# Generative Foundation Model for Structured and Unstructured Electronic Health Records

arXiv: https://arxiv.org/abs/2508.16054 · HTML: https://mlsanity.com/paper/2508.16054/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 36 references that are in the map.
- First posted on arXiv 22 Aug 2025.

## Builds on (most cited first, 19 of 19)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Deep reinforcement learning from human preferences](https://mlsanity.com/paper/1706.03741/) (2017)
- [REALM: Retrieval-Augmented Language Model Pre-Training](https://mlsanity.com/paper/2002.08909/) (2020)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [An Empirical Evaluation of Generic Convolutional and Recurrent Networks for Sequence Modeling](https://mlsanity.com/paper/1803.01271/) (2018)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Generating Sequences With Recurrent Neural Networks](https://mlsanity.com/paper/1308.0850/) (2013)
- [How Far Can Camels Go? Exploring the State of Instruction Tuning on Open Resources](https://mlsanity.com/paper/2306.04751/) (2023)
- [Med-Flamingo: a Multimodal Medical Few-shot Learner](https://mlsanity.com/paper/2307.15189/) (2023)
- [RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism](https://mlsanity.com/paper/1608.05745/) (2016)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [BiomedGPT: A Generalist Vision-Language Foundation Model for Diverse Biomedical Tasks](https://mlsanity.com/paper/2305.17100/) (2023)
- [CEHR-BERT: Incorporating temporal information from structured EHR data to improve prediction tasks](https://mlsanity.com/paper/2111.08585/) (2021)
- [A Framework for Human Evaluation of Large Language Models in Healthcare Derived from Literature Review](https://mlsanity.com/paper/2405.02559/) (2024)
- [Med42 -- Evaluating Fine-Tuning Strategies for Medical LLMs: Full-Parameter vs. Parameter-Efficient Approaches](https://mlsanity.com/paper/2404.14779/) (2024)
- [HELM: Hierarchical Encoding for mRNA Language Modeling](https://mlsanity.com/paper/2410.12459/) (2024)
- [The Foundational Capabilities of Large Language Models in Predicting Postoperative Risks Using Clinical Notes](https://mlsanity.com/paper/2402.17493/) (2024)

## Abstract (arXiv)

Electronic health records (EHRs) are rich clinical data sources but complex repositories of patient data, spanning structured elements (demographics, vitals, lab results, codes), unstructured clinical notes and other modalities of data. Harnessing this heterogeneity is critical for improving patient outcomes. Recent advances in large language models (LLMs) have enabled foundation models that can learn from multiple data modalities and support clinical tasks. However, most current approaches simply serialize numeric EHR data into text, which risks losing temporal and quantitative detail. We introduce Generative Deep Patient (GDP), a multimodal foundation model that natively encodes structured EHR time-series via a CNN-Transformer encoder and fuses it with unstructured EHRs through cross-modal attention into a LLaMA-based decoder. GDP is trained in two stages: (1) generative pretraining, where it learns to produce clinical narratives from raw patient timelines while also performing masked feature prediction (MFP) and next time-step prediction (NTP) to capture temporal dynamics; and (2) multi-task fine-tuning for clinically meaningful predictions (e.g., heart failure, type 2 diabetes, 30-day readmission). In clinical prediction, GDP demonstrated superior performance on MIMIC-IV: heart failure AUROC = 0.923, type 2 diabetes AUROC = 0.817, and 30-day readmission AUROC = 0.627. For narrative generation, GDP achieved ROUGE-L = 0.135 and BERTScore-F1 = 0.545. In a blinded human evaluation, GDP-Instruct scored highest on faithfulness, fluency, and overall clinical utility, suggesting reduced hospital documentation workload without sacrificing accuracy. Our results demonstrate that a single multimodal foundation model can both predict clinically actionable events and generate high-quality clinical narratives. Furthermore, GDP's flexible architecture can be extended to additional modalities.