SapBERT-from-PubMedBERT-fulltext EU AI Act Compliance Profile

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). Trained with UMLS 2020AA (English only), using microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext as the base model.

Expected input and output

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.

Extracting embeddings from SapBERT

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_e

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