EMPHCN

Install

To use EMPHCN you must make sure that your python version is greater than 3.7. If you don’t know the version of python you can check it by:

python
>>> import platform
>>> platform.python_version()
'3.7.13'

Environment Requirement

The required packages are as follows:

• PyTorch==1.7.0
• PyTorch-Geometric==1.5.0
• numpy==1.19.2
• scikit-learn==0.21.3

Data availability

we provide the compressed format of the datasets T1,T2 used in the paper. If you want to use them, please download and unzip the "datasets.zip" file.

T1 dataset

drug-disease associations in the T1 dataset were selected from ZhangDDA

• sim_pathway.txt: pathway similarity matrix
• sim_target.txt: target similarity matrix
• sim_rr.txt:drug-drug interactions similarity matrix
• sim_enzyme.txt:drug enzymes similarity matrix
• spilt_x.mat:10 cross validation index
• d_p.pt:drug-protein associations
• r_p.pt:diseas-protein associations
• p_p.pt:protein-protein associations

T2 dataset

drug-disease associations in the T2 dataset were selected from repoDB

• sim_chemical.txt: chemical similarity matrix
• sim_clinical.txt: clinical similarity matrix
• sim_drugside_effect’s .txt:drugside_effect’s similarity matrix
• spilt_x.mat:10 cross validation index
• d_p.pt:drug-protein associations
• r_p.pt:diseas-protein associations
• p_p.pt:protein-protein associations

Usage

Quick start

We use the dataset T1 to illustrate an example. You should first unzip the "code.zip" file and unzip the "datasets.zip" file. Then you just need to go to the "code" file directory and run the following code:

python main.py --dataset T1

T2 dataset

python main.py --dataset folder_name