SYNPRED: A Synergistic Approach to Multimodal Learning for Clinical Prediction

Abstract

Multimodal medical data captures complementary aspects of disease. It provides a comprehensive basis for diagnosis and the identification of biological associations linked to progression or treatment response. Established contrastive learning approaches exploit shared information across modalities, but fall short in exploiting complementary, modality-specific signals relevant for a task. Here, we propose a synergistic multimodal variational autoencoder (VAE) framework that separates task-relevant unimodal and multimodal information from instance-specific variation task-irrelevant, allowing complementary signals across modalities to be leveraged for prediction. The method yields benefits even if modalities are missing at test time. We evaluate the method on a treatment response prediction task using medical imaging and RNA data. Empirical comparison with alignment-based and multimodal VAE state-of-the-art approaches demonstrates improved multimodal prediction performance, and consistent benefits for prediction from a single modality after multimodal training. The full code can be found here: https://github.com/cirmuw/SYNPRED.