Interpretable Prototype-based Graph Information Bottleneck
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Abstract (arXiv)
The success of Graph Neural Networks (GNNs) has led to a need for understanding their decision-making process and providing explanations for their predictions, which has given rise to explainable AI (XAI) that offers transparent explanations for black-box models. Recently, the use of prototypes has successfully improved the explainability of models by learning prototypes to imply training graphs that affect the prediction. However, these approaches tend to provide prototypes with excessive information from the entire graph, leading to the exclusion of key substructures or the inclusion of irrelevant substructures, which can limit both the interpretability and the performance of the model in downstream tasks. In this work, we propose a novel framework of explainable GNNs, called interpretable Prototype-based Graph Information Bottleneck (PGIB) that incorporates prototype learning within the information bottleneck framework to provide prototypes with the key subgraph from the input graph that is important for the model prediction. This is the first work that incorporates prototype learning into the process of identifying the key subgraphs that have a critical impact on the prediction performance. Extensive experiments, including qualitative analysis, demonstrate that PGIB outperforms state-of-the-art methods in terms of both prediction performance and explainability.
Key facts. Cited by 23 papers in the map (data through 7 Oct 2026). Builds on 22 of its 35 references that are in the map. First posted on arXiv 30 Oct 2023.
Builds on
22 of 35 references.
References · 22
- 2016Semi-Supervised Classification with Graph Convolutional Networkscited by 11,282
- 2017Graph Attention Networkscited by 8,854
- 2018How Powerful are Graph Neural Networks?cited by 4,355
- 2019Contrastive Multiview Codingcited by 1,297
- 2018Learning deep representations by mutual information estimation and maximizationcited by 1,265
- 2020Graph Contrastive Learning with Augmentationscited by 1,203
- 2019GNNExplainer: Generating Explanations for Graph Neural Networkscited by 735
- 2018This Looks Like That: Deep Learning for Interpretable Image Recognitioncited by 731
- 2020Parameterized Explainer for Graph Neural Networkcited by 423
- 2020Explainability in Graph Neural Networks: A Taxonomic Surveycited by 383
- 2020Discovering Symbolic Models from Deep Learning with Inductive Biasescited by 335
- 2020XGNN: Towards Model-Level Explanations of Graph Neural Networkscited by 211
10 more
- 2020PGM-Explainer: Probabilistic Graphical Model Explanations for Graph Neural Networkscited by 210
- 2022Interpretable and Generalizable Graph Learning via Stochastic Attention Mechanismcited by 171
- 2020Graph Information Bottleneckcited by 168
- 2020Graph Information Bottleneck for Subgraph Recognitioncited by 119
- 2021ProtGNN: Towards Self-Explaining Graph Neural Networkscited by 96
- 2020ProtoPShare: Prototype Sharing for Interpretable Image Classification and Similarity Discoverycited by 89
- 2021Graph Structure Learning with Variational Information Bottleneckcited by 81
- 2021Improving Subgraph Recognition with Variational Graph Information Bottleneckcited by 45
- 2020Quantifying Explainers of Graph Neural Networks in Computational Pathologycited by 35
- 2023Conditional Graph Information Bottleneck for Molecular Relational Learningcited by 24
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Citing papers per year: 2024: 6; 2025: 9; 2026: 8.
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- 2024Contrastive Graph Representation Learning with Adversarial Cross-view Reconstruction and Information Bottleneckcited by 21
- 2025A Comprehensive Survey on Self-Interpretable Neural Networkscited by 18
- 2025ProtoMol: Enhancing Molecular Property Prediction via Prototype-Guided Multimodal Learningcited by 11
- 2025Raising the Bar in Graph OOD Generalization: Invariant Learning Beyond Explicit Environment Modelingcited by 9
- 2024Self-Explainable Graph Transformer for Link Sign Predictioncited by 8
- 2024A Self-Explainable Heterogeneous GNN for Relational Deep Learningcited by 7
- 2025SoREX: Towards Self-Explainable Social Recommendation with Relevant Ego-Path Extractioncited by 5
- 2024Towards Few-shot Self-explaining Graph Neural Networkscited by 4
- 2026PIME: Prototype-based Interpretable MCTS-Enhanced Brain Network Analysis for Disorder Diagnosiscited by 2
- 2025Towards Faithful Class-level Self-explainability in Graph Neural Networks by Subgraph Dependenciescited by 1
- 2025Think as a Doctor: An Interpretable AI Approach for ICU Mortality Predictioncited by 1
- 2026WaterVIB: Learning Minimal Sufficient Watermark Representations via Variational Information Bottleneckcited by 1
11 more
- 2026Revealing Combinatorial Reasoning of GNNs via Graph Concept Bottleneck Layercited by 1
- 2024Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networkscited by 0
- 2024GINTRIP: Interpretable Temporal Graph Regression using Information bottleneck and Prototype-based methodcited by 0
- 2025Interpretable High-order Knowledge Graph Neural Network for Predicting Synthetic Lethality in Human Cancerscited by 0
- 2025Enhancing Job Salary Prediction with Disentangled Composition Effect Modeling: A Neural Prototyping Approachcited by 0
