MIRACLE: Causally-Aware Imputation via Learning Missing Data Mechanisms

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

Keywords: Missing data, Multiple imputation, Deep learning

TL;DR: We introduce a framework for missing data imputation that leverages causal structure and missing data indicators.

Abstract: 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.

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Community Implementations: [ 1 code implementation](https://www.catalyzex.com/paper/arxiv:2111.03187/code)