M3Care: Learning with Missing Modalities in Multimodal Healthcare Data

TLDR

Multimodal electronic health record data are widely used, yet conventional methods assume all modalities are present, whereas missing modalities—common in real‑world settings—are typically handled by unstable generative models. The authors introduce M3Care, a direct‑problem model designed to address the underdetermined issue of missing modalities in multimodal healthcare data. M3Care imputes task‑related information for missing modalities in the latent space by leveraging a task‑guided modality‑adaptive similarity metric that identifies similar patients based on their available modalities, enabling end‑to‑end clinical analysis without generating raw missing data. Experiments on real‑world datasets demonstrate that M3Care outperforms state‑of‑the‑art baselines and yields findings aligned with expert knowledge, highlighting its potential for useful insights and explanations.

Abstract

Multimodal electronic health record (EHR) data are widely used in clinical applications. Conventional methods usually assume that each sample (patient) is associated with the unified observed modalities, and all modalities are available for each sample. However, missing modality caused by various clinical and social reasons is a common issue in real-world clinical scenarios. Existing methods mostly rely on solving a generative model that learns a mapping from the latent space to the original input space, which is an unstable ill-posed inverse problem. To relieve the underdetermined system, we propose a model solving a direct problem, dubbed learning with Missing Modalities in Multimodal healthcare data (M3Care). M3Care is an end-to-end model compensating the missing information of the patients with missing modalities to perform clinical analysis. Instead of generating raw missing data, M3Care imputes the task-related information of the missing modalities in the latent space by the auxiliary information from each patient's similar neighbors, measured by a task-guided modality-adaptive similarity metric, and thence conducts the clinical tasks. The task-guided modality-adaptive similarity metric utilizes the uncensored modalities of the patient and the other patients who also have the same uncensored modalities to find similar patients. Experiments on real-world datasets show that M3Care outperforms the state-of-the-art baselines. Moreover, the findings discovered by M3Care are consistent with experts and medical knowledge, demonstrating the capability and the potential of providing useful insights and explanations.