How to use the pretrained UMLSBERT for NER task prediction

[kswamy15]

This is not a real issue about this repo. But want to know how to use the UmlsBERT for NER prediction on a bunch of clinical text - without any fine tuning or training of the pre-trained model. Is there a jupyter notebook that points to using the pre-trained model on a batch of clinical text for NER prediction?

[gmichalo]

Thank you for your interest in UmlsBert. You can find a Jupiter notebook for the NER task in : https://github.com/gmichalo/UmlsBERT/blob/master/experiments/NER_task.ipynb

where we have an example-code for UmlsBert and the standard Bert architecture (bert, biobert, bio_clinicalbert).