mlsanityData to 7 Oct 2026

CLEAR: Generative Counterfactual Explanations on Graphs

arXiv 2210.08443 ↗First posted 16 Oct 2022cs.LGcited by 48

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Abstract (arXiv)

Counterfactual explanations promote explainability in machine learning models by answering the question "how should an input instance be perturbed to obtain a desired predicted label?". The comparison of this instance before and after perturbation can enhance human interpretation. Most existing studies on counterfactual explanations are limited in tabular data or image data. In this work, we study the problem of counterfactual explanation generation on graphs. A few studies have explored counterfactual explanations on graphs, but many challenges of this problem are still not well-addressed: 1) optimizing in the discrete and disorganized space of graphs; 2) generalizing on unseen graphs; and 3) maintaining the causality in the generated counterfactuals without prior knowledge of the causal model. To tackle these challenges, we propose a novel framework CLEAR which aims to generate counterfactual explanations on graphs for graph-level prediction models. Specifically, CLEAR leverages a graph variational autoencoder based mechanism to facilitate its optimization and generalization, and promotes causality by leveraging an auxiliary variable to better identify the underlying causal model. Extensive experiments on both synthetic and real-world graphs validate the superiority of CLEAR over the state-of-the-art methods in different aspects.

Key facts. Cited by 48 papers in the map (data through 7 Oct 2026). Builds on 38 of its 54 references that are in the map. First posted on arXiv 16 Oct 2022.

Builds on

38 of 54 references.

References · 38

  1. 2016Semi-Supervised Classification with Graph Convolutional Networkscited by 11,282
  2. 2017Graph Attention Networkscited by 8,854
  3. 2019Fast Graph Representation Learning with PyTorch Geometriccited by 2,414
  4. 2016Variational Graph Auto-Encoderscited by 1,373
  5. 2017Counterfactual Explanations without Opening the Black Box: Automated Decisions and the GDPRcited by 1,086
  6. 2017MoleculeNet: A Benchmark for Molecular Machine Learningcited by 1,037
  7. 2019GNNExplainer: Generating Explanations for Graph Neural Networkscited by 735
  8. 2018Junction Tree Variational Autoencoder for Molecular Graph Generationcited by 647
  9. 2019Explaining Machine Learning Classifiers through Diverse Counterfactual Explanationscited by 612
  10. 2019Variational Autoencoders and Nonlinear ICA: A Unifying Frameworkcited by 494
  11. 2018GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Modelscited by 406
  12. 2018MolGAN: An implicit generative model for small molecular graphscited by 392
26 more
  1. 2020Explainability in Graph Neural Networks: A Taxonomic Surveycited by 383
  2. 2018GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoderscited by 375
  3. 2018Actionable Recourse in Linear Classificationcited by 327
  4. 2018Nonlinear ICA Using Auxiliary Variables and Generalized Contrastive Learningcited by 278
  5. 2018Explanations based on the Missing: Towards Contrastive Explanations with Pertinent Negativescited by 261
  6. 2020Algorithmic Recourse: from Counterfactual Explanations to Interventionscited by 250
  7. 2019FACE: Feasible and Actionable Counterfactual Explanationscited by 232
  8. 2018Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discoverycited by 191
  9. 2018Local Rule-Based Explanations of Black Box Decision Systemscited by 165
  10. 2020Multi-Objective Counterfactual Explanationscited by 157
  11. 2019Learning Model-Agnostic Counterfactual Explanations for Tabular Datacited by 146
  12. 2019Preserving Causal Constraints in Counterfactual Explanations for Machine Learning Classifierscited by 143
  13. 2020Algorithmic recourse under imperfect causal knowledge: a probabilistic approachcited by 139
  14. 2022Data Augmentation for Deep Graph Learning: A Surveycited by 132
  15. 2017GraphGAN: Graph Representation Learning with Generative Adversarial Netscited by 121
  16. 2021CF-GNNExplainer: Counterfactual Explanations for Graph Neural Networkscited by 118
  17. 2018Graphite: Iterative Generative Modeling of Graphscited by 112
  18. 2019Efficient Search for Diverse Coherent Explanationscited by 111
  19. 2020Sub-graph Contrast for Scalable Self-Supervised Graph Representation Learningcited by 90
  20. 2017Interpretable Predictions of Tree-based Ensembles via Actionable Feature Tweakingcited by 76
  21. 2021Robust Counterfactual Explanations on Graph Neural Networkscited by 72
  22. 2019Causal Discovery with General Non-Linear Relationships Using Non-Linear ICAcited by 58
  23. 2019Model Agnostic Contrastive Explanations for Structured Datacited by 41
  24. 2021A Survey on the Robustness of Feature Importance and Counterfactual Explanationscited by 38
  25. 2021Counterfactual Graphs for Explainable Classification of Brain Networkscited by 33
  26. 2021MEG: Generating Molecular Counterfactual Explanations for Deep Graph Networkscited by 32

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2022: 1; 2023: 16; 2024: 17; 2025: 5; 2026: 9.

48 papers.

