# EHR-RAG: Bridging Long-Horizon Structured Electronic Health Records and Large Language Models via Enhanced Retrieval-Augmented Generation

arXiv: https://arxiv.org/abs/2601.21340 · HTML: https://mlsanity.com/paper/2601.21340/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- Placed in Medical and biomedical RAG, one of 15 directions in Retrieval-augmented generation.
- Builds on 35 of its 61 references that are in the map.
- First posted on arXiv 29 Jan 2026.

## Placed in

- Retrieval-augmented generation / [Medical and biomedical RAG](https://mlsanity.com/rag/medical-and-biomedical-rag/)

## Builds on (most cited first, 30 of 35)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Large Language Models are Zero-Shot Reasoners](https://mlsanity.com/paper/2205.11916/) (2022)
- [Lost in the Middle: How Language Models Use Long Contexts](https://mlsanity.com/paper/2307.03172/) (2023)
- [Retrieval-Augmented Generation for Large Language Models: A Survey](https://mlsanity.com/paper/2312.10997/) (2023)
- [Self-RAG: Learning to Retrieve, Generate, and Critique through Self-Reflection](https://mlsanity.com/paper/2310.11511/) (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)
- [Do NLP Models Know Numbers? Probing Numeracy in Embeddings](https://mlsanity.com/paper/1909.07940/) (2019)
- [EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models](https://mlsanity.com/paper/2307.02028/) (2023)
- [Language Models Are An Effective Patient Representation Learning Technique For Electronic Health Record Data](https://mlsanity.com/paper/2001.05295/) (2020)
- [GAMENet: Graph Augmented MEmory Networks for Recommending Medication Combination](https://mlsanity.com/paper/1809.01852/) (2018)
- [EHRAgent: Code Empowers Large Language Models for Few-shot Complex Tabular Reasoning on Electronic Health Records](https://mlsanity.com/paper/2401.07128/) (2024)
- [DeepRetrieval: Hacking Real Search Engines and Retrievers with Large Language Models via Reinforcement Learning](https://mlsanity.com/paper/2503.00223/) (2025)
- [Do Language Embeddings Capture Scales?](https://mlsanity.com/paper/2010.05345/) (2020)
- [GraphCare: Enhancing Healthcare Predictions with Personalized Knowledge Graphs](https://mlsanity.com/paper/2305.12788/) (2023)
- [Reasoning-Enhanced Healthcare Predictions with Knowledge Graph Community Retrieval](https://mlsanity.com/paper/2410.04585/) (2024)
- [ClinicalBench: Can LLMs Beat Traditional ML Models in Clinical Prediction?](https://mlsanity.com/paper/2411.06469/) (2024)
- [Biomedical knowledge graph-optimized prompt generation for large language models](https://mlsanity.com/paper/2311.17330/) (2023)
- [Large Language Models are Powerful Electronic Health Record Encoders](https://mlsanity.com/paper/2502.17403/) (2025)
- [REALM: RAG-Driven Enhancement of Multimodal Electronic Health Records Analysis via Large Language Models](https://mlsanity.com/paper/2402.07016/) (2024)
- [Prompting Large Language Models for Zero-Shot Clinical Prediction with Structured Longitudinal Electronic Health Record Data](https://mlsanity.com/paper/2402.01713/) (2024)
- [MIRA: Medical Time Series Foundation Model for Real-World Health Data](https://mlsanity.com/paper/2506.07584/) (2025)
- [EHR-R1: A Reasoning-Enhanced Foundational Language Model for Electronic Health Record Analysis](https://mlsanity.com/paper/2510.25628/) (2025)
- [EMERGE: Enhancing Multimodal Electronic Health Records Predictive Modeling with Retrieval-Augmented Generation](https://mlsanity.com/paper/2406.00036/) (2024)
- [RAS: Retrieval-And-Structuring for Knowledge-Intensive LLM Generation](https://mlsanity.com/paper/2502.10996/) (2025)
- [Training LLMs for EHR-Based Reasoning Tasks via Reinforcement Learning](https://mlsanity.com/paper/2505.24105/) (2025)
- [Large Language Models with Temporal Reasoning for Longitudinal Clinical Summarization and Prediction](https://mlsanity.com/paper/2501.18724/) (2025)
- [LLMs-based Few-Shot Disease Predictions using EHR: A Novel Approach Combining Predictive Agent Reasoning and Critical Agent Instruction](https://mlsanity.com/paper/2403.15464/) (2024)

## Built on by (most cited first, 6 of 6)

- [MedGuideX: Internalizing Decision Logic from Executable Guidelines into Large Language Models for Clinical Reasoning](https://mlsanity.com/paper/2605.26567/) (2026)
- [Discriminative Representation Learning for Clinical Prediction](https://mlsanity.com/paper/2603.20921/) (2026)
- [ClinicalBench: Stress-Testing Assertion-Aware Retrieval for Cross-Admission Clinical QA on MIMIC-IV](https://mlsanity.com/paper/2605.11143/) (2026)
- [GuideSkill: Evolving Executable LLM Agent Skills for Guideline-Grounded Clinical Reasoning](https://mlsanity.com/paper/2607.26160/) (2026)
- [EviGen: Predictive Evidence Scaffolding for Verifiable Clinical Rationale Generation](https://mlsanity.com/paper/2609.18852/) (2026)
- [MedRouter: Demystifying Knowledge Differences Across Medical LLMs for Routing-Based Reasoning](https://mlsanity.com/paper/2609.33119/) (2026)

## Abstract (arXiv)

Electronic Health Records (EHRs) provide rich longitudinal clinical evidence that is central to medical decision-making, motivating the use of retrieval-augmented generation (RAG) to ground large language model (LLM) predictions. However, long-horizon EHRs often exceed LLM context limits, and existing approaches commonly rely on truncation or vanilla retrieval strategies that discard clinically relevant events and temporal dependencies. To address these challenges, we propose EHR-RAG, a retrieval-augmented framework designed for accurate interpretation of long-horizon structured EHR data. EHR-RAG introduces three components tailored to longitudinal clinical prediction tasks: Event- and Time-Aware Hybrid EHR Retrieval to preserve clinical structure and temporal dynamics, Adaptive Iterative Retrieval to progressively refine queries in order to expand broad evidence coverage, and Dual-Path Evidence Retrieval and Reasoning to jointly retrieves and reasons over both factual and counterfactual evidence. Experiments across four long-horizon EHR prediction tasks show that EHR-RAG consistently outperforms the strongest LLM-based baselines, achieving an average Macro-F1 improvement of 10.76%. Overall, our work highlights the potential of retrieval-augmented LLMs to advance clinical prediction on structured EHR data in practice.