Explainability in Graph Neural Networks: A Taxonomic Survey
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Abstract (arXiv)
Deep learning methods are achieving ever-increasing performance on many artificial intelligence tasks. A major limitation of deep models is that they are not amenable to interpretability. This limitation can be circumvented by developing post hoc techniques to explain the predictions, giving rise to the area of explainability. Recently, explainability of deep models on images and texts has achieved significant progress. In the area of graph data, graph neural networks (GNNs) and their explainability are experiencing rapid developments. However, there is neither a unified treatment of GNN explainability methods, nor a standard benchmark and testbed for evaluations. In this survey, we provide a unified and taxonomic view of current GNN explainability methods. Our unified and taxonomic treatments of this subject shed lights on the commonalities and differences of existing methods and set the stage for further methodological developments. To facilitate evaluations, we generate a set of benchmark graph datasets specifically for GNN explainability. We summarize current datasets and metrics for evaluating GNN explainability. Altogether, this work provides a unified methodological treatment of GNN explainability and a standardized testbed for evaluations.
Key facts. Cited by 383 papers in the map (data through 7 Oct 2026). First posted on arXiv 31 Dec 2020.
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Citing papers per year: 2021: 31; 2022: 67; 2023: 87; 2024: 94; 2025: 60; 2026: 44.
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- 2021On Explainability of Graph Neural Networks via Subgraph Explorationscited by 280
- 2022Discovering Invariant Rationales for Graph Neural Networkscited by 186
- 2021Self-Supervised Learning of Graph Neural Networks: A Unified Reviewcited by 184
- 2022Interpretable and Generalizable Graph Learning via Stochastic Attention Mechanismcited by 171
- 2022Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphscited by 144
- 2022GOOD: A Graph Out-of-Distribution Benchmarkcited by 140
- 2021Benchmarking and Survey of Explanation Methods for Black Box Modelscited by 136
- 2021Explainable AI (XAI): A Systematic Meta-Survey of Current Challenges and Future Opportunitiescited by 125
- 2021CF-GNNExplainer: Counterfactual Explanations for Graph Neural Networkscited by 118
- 2022A Comprehensive Survey on Trustworthy Graph Neural Networks: Privacy, Robustness, Fairness, and Explainabilitycited by 118
- 2022A Survey of Knowledge Graph Reasoning on Graph Types: Static, Dynamic, and Multimodalcited by 106
- 2022Out-Of-Distribution Generalization on Graphs: A Surveycited by 97
38 more
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- 2022Evaluating Explainability for Graph Neural Networkscited by 85
- 2023Generative Diffusion Models on Graphs: Methods and Applicationscited by 79
- 2022Learning and Evaluating Graph Neural Network Explanations based on Counterfactual and Factual Reasoningcited by 78
- 2021DIG: A Turnkey Library for Diving into Graph Deep Learning Researchcited by 76
- 2022Global Explainability of GNNs via Logic Combination of Learned Conceptscited by 64
- 2021GraphSVX: Shapley Value Explanations for Graph Neural Networkscited by 63
- 2022Interpretable Graph Neural Networks for Connectome-Based Brain Disorder Analysiscited by 58
- 2022GraphFramEx: Towards Systematic Evaluation of Explainability Methods for Graph Neural Networkscited by 57
- 2022Federated Graph Neural Networks: Overview, Techniques and Challengescited by 52
- 2022Graph Pooling for Graph Neural Networks: Progress, Challenges, and Opportunitiescited by 52
- 2022CLEAR: Generative Counterfactual Explanations on Graphscited by 48
- 2024Usable XAI: 10 Strategies Towards Exploiting Explainability in the LLM Eracited by 45
- 2022GStarX: Explaining Graph Neural Networks with Structure-Aware Cooperative Gamescited by 42
- 2023Does Invariant Graph Learning via Environment Augmentation Learn Invariance?cited by 42
- 2023Towards Self-Interpretable Graph-Level Anomaly Detectioncited by 41
- 2021Sampling methods for efficient training of graph convolutional networks: A surveycited by 40
- 2021Automated Machine Learning on Graphs: A Surveycited by 38
- 2021Probing GNN Explainers: A Rigorous Theoretical and Empirical Analysis of GNN Explanation Methodscited by 36
- 2021Zorro: Valid, Sparse, and Stable Explanations in Graph Neural Networkscited by 34
- 2022GNNInterpreter: A Probabilistic Generative Model-Level Explanation for Graph Neural Networkscited by 34
- 2022Explaining the Explainers in Graph Neural Networks: a Comparative Studycited by 34
