pytorch jax bert feature-extraction arxiv:2010.11784 transformers
---
language: en

tags:
- biomedical
- lexical-semantics

datasets:
- UMLS
**[news]** A cross-lingual extension of SapBERT will appear in the main onference of **ACL 2021**! <br>
**[news]** SapBERT will appear in the conference proceedings of **NAACL 2021**!

### SapBERT-PubMedBERT
SapBERT by [Liu et al. (2020)](https://arxiv.org/pdf/2010.11784.pdf). Trained with [UMLS](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html) 2020AA (English only), using [microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) as the base model. Please use the mean-pooling of the output as the representation.

### Citation
```bibtex
@inproceedings{liu-etal-2021-self,
    title = "Self-Alignment Pretraining for Biomedical Entity Representations",
    author = "Liu, Fangyu  and
      Shareghi, Ehsan  and
      Meng, Zaiqiao  and
      Basaldella, Marco  and
      Collier, Nigel",
    booktitle = "Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies",
    month = jun,
    year = "2021",
    address = "Online",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/2021.naacl-main.334",
    pages = "4228--4238",
    abstract = "Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologies with 4M+ concepts. In contrast with previous pipeline-based hybrid systems, SapBERT offers an elegant one-model-for-all solution to the problem of medical entity linking (MEL), achieving a new state-of-the-art (SOTA) on six MEL benchmarking datasets. In the scientific domain, we achieve SOTA even without task-specific supervision. With substantial improvement over various domain-specific pretrained MLMs such as BioBERT, SciBERTand and PubMedBERT, our pretraining scheme proves to be both effective and robust.",
}
```
