Clinical Entity Linking in Spanish with Knowledge-Graph Enhanced Biencoders

Welcome to the official repository of the ClinLinker-KB, developed by the Computational Intelligence and Biomedicine (ICB) group at the University of Málaga and Barcelona Super Computing Center (BSC).

Environment main settings

• Python 3.10+
• PyTorch 2.1.0

Installation

Clone the repository and install the required packages:

git clone https://github.com/ICB-UMA/ClinLinker-KB.git

Requirements

cd ClinLinker-KB
pip install -r requirements

Usage

The repository includes scripts for data generation and model training. Here are examples of how to use these scripts:

Data Generation

Create your own data from:

generate_pretraining_data.ipynb

Train your cross-encoder

cd scripts/
python cross_encoder_training.py 

Features

• Multilingual Support: Capable of processing and understanding multiple languages.
• Advanced Machine Learning Techniques: Utilizes state-of-the-art models and frameworks.
• High-Performance Computing: Initially deployed and tested on an NVIDIA RTX 2080 Ti GPU, though not a mandatory requirement.

Contributing

We welcome contributions from the community. Please submit your pull requests to the main branch and ensure your code adheres to the existing style.