| --- | |
| language: multilingual | |
| tags: | |
| - biomedical | |
| - lexical-semantics | |
| - cross-lingual | |
| 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-XLMR | |
| SapBERT [(Liu et al. 2020)](https://arxiv.org/pdf/2010.11784.pdf) trained with [UMLS](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html) 2020AB, using [xlm-roberta-base](https://huggingface.co/xlm-roberta-base) as the base model. Please use [CLS] as the representation of the input. | |
| #### Extracting embeddings from SapBERT | |
| The following script converts a list of strings (entity names) into embeddings. | |
| ```python | |
| import numpy as np | |
| import torch | |
| from tqdm.auto import tqdm | |
| from transformers import AutoTokenizer, AutoModel | |
| tokenizer = AutoTokenizer.from_pretrained("cambridgeltl/SapBERT-from-PubMedBERT-fulltext") | |
| model = AutoModel.from_pretrained("cambridgeltl/SapBERT-from-PubMedBERT-fulltext").cuda() | |
| # replace with your own list of entity names | |
| all_names = ["covid-19", "Coronavirus infection", "high fever", "Tumor of posterior wall of oropharynx"] | |
| bs = 128 # batch size during inference | |
| all_embs = [] | |
| for i in tqdm(np.arange(0, len(all_names), bs)): | |
| toks = tokenizer.batch_encode_plus(all_names[i:i+bs], | |
| padding="max_length", | |
| max_length=25, | |
| truncation=True, | |
| return_tensors="pt") | |
| toks_cuda = {} | |
| for k,v in toks.items(): | |
| toks_cuda[k] = v.cuda() | |
| cls_rep = model(**toks_cuda)[0][:,0,:] # use CLS representation as the embedding | |
| all_embs.append(cls_rep.cpu().detach().numpy()) | |
| all_embs = np.concatenate(all_embs, axis=0) | |
| ``` | |
| For more details about training and eval, see SapBERT [github repo](https://github.com/cambridgeltl/sapbert). | |
| ### Citation | |
| ```bibtex | |
| @inproceedings{liu2021learning, | |
| title={Learning Domain-Specialised Representations for Cross-Lingual Biomedical Entity Linking}, | |
| author={Liu, Fangyu and Vuli{\'c}, Ivan and Korhonen, Anna and Collier, Nigel}, | |
| booktitle={Proceedings of ACL-IJCNLP 2021}, | |
| month = aug, | |
| year={2021} | |
| } | |
| ``` |