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run_transformer_batch_prediction.py requires label2idx.json file for input, but this file is missing from provided mimic-III trained models #7

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stewacad000 opened this issue Dec 15, 2022 · 1 comment
Open

run_transformer_batch_prediction.py requires label2idx.json file for input, but this file is missing from provided mimic-III trained models #7

stewacad000 opened this issue Dec 15, 2022 · 1 comment

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@stewacad000
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I am trying to run the mimic-III pretrained BERT model with the ClinicalTransformerNER package but the package file run_tranformer_batch_prediction.py requires a file named label2idx.json, which is not contained in the model zip file. Is this file created in a step that I may have missed?
@bugface
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bugface commented Dec 24, 2022

see uf-hobi-informatics-lab/ClinicalTransformerNER#13

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@bugface @stewacad000