main_PCQM4.py
--train_subset: Whether to use only a fraction of train data
--gnn: select the gnn type
If you run main_PCQM4.py, there will be a preprocessing stage. After you run the code, you will find dataset/pcqm4m-v2 folder.
Please save this folder. If there is a dataset/pcqm4m-v2 folder, the preprocessing stage will be skipped.
Please do not pretrain on Colab notebook. The file is too big.
main_bbbp.py
train/val/test dataset is already in the folder.
There was a problem when installing ogb before the torch-geometry. Please install in order by torch-geometry > rdkit > ogb
import os
import torch
os.environ['TORCH'] = torch.__version__
print(torch.__version__)
!pip install -q torch-scatter -f https://data.pyg.org/whl/torch-${TORCH}.html
!pip install -q torch-sparse -f https://data.pyg.org/whl/torch-${TORCH}.html
!pip install -q git+https://github.com/pyg-team/pytorch_geometric.git
!pip install rdkit-pypi
!pip install ogb