mlsanityData to 7 Oct 2026

A Comparative Study of Counterfactual Explainers for Graph Neural Networks Enabling Multiple Types of Graph Edit

arXiv 2609.05113 ↗First posted 4 Sep 2026cs.LGcited by 0

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Abstract (arXiv)

Counterfactual explanations for graph-structured data seek to determine minimal and realistic modifications required in an input graph to alter a model's prediction to a predefined output. Although counterfactual explainers that support modifying the graph by both adding and removing edges have recently emerged, there is still a lack of general and efficient methods, especially when considering the quality of the generated explanations. Moreover, the problem remains far from solved, as existing methods exhibit different strengths and weaknesses, often trading off between explanation size, coverage and quality. For this reason, it is important to identify where each method performs well and where it falls short, so as to guide future research in the field. Thus, our study compares six state-of-the-art (SOTA) models on a diverse set of real-world and synthetic datasets, covering both binary and multi-class graph and node classification tasks, and evaluates their performance using diverse quantitative and qualitative metrics.

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References · 17

  1. 2016Revisiting Semi-Supervised Learning with Graph Embeddingscited by 970
  2. 2020Parameterized Explainer for Graph Neural Networkcited by 423
  3. 2021On Explainability of Graph Neural Networks via Subgraph Explorationscited by 280
  4. 2020XGNN: Towards Model-Level Explanations of Graph Neural Networkscited by 211
  5. 2020Interpreting Graph Neural Networks for NLP With Differentiable Edge Maskingcited by 152
  6. 2022A Comprehensive Survey on Trustworthy Graph Neural Networks: Privacy, Robustness, Fairness, and Explainabilitycited by 118
  7. 2022Learning and Evaluating Graph Neural Network Explanations based on Counterfactual and Factual Reasoningcited by 78
  8. 2021Towards Self-Explainable Graph Neural Networkcited by 75
  9. 2021Robust Counterfactual Explanations on Graph Neural Networkscited by 72
  10. 2022CLEAR: Generative Counterfactual Explanations on Graphscited by 48
  11. 2021MEG: Generating Molecular Counterfactual Explanations for Deep Graph Networkscited by 32
  12. 2023Counterfactual Learning on Graphs: A Surveycited by 22
5 more
  1. 2024Graph Neural Networks for Vulnerability Detection: A Counterfactual Explanationcited by 12
  2. 2021Multi-objective Explanations of GNN Predictionscited by 10
  3. 2023D4Explainer: In-Distribution GNN Explanations via Discrete Denoising Diffusioncited by 9
  4. 2023Robust Stochastic Graph Generator for Counterfactual Explanationscited by 7
  5. 2025Graph Inverse Style Transfer for Counterfactual Explainabilitycited by 2

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