- 2024A Review of Graph Neural Networks in Epidemic Modelingcited by 31
- 2022A Survey on Graph Counterfactual Explanations: Definitions, Methods, Evaluation, and Research Challengescited by 30
- 2022Parallel and Distributed Graph Neural Networks: An In-Depth Concurrency Analysiscited by 29
- 2023Joint Learning of Label and Environment Causal Independence for Graph Out-of-Distribution Generalizationcited by 29
- 2023A Survey on Explainability of Graph Neural Networkscited by 28
- 2022Graph Neural Networks in IoT: A Surveycited by 27
- 2023DAG Matters! GFlowNets Enhanced Explainer For Graph Neural Networkscited by 27
- 2022A Survey of Explainable Graph Neural Networks: Taxonomy and Evaluation Metricscited by 26
- 2023PaGE-Link: Path-based Graph Neural Network Explanation for Heterogeneous Link Predictioncited by 25
- 2023Towards Fair Graph Neural Networks via Graph Counterfactualcited by 23
- 2023Over-Squashing in Graph Neural Networks: A Comprehensive surveycited by 23
- 2023Interpretable Prototype-based Graph Information Bottleneckcited by 23
- 2024Graph Condensation: A Surveycited by 23
50 most cited of 383 All 383 (JSON)
- 2026WOMBAT: Whitebox Oracle for Molecular Benchmarking and Attribution Testing30 Sep 2026
- 2026Where Privacy Belongs: Placement Diagnosis and Certified Selection for Private Counterfactual Explanations on Graphs29 Sep 2026
- 2026Controllable GNN Explanations via Multi-Metric Preference Selection26 Sep 2026
- 2026Self-Explainable Multi-Label Graph Neural Network for Correlated Evidence Attribution27 Aug 2026
- 2026From Abductive Explanations to Global Logical Rules for Node Classification in SGCs17 Aug 2026
- 2026NICE: Scale-Stable Perturbations for Graph Neural Network Explanations via Noise Corruption17 Aug 2026
- 2026Amortised Post-Hoc Explanation with Exact Preservation for Dynamic Graph Anomaly Detectors16 Aug 2026
- 2026Overcoming Shortcut Learning in Graph Neural Networks through Active Explanation Guidance14 Aug 2026
- 2026Faithful, Sufficient and Understandable: Rethinking Graph Counterfactual Explanations via Discrete Diffusion Inversion12 Aug 2026
- 2026Explaining spatial information flow in short-term traffic forecasting models using a gated graph attention network9 Aug 2026
- 2026Towards Faithful Graph Explanations with Synergistic Edge Effects via Granular Balls23 Jul 2026
- 2026A Polynomial Architecture-Attribution Co-Design Framework for Exact Aumann-Shapley Attribution in GNNs23 Jul 2026
38 more
- 2026Toward Auditable Fraud Detection: Combining Graph Features, Model Explanations, and Agentic Case Investigation21 Jul 2026
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- 2026Explaining Temporal Graph Neural Networks via Feature-induced Information Flow25 Jun 2026
- 2026Auto-Configured Explainable Graph Neural Networks for Multi-Site Pollution Prediction23 Jun 2026
- 2026A Completion-Aware Framework for Impactful Counterfactual Explainability in Graph Neural Networks20 Jun 2026
- 2026CIExplainer++: Generating Causal and Interpretable Explanations for Graph Neural Networks17 Jun 2026
- 2026Self-Evolving Agents as Dynamic Graph Transformation: A Survey and New Perspective10 Jun 2026
- 2026TN-SHAP-G: Graph-Structured Tensor Network Surrogates for Shapley Values and Interactions1 Jun 2026
- 2026Relevant Walk Search for Explaining Graph Neural Networks22 May 2026
- 2026Efficient Higher-order Subgraph Attribution via Message Passing21 May 2026
- 2026Ex-GraphRAG: Interpretable Evidence Routing for Graph-Augmented LLMs21 May 2026
- 2026B-cos GNNs: Faithful Explanations through Dynamic Linearity19 May 2026
- 2026UNR-Explainer: Counterfactual Explanations for Unsupervised Node Representation Learning Models17 May 2026
- 2026AIMing for Standardised Explainability Evaluation in GNNs: A Framework and Case Study on Graph Kernel Networks14 May 2026
- 2026SLASH the Sink: Sharpening Structural Attention Inside LLMs11 May 2026
- 2026Structural Interpretations of Protein Language Model Representations via Differentiable Graph Partitioning9 May 2026
- 2026Attention-based graph neural networks: a survey9 May 2026
- 2026Graph neural network explanations reveal a topological signature of disease-associated hubs in biological networks8 May 2026
- 2026Why Self-Inconsistency Arises in GNN Explanations and How to Exploit It8 May 2026
- 2026Explainable AI for Jet Tagging: A Comparative Study of GNNExplainer, GNNShap, and GradCAM for Jet Tagging in the Lund Jet Plane28 Apr 2026
- 2026Foundation models for discovering robust biomarkers of neurological disorders from dynamic functional connectivity23 Apr 2026
- 2026TACENR: Task-Agnostic Contrastive Explanations for Node Representations21 Apr 2026
