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stanfordmlgroup / chexpert-labeler

CheXpert NLP tool to extract observations from radiology reports.
MIT License
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Compatibility with NegBio #5

Closed cshivade closed 5 years ago

cshivade commented 5 years ago

Hello, It seems the NegBio underwent significant changes recently. This results in a bunch of errors. Can you please the update the repo to absorb those?

alistairewj commented 5 years ago

Can you provide any information about what the errors are? Traceback, etc?

cshivade commented 5 years ago

Thanks for the response. Specifically the following calls have changed in NegBio:

Line 28 in load.py Lines 100 to 104 in stages/classify.py

cshivade commented 5 years ago

I tried merging the pull request here and running it at my end. It addresses the issues in my prebious comment. It does throws a different error but does generate the output file labeled_reports.csv. Can you please add the expected output file for the sample_reports.csv to this repo? That would help users verify if their output is correct. Thanks !

jirvin16 commented 5 years ago

Great to hear! I've added the sample output file and seems the original issue is resolved, so closing this.