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Improving Information Extraction from Pathology Reports using Named Entity Recognition

License: GNU General Public License v3.0

Jupyter Notebook 44.47% Shell 0.86% Python 54.67%
medical-application named-entity-recognition nlp-machine-learning breast-cancer cancer-data pathology-report

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andersoneduardo taylor-kelce

pathology_extraction's Issues

Where are the models in your code?

to parse a txt file

outputs = ner.extract_entity_from_report(
'data/example_diagnosis.negation_1.txt',
weights_path ='models/model.all_augmentations.pt'
)

Here, you didn't mention anything about 'models/model.all_augmentations.pt' . while running your run.sh code I am having the error below ,

FileNotFoundError Traceback (most recent call last)
in <cell line: 2>()
1 # basic example
----> 2 basic_output = ner.extract_entity_from_text(
3 "a. breast, left 11:00 o'clock 5cm from the nipple - ductal carcinoma in situ",
4 weights_path ='models/model.all_augmentations.pt'
5 )

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