Dataset Specifications for MoleculeSTM

We provide the raw dataset (after preprocessing) at this Hugging Face link. Or you can download them by running python download_datasets.py.

1. Pretraining Dataset: PubChemSTM

For PubChemSTM, please note that we can only release the chemical structure information. If you need the textual data, please follow our preprocessing scripts.

2. Downstream Datasets

Please refer to the following for three downstream tasks:

• DrugBank_data for zero-shot structure-text retrieval
• ZINC250K_data for space alignment (step 1 in editing)
• Editing_data for zero-shot text-guided (step 2 in editing)
  • single_multi_property_SMILES.txt for single-objective, multi-objective, binding-affinity-based, and drug relevance editing
  • neighbor2drug for neighborhood searching for patent drug molecules
  • ChEMBL_data for binding editing
• MoleculeNet_data for molecular property prediction

Checkpoints Specifications for MoleculeSTM

We provide the optimal checkpoints at this Hugging Face link. Or you can download them by running python download_checkpoints.py.