MedDiTPro: A Prompt-Guided Diffusion Transformer for Multimodal Longitudinal Medical Data Synthesis

Diffusion models have recently emerged as a state-of-the-art approach for synthetic Electronic Health Record (EHR) generation, offering superior fidelity and diversity over traditional generative models. However, existing diffusion-based methods struggle with unique challenges: limited representation learning and modality utilization, where they fail to explicitly capture inter-modality dependencies and fine-grained code-level interactions, and constrained adaptability due to reliance on U-Net-based architectures, which are not well-suited for handling the heterogeneous and evolving nature of EHR data. Furthermore, current evaluation paradigms rely on either perplexity-based sequence modeling or global distributional measures, lacking robustness in assessing both intra-visit code relationships and inter-visit temporal patterns. To address these limitations, we propose MedDiTPro, a diffusion transformer-based framework that enhances multimodal EHR generation by integrating structured modality-aware guidance. Through a unified transformer for intra-visit representation learning, a modality-specific and datawise prompt learner, and a diffusion transformer with structured guidance, MedDiTPro achieves state-of-the-art performance in generating diverse and clinically meaningful synthetic records. Extensive experiments on publicly available datasets demonstrate that MedDiTPro achieves state-of-the-art fidelity, privacy preservation, and utility. © 2025 ACM.