Comments (1)
I'm sorry to reply late.
When fine-tune turn, you need to put your favorite SMILES set into ./dataset/
directory. (In this context, your SMILES set named your-favorite-smiles.smi
.)
And edit line like: "finetune_data_filename": "./datasets/your-favorite-smiles.smi"
, in ./configs/LSTMChem_config.json
.
Finally, run finetune.py
, you get newly generated SMILES in WantsChems.smi
.
If you don't have relevant SMILES set for fine-tune, please get wet data in your organization.
Or, please remake ./datasets/datasets.smi
, because train dataset chemicals in datasets.smi
were extracted from whole ChEMBL DataBase on condition that chemical shows IC50, EC50, Ki < nM.
For example, if you want to generate new kinase inhibitor, care must be taken you may avoid kinase inhibitor when you extract from ChEMBL DataBase. And make extracted SMILES set to train dataset and make avoided kinase inhibitor SMILES set for test set (fine-tune set).
Perhaps, you may not need this steps. Train NN ./datasets/datasets.smi
of this repo and fin-tune kinase inhibitor SMILES that is extracted from ChEMBL DB.
If you are not familiar with handling ChEMBL DB, this article is useful.
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Related Issues (16)
- where to get finetune's corpors? HOT 2
- different result about dataset query HOT 1
- Fragment growing' implemented in code? HOT 1
- AttributeError: 'NoneType' object has no attribute 'shape' HOT 6
- Run on only 1 GPU, how to run on all the 4 available GPUs HOT 1
- Batchsize in Finetuning is irrelevant HOT 1
- About GPU memory usage? HOT 1
- Issue while importing functions
- GPU for Tensorflow
- How I can get the file named ' LSTM_Chem-22-0.42.hdf5' HOT 1
- How I can get the file 'LSTM_Chem-22-0.42.hdf5'? HOT 8
- RuntimeError: dictionary changed size during iteration HOT 2
- Please update the dataset link to the one provided here! HOT 1
- Could you public the saved model for tranfer learning? HOT 1
- AttributeError: 'NoneType' object has no attribute 'shape'
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