--- a/README.md +++ b/README.md @@ -1,50 +1,50 @@ -# Knowledge Graph Neural Network -This is our implementation for the paper -> Xuan Lin, Zhe Quan, Zhi-Jie Wang, Tengfei Ma and Xiangxiang Zeng. KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction. IJCAI' 20 accepted. - -<img align="center" src="Figure1.png"> -Figure 1 shows the overview of KGNN. It takes the parsed DDI matrix and knowledge graph obtained from preprocessing of dataset as the input. It outputs the interaction value for the drug-drug pair. - -# Requirement -To run the code, you need the following dependencies: -* Python == 3.6.6 -* Keras == 2.3.0 -* Tensorflow == 1.13.1 -* scikit-learn == 0.22 - -# Installation -You can create a virtual environment using [conda](https://github.com/conda/conda). -```bash -conda create -n kgnn python=3.6.6 -source activate kgnn -git clone https://github.com/xzenglab/KGNN.git -cd KGNN -pip install -r requirement.txt -``` - -# Dataset -We just provide the preprocessed KG from KEGG-drug dataset owing to the size limited. And you can directly download the original DrugBank dataset ([V5.1.4](https://www.drugbank.ca/releases/5-1-4)). Note that the construction of KG please refer to [Bio2RDF](https://github.com/bio2rdf/bio2rdf-scripts/wiki) tool in detail. - -# Usage -```bash -python run.py -``` - -# Citation -```bash -@inproceedings{ijcai2020-380, - title = {KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction}, - author = {Lin, Xuan and Quan, Zhe and Wang, Zhi-Jie and Ma, Tengfei and Zeng, Xiangxiang}, - booktitle = {Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, {IJCAI-20}}, - publisher = {International Joint Conferences on Artificial Intelligence Organization}, - editor = {Christian Bessiere}, - pages = {2739--2745}, - year = {2020}, - month = {7}, - note = {Main track}, - doi = {10.24963/ijcai.2020/380}, - url = {https://doi.org/10.24963/ijcai.2020/380}, -} -``` - -For any clarification, comments, or suggestions please create an issue or contact [Jacklin](Jack_lin@hnu.edu.cn). +# Knowledge Graph Neural Network +This is our implementation for the paper + Xuan Lin, Zhe Quan, Zhi-Jie Wang, Tengfei Ma and Xiangxiang Zeng. KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction. IJCAI' 20 accepted. + +<img align="center" src="https://github.com/xzenglab/KGNN/blob/master/Figure1.png?raw=true"> +Figure 1 shows the overview of KGNN. It takes the parsed DDI matrix and knowledge graph obtained from preprocessing of dataset as the input. It outputs the interaction value for the drug-drug pair. + +# Requirement +To run the code, you need the following dependencies: +* Python == 3.6.6 +* Keras == 2.3.0 +* Tensorflow == 1.13.1 +* scikit-learn == 0.22 + +# Installation +You can create a virtual environment using [conda](https://github.com/conda/conda). +```bash +conda create -n kgnn python=3.6.6 +source activate kgnn +git clone https://github.com/xzenglab/KGNN.git +cd KGNN +pip install -r requirement.txt +``` + +# Dataset +We just provide the preprocessed KG from KEGG-drug dataset owing to the size limited. And you can directly download the original DrugBank dataset ([V5.1.4](https://www.drugbank.ca/releases/5-1-4)). Note that the construction of KG please refer to [Bio2RDF](https://github.com/bio2rdf/bio2rdf-scripts/wiki) tool in detail. + +# Usage +```bash +python run.py +``` + +# Citation +```bash +@inproceedings{ijcai2020-380, + title = {KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction}, + author = {Lin, Xuan and Quan, Zhe and Wang, Zhi-Jie and Ma, Tengfei and Zeng, Xiangxiang}, + booktitle = {Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, {IJCAI-20}}, + publisher = {International Joint Conferences on Artificial Intelligence Organization}, + editor = {Christian Bessiere}, + pages = {2739--2745}, + year = {2020}, + month = {7}, + note = {Main track}, + doi = {10.24963/ijcai.2020/380}, + url = {https://doi.org/10.24963/ijcai.2020/380}, +} +``` + +For any clarification, comments, or suggestions please create an issue or contact [Jacklin](Jack_lin@hnu.edu.cn).