Robust Multi-View Co-Expression Network Inference

Abstract

Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including the high-dimensionality of the data relative to the number of samples, sample correlations, and batch effects. To address these complexities, we introduce a robust method for high-dimensional graph inference from multiple independent studies. We base our approach on the premise that each dataset is essentially a noisy linear mixture of gene loadings that follow a multivariate $t$-distribution with a sparse precision matrix, which is shared across studies. This allows us to show that we can identify the co-expression matrix up to a scaling factor among other model parameters. Our method employs an Expectation-Maximization procedure for parameter estimation. Empirical evaluation on synthetic and gene expression data demonstrates our method’s improved ability to learn the underlying graph structure compared to baseline methods.