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Train_test_validate function does not work for nci60 dataset #322

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jjacobson95 opened this issue Feb 4, 2025 · 2 comments
Open

Train_test_validate function does not work for nci60 dataset #322

jjacobson95 opened this issue Feb 4, 2025 · 2 comments
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@jjacobson95
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jjacobson95 commented Feb 4, 2025

The train_test_validate function currently fails when it encounters an NaN value such as in nci60.

Image Image

Edit - for more info: This is still present even after dropping NaN values from each datatype using the following command:

cd_nci60.experiments.dropna(inplace = True)
cd_nci60.transcriptomics.dropna(inplace = True)
cd_nci60.mutations.dropna(inplace = True)
cd_nci60.copy_number.dropna(inplace = True)
cd_nci60.drug_descriptors.dropna(inplace = True)
cd_nci60.drugs.dropna(inplace = True)
cd_nci60.proteomics.dropna(inplace = True)
cd_nci60.samples.dropna(inplace = True)
@jjacobson95 jjacobson95 added bug Something isn't working package labels Feb 4, 2025
@ymahlich
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ymahlich commented Feb 4, 2025

This is a dataset problem. Those NaNs are generated because there is no fit_auc for certain entries in the nci60.experiments object. See attached screenshot.

Image

This needs to be either fixed on the dataset / build side or, we need to exclude those experiments (which should probably also happen on the build side of things)

@sgosline
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This will be fixed when #340 is fixed.

@jjacobson95 jjacobson95 added this to the v2.2 milestone May 8, 2025
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