# CLEAR: Generative Counterfactual Explanations on Graphs

arXiv: https://arxiv.org/abs/2210.08443 · HTML: https://mlsanity.com/paper/2210.08443/

## Key facts

- Cited by 48 papers in the map (data through 14 Oct 2026).
- Builds on 38 of its 54 references that are in the map.
- First posted on arXiv 16 Oct 2022.

## Builds on (most cited first, 30 of 38)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Counterfactual Explanations without Opening the Black Box: Automated Decisions and the GDPR](https://mlsanity.com/paper/1711.00399/) (2017)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [Explaining Machine Learning Classifiers through Diverse Counterfactual Explanations](https://mlsanity.com/paper/1905.07697/) (2019)
- [Variational Autoencoders and Nonlinear ICA: A Unifying Framework](https://mlsanity.com/paper/1907.04809/) (2019)
- [GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models](https://mlsanity.com/paper/1802.08773/) (2018)
- [MolGAN: An implicit generative model for small molecular graphs](https://mlsanity.com/paper/1805.11973/) (2018)
- [Explainability in Graph Neural Networks: A Taxonomic Survey](https://mlsanity.com/paper/2012.15445/) (2020)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [Actionable Recourse in Linear Classification](https://mlsanity.com/paper/1809.06514/) (2018)
- [Nonlinear ICA Using Auxiliary Variables and Generalized Contrastive Learning](https://mlsanity.com/paper/1805.08651/) (2018)
- [Explanations based on the Missing: Towards Contrastive Explanations with Pertinent Negatives](https://mlsanity.com/paper/1802.07623/) (2018)
- [Algorithmic Recourse: from Counterfactual Explanations to Interventions](https://mlsanity.com/paper/2002.06278/) (2020)
- [FACE: Feasible and Actionable Counterfactual Explanations](https://mlsanity.com/paper/1909.09369/) (2019)
- [Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discovery](https://mlsanity.com/paper/1803.09518/) (2018)
- [Local Rule-Based Explanations of Black Box Decision Systems](https://mlsanity.com/paper/1805.10820/) (2018)
- [Multi-Objective Counterfactual Explanations](https://mlsanity.com/paper/2004.11165/) (2020)
- [Learning Model-Agnostic Counterfactual Explanations for Tabular Data](https://mlsanity.com/paper/1910.09398/) (2019)
- [Preserving Causal Constraints in Counterfactual Explanations for Machine Learning Classifiers](https://mlsanity.com/paper/1912.03277/) (2019)
- [Algorithmic recourse under imperfect causal knowledge: a probabilistic approach](https://mlsanity.com/paper/2006.06831/) (2020)
- [Data Augmentation for Deep Graph Learning: A Survey](https://mlsanity.com/paper/2202.08235/) (2022)
- [GraphGAN: Graph Representation Learning with Generative Adversarial Nets](https://mlsanity.com/paper/1711.08267/) (2017)
- [CF-GNNExplainer: Counterfactual Explanations for Graph Neural Networks](https://mlsanity.com/paper/2102.03322/) (2021)
- [Graphite: Iterative Generative Modeling of Graphs](https://mlsanity.com/paper/1803.10459/) (2018)
- [Efficient Search for Diverse Coherent Explanations](https://mlsanity.com/paper/1901.04909/) (2019)

## Built on by (most cited first, 30 of 48)

- [A Survey on Graph Counterfactual Explanations: Definitions, Methods, Evaluation, and Research Challenges](https://mlsanity.com/paper/2210.12089/) (2022)
- [A Survey on Explainability of Graph Neural Networks](https://mlsanity.com/paper/2306.01958/) (2023)
- [Counterfactual Learning on Graphs: A Survey](https://mlsanity.com/paper/2304.01391/) (2023)
- [LLM-Generated Black-box Explanations Can Be Adversarially Helpful](https://mlsanity.com/paper/2405.06800/) (2024)
- [PowerGraph: A power grid benchmark dataset for graph neural networks](https://mlsanity.com/paper/2402.02827/) (2024)
- [Towards Robust Fidelity for Evaluating Explainability of Graph Neural Networks](https://mlsanity.com/paper/2310.01820/) (2023)
- [Efficient XAI Techniques: A Taxonomic Survey](https://mlsanity.com/paper/2302.03225/) (2023)
- [How Interpretable Are Interpretable Graph Neural Networks?](https://mlsanity.com/paper/2406.07955/) (2024)
- [Graph Neural Networks for Vulnerability Detection: A Counterfactual Explanation](https://mlsanity.com/paper/2404.15687/) (2024)
- [GNNX-BENCH: Unravelling the Utility of Perturbation-based GNN Explainers through In-depth Benchmarking](https://mlsanity.com/paper/2310.01794/) (2023)
- [Causality-Aware Spatiotemporal Graph Neural Networks for Spatiotemporal Time Series Imputation](https://mlsanity.com/paper/2403.11960/) (2024)
- [GInX-Eval: Towards In-Distribution Evaluation of Graph Neural Network Explanations](https://mlsanity.com/paper/2309.16223/) (2023)
- [Deep Backtracking Counterfactuals for Causally Compliant Explanations](https://mlsanity.com/paper/2310.07665/) (2023)
- [D4Explainer: In-Distribution GNN Explanations via Discrete Denoising Diffusion](https://mlsanity.com/paper/2310.19321/) (2023)
- [Exploring Causal Learning through Graph Neural Networks: An In-depth Review](https://mlsanity.com/paper/2311.14994/) (2023)
- [Factorized Explainer for Graph Neural Networks](https://mlsanity.com/paper/2312.05596/) (2023)
- [LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework](https://mlsanity.com/paper/2405.13902/) (2024)
- [Robust Stochastic Graph Generator for Counterfactual Explanations](https://mlsanity.com/paper/2312.11747/) (2023)
- [Recent Advances in Malware Detection: Graph Learning and Explainability](https://mlsanity.com/paper/2502.10556/) (2025)
- [Generative Explanations for Graph Neural Network: Methods and Evaluations](https://mlsanity.com/paper/2311.05764/) (2023)
- [When Graph Neural Network Meets Causality: Opportunities, Methodologies and An Outlook](https://mlsanity.com/paper/2312.12477/) (2023)
- [QUCE: The Minimisation and Quantification of Path-Based Uncertainty for Generative Counterfactual Explanations](https://mlsanity.com/paper/2402.17516/) (2024)
- [Causal Inference with Latent Variables: Recent Advances and Future Prospectives](https://mlsanity.com/paper/2406.13966/) (2024)
- [Graph AI in Medicine](https://mlsanity.com/paper/2310.13767/) (2023)
- [A Survey of Out-of-distribution Generalization for Graph Machine Learning from a Causal View](https://mlsanity.com/paper/2409.09858/) (2024)
- [Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction](https://mlsanity.com/paper/2410.15165/) (2024)
- [Graph Counterfactual Explainable AI via Latent Space Traversal](https://mlsanity.com/paper/2501.08850/) (2025)
- [Unstructured and structured data: Can we have the best of both worlds with large language models?](https://mlsanity.com/paper/2304.13010/) (2023)
- [Game-theoretic Counterfactual Explanation for Graph Neural Networks](https://mlsanity.com/paper/2402.06030/) (2024)
- [Fast Inference of Removal-Based Node Influence](https://mlsanity.com/paper/2403.08333/) (2024)

## 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.