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stanfordmlgroup / chexpert-labeler

CheXpert NLP tool to extract observations from radiology reports.
MIT License
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Running CheXpert labeler on Google Colab? #38

Open PabloMessina opened 1 year ago

PabloMessina commented 1 year ago

Hi. I'm trying to run CheXpert labeler on Google Colab, but I'm unable to generate labels for the sample_reports.csv. You can find my attempt here: https://colab.research.google.com/drive/17ABqvLdJd5GcuxRGPMgQwS5HqtWSIcww?usp=sharing

Do you have, or at least know how to implement, a minimal working example of CheXpert labeler running on colab?

Thanks in advance, Pablo

jirvin16 commented 1 year ago

I'm not aware of a working example in Colab. Instead of running a shell command you could try importing the label function and running it from within Colab instead?

PabloMessina commented 1 year ago

Do you mean using Colab's Python instead of the Python that comes with conda? What should I do instead of running conda env create -f environment.yml?

jirvin16 commented 1 year ago

I mean something like:

from chexpert_labeler.label import label

label(...)
njan-creative commented 1 year ago

I am also trying to setup on Google colab without success.. Were you able to get it to work ?