Counting Graph Substructures with Graph Neural Networks

Graph Neural Networks (GNNs) are powerful representation learning tools that have achieved remarkable performance in various downstream tasks. However, there are still open questions regarding their ability to count and list substructures, which play a crucial role in biological and social networks. In this work, we fill this gap and characterize the representation and generalization power of GNNs in terms of their ability to produce powerful representations that count substructures. In particular, we study the message-passing operations of GNNs with random node input in a novel fashion, and show how they can produce equivariant representations that are associated with high-order statistical moments. Using these representations, we prove that GNNs can learn how to count cycles, cliques, quasi-cliques, and the number of connected components in a graph. We also provide new insights into the generalization capacity of GNNs. Our analysis is constructive and enables the design of a generic GNN architecture that shows remarkable performance in four distinct tasks: cycle detection, cycle counting, graph classification, and molecular property prediction.