- 2026BAED: a New Paradigm for Few-shot Graph Learning with Explanation in the Loop2 Mar 2026
- 2026GlassMol: Interpretable Molecular Property Prediction with Concept Bottleneck Models1 Mar 2026
- 2026Quantifying Explanation Quality in Graph Neural Networks using Out-of-Distribution Generalization7 Feb 2026
- 2026ATEX-CF: Attack-Informed Counterfactual Explanations for Graph Neural Networks5 Feb 2026
- 2026PIMPC-GNN: Physics-Informed Multi-Phase Consensus Learning for Enhancing Imbalanced Node Classification in Graph Neural Networks2 Feb 2026
- 2026GraphNNK -- Graph Classification and Interpretability31 Jan 2026
- 2026GNN Explanations that do not Explain and How to find Them28 Jan 2026
- 2026FSX: Message Flow Sensitivity Enhanced Structural Explainer for Graph Neural Networks21 Jan 2026
- 2026Improving LLM Reasoning with Homophily-aware Structural and Semantic Text-Attributed Graph Compression13 Jan 2026
- 2026Parallelizing Node-Level Explainability in Graph Neural Networks8 Jan 2026
- 2025GRExplainer: A Universal Explanation Method for Temporal Graph Neural Networks28 Dec 2025
- 2025From Cells to Survival: Hierarchical Analysis of Cell Inter-Relations in Multiplex Microscopy for Lung Cancer Prognosis9 Dec 2025
- 2025Mitigating Bias in Graph Hyperdimensional Computing8 Dec 2025
- 2025PISA: Prioritized Invariant Subgraph Aggregation for Out-of-Distribution Generalization on Graphs27 Nov 2025
- 2025InteractiveGNNExplainer: A Visual Analytics Framework for Multi-Faceted Understanding and Probing of Graph Neural Network Predictions17 Nov 2025
- 2025PruneGCRN: Minimizing and explaining spatio-temporal problems through node pruning12 Oct 2025
50 newest of 383 All 383 (JSON)
- 2023Generative Diffusion Models on Graphs: Methods and Applicationscited by 79
- 2023D4Explainer: In-Distribution GNN Explanations via Discrete Denoising Diffusioncited by 9
- 2026Faithful, Sufficient and Understandable: Rethinking Graph Counterfactual Explanations via Discrete Diffusion Inversioncited by 1
- 2026Faithful, Sufficient and Understandable: Rethinking Graph Counterfactual Explanations via Discrete Diffusion Inversion12 Aug 2026
- 2023D4Explainer: In-Distribution GNN Explanations via Discrete Denoising Diffusion30 Oct 2023
- 2023Generative Diffusion Models on Graphs: Methods and Applications6 Feb 2023
- 2021On Explainability of Graph Neural Networks via Subgraph Explorationscited by 280
- 2022Discovering Invariant Rationales for Graph Neural Networkscited by 186
- 2021Self-Supervised Learning of Graph Neural Networks: A Unified Reviewcited by 184
- 2022Interpretable and Generalizable Graph Learning via Stochastic Attention Mechanismcited by 171
- 2022Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphscited by 144
- 2022GOOD: A Graph Out-of-Distribution Benchmarkcited by 140
- 2021Benchmarking and Survey of Explanation Methods for Black Box Modelscited by 136
- 2021Explainable AI (XAI): A Systematic Meta-Survey of Current Challenges and Future Opportunitiescited by 125
- 2021CF-GNNExplainer: Counterfactual Explanations for Graph Neural Networkscited by 118
- 2022A Comprehensive Survey on Trustworthy Graph Neural Networks: Privacy, Robustness, Fairness, and Explainabilitycited by 118
- 2022A Survey of Knowledge Graph Reasoning on Graph Types: Static, Dynamic, and Multimodalcited by 106
- 2022Out-Of-Distribution Generalization on Graphs: A Surveycited by 97
12 most cited of 375 All 375 (JSON)
- 2026WOMBAT: Whitebox Oracle for Molecular Benchmarking and Attribution Testing30 Sep 2026
- 2026Where Privacy Belongs: Placement Diagnosis and Certified Selection for Private Counterfactual Explanations on Graphs29 Sep 2026
- 2026Controllable GNN Explanations via Multi-Metric Preference Selection26 Sep 2026
- 2026Self-Explainable Multi-Label Graph Neural Network for Correlated Evidence Attribution27 Aug 2026
- 2026From Abductive Explanations to Global Logical Rules for Node Classification in SGCs17 Aug 2026
- 2026NICE: Scale-Stable Perturbations for Graph Neural Network Explanations via Noise Corruption17 Aug 2026
- 2026Amortised Post-Hoc Explanation with Exact Preservation for Dynamic Graph Anomaly Detectors16 Aug 2026
- 2026Overcoming Shortcut Learning in Graph Neural Networks through Active Explanation Guidance14 Aug 2026
- 2026Explaining spatial information flow in short-term traffic forecasting models using a gated graph attention network9 Aug 2026
- 2026Towards Faithful Graph Explanations with Synergistic Edge Effects via Granular Balls23 Jul 2026
- 2026A Polynomial Architecture-Attribution Co-Design Framework for Exact Aumann-Shapley Attribution in GNNs23 Jul 2026
- 2026Toward Auditable Fraud Detection: Combining Graph Features, Model Explanations, and Agentic Case Investigation21 Jul 2026
12 newest of 375 All 375 (JSON)