usage/README.md

Knowledge-Rich Self-Supervision (KRISS) for Biomedical Entity Linking

Usage code for the entity linking approach described in the following paper:

@article{kriss,
  author = {Sheng Zhang, Hao Cheng, Shikhar Vashishth, Cliff Wong, Jinfeng Xiao, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon},
  title = {Knowledge-Rich Self-Supervision for Biomedical Entity Linking},
  year = {2021},
  url = {https://arxiv.org/abs/2112.07887},
  eprinttype = {arXiv},
  eprint = {2112.07887},
}

https://arxiv.org/pdf/2112.07887.pdf

Usage of KRISS for Entity Linking

Here, we use the MedMentions data to show you how to 1) generate prototype embeddings, and 2) run entity linking.

(We are currently unable to release the self-supervised mention examples, because they requires UMLS and PubMed licenses.)

1. Create conda environment and install requirements

conda create -n kriss -y python=3.8 && conda activate kriss
pip install -r requirements.txt

2. Download the MedMentions dataset

git clone https://github.com/chanzuckerberg/MedMentions.git

3. Generate prototype embeddings

python generate_prototypes.py

4. Run entity linking

python run_entity_linking.py