base environment: python 3.7, cuda 10.2, pytorch 1.6, torchvision 0.7.0, tensorboardX 2.1
pytorch-geometric:
pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.6.0+cu102.html
pip install torch-sparse -f https://pytorch-geometric.com/whl/torch-1.6.0+cu102.html
pip install torch-cluster -f https://pytorch-geometric.com/whl/torch-1.6.0+cu102.html
pip install torch-spline-conv -f https://pytorch-geometric.com/whl/torch-1.6.0+cu102.html
pip install torch-geometric
Training codes in gnn_train.py, and the run script in run.py.
STRING(we use Homo sapiens subset):
- PPI: https://stringdb-static.org/download/protein.actions.v11.0/9606.protein.actions.v11.0.txt.gz
- Protein sequence: https://stringdb-static.org/download/protein.sequences.v11.0/9606.protein.sequences.v11.0.fa.gz Dataset： SHS27k and SHS148k:
- http://yellowstone.cs.ucla.edu/~muhao/pipr/SHS_ppi_beta.zip