The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.
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Fixing is_class Determination in featurization.py #354
Hi, when running a multitask classification model, the NaNs in out_vals were not being replaced with zeros in the make_weights function in featurization.py. The root cause was that the is_class variable was incorrectly determined based on params.model_type instead of params.prediction_type, causing it to always return False and consequently not replacing the NaNs in out_vals.
I corrected the is_class assignments in featurization.py to ensure they reflect the prediction_type. I ran the multitask classification tests for atomsci/ddm/test/integrative/delaney_Panel, which initially passed even without the changes. However, after closer inspection, I found that there were no NaNs in the response columns of test data, which is why the tests passed. When I introduced NaNs into the response columns, the models failed to train with the old code. After applying the is_class fix, the models trained successfully.
Hi, when running a multitask classification model, the NaNs in
out_vals
were not being replaced with zeros in the make_weights function infeaturization.py
. The root cause was that theis_class
variable was incorrectly determined based onparams.model_type
instead ofparams.prediction_type
, causing it to always return False and consequently not replacing the NaNs inout_vals
. I corrected theis_class
assignments infeaturization.py
to ensure they reflect theprediction_type
. I ran the multitask classification tests foratomsci/ddm/test/integrative/delaney_Panel
, which initially passed even without the changes. However, after closer inspection, I found that there were no NaNs in the response columns of test data, which is why the tests passed. When I introduced NaNs into the response columns, the models failed to train with the old code. After applying theis_class
fix, the models trained successfully.