high_level.md

High Level Models

2021

• GraphSynergy: Network Inspired Deep Learning Model for Anti-Cancer Drug Combination Prediction (ResearchSquare 2021)

  • Jiannan Yang, Zhongzhi Xu, William Wu, Qian Chu, Qingpeng Zhang
  • [Paper]
  • [Tensorflow]

• Relation Matters in Sampling: A Scalable Multi-Relational Graph Neural Network for Drug-Drug Interaction Prediction (BioArxiv 2021)

  • Arthur Feeney, Rishabh Gupta, Veronika Thost, Rico Angell, Gayathri Chandu, Yash Adhikari, Tengfei Ma
  • [Paper]

• Drug-Drug Interaction Prediction with Wasserstein Adversarial Autoencoder-Based Knowledge Graph Embeddings (Bioinformatics 2021)

  • Yuanfei Dai, Chenhao Guo, Wenzhong Guo, Carsten Eickhoff
  • [Paper]

• Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks (BioArxiv 2021)

  • Shichao Liu, Yang Zhang, Yuxin Cui, Yang Qiu, Yifan Deng, Wen Zhang, Zhongfei Zhang
  • [Paper]
  • [Python TensorFlow]

• SumGNN: Multi-Typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization (Bioinformatics 2021)

  • Yue Yu, Kexin Huang, Chao Zhang, Lucas M Glass, Jimeng Sun, Cao Xiao
  • [Paper]
  • [Python PyTorch]

2020

• DTF: Deep Tensor Factorization for Predicting Anticancer Drug Synergy (IJCAI 2020)

  • Zexuan Sun, Shujun Huang, Peiran Jiang, Pingzhao Hu
  • [Paper]
  • [PyTorch]

• GoGNN: Graph of Graphs Neural Network for Predicting Structured Entity Interactions (IJCAI 2020)

  • Hanchen Wang, Defu Lian, Ying Zhang, Lu Qin, Xuemin Lin
  • [Paper]
  • [PyTorch]

• SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks (Nature Scientific Reports 2020)

  • Kexin Huang, Cao Xiao, Lucas Glass, Marinka Zitnik, Jimeng Sun
  • [Paper]
  • [PyTorch]

• KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction (AAAI 2020)

  • Xuan Lin, Zhe Quan, Zhi-Jie Wang, Tengfei Ma, Xiangxiang Zeng
  • [Paper]
  • [PyTorch]

• SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks (Nature Scientific Reports 2020)

  • Kexin Huang, Cao Xiao, Lucas Glass, Marinka Zitnik, Jimeng Sun
  • [Paper]
  • [PyTorch]

2019

• Tri-graph Information Propagation for Polypharmacy Side Effect Prediction (NeurIPS 2019)
  • Hao Xu, Shengqi Sang, and Haiping Lu
  • [Paper]
  • [PyTorch]

2018

• Modeling Polypharmacy Side Effects with Graph Convolutional Networks (NeurIPS 2019)

  • Marinka Zitnik, Monica Agrawal, Jure Leskovec
  • [Paper]
  • [Tensorflow]

• Adverse Drug Reaction Predictions Using Stacking Deep Heterogeneous Information Network Embedding Approach (MDPI 2018)

  • Baofang Hu, Hong Wang, Lutong Wang and Weihua Yuan
  • [Paper]

• Knowledge Graph Completion to Predict Polypharmacy Side Effects (MDPI 2018)

  • Baofang Hu, Hong Wang, Lutong Wang and Weihua Yuan
  • [Paper]

• Knowledge Graph Completion to Predict Polypharmacy Side Effects (DILS 2018)

  • Brandon Malone, Alberto García-Durán, Mathias Niepert
  • [Paper]