Subgraph Concept Networks: Concept Levels in Graph Classification

Lucie Charlotte Magister, Alexander Norcliffe, Iulia Duta, Pietro Lio
4/20/2026
cs.LG

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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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@article{magister2026subgraph,
  title  = {Subgraph Concept Networks: Concept Levels in Graph Classification},
  author = {Lucie Charlotte Magister and Alexander Norcliffe and Iulia Duta and Pietro Lio},
  year   = {2026},
  eprint = {2604.18868},
  archivePrefix = {arXiv},
  url    = {http://arxiv.org/abs/2604.18868v1}
}

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