# B-XAIC Dataset: Benchmarking Explainable AI for Graph Neural Networks Using Chemical Data

arXiv: https://arxiv.org/abs/2505.22252 · HTML: https://mlsanity.com/paper/2505.22252/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 36 of its 52 references that are in the map.
- First posted on arXiv 28 May 2025.

## Builds on (most cited first, 30 of 36)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Deep Inside Convolutional Networks: Visualising Image Classification Models and Saliency Maps](https://mlsanity.com/paper/1312.6034/) (2013)
- [Striving for Simplicity: The All Convolutional Net](https://mlsanity.com/paper/1412.6806/) (2014)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [Parameterized Explainer for Graph Neural Network](https://mlsanity.com/paper/2011.04573/) (2020)
- [Explainability in Graph Neural Networks: A Taxonomic Survey](https://mlsanity.com/paper/2012.15445/) (2020)
- [From Anecdotal Evidence to Quantitative Evaluation Methods: A Systematic Review on Evaluating Explainable AI](https://mlsanity.com/paper/2201.08164/) (2022)
- [Not Just a Black Box: Learning Important Features Through Propagating Activation Differences](https://mlsanity.com/paper/1605.01713/) (2016)
- [On Explainability of Graph Neural Networks via Subgraph Explorations](https://mlsanity.com/paper/2102.05152/) (2021)
- [Discovering Invariant Rationales for Graph Neural Networks](https://mlsanity.com/paper/2201.12872/) (2022)
- [Interpretable and Generalizable Graph Learning via Stochastic Attention Mechanism](https://mlsanity.com/paper/2201.12987/) (2022)
- [Understanding Attention and Generalization in Graph Neural Networks](https://mlsanity.com/paper/1905.02850/) (2019)
- [Graph Information Bottleneck](https://mlsanity.com/paper/2010.12811/) (2020)
- [Interpreting Graph Neural Networks for NLP With Differentiable Edge Masking](https://mlsanity.com/paper/2010.00577/) (2020)
- [Towards a Unified Framework for Fair and Stable Graph Representation Learning](https://mlsanity.com/paper/2102.13186/) (2021)
- [CF-GNNExplainer: Counterfactual Explanations for Graph Neural Networks](https://mlsanity.com/paper/2102.03322/) (2021)
- [Drug discovery with explainable artificial intelligence](https://mlsanity.com/paper/2007.00523/) (2020)
- [ProtGNN: Towards Self-Explaining Graph Neural Networks](https://mlsanity.com/paper/2112.00911/) (2021)
- [Evaluating Explainability for Graph Neural Networks](https://mlsanity.com/paper/2208.09339/) (2022)
- [Learning and Evaluating Graph Neural Network Explanations based on Counterfactual and Factual Reasoning](https://mlsanity.com/paper/2202.08816/) (2022)
- [Towards Self-Explainable Graph Neural Network](https://mlsanity.com/paper/2108.12055/) (2021)
- [Robust Counterfactual Explanations on Graph Neural Networks](https://mlsanity.com/paper/2107.04086/) (2021)
- [Global Explainability of GNNs via Logic Combination of Learned Concepts](https://mlsanity.com/paper/2210.07147/) (2022)
- [GraphFramEx: Towards Systematic Evaluation of Explainability Methods for Graph Neural Networks](https://mlsanity.com/paper/2206.09677/) (2022)
- [RelEx: A Model-Agnostic Relational Model Explainer](https://mlsanity.com/paper/2006.00305/) (2020)
- [KerGNNs: Interpretable Graph Neural Networks with Graph Kernels](https://mlsanity.com/paper/2201.00491/) (2022)
- [Improving Subgraph Recognition with Variational Graph Information Bottleneck](https://mlsanity.com/paper/2112.09899/) (2021)
- [Explaining the Explainers in Graph Neural Networks: a Comparative Study](https://mlsanity.com/paper/2210.15304/) (2022)

## Built on by (most cited first, 4 of 4)

- [Fragment-Wise Interpretability in Graph Neural Networks via Molecule Decomposition and Contribution Analysis](https://mlsanity.com/paper/2508.15015/) (2025)
- [FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization](https://mlsanity.com/paper/2605.10230/) (2026)
- [Measuring What Matters: A Unified Evaluation Framework for GNN Explainability](https://mlsanity.com/paper/2607.04600/) (2026)
- [WOMBAT: Whitebox Oracle for Molecular Benchmarking and Attribution Testing](https://mlsanity.com/paper/2610.00713/) (2026)

## Abstract (arXiv)

Understanding the reasoning behind deep learning model predictions is crucial in cheminformatics and drug discovery, where molecular design determines their properties. However, current evaluation frameworks for Explainable AI (XAI) in this domain often rely on artificial datasets or simplified tasks, employing data-derived metrics that fail to capture the complexity of real-world scenarios and lack a direct link to explanation faithfulness. To address this, we introduce B-XAIC, a novel benchmark constructed from real-world molecular data and diverse tasks with known ground-truth rationales for assigned labels. Through a comprehensive evaluation using B-XAIC, we reveal limitations of existing XAI methods for Graph Neural Networks (GNNs) in the molecular domain. This benchmark provides a valuable resource for gaining deeper insights into the faithfulness of XAI, facilitating the development of more reliable and interpretable models.