mlsanityData to 14 Oct 2026

A Unified View of Relational Deep Learning for Drug Pair Scoring

arXiv 2111.02916 ↗First posted 4 Nov 2021cs.LG cs.AI cs.SIcited by 7

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Abstract (arXiv)

In recent years, numerous machine learning models which attempt to solve polypharmacy side effect identification, drug-drug interaction prediction and combination therapy design tasks have been proposed. Here, we present a unified theoretical view of relational machine learning models which can address these tasks. We provide fundamental definitions, compare existing model architectures and discuss performance metrics, datasets and evaluation protocols. In addition, we emphasize possible high impact applications and important future research directions in this domain.

Key facts. Cited by 7 papers in the map (data through 14 Oct 2026). Builds on 27 of its 99 references that are in the map. First posted on arXiv 4 Nov 2021.

Builds on

27 of 99 references.

References · 27

  1. 2017Inductive Representation Learning on Large Graphscited by 6,320
  2. 2016PointNet: Deep Learning on Point Sets for 3D Classification and Segmentationcited by 5,248
  3. 2019Fast Graph Representation Learning with PyTorch Geometriccited by 2,434
  4. 2021Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Developmentcited by 264
  5. 2019Deep Graph Library: A Graph-Centric, Highly-Performant Package for Graph Neural Networkscited by 242
  6. 2015Order Matters: Sequence to sequence for setscited by 237
  7. 2018Modeling polypharmacy side effects with graph convolutional networkscited by 237
  8. 2017SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernelscited by 161
  9. 2021Accurate Learning of Graph Representations with Graph Multiset Poolingcited by 120
  10. 2021PyTorch Geometric Temporal: Spatiotemporal Signal Processing with Neural Machine Learning Modelscited by 118
  11. 2020SkipGNN: Predicting Molecular Interactions with Skip-Graph Networkscited by 44
  12. 2020Multi-view Graph Contrastive Representation Learning for Drug-Drug Interaction Predictioncited by 41
15 more
  1. 2020SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarizationcited by 33
  2. 2020GoGNN: Graph of Graphs Neural Network for Predicting Structured Entity Interactionscited by 29
  3. 2021DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinationscited by 27
  4. 2019MR-GNN: Multi-Resolution and Dual Graph Neural Network for Predicting Structured Entity Interactionscited by 24
  5. 2019CASTER: Predicting Drug Interactions with Chemical Substructure Representationcited by 24
  6. 2019Drug-Drug Adverse Effect Prediction with Graph Co-Attentioncited by 20
  7. 2018Drug Similarity Integration Through Attentive Multi-view Graph Auto-Encoderscited by 17
  8. 2018Synergistic Drug Combination Prediction by Integrating Multi-omics Data in Deep Learning Modelscited by 9
  9. 2020Bi-Level Graph Neural Networks for Drug-Drug Interaction Predictioncited by 8
  10. 2021Relation Matters in Sampling: A Scalable Multi-Relational Graph Neural Network for Drug-Drug Interaction Predictioncited by 6
  11. 2021MOOMIN: Deep Molecular Omics Network for Anti-Cancer Drug Combination Therapycited by 6
  12. 2019Drug-drug interaction prediction based on co-medication patterns and graph matchingcited by 3
  13. 2017DeepCCI: End-to-end Deep Learning for Chemical-Chemical Interaction Predictioncited by 2
  14. 2018Knowledge Graph Completion to Predict Polypharmacy Side Effectscited by 2
  15. 2020Tri-graph Information Propagation for Polypharmacy Side Effect Predictioncited by 2

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Cited by year

Citing papers per year: 2022: 2; 2023: 3; 2024: 1; 2025: 1.

7 papers.

  1. 2023Conditional Graph Information Bottleneck for Molecular Relational Learningcited by 24
  2. 2025Large Language Models are Good Relational Learnerscited by 24
  3. 2024MolTC: Towards Molecular Relational Modeling In Language Modelscited by 22
  4. 2023Shift-Robust Molecular Relational Learning with Causal Substructurecited by 15
  5. 2022ChemicalX: A Deep Learning Library for Drug Pair Scoringcited by 11
  6. 2022Distributed representations of graphs for drug pair scoringcited by 1
  7. 2023CongFu: Conditional Graph Fusion for Drug Synergy Predictioncited by 1