README.md

HunFlair experiments

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".

Usage

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.}

Citing HunFlair

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}
}