PiCME: Pipeline for Contrastive Modality Evaluation and Encoding in the MIMIC Dataset

Abstract

Multimodal deep learning holds promise for improving clinical prediction by integrating diverse patient data, including text, imaging, time-series, and structured demographics. Contrastive learning facilitates this integration by producing a unified representation that can be reused across tasks, reducing the need for separate models or encoders. Although contrastive learning has seen success in vision-language domains, its use in clinical settings remains largely limited to image and text pairs. We propose the Pipeline for Contrastive Modality Evaluation and Encoding (PiCME), which systematically assesses five clinical data types from MIMIC: discharge summaries, radiology reports, chest X-rays, demographics, and time-series. We pre-train contrastive models on all 26 combinations of two to five modalities and evaluate their utility on in-hospital mortality and phenotype prediction. To address performance plateaus with more modalities, we introduce a Modality-Gated LSTM that weights each modality according to its contrastively learned importance. Our results show that contrastive models remain competitive with supervised baselines, particularly in three-modality settings. Performance declines beyond three modalities, which supervised models fail to recover. The Modality-Gated LSTM mitigates this drop, improving AUROC from 73.19% to 76.93% and AUPRC from 51.27% to 62.26% in the five-modality setting. We also compare contrastively learned modality importance scores with attribution scores and evaluate generalization across demographic subgroups, highlighting strengths in interpretability and fairness. PiCME is the first to scale contrastive learning across all modality combinations in MIMIC, offering guidance for modality selection, training strategies, and equitable clinical prediction.