Subgraph Concept Networks: Concept Levels in Graph Classification

arXiv cs.LG / 4/22/2026

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Key Points

  • The paper addresses the opacity of Graph Neural Network (GNN) reasoning and the trust gap in their predictions by focusing on concept-based explanations.
  • It critiques existing concept-based methods for graph classification as being limited to the node-embedding space and obscured by pooling operations.
  • The authors introduce the Subgraph Concept Network, the first architecture aimed at extracting both subgraph-level and graph-level concepts within a single GNN framework.
  • The approach uses soft clustering on node concept embeddings to derive concepts at multiple granularities, enabling more interpretable reasoning.
  • Experiments indicate that the model maintains competitive accuracy while discovering meaningful concepts at different network levels.

Abstract

The reasoning process of Graph Neural Networks is complex and considered opaque, limiting trust in their predictions. To alleviate this issue, prior work has proposed concept-based explanations, extracted from clusters in the model's node embeddings. However, a limitation of concept-based explanations is that they only explain the node embedding space and are obscured by pooling in graph classification. To mitigate this issue and provide a deeper level of understanding, we propose the Subgraph Concept Network. The Subgraph Concept Network is the first graph neural network architecture that distils subgraph and graph-level concepts. It achieves this by performing soft clustering on node concept embeddings to derive subgraph and graph-level concepts. Our results show that the Subgraph Concept Network allows to obtain competitive model accuracy, while discovering meaningful concepts at different levels of the network.

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