Establishing causal dependencies is crucial in applied domains, such as medicine and healthcare, where decision-making must be explainable. In these settings, small sample sizes and missing data call for federated approaches to maximise the amount of information we can use.

We propose a novel federated causal discovery algorithm capable of pooling information from multiple sources with heterogeneous missing data to learn a graph representing cause–effect relationships. In particular, we learn a causal graph on a centralised server while taking into account both prior knowledge and missingness mechanism specific to each client.

We applied the proposed algorithm to synthetic data and real-world data from a multicentric study on endometrial cancer, validating the obtained causal graph through quantitative analyses and a clinical literature review.

Our approach learns an accurate model despite data missing not-at-random.

Federated learning

Multiple sources

Missing data

© 2025 The Authors. Published by Elsevier Inc.