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usage/README.md

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-# Knowledge-Rich Self-Supervision (KRISS) for Biomedical Entity Linking
-
-Usage code for the entity linking approach described in the following paper:
-```bibtex
-@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](https://arxiv.org/pdf/2112.07887.pdf)
-
-## Usage of KRISS for Entity Linking
-
-Here, we use the [MedMentions](https://github.com/chanzuckerberg/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
-```bash
-conda create -n kriss -y python=3.8 && conda activate kriss
-pip install -r requirements.txt
-```
-
-### 2. Download the MedMentions dataset
-
-```bash
-git clone https://github.com/chanzuckerberg/MedMentions.git
-```
-
-### 3. Generate prototype embeddings
-```bash
-python generate_prototypes.py
-```
-
-### 4. Run entity linking
-```bash
-python run_entity_linking.py
-```