Graph Neural Networks (GNNs) have emerged as a dominant approach in graph representation learning, yet they often struggle to capture consistent similarity relationships among graphs. To capture similarity relationships, while graph kernel methods like the Weisfeiler-Lehman subtree (WL-subtree) and Weisfeiler-Lehman optimal assignment (WLOA) perform effectively, they are heavily reliant on predefined kernels and lack sufficient non-linearities. Our work aims to bridge the gap between neural network methods and kernel approaches by enabling GNNs to consistently capture relational structures in their learned representations. Given the analogy between the message-passing process of GNNs and WL algorithms, we thoroughly compare and analyze the properties of WL-subtree and WLOA kernels. We find that the similarities captured by WLOA at different iterations are asymptotically consistent, ensuring that similar graphs remain similar in subsequent iterations, thereby leading to superior performance over the WL-subtree kernel. Inspired by these findings, we conjecture that the consistency in the similarities of graph representations across GNN layers is crucial in capturing relational structures and enhancing graph classification performance. Thus, we propose a loss to enforce the similarity of graph representations to be consistent across different layers. Our empirical analysis verifies our conjecture and shows that our proposed consistency loss can significantly enhance graph classification performance across several GNN backbones on various datasets.

We investigate the distance function learned by message passing neural networks (MPNNs) in specific tasks, aiming to capture the functional distance between prediction targets that MPNNs implicitly learn. This contrasts with previous work, which links MPNN distances on arbitrary tasks to structural distances on graphs that ignore task-specific information. To address this gap, we distill the distance between MPNN embeddings into an interpretable graph distance. Our method uses optimal transport on the Weisfeiler Leman Labeling Tree (WILT), where the edge weights reveal subgraphs that strongly influence the distance between embeddings. This approach generalizes two well-known graph kernels and can be computed in linear time. Through extensive experiments, we demonstrate that MPNNs define the relative position of embeddings by focusing on a small set of subgraphs that are known to be functionally important in the domain.

Graph Neural Networks (GNNs) have emerged as a dominant approach in graph representation learning, yet they often struggle to capture consistent similarity relationships among graphs. To capture similarity relationships, while graph kernel methods like the Weisfeiler-Lehman subtree (WL-subtree) and Weisfeiler-Lehman optimal assignment (WLOA) perform effectively, they are heavily reliant on predefined kernels and lack sufficient non-linearities. Our work aims to bridge the gap between neural network methods and kernel approaches by enabling GNNs to consistently capture relational structures in their learned representations. Given the analogy between the message-passing process of GNNs and WL algorithms, we thoroughly compare and analyze the properties of WL-subtree and WLOA kernels. We find that the similarities captured by WLOA at different iterations are asymptotically consistent, ensuring that similar graphs remain similar in subsequent iterations, thereby leading to superior performance over the WL-subtree kernel.

The Weisfeiler-Leman algorithm ($1$-WL) is a well-studied heuristic for the graph isomorphism problem. Recently, the algorithm has played a prominent role in understanding the expressive power of message-passing graph neural networks (MPNNs) and being effective as a graph kernel. Despite its success, $1$-WL faces challenges in distinguishing non-isomorphic graphs, leading to the development of more expressive MPNN and kernel architectures. However, the relationship between enhanced expressivity and improved generalization performance remains unclear. Here, we show that an architecture's expressivity offers limited insights into its generalization performance when viewed through graph isomorphism. Moreover, we focus on augmenting $1$-WL and MPNNs with subgraph information and employ classical margin theory to investigate the conditions under which an architecture's increased expressivity aligns with improved generalization performance. In addition, we show that gradient flow pushes the MPNN's weights toward the maximum margin solution. Further, we introduce variations of expressive $1$-WL-based kernel and MPNN architectures with provable generalization properties. Our empirical study confirms the validity of our theoretical findings.