Temporary repository for KEDD

⚠️This repository is still under development. Unexpected errors could occur when running the code.

The codebase is built on OpenBioMed. We are endavouring for a future release that incorporates the revised KEDD model.

To reproduce KEDD, install BMKG and put it under assets/kg/.

DTI

Yamanishi08 and BMKG_DTI can download from here. The 2 datasets should put under datasets/dti/.

To run KEDD for drug-target interaction, use the following command:

bash scripts/dti/train_kedd.sh

DP

Download MoleculeNet datasets here, unzip the file, and put the dataset fold under datasets/dp/. You can use the following commands from within OpenBioMed/:

wget http://snap.stanford.edu/gnn-pretrain/data/chem_dataset.zip
unzip chem_dataset.zip
mkdir -p datasets/dp
mv dataset datasets/dp/moleculenet
rm chem_dataset.zip

After downloading and unzipping, you should remove all the processed/ directories of 8 datasets in the dataset/ folder.

To run KEDD for drug property prediction, use the following command:

bash scripts/dp/train_kedd.sh

DDI

Luo's dataset is available here. Put them under the datasets/ddi/ folder.

To run KEDD for drug-drug interaction prediction, use the following command:

bash scripts/ddi/train_kedd.sh

PPI

The SHS27k and SHS148k datasets are available here. Put them under datasets/ppi/

To run KEDD for protein-protein interaction prediction, use the following command:

bash scripts/ppi/run.sh