low_level.md

Low Level Models

2021

• GCN-BMP: Investigating graph representation learning for DDI prediction task

  • Xin Chena, Xien Liua, Ji Wu
  • [Paper]

• Synergistic Drug Combination Prediction by Integrating Multiomics Data in Deep Learning Models (Translational Bioinformatics for Therapeutic Development 2021)

  • Tianyu Zhang, Liwei Zhang, Philip R. O. Payne, Fuhai Li
  • [Paper]

• MatchMaker: A Deep Learning Framework for Drug Synergy Prediction (IEEE/ACM Transactions on Computational Biology and Bioinformatics 2021)

  • Halil Ibrahim Kuru, Oznur Tastan, A. Ercument Cicek
  • [Paper]
  • [Tensorflow]

• Cold-Start Problems in Data-Driven Prediction of Drug–Drug Interaction Effects (MDPI 2021)

  • Pieter Dewulf, Michiel Stock and Bernard De Baets
  • [Paper]

• SmileGNN: Drug-Drug Interaction Prediction Based on SMILES and Graph Neural Network (ResearchSquare 2021)

  • Xueting Han, Xutao Li, Junyi Li
  • [Paper]
  • [TensorFlow]

• DeepDDS: Deep Graph Neural Network with Attention Mechanism to Predict Synergistic Drug Combinations (Arxiv 2021)

  • Jinxian Wang, Wenhao Zhang, Siyuan Shen, Lei Deng, Hui Liu
  • [Paper]
  • [PyTorch]

• SSI–DDI: Substructure–Substructure Interactions for Drug–Drug Interaction Prediction (Briefings in Bioinformatics 2021)

  • Arnold K. Nyamabo, Hui Yu and Jian-Yu Shi
  • [Paper]
  • [PyTorch]

2020

• DeepDrug: A General Graph-Based Deep Learning Framework for Drug Relation Prediction (BioArxiv 2020)

  • Xusheng Cao, Rui Fan, Wanwen Zeng
  • [Paper]
  • [Python TensorFlow]

• DPDDI: A Deep Predictor for Drug-Drug Interactions (BMC Bioinformatics 2020)

  • Yue-Hua Feng, Shao-Wu Zhang, Jian-Yu Shi
  • [Paper]
  • [Python TensorFlow]

• CASTER: Predicting Drug Interactions with Chemical Substructure Representation (AAAI 2020)

  • Kexin Huang, Cao Xiao, Trong Nghia Hoang, Lucas M. Glass, Jimeng Sun
  • [Paper]
  • [PyTorch]

2019

• Drug-Drug Adverse Effect Prediction with Graph Co-Attention (ICML 2019)

  • Andreea Deac, Yu-Hsiang Huang, Petar Veličković, Pietro Liò, Jian Tang
  • [Paper]
  • [PyTorch]

• MR-GNN: Multi-Resolution and Dual Graph Neural Network for Predicting Structured Entity Interactions (IJCAI 2019)

  • Nuo Xu, Pinghui Wang, Long Chen, Jing Tao, Junzhou Zhao
  • [Paper]
  • [Python Tensorflow]

2018

• Deep Learning Improves Prediction of Drug--Drug and Drug-Food Interactions (PNAS 2018)

  • Jae Yong Ryu, Hyun Uk Kim, Sang Yup Lee
  • [Paper]
  • [TensorFlow]

• DeepCCI: End-to-end Deep Learning for Chemical-Chemical Interaction Prediction (BCB 2017)

  • Sunyoung Kwon, Sungroh Yoon
  • [Paper]

• DeepSynergy: Predicting Anti-Cancer Drug Synergy with Deep Learning (Bioinformatics 2018)

  • Kristina Preuer, Richard P I Lewis, Sepp Hochreiter, Andreas Bender, Krishna C Bulusu, Günter Klambauer
  • [Paper]
  • [TensorFlow]