Bayesian Optimal Experimental Design for Inferring Causal Structure

Abstract

Inferring the causal structure of a system typically requires interventional data, rather than just observational data. Since interventional experiments can be costly, it is preferable to select interventions that yield the maximum amount of information about a system. We propose a novel Bayesian method for optimal experimental design by sequentially selecting interventions that minimize the expected posterior entropy as rapidly as possible. A key feature is that the method can be implemented by computing simple summaries of the current posterior, avoiding the computationally burdensome task of repeatedly performing posterior inference on hypothetical future datasets drawn from the posterior predictive. After deriving the method in a general setting, we apply it to the problem of inferring causal networks. We present a series of simulation studies, in which we find that the proposed method performs favorably compared to existing alternative methods. Finally, we apply the method to real data from two gene regulatory networks.