- 2025Interpreting Graph Inference with Skyline Explanationscited by 0
- 2026Exploring Concept Subspace for Self-explainable Text-Attributed Graph Learningcited by 0
- 2026Why Self-Inconsistency Arises in GNN Explanations and How to Exploit Itcited by 0
- 2026ST-TGExplainer: Disentangling Stability and Transition Patterns for Temporal GNN Interpretabilitycited by 0
- 2026CalibHyper: Chance-Corrected Relational Hypergraphs for Few-Shot Molecular Property Predictioncited by 0
- 2026WOMBAT: Whitebox Oracle for Molecular Benchmarking and Attribution Testingcited by 0
- 2026WOMBAT: Whitebox Oracle for Molecular Benchmarking and Attribution Testing30 Sep 2026
- 2026CalibHyper: Chance-Corrected Relational Hypergraphs for Few-Shot Molecular Property Prediction27 Sep 2026
- 2026ST-TGExplainer: Disentangling Stability and Transition Patterns for Temporal GNN Interpretability19 May 2026
- 2026Why Self-Inconsistency Arises in GNN Explanations and How to Exploit It8 May 2026
- 2026Exploring Concept Subspace for Self-explainable Text-Attributed Graph Learning13 Apr 2026
- 2026Revealing Combinatorial Reasoning of GNNs via Graph Concept Bottleneck Layer2 Mar 2026
- 2026WaterVIB: Learning Minimal Sufficient Watermark Representations via Variational Information Bottleneck25 Feb 2026
- 2026PIME: Prototype-based Interpretable MCTS-Enhanced Brain Network Analysis for Disorder Diagnosis24 Feb 2026
- 2025ProtoMol: Enhancing Molecular Property Prediction via Prototype-Guided Multimodal Learning19 Oct 2025
- 2025Think as a Doctor: An Interpretable AI Approach for ICU Mortality Prediction11 Oct 2025
- 2025SoREX: Towards Self-Explainable Social Recommendation with Relevant Ego-Path Extraction30 Sep 2025
- 2025Towards Faithful Class-level Self-explainability in Graph Neural Networks by Subgraph Dependencies15 Aug 2025
11 more
- 2025Interpreting Graph Inference with Skyline Explanations12 May 2025
- 2025Enhancing Job Salary Prediction with Disentangled Composition Effect Modeling: A Neural Prototyping Approach17 Mar 2025
- 2025Interpretable High-order Knowledge Graph Neural Network for Predicting Synthetic Lethality in Human Cancers8 Mar 2025
- 2025Raising the Bar in Graph OOD Generalization: Invariant Learning Beyond Explicit Environment Modeling15 Feb 2025
- 2025A Comprehensive Survey on Self-Interpretable Neural Networks26 Jan 2025
- 2024A Self-Explainable Heterogeneous GNN for Relational Deep Learning30 Nov 2024
- 2024GINTRIP: Interpretable Temporal Graph Regression using Information bottleneck and Prototype-based method17 Sep 2024
- 2024Self-Explainable Graph Transformer for Link Sign Prediction16 Aug 2024
- 2024Towards Few-shot Self-explaining Graph Neural Networks14 Aug 2024
- 2024Contrastive Graph Representation Learning with Adversarial Cross-view Reconstruction and Information Bottleneck1 Aug 2024
- 2024Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks7 Feb 2024
- 2024Contrastive Graph Representation Learning with Adversarial Cross-view Reconstruction and Information Bottleneckcited by 21
- 2025A Comprehensive Survey on Self-Interpretable Neural Networkscited by 18
- 2025ProtoMol: Enhancing Molecular Property Prediction via Prototype-Guided Multimodal Learningcited by 11
- 2025Raising the Bar in Graph OOD Generalization: Invariant Learning Beyond Explicit Environment Modelingcited by 9
- 2024Self-Explainable Graph Transformer for Link Sign Predictioncited by 8
- 2024A Self-Explainable Heterogeneous GNN for Relational Deep Learningcited by 7
- 2025SoREX: Towards Self-Explainable Social Recommendation with Relevant Ego-Path Extractioncited by 5
- 2024Towards Few-shot Self-explaining Graph Neural Networkscited by 4
- 2026PIME: Prototype-based Interpretable MCTS-Enhanced Brain Network Analysis for Disorder Diagnosiscited by 2
- 2025Towards Faithful Class-level Self-explainability in Graph Neural Networks by Subgraph Dependenciescited by 1
- 2025Think as a Doctor: An Interpretable AI Approach for ICU Mortality Predictioncited by 1
- 2026WaterVIB: Learning Minimal Sufficient Watermark Representations via Variational Information Bottleneckcited by 1
12 most cited of 22 All 22 (JSON)
- 2026WOMBAT: Whitebox Oracle for Molecular Benchmarking and Attribution Testing30 Sep 2026
- 2026CalibHyper: Chance-Corrected Relational Hypergraphs for Few-Shot Molecular Property Prediction27 Sep 2026
- 2026ST-TGExplainer: Disentangling Stability and Transition Patterns for Temporal GNN Interpretability19 May 2026
- 2026Why Self-Inconsistency Arises in GNN Explanations and How to Exploit It8 May 2026
- 2026Exploring Concept Subspace for Self-explainable Text-Attributed Graph Learning13 Apr 2026
- 2026WaterVIB: Learning Minimal Sufficient Watermark Representations via Variational Information Bottleneck25 Feb 2026
- 2026PIME: Prototype-based Interpretable MCTS-Enhanced Brain Network Analysis for Disorder Diagnosis24 Feb 2026
- 2025ProtoMol: Enhancing Molecular Property Prediction via Prototype-Guided Multimodal Learning19 Oct 2025
- 2025Think as a Doctor: An Interpretable AI Approach for ICU Mortality Prediction11 Oct 2025
- 2025SoREX: Towards Self-Explainable Social Recommendation with Relevant Ego-Path Extraction30 Sep 2025
- 2025Towards Faithful Class-level Self-explainability in Graph Neural Networks by Subgraph Dependencies15 Aug 2025
- 2025Interpreting Graph Inference with Skyline Explanations12 May 2025
12 newest of 22 All 22 (JSON)