Random Probing for Structural Self-Interactions in Graph Neural Networks

Saku Peltonen, H. Çağrı Bilgi, Kubilay Atasu

Graph Neural Networks (GNNs) fundamentally lack the ability to capture structural properties defined by node self-interactions, such as cycle counts, subgraph centrality, and heat kernel signatures. Existing solutions often rely on computationally expensive higher-order architectures or hand-crafted features. In this work, we introduce DIAL, a message-passing layer that gives nodes access to graph structure through the diagonal of graph-derived operators. Our approach uses randomized probing to provide nodes with learnable, permutation equivariant access to diagonal entries. We prove that our approach can express important structural features, including cycle counts, subgraph centrality, and heat kernel signatures. The proposed method can be integrated directly into message passing layers. Experiments on molecular property prediction, cycle counting, and pattern detection demonstrate the effectiveness of DIAL across a range of graph learning tasks.