MIRACLE: Causally-Aware Imputation via Learning Missing Data Mechanisms

Part of Advances in Neural Information Processing Systems 34 pre-proceedings (NeurIPS 2021)

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Trent Kyono, Yao Zhang, Alexis Bellot, Mihaela van der Schaar


Missing data is an important problem in machine learning practice. Starting from the premise that imputation methods should preserve the causal structure of the data, we develop a regularization scheme that encourages any baseline imputation method to be causally consistent with the underlying data generating mechanism. Our proposal is a causally-aware imputation algorithm (MIRACLE). MIRACLE iteratively refines the imputation of a baseline by simultaneously modeling the missingness generating mechanism, encouraging imputation to be consistent with the causal structure of the data. We conduct extensive experiments on synthetic and a variety of publicly available datasets to show that MIRACLE is able to consistently improve imputation over a variety of benchmark methods across all three missingness scenarios: at random, completely at random, and not at random.