Till Hendrik Schulz

Dexiong Chen, Till Hendrik Schulz, Karsten Borgwardt

Subgraph detection seeks to identify whether and where instances of query patterns occur within a larger graph. This problem is fundamental across scientific domains and is closely related to subgraph isomorphism, which is NP-complete, limiting combinatorial approaches to small patterns or moderately sized graphs. We introduce GraphDETR, a deep learning framework that formulates subgraph detection as a set prediction problem, analogous to DETR in object detection. GraphDETR encodes the target graph with a graph neural network, and employs a fixed set of learnable query vectors, decoded via a transformer decoder, to predict all pattern occurrences jointly in a single forward pass. This is enabled by training the model end-to-end with bipartite matching. Unlike traditional combinatorial methods that only solve exact structural matching, GraphDETR naturally extends to approximate matching, enabling detection beyond exact pattern correspondence. Empirically, we show that GraphDETR can detect diverse patterns, such as molecular structures, cycles, cliques, and fuzzy patterns of up to 50 nodes, in target graphs with up to 1000 nodes. We further evaluate on molecular functional group detection over the ChEMBL dataset, where GraphDETR predicts the complete set of functional groups per molecule, achieving a strong performance of $\text{AP}_{100} = 91.2$.

Dexiong Chen, Till Hendrik Schulz, Karsten Borgwardt

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 significant performance improvements on 19 graph and node benchmark datasets, notably outperforming existing methods by up to 13\% on the PascalVoc-SP and COCO-SP datasets. The code is available at https://github.com/BorgwardtLab/NeuralWalker.

Till Hendrik Schulz, Pascal Welke, Stefan Wrobel

The majority of popular graph kernels is based on the concept of Haussler's $\mathcal{R}$-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. For one thing, this provides access to features on different levels of resolution. Furthermore, rather than to simply compare frequencies of features in graphs, it 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.

Till Hendrik Schulz, Tamás Horváth, Pascal Welke et al.

The Weisfeiler-Lehman graph kernels are among the most prevalent graph kernels due to their remarkable time complexity and predictive performance. Their key concept is based on an implicit comparison of neighborhood representing trees with respect to equality (i.e., isomorphism). This binary valued comparison is, however, arguably too rigid for defining suitable similarity measures over graphs. To overcome this limitation, we propose a generalization of Weisfeiler-Lehman graph kernels which takes into account the similarity between trees rather than equality. We achieve this using a specifically fitted variation of the well-known tree edit distance which can efficiently be calculated. We empirically show that our approach significantly outperforms state-of-the-art methods in terms of predictive performance on datasets containing structurally more complex graphs beyond the typically considered molecular graphs.