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DDs(Drug Drug synergy)

中文版本 English Version

Background

Drug combinations, also known as combinatorial therapy, are frequently prescribed to treat patients with complex disease. Graph convolutional network(GCN) can be used to predict drug-drug synergy by intergrating multiple biological networks.

Datasets

Drug-drug synergy information and drug physi-chemical features can be put under data folder.

ddi

mkdir data && cd data && mkdir DDI && wget "http://www.bioinf.jku.at/software/DeepSynergy/labels.csv"

dti

cd data && wget "https://baidu-nlp.bj.bcebos.com/PaddleHelix/datasets/drug_synergy_datasets/dti.tgz" && tar xzvf dti.tgz

ppi

cd data && wget "https://baidu-nlp.bj.bcebos.com/PaddleHelix/datasets/drug_synergy_datasets/ppi.tgz" && tar xzvf ppi.tgz

drug features

cd data && wget "https://baidu-nlp.bj.bcebos.com/PaddleHelix/datasets/drug_synergy_datasets/drug_feat.tgz" && tar xzvf drug_feat.tgz

Instructions

For illustration, we provide a python script train.py. Its usage is:

CUDA_VISIBLE_DEVICES=0 python3 train.py 
                         --ddi ./data/DDI/DDs.csv
                         --dti ./data/DTI/drug_protein_links.tsv
                         --ppi ./data/PPI/protein_protein_links.txt
                         --d_feat ./data/all_drugs_name.fet
                         --epochs 10
                         --num_graph 10
                         --sub_neighbours 10 10
                         --cuda

Notice that if you only have CPU machine, just remove --cuda.

Reference

RGCN

@article{jiang2020deep, title={Deep graph embedding for prioritizing synergistic anticancer drug combinations}, author={Jiang, Peiran and Huang, Shujun and Fu, Zhenyuan and Sun, Zexuan and Lakowski, Ted M and Hu, Pingzhao}, journal={Computational and structural biotechnology journal}, volume={18}, pages={427--438}, year={2020}, publisher={Elsevier} }