MedError

A project for medical error detection and analysis

🌐 Try the App

https://ohnlp.org/MedError/

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System Requirements

Operating Systems

This software has been tested on:

• macOS (Darwin 24.2.0 and later)
• Linux (Ubuntu 20.04, 22.04)
• Windows (Windows 10/11 with WSL2 recommended)

📊 Sample Data

Sample data files are available in the assets/ folder:

• error_definition.yaml - Error category definitions
• error_labels.json - Annotated medical text examples

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Installation Guide

Step 1: Clone the Repository

git clone https://github.com/OHNLP/MedError.git
cd MedError

Step 2: Create a Virtual Environment

conda env create -f environment.yml
conda activate mederror

Step 3: Install Dependencies

pip install -e .

For development dependencies:

pip install -e .[dev]

Typical Install Time

• With Conda: ~5 minutes

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Demo

** Edit path in the code to run the demo**

1. Run error classification:

   python src/mederror/prompt.py

2. Post-process results:

   python src/mederror/postprocess.py

3. Evaluate results:

   python src/mederror/eval.py

Contribution Guidelines

If you plan to contribute to this repository, follow these steps:

1. Fork the repository and create a new branch for your changes:

git checkout -b your-branch-name

2. Install development dependencies:

pip install .[dev]

3. Set up pre-commit hooks:

pre-commit install

4. Commit your changes and open pull request with a clear description of changes.