A Survey on Graph Kernels

Graph kernels have become an established and widely-used technique for solving classification tasks on graphs. This survey gives a comprehensive overview of techniques for kernel-based graph classification developed in the past 15 years. We describe and categorize graph kernels based on properties inherent to their design, such as the nature of their extracted graph features, their method of computation and their applicability to problems in practice. In an extensive experimental evaluation, we study the classification accuracy of a large suite of graph kernels on established benchmarks as well as new datasets. We compare the performance of popular kernels with several baseline methods and study the effect of applying a Gaussian RBF kernel to the metric induced by a graph kernel. In doing so, we find that simple baselines become competitive after this transformation on some datasets. Moreover, we study the extent to which existing graph kernels agree in their predictions (and prediction errors) and obtain a data-driven categorization of kernels as result. Finally, based on our experimental results, we derive a practitioner's guide to kernel-based graph classification

Curvature Filtrations for Graph Generative Model Evaluation

Graph generative model evaluation necessitates understanding differences between graphs on the distributional level. This entails being able to harness salient attributes of graphs in an efficient manner. Curvature constitutes one such property of graphs, and has recently started to prove useful in characterising graphs. Its expressive properties, stability, and practical utility in model evaluation remain largely unexplored, however. We combine graph curvature descriptors with emerging methods from topological data analysis to obtain robust, expressive descriptors for evaluating graph generative models

Wide Graph Neural Networks: Aggregation Provably Leads to Exponentially Trainability Loss

Graph convolutional networks (GCNs) and their variants have achieved great success in dealing with graph-structured data. However, it is well known that deep GCNs will suffer from over-smoothing problem, where node representations tend to be indistinguishable as we stack up more layers. Although extensive research has confirmed this prevailing understanding, few theoretