# EMR-AGENT: Automating Cohort and Feature Extraction from EMR Databases

arXiv: https://arxiv.org/abs/2510.00549 · HTML: https://mlsanity.com/paper/2510.00549/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 28 of its 47 references that are in the map.
- First posted on arXiv 1 Oct 2025.

## Builds on (most cited first, 28 of 28)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
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- [Qwen2.5 Technical Report](https://mlsanity.com/paper/2412.15115/) (2024)
- [DIN-SQL: Decomposed In-Context Learning of Text-to-SQL with Self-Correction](https://mlsanity.com/paper/2304.11015/) (2023)
- [A Real-World WebAgent with Planning, Long Context Understanding, and Program Synthesis](https://mlsanity.com/paper/2307.12856/) (2023)
- [Multitask learning and benchmarking with clinical time series data](https://mlsanity.com/paper/1703.07771/) (2017)
- [Multi-Time Attention Networks for Irregularly Sampled Time Series](https://mlsanity.com/paper/2101.10318/) (2021)
- [Spider 2.0: Evaluating Language Models on Real-World Enterprise Text-to-SQL Workflows](https://mlsanity.com/paper/2411.07763/) (2024)
- [CHESS: Contextual Harnessing for Efficient SQL Synthesis](https://mlsanity.com/paper/2405.16755/) (2024)
- [Is Your LLM Secretly a World Model of the Internet? Model-Based Planning for Web Agents](https://mlsanity.com/paper/2411.06559/) (2024)
- [Set Functions for Time Series](https://mlsanity.com/paper/1909.12064/) (2019)
- [MIMIC-Extract: A Data Extraction, Preprocessing, and Representation Pipeline for MIMIC-III](https://mlsanity.com/paper/1907.08322/) (2019)
- [EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models](https://mlsanity.com/paper/2307.02028/) (2023)
- [Self-Supervised Transformer for Sparse and Irregularly Sampled Multivariate Clinical Time-Series](https://mlsanity.com/paper/2107.14293/) (2021)
- [Time Series as Images: Vision Transformer for Irregularly Sampled Time Series](https://mlsanity.com/paper/2303.12799/) (2023)
- [EHRAgent: Code Empowers Large Language Models for Few-shot Complex Tabular Reasoning on Electronic Health Records](https://mlsanity.com/paper/2401.07128/) (2024)
- [Event Stream GPT: A Data Pre-processing and Modeling Library for Generative, Pre-trained Transformers over Continuous-time Sequences of Complex Events](https://mlsanity.com/paper/2306.11547/) (2023)
- [EHRSQL: A Practical Text-to-SQL Benchmark for Electronic Health Records](https://mlsanity.com/paper/2301.07695/) (2023)
- [Benchmarking machine learning models on multi-centre eICU critical care dataset](https://mlsanity.com/paper/1910.00964/) (2019)
- [Yet Another ICU Benchmark: A Flexible Multi-Center Framework for Clinical ML](https://mlsanity.com/paper/2306.05109/) (2023)
- [Learning Missing Modal Electronic Health Records with Unified Multi-modal Data Embedding and Modality-Aware Attention](https://mlsanity.com/paper/2305.02504/) (2023)
- [Unifying Heterogeneous Electronic Health Records Systems via Text-Based Code Embedding](https://mlsanity.com/paper/2108.03625/) (2021)
- [Clairvoyance: A Pipeline Toolkit for Medical Time Series](https://mlsanity.com/paper/2310.18688/) (2023)
- [ACES: Automatic Cohort Extraction System for Event-Stream Datasets](https://mlsanity.com/paper/2406.19653/) (2024)
- [LG AI Research & KAIST at EHRSQL 2024: Self-Training Large Language Models with Pseudo-Labeled Unanswerable Questions for a Reliable Text-to-SQL System on EHRs](https://mlsanity.com/paper/2405.11162/) (2024)
- [EHR-SeqSQL : A Sequential Text-to-SQL Dataset For Interactively Exploring Electronic Health Records](https://mlsanity.com/paper/2406.00019/) (2024)
- [Self-Supervised Predictive Coding with Multimodal Fusion for Patient Deterioration Prediction in Fine-grained Time Resolution](https://mlsanity.com/paper/2210.16598/) (2022)

## Abstract (arXiv)

Machine learning models for clinical prediction rely on structured data extracted from Electronic Medical Records (EMRs), yet this process remains dominated by hardcoded, database-specific pipelines for cohort definition, feature selection, and code mapping. These manual efforts limit scalability, reproducibility, and cross-institutional generalization. To address this, we introduce EMR-AGENT (Automated Generalized Extraction and Navigation Tool), an agent-based framework that replaces manual rule writing with dynamic, language model-driven interaction to extract and standardize structured clinical data. Our framework automates cohort selection, feature extraction, and code mapping through interactive querying of databases. Our modular agents iteratively observe query results and reason over schema and documentation, using SQL not just for data retrieval but also as a tool for database observation and decision making. This eliminates the need for hand-crafted, schema-specific logic. To enable rigorous evaluation, we develop a benchmarking codebase for three EMR databases (MIMIC-III, eICU, SICdb), including both seen and unseen schema settings. Our results demonstrate strong performance and generalization across these databases, highlighting the feasibility of automating a process previously thought to require expert-driven design. The code will be released publicly at https://github.com/AITRICS/EMR-AGENT/tree/main. For a demonstration, please visit our anonymous demo page: https://anonymoususer-max600.github.io/EMR_AGENT/