Features for the antibiotics checkpoints
See original GitHub issueHi,
I want to make predictions using the Antibiotics checkpoints provided here: http://chemprop.csail.mit.edu/checkpoints
I do this by running the following command:
chemprop_predict --test_path data/smiles.csv --checkpoint_dir checkpoint --preds_path test_preds.csv --features_generator rdkit_2d_normalized --no_features_scaling
Am I using the correct features generator for this checkpoint?
In addition, when running predictions, I get the following warning:
Warning: Pretrained parameter "encoder.encoder.cached_zero_vector" cannot be found in model parameters.
Warning: Pretrained parameter "encoder.encoder.W_i.weight" cannot be found in model parameters.
Warning: Pretrained parameter "encoder.encoder.W_h.weight" cannot be found in model parameters.
Warning: Pretrained parameter "encoder.encoder.W_o.weight" cannot be found in model parameters.
Warning: Pretrained parameter "encoder.encoder.W_o.bias" cannot be found in model parameters.
Loading pretrained parameter "ffn.1.weight".
Loading pretrained parameter "ffn.1.bias".
I wonder if this something I should be worried about.
Thanks!
M
Issue Analytics
- State:
- Created 3 years ago
- Comments:12 (7 by maintainers)
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We just fixed the features scaling bug. You should now be able to run:
python scripts/save_features.py --data_path data/smiles.csv --save_path data/smiles_features.npz --features_generator rdkit_2d_normalized
python predict.py --test_path data/smiles.csv --checkpoint_dir checkpoint --preds_path test_preds.csv --features_path data/smiles_features.npz --no_features_scaling
(This will produce the exact same predictions you had before, the only difference is that you can correctly set the
--no_features_scaling
option now).@miquelduranfrigola - no worries at all, am happy that it all works now. This also reminded me that I wanted to write a bug report to the descriptastorus team regarding all the warning, which I now finally did - thanks for the reminder!