Causal Discovery and Optimal Experimental Design for Genome-Scale Biological Network Recovery

Abstract

Causal discovery of genome-scale networks is important for identifying pathways from genes to observable traits - e.g. differences in cell function, disease, drug resistance and others. Causal learners based on graphical models rely on interventional samples to orient edges in the network. However, these models have not been shown to scale up the size of the genome, which are on the order of 1e3-1e4 genes. We introduce a new learner, SP-GIES, that jointly learns from interventional and observational datasets and achieves almost 4x speedup against an existing learner for 1,000 node networks. SP-GIES achieves an AUC-PR score of 0.91 on 1,000 node networks, and scales up to 2,000 node networks - this is 4x larger than existing works. We also show how SP-GIES improves downstream optimal experimental design strategies for selecting interventional experiments to perform on the system. This is an important step forward in realizing causal discovery at scale via autonomous experimental design.