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  1. 2022A Survey on Graph Counterfactual Explanations: Definitions, Methods, Evaluation, and Research Challengescited by 30
  2. 2023A Survey on Explainability of Graph Neural Networkscited by 28
  3. 2023Counterfactual Learning on Graphs: A Surveycited by 22
  4. 2024LLM-Generated Black-box Explanations Can Be Adversarially Helpfulcited by 20
  5. 2024PowerGraph: A power grid benchmark dataset for graph neural networkscited by 19
  6. 2023Towards Robust Fidelity for Evaluating Explainability of Graph Neural Networkscited by 16
  7. 2023Efficient XAI Techniques: A Taxonomic Surveycited by 14
  8. 2024How Interpretable Are Interpretable Graph Neural Networks?cited by 13
  9. 2024Graph Neural Networks for Vulnerability Detection: A Counterfactual Explanationcited by 12
  10. 2023GNNX-BENCH: Unravelling the Utility of Perturbation-based GNN Explainers through In-depth Benchmarkingcited by 11
  11. 2024Causality-Aware Spatiotemporal Graph Neural Networks for Spatiotemporal Time Series Imputationcited by 11
  12. 2023GInX-Eval: Towards In-Distribution Evaluation of Graph Neural Network Explanationscited by 9
36 more
  1. 2023D4Explainer: In-Distribution GNN Explanations via Discrete Denoising Diffusioncited by 9
  2. 2023Deep Backtracking Counterfactuals for Causally Compliant Explanationscited by 8
  3. 2023Exploring Causal Learning through Graph Neural Networks: An In-depth Reviewcited by 8
  4. 2023Factorized Explainer for Graph Neural Networkscited by 8
  5. 2024LOGIN: A Large Language Model Consulted Graph Neural Network Training Frameworkcited by 8
  6. 2023Robust Stochastic Graph Generator for Counterfactual Explanationscited by 7
  7. 2025Recent Advances in Malware Detection: Graph Learning and Explainabilitycited by 6
  8. 2023Generative Explanations for Graph Neural Network: Methods and Evaluationscited by 4
  9. 2023When Graph Neural Network Meets Causality: Opportunities, Methodologies and An Outlookcited by 4
  10. 2024QUCE: The Minimisation and Quantification of Path-Based Uncertainty for Generative Counterfactual Explanationscited by 4
  11. 2024Causal Inference with Latent Variables: Recent Advances and Future Prospectivescited by 4
  12. 2023Graph AI in Medicinecited by 3
  13. 2024A Survey of Out-of-distribution Generalization for Graph Machine Learning from a Causal Viewcited by 3
  14. 2024Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Predictioncited by 3
  15. 2025Graph Counterfactual Explainable AI via Latent Space Traversalcited by 3
  16. 2023Unstructured and structured data: Can we have the best of both worlds with large language models?cited by 2
  17. 2024Game-theoretic Counterfactual Explanation for Graph Neural Networkscited by 2
  18. 2024Fast Inference of Removal-Based Node Influencecited by 2
  19. 2024Towards Non-Adversarial Algorithmic Recoursecited by 2
  20. 2023Adapting to Change: Robust Counterfactual Explanations in Dynamic Data Landscapescited by 1
  21. 2024Global Human-guided Counterfactual Explanations for Molecular Properties via Reinforcement Learningcited by 1
  22. 2024Explanation-Preserving Augmentation for Semi-Supervised Graph Representation Learningcited by 1
  23. 2025Finding Counterfactual Evidences for Node Classificationcited by 1
  24. 2025Causal Graph Neural Networks for Healthcarecited by 1
  25. 2026Beyond Edge Deletion: A Comprehensive Approach to Counterfactual Explanation in Graph Neural Networkscited by 1
  26. 2026UNR-Explainer: Counterfactual Explanations for Unsupervised Node Representation Learning Modelscited by 1
  27. 2026Faithful, Sufficient and Understandable: Rethinking Graph Counterfactual Explanations via Discrete Diffusion Inversioncited by 1
  28. 2024PAC Learnability under Explanation-Preserving Graph Perturbationscited by 0
  29. 2024Global Graph Counterfactual Explanation: A Subgraph Mapping Approachcited by 0
  30. 2025ARM-Explainer -- Explaining and improving graph neural network predictions for the maximum clique problem using node features and association rule miningcited by 0
  31. 2026CFRecs: Counterfactual Recommendations on Real Estate User Listing Interaction Graphscited by 0
  32. 2026From Top-1 to Top-K: A Reproducibility Study and Benchmarking of Counterfactual Explanations for Recommender Systemscited by 0
  33. 2026Querying Counterfactuals on Tissue Graphs with Supervised Disentanglementcited by 0
  34. 2026A Completion-Aware Framework for Impactful Counterfactual Explainability in Graph Neural Networkscited by 0
  35. 2026Measuring What Matters: A Unified Evaluation Framework for GNN Explainabilitycited by 0
  36. 2026A Comparative Study of Counterfactual Explainers for Graph Neural Networks Enabling Multiple Types of Graph Editcited by 0