Multimodal Training to Unimodal Deployment: Leveraging Unstructured Data During Training to Optimize Structured Data Only Deployment

Large Language Models (LLMs) have shown strong promise for mining Electronic Health Records (EHRs) by reasoning over longitudinal clinical information to capture context-rich patient trajectories. However, leveraging LLMs for structured EHRs (e.g., standardized diagnosis and medication codes) presents two key challenges. First, translating time-stamped EHR sequences into plain text can obscure both temporal structure and code identities, weakening the ability to capture code co-occurrence and longitudinal regularities. Second, unlike cohort-trained predictive models that learn a shared, task-aligned representation space across patients, LLMs are often applied in a case-isolated inference setting where each patient is processed independently without leveraging population-level patterns. To address these challenges, we introduce RePrompT, a time-aware LLM framework that integrates structured EHR encoders through prompt tuning, without modifying underlying architectures. Specifically, RePrompT recurrently incorporates latent states from prior visits to preserve longitudinal information, and injects population-level information through trainable prompt tokens derived from a cohort-trained, task-aligned EHR encoder. Experiments on MIMIC-III and MIMIC-IV demonstrate that RePrompT consistently outperforms both EHR-based and LLM-based baselines across multiple clinical prediction tasks.

Autoregressive foundation models trained on tokenized electronic health records (EHRs) can support zero-shot clinical prediction, yet most operate on structured event codes alone, and do not incorporate multiple modalities in a principled way. We present a framework for conditioning such models on auxiliary clinical modalities, including ECG waveforms, chest X-ray images, and clinical notes, using modality-specific latent compression and gated cross-attention with temporal alignment. We investigate two key design choices: (1) how to compress long per-modality sequences (e.g., ECG time series) before they enter the multi-modal cross-attention. This feature may be essential to reduce compute overheads and may be beneficial for generalization; (2) how the choice of pretrained encoder for each modality impacts downstream performance. Through controlled ablations on MIMIC-IV, we show that the best latent-compression configurations outperforms both uncompressed cross-attention and mean pooling. Encoder choice has a clear within-modality effect, with stronger pretrained encoders consistently outperforming weaker alternatives. We further show that merely adding auxiliary modalities does not guarantee improvement on ICU mortality prediction over an EHR-only baseline. This implies that careful design of the fusion architecture and an appropriate evaluation in the clinical context are required.

Machine learning holds promise for advancing clinical decision support, yet it remains unclear when multimodal learning truly helps in practice, particularly under modality missingness and fairness constraints. In this work, we conduct a systematic benchmark of multimodal fusion between Electronic Health Records (EHR) and chest X-rays (CXR) on standardized cohorts from MIMIC-IV and MIMIC-CXR, aiming to answer four fundamental questions: when multimodal fusion improves clinical prediction, how different fusion strategies compare, how robust existing methods are to missing modalities, and whether multimodal models achieve algorithmic fairness. Our study reveals several key insights. Multimodal fusion improves performance when modalities are complete, with gains concentrating in diseases that require complementary information from both EHR and CXR. While cross-modal learning mechanisms capture clinically meaningful dependencies beyond simple concatenation, the rich temporal structure of EHR introduces strong modality imbalance that architectural complexity alone cannot overcome. Under realistic missingness, multimodal benefits rapidly degrade unless models are explicitly designed to handle incomplete inputs. Moreover, multimodal fusion does not inherently improve fairness, with subgroup disparities mainly arising from unequal sensitivity across demographic groups. To support reproducible and extensible evaluation, we further release a flexible benchmarking toolkit that enables plug-and-play integration of new models and datasets. Together, this work provides actionable guidance on when multimodal learning helps, when it fails, and why, laying the foundation for developing clinically deployable multimodal systems that are both effective and reliable. The open-source toolkit can be found at https://github.com/jakeykj/CareBench.