Message-passing graph neural networks (GNNs) excel at capturing local relationships but struggle with long-range dependencies in graphs. In contrast, graph transformers (GTs) enable global information exchange but often oversimplify the graph structure by representing graphs as sets of fixed-length vectors. This work introduces a novel architecture that overcomes the shortcomings of both approaches by combining the long-range information of random walks with local message passing. By treating random walks as sequences, our architecture leverages recent advances in sequence models to effectively capture long-range dependencies within these walks. Based on this concept, we propose a framework that offers (1) more expressive graph representations through random walk sequences, (2) the ability to utilize any sequence model for capturing long-range dependencies, and (3) the flexibility by integrating various GNN and GT architectures. Our experimental evaluations demonstrate that our approach achieves competitive performance on 19 graph and node benchmark datasets, notably outperforming existing methods by up to 13\% on the PascalVoc-SP and COCO-SP datasets. Code: https://github.com/BorgwardtLab/NeuralWalker

Message passing graph neural networks (GNNs) are known to have limited expressive power in their ability to distinguish some non-isomorphic graphs. Because of this, it is well known that they are unable to detect or count arbitrary graph substructures (i.e., solving the subgraph isomorphism problem), a task that is of great importance for several types of graph-structured data. However, we observe that GNNs are in fact able to count graph patterns quite accurately across several real-world graph datasets. Motivated by this observation, we provide an analysis of the subgraph-counting capabilities of GNNs beyond the worst case, deriving several sufficient conditions for GNNs to be able to count subgraphs and, more importantly, to be able to sample-efficiently learn to count subgraphs. Moreover, we develop novel dynamic programming algorithms for solving the subgraph isomorphism problem on restricted classes of pattern and target graphs, and show that message-passing GNNs can efficiently simulate these dynamic programs. Finally, we empirically validate that our sufficient conditions for GNNs to count subgraphs hold on many real-world datasets, providing a theoretically-grounded explanation to our motivating observations.

Graph neural networks (GNNs) employing message passing for graph classification are inherently limited by the expressive power of the Weisfeiler-Leman (WL) test for graph isomorphism. Node individualization schemes, which assign unique identifiers to nodes (e.g., by adding random noise to features), are a common approach for achieving universal expressiveness. However, the ability of GNNs endowed with individualization schemes to generalize beyond the training data is still an open question. To address this question, this paper presents a theoretical analysis of the sample complexity of such GNNs from a statistical learning perspective, employing Vapnik–Chervonenkis (VC) dimension and covering number bounds. We demonstrate that node individualization schemes that are permutation-equivariant result in lower sample complexity, and design novel individualization schemes that exploit these results. As an application of this analysis, we also develop a novel architecture that can perform substructure identification (i.e., subgraph isomorphism) while having a lower VC dimension compared to competing methods. Finally, our theoretical findings are validated experimentally on both synthetic and real-world datasets.

The majority of popular graph kernels is based on the concept of Haussler's R-convolution kernel and defines graph similarities in terms of mutual substructures. In this work, we enrich these similarity measures by considering graph filtrations: Using meaningful orders on the set of edges, which allow to construct a sequence of nested graphs, we can consider a graph at multiple granularities. A key concept of our approach is to track graph features over the course of such graph resolutions. Rather than to simply compare frequencies of features in graphs, this allows for their comparison in terms of when and for how long they exist in the sequences. In this work, we propose a family of graph kernels that incorporate these existence intervals of features. While our approach can be applied to arbitrary graph features, we particularly highlight Weisfeiler-Lehman vertex labels, leading to efficient kernels. We show that using Weisfeiler-Lehman labels over certain filtrations strictly increases the expressive power over the ordinary Weisfeiler-Lehman procedure in terms of deciding graph isomorphism. In fact, this result directly yields more powerful graph kernels based on such features and has implications to graph neural networks due to their close relationship to the Weisfeiler-Lehman method. We empirically validate the expressive power of our graph kernels and show significant improvements over state-of-the-art graph kernels in terms of predictive performance on various real-world benchmark datasets.

Abstract After more than one decade, Weisfeiler-Lehman graph kernels are still among the most prevalent graph kernels due to their remarkable predictive performance and time complexity. They are based on a fast iterative partitioning of vertices, originally designed for deciding graph isomorphism with one-sided error. The Weisfeiler-Lehman graph kernels retain this idea and compare such labels with respect to equality. This binary valued comparison is, however, arguably too rigid for defining suitable graph kernels for certain graph classes. To overcome this limitation, we propose a generalization of Weisfeiler-Lehman graph kernels which takes into account a more natural and finer grade of similarity between Weisfeiler-Lehman labels than equality. We show that the proposed similarity can be calculated efficiently by means of the Wasserstein distance between certain vectors representing Weisfeiler-Lehman labels. This and other facts give rise to the natural choice of partitioning the vertices with the Wasserstein k-means algorithm. We empirically demonstrate on the Weisfeiler-Lehman subtree kernel, which is one of the most prominent Weisfeiler-Lehman graph kernels, that our generalization significantly outperforms this and other state-of-the-art graph kernels in terms of predictive performance on datasets which contain structurally more complex graphs beyond the typically considered molecular graphs.