Title: Expressive and Invariant Graph Learning via Canonical Tree Cover Neural Networks
Primary area: learning on graphs and other geometries & topologies
Keywords: graph neural networks, canonicalization, invariance, tree, molecule graph

Abstract: While message-passing NNs (MPNNs) are naturally invariant on graphs, they are fundamentally limited in expressive power. Canonicalization offers a powerful alternative by mapping each graph to a unique, invariant representation on which expressive encoders can operate. However, existing approaches rely on a single canonical sequence, which flattens the structure, distorts graph distances, and restricts expressivity. To address these limitations, we introduce Canonical Tree Cover Neural Networks (CTNNs), which represent the graph with a canonical spanning tree cover, i.e., a small collection of canonical trees covering all edges. Each tree is then processed with an existing expressive tree encoder. Theoretically, tree covers better preserve graph distances than sequences, and on sparse graphs, the cover recovers all edges with a logarithmic number of trees in the graph size, making CTNNs strictly more expressive than sequence-based canonicalization pipelines. Empirically, CTNNs consistently outperform invariant GNNs, random samplers, and sequence canonicalizations across graph classification benchmarks. Overall, CTNNs advance graph learning by providing an efficient, invariant, and expressive representation learning framework via tree cover-based canonicalization.