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Paper · 2506.13911 · NeurIPS · 2025

Logical Expressiveness of Graph Neural Networks with Hierarchical Node Individualization

Arie Soeteman, Balder Ten Cate

arXiv · PDF · Open in the Atlas

Code that ran

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RepositoryRoleRan
ariesoeteman/hegnn canonical 0 of 8
FunctionStatusWhere it lives
array_list_to_tensor_list Not yet run ariesoeteman/hegnn/hegnn/data_processing/hdf5_structures.py
code served (permissive licence) · get_code("5f06c3eac54e5a1a")
count_cycles Not yet run ariesoeteman/hegnn/hegnn/data_processing/cycle_counts.py
code served (permissive licence) · get_code("741b7ffa6d75215b")
merge_batch_list Not yet run ariesoeteman/hegnn/hegnn/data_processing/data_structures.py
code served (permissive licence) · get_code("f46e7cceda763952")
recursive_dict_update Not yet run ariesoeteman/hegnn/hegnn/config/parse_config.py
code served (permissive licence) · get_code("efbd80279eae3407")
square_edge_index Not yet run ariesoeteman/hegnn/hegnn/data_processing/data_preprocessing.py
code served (permissive licence) · get_code("1df314f5090b4621")
square_x Not yet run ariesoeteman/hegnn/hegnn/data_processing/data_preprocessing.py
code served (permissive licence) · get_code("7486d5df90e40102")
to_numpy Not yet run ariesoeteman/hegnn/hegnn/data_processing/hdf5_structures.py
code served (permissive licence) · get_code("a0d88b4d6461590b")
to_tensor Not yet run ariesoeteman/hegnn/hegnn/data_processing/hdf5_structures.py
code served (permissive licence) · get_code("273d3b1783ffc1ae")

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Abstract

We propose and study Hierarchical Ego Graph Neural Networks (HE-GNNs), an expressive extension of graph neural networks (GNNs) with hierarchical node individualization, inspired by the Individualization-Refinement paradigm for isomorphism testing. HE-GNNs generalize subgraph-GNNs and form a hierarchy of increasingly expressive models that, in the limit, distinguish graphs up to isomorphism. We show that, over graphs of bounded degree, the separating power of HE-GNN node classifiers equals that of graded hybrid logic. This characterization enables us to relate the separating power of HE-GNNs to that of higher-order GNNs, GNNs enriched with local homomorphism count features, and color refinement algorithms based on Individualization-Refinement. Our experimental results confirm the practical feasibility of HE-GNNs and show benefits in comparison with traditional GNN architectures, both with and without local homomorphism count features.

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