# Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction

arXiv: https://arxiv.org/abs/2410.15165 · HTML: https://mlsanity.com/paper/2410.15165/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 42 references that are in the map.
- First posted on arXiv 19 Oct 2024.

## Builds on (most cited first, 18 of 18)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [Self-Refine: Iterative Refinement with Self-Feedback](https://mlsanity.com/paper/2303.17651/) (2023)
- [Sequence to Sequence Learning with Neural Networks](https://mlsanity.com/paper/1409.3215/) (2014)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [TUDataset: A collection of benchmark datasets for learning with graphs](https://mlsanity.com/paper/2007.08663/) (2020)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [Talking About Large Language Models](https://mlsanity.com/paper/2212.03551/) (2022)
- [Preserving Causal Constraints in Counterfactual Explanations for Machine Learning Classifiers](https://mlsanity.com/paper/1912.03277/) (2019)
- [Learning and Evaluating Graph Neural Network Explanations based on Counterfactual and Factual Reasoning](https://mlsanity.com/paper/2202.08816/) (2022)
- [Robust Counterfactual Explanations on Graph Neural Networks](https://mlsanity.com/paper/2107.04086/) (2021)
- [CLEAR: Generative Counterfactual Explanations on Graphs](https://mlsanity.com/paper/2210.08443/) (2022)
- [Usable XAI: 10 Strategies Towards Exploiting Explainability in the LLM Era](https://mlsanity.com/paper/2403.08946/) (2024)
- [Counterfactual Graphs for Explainable Classification of Brain Networks](https://mlsanity.com/paper/2106.08640/) (2021)
- [RegExplainer: Generating Explanations for Graph Neural Networks in Regression Tasks](https://mlsanity.com/paper/2307.07840/) (2023)

## Built on by (most cited first, 3 of 3)

- [GraphXAIN: Narratives to Explain Graph Neural Networks](https://mlsanity.com/paper/2411.02540/) (2024)
- [MolEvolve: LLM-Guided Evolutionary Search for Interpretable Molecular Optimization](https://mlsanity.com/paper/2603.24382/) (2026)
- [Implicit Neural Representations of Molecular Vector-Valued Functions](https://mlsanity.com/paper/2502.10848/) (2025)

## Abstract (arXiv)

In recent years, Graph Neural Networks (GNNs) have become successful in molecular property prediction tasks such as toxicity analysis. However, due to the black-box nature of GNNs, their outputs can be concerning in high-stakes decision-making scenarios, e.g., drug discovery. Facing such an issue, Graph Counterfactual Explanation (GCE) has emerged as a promising approach to improve GNN transparency. However, current GCE methods usually fail to take domain-specific knowledge into consideration, which can result in outputs that are not easily comprehensible by humans. To address this challenge, we propose a novel GCE method, LLM-GCE, to unleash the power of large language models (LLMs) in explaining GNNs for molecular property prediction. Specifically, we utilize an autoencoder to generate the counterfactual graph topology from a set of counterfactual text pairs (CTPs) based on an input graph. Meanwhile, we also incorporate a CTP dynamic feedback module to mitigate LLM hallucination, which provides intermediate feedback derived from the generated counterfactuals as an attempt to give more faithful guidance. Extensive experiments demonstrate the superior performance of LLM-GCE. Our code is released on https://github.com/YinhanHe123/newLLM4GNNExplanation.