Installation

1. Clone repository.

git clone https://github.com/BML-cbnu/DrugGCN
cd DrugGCN

2. Install the requirments.

pip install -r requirements.txt

GCN configuration

Input:

n of samples
p of features
d of drugs

Gene_data: (n * p) Gene Expression matrix.
PPI_data: (p * p) PPI Network matrix.
Respond_data: (n * d) Drug-Respond matrix.

F: Number of features.
K: List of polynomial orders. (Filter sizes)
p: Pooling size.

Output:

Y_pred : y * d ( y is a test set of n )

Reproducing our experiments

Edit the Configuration file to produce experiments differently.

vim config.yaml

Run experiments.

python GraphCNN.py config.yaml
python Compare.py config.yaml