# ChatHealthAI: Aligning Electronic Health Record Representations with Large Language Models for Grounded Clinical Reasoning

arXiv: https://arxiv.org/abs/2606.02802 · HTML: https://mlsanity.com/paper/2606.02802/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 16 of its 45 references that are in the map.
- First posted on arXiv 1 Jun 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 16 of 16)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Flamingo: a Visual Language Model for Few-Shot Learning](https://mlsanity.com/paper/2204.14198/) (2022)
- [MiniGPT-4: Enhancing Vision-Language Understanding with Advanced Large Language Models](https://mlsanity.com/paper/2304.10592/) (2023)
- [Retrieval-Augmented Generation for Large Language Models: A Survey](https://mlsanity.com/paper/2312.10997/) (2023)
- [Orca: Progressive Learning from Complex Explanation Traces of GPT-4](https://mlsanity.com/paper/2306.02707/) (2023)
- [BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains](https://mlsanity.com/paper/2402.10373/) (2024)
- [Capabilities of Gemini Models in Medicine](https://mlsanity.com/paper/2404.18416/) (2024)
- [MedRAG: Enhancing Retrieval-augmented Generation with Knowledge Graph-Elicited Reasoning for Healthcare Copilot](https://mlsanity.com/paper/2502.04413/) (2025)
- [Explainable artificial intelligence model to predict acute critical illness from electronic health records](https://mlsanity.com/paper/1912.01266/) (2019)
- [A Survey on Medical Large Language Models: Technology, Application, Trustworthiness, and Future Directions](https://mlsanity.com/paper/2406.03712/) (2024)
- [Ask Patients with Patience: Enabling LLMs for Human-Centric Medical Dialogue with Grounded Reasoning](https://mlsanity.com/paper/2502.07143/) (2025)
- [EHR-R1: A Reasoning-Enhanced Foundational Language Model for Electronic Health Record Analysis](https://mlsanity.com/paper/2510.25628/) (2025)
- [PaLM2-VAdapter: Progressively Aligned Language Model Makes a Strong Vision-language Adapter](https://mlsanity.com/paper/2402.10896/) (2024)
- [Evaluating Retrieval-Augmented Generation vs. Long-Context Input for Clinical Reasoning over EHRs](https://mlsanity.com/paper/2508.14817/) (2025)

## Abstract (arXiv)

Large language models (LLMs) exhibit strong natural-language reasoning abilities for clinical decision support, but struggle to effectively model structured longitudinal electronic health records (EHRs). In contrast, EHR foundation models can learn predictive patient representations, yet lack interpretable language-based reasoning. To bridge this gap, we propose ChatHealthAI, a multimodal reasoning framework that aligns structured EHR representations from a pretrained EHR foundation model with the semantic space of a frozen LLM through a task-aware resampler. By integrating longitudinal patient representations with refined clinical event descriptions, ChatHealthAI enables clinically grounded natural-language reasoning while maintaining accurate patient prediction. We evaluated ChatHealthAI on three clinical predictive tasks from the EHRSHOT benchmark. Results show that ChatHealthAI improves reasoning quality and interpretability while preserving competitive predictive performance. These findings highlight the potential of integrating EHR foundation models with pretrained LLMs for interpretable clinical prediction.