Amortized Inference for Causal Structure Learning

Lars Lorch, Scott Sussex, Jonas Rothfuss, Andreas Krause, Bernhard Schölkopf

Keywords: causality, amortized inference, causal discovery, structure learning, Bayesian causal discovery

TL;DR: Amortizing causal discovery for learning domain-specific inductive bias

Abstract: Learning causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to predict the causal structure from observational or interventional data. This allows us to bypass both the search over graphs and the hand-engineering of suitable score functions. Instead, our inference model acquires domain-specific inductive biases for causal discovery solely from data generated by a simulator. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici

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