginals using Gaussian scale mixtures to account for node-level non-normality in continuous multivariate data. This flexible modeling strategy facilitates identification of conditional sign dependencies among non-normal nodes while still being able to infer conditional dependencies among normal nodes. In simulations, we demonstrate that RCGM outperforms existing Gaussian chain graph inference methods in data generated from various non-normal mechanisms. We apply our method to genomic, transcriptomic and proteomic data to understand underlying biological processes holistically for drug response and resistance in lung cancer cell lines. Our analysis reveals inter- and intra- platform dependencies of key signaling pathways to monotherapies of icotinib, erlotinib and osimertinib among other drugs, along with shared patterns of molecular mechanisms behind drug actions.