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Do Graph Neural Network States Contain Graph Properties?

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Deep neural networks (DNNs) achieve state-of-the-art performance on many tasks, but this often requires increasingly larger model sizes, which in turn leads to more complex internal representations. Explain ability techniques (XAI) have made remarkable progress in the interpretability of ML models. However, the non-euclidean nature of Graph Neural Networks (GNNs) makes it difficult to reuse already existing XAI methods. While other works have focused on instance-based explanation methods for GNNs, very few have investigated model-based methods and, to our knowledge, none have tried to probe the embedding of the GNNs for structural graph properties. In this paper we present a model agnostic explain ability pipeline for Graph Neural Networks (GNNs) employing diagnostic classifiers. We propose to consider graph-theoretic properties as the features of choice for studying the emergence of representations in GNNs. This pipeline aims to probe and interpret the learned representations in GNNs across various architectures and datasets, refining our understanding and trust in these models.

Original languageEnglish
Pages (from-to)1-37
Number of pages37
JournalProceedings of Machine Learning Research
Volume284
Early online date29 Aug 2025
DOIs
Publication statusPublished - 2025
Event19th Conference on Neurosymbolic Learning and Reasoning, NeSy 2025 - Santa Cruz, United States
Duration: 8 Sept 202510 Sept 2025

Bibliographical note

Publisher Copyright:
© 2025 T. Pelletreau-Duris, R.v. Bakel & M. Cochez.

Funding

This work is based on the MSc. AI thesis by Tom Pelletreau-Duris, a large part of the results were also presented in that work. Michael Cochez is partially funded by the Elsevier Discovery Lab, partially funded by the Graph-Massivizer project, funded by the Horizon Europe programme of the European Union (grant 101093202), and supported by a gift from Accenture LLP. His work on this publication is in part based upon work from COST Action CA23147 GOBLIN - Global Network on Large-Scale, Cross-domain and Multilingual Open Knowledge Graphs, supported by COST (European Cooperation in Science and Technology, https://www.cost.eu). We would also want to thank the anonymous reviewers for their comments and suggestions that helped us improve the manuscript.

FundersFunder number
European Cooperation in Science and Technology
HORIZON EUROPE Framework Programme101093202

    Keywords

    • Explainable AI
    • Graph Neural Networks
    • linear probing
    • Mechanistic Interpretability
    • XAI

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