by cambridgeltl
Open source · 540k downloads · 67 likes
SapBERT from PubMedBERT fulltext is an artificial intelligence model specialized in the semantic representation of biomedical terms. It generates embeddings (numerical vectors) from medical entity names, enabling the capture of their semantic relationships and facilitating their comparison or grouping. This model stands out for its ability to understand and encode complex medical concepts, even when they are expressed differently, thanks to training on data from the UMLS. It is particularly useful for applications such as terminology normalization, biomedical information retrieval, or clinical data analysis. Its cross-lingual approach and integration with PubMedBERT make it a powerful tool for healthcare professionals and medical researchers.
datasets:
[news] A cross-lingual extension of SapBERT will appear in the main onference of ACL 2021!
[news] SapBERT will appear in the conference proceedings of NAACL 2021!
SapBERT by Liu et al. (2020). Trained with UMLS 2020AA (English only), using microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext as the base model.
The input should be a string of biomedical entity names, e.g., "covid infection" or "Hydroxychloroquine". The [CLS] embedding of the last layer is regarded as the output.
The following script converts a list of strings (entity names) into embeddings.
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.
@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.",
}