This repository contains the source code to reproduce the experiments conducted in Weber et al. "HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition".
To reproduce the experiments the following steps have to be performed:
- Setup environment and install necessary packages / models:
pip install -r requirements.txt
chmod u+x install_scispacy_models.sh
./install_scispacy_models.sh
- Download and prepare the evaluation corpora
python download_and_prepare_corpora.py
- Run experiments
chmod u+x run_experiments.sh
./run_experiments.sh
Note for the competitors HUNER and MISC we provide the annotations in annotations
.
Please cite the following paper when using HunFlair:
@article{weber2020hunflair,
title={HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition},
author={Weber, Leon and S{\"a}nger, Mario and M{\"u}nchmeyer, Jannes and Habibi, Maryam and Leser, Ulf and Akbik, Alan},
journal={arXiv preprint arXiv:2008.07347},
year={2020}
}