Features for the antibiotics checkpoints

Hi,

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

[hesther]

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).

[hesther]

@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!