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Context: NER (named entity recognition) and RE (relation extraction) from sentences obtained from radiology reports (medical text).

There is a BERT-based model from HuggingFace I would like to use for this: https://huggingface.co/microsoft/BiomedVLP-CXR-BERT-specialized

I already have experience using this model for simple tasks, such as comparing vector representations of sentences and classifying sentences. I've already written scripts for fine-tuning and evaluating this model on said tasks.

Now I want to do NER and RE using this model. I plan to use the following dataset for that purpose: https://physionet.org/content/radgraph/1.0.0/

Here is a figure from the paper:

enter image description here

Implementation-wise, I foresee the following challenges:

  • I need to obtain the token representations from the last layer of CXR-BERT.
  • I need to add a layer for NER on top of those tokens.
  • I need to represent entities.
  • I need to add a layer for RE given the representations of a pair of entities.
  • I need to convert the raw dataset into labels for NER and RE somehow, making sure that the labels are consistent with the tokenizer of CXR-BERT.
  • I need to define some appropriate loss function(s) to train the model. I've read that CRF (conditional random fields) are useful in this case, but I have zero experience using them.

I need help figuring out a way of implementing (coding) all of the points above. Ideally I'd like to make reasonable design decisions based on what usually works well for people doing NER/RE (I don't have much experience with those tasks, this is my first time).

Any suggestions and insights will be much appreciated.

Thanks a lot in advance.

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