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Enhancing Clinical BERT Embedding using a Biomedical Knowledge Base

This repo provides two pretrained models for paper Enhancing Clinical BERT Embedding using a Biomedical Knowledge Base by Boran Hao, Henghui Zhu and Ioannis Ch. Paschalidis. The models are originally trained using Tensorflow and has been converted to PyTorch huggingface transformers models.

Quick tour

To use our pretrained models, download the models from the release pages and unzip them. A sample code for using the models are shown as follows. The code is based on tranformers==3.3.0 and it should works for tranformers version 3.x. For tranformers version 2.x, you need to change the way to perform tokenization.

from transformers import AutoModel, AutoTokenizer

model = AutoModel.from_pretrained('./clinical_kb_albert')
tokenizer = AutoTokenizer.from_pretrained('./clinical_kb_albert')

inputs = tokenizer("Hello world!", return_tensors="pt")
outputs = model(**inputs)