README.md

metadata

language:
  - en
  - es
  - fr
  - nl
  - de
  - fi
  - ru
  - tr
  - ko
  - zh
  - ja
  - th
  - pt
  - it
  - sv
  - hu
  - pl
  - et
  - hr
  - uk
  - el
  - da
  - he
tags:
  - biomedical
  - bionlp
  - entity linking
  - embedding
  - bert

A multilingual BERGAMOT: Biomedical Entity Representation with Graph-Augmented Multi-Objective Transformer model with pre-trained on UMLS (version 2020AB) using a Graph Attention Network (GAT) encoder.

For technical details see our NAACL 2024 paper.

Here is the poster of our paper.

For pretraining code see our github: https://github.com/Andoree/BERGAMOT.

Citation

@inproceedings{sakhovskiy-et-al-2024-bergamot,
    title = "Biomedical Entity Representation with Graph-Augmented Multi-Objective Transformer",
    author = "Sakhovskiy, Andrey and Semenova, Natalia and Kadurin, Artur and Tutubalina, Elena",
    booktitle = "Findings of the Association for Computational Linguistics: NAACL 2024",
    month = jun,
    year = "2024",
    address = "Mexico City, Mexico",
    publisher = "Association for Computational Linguistics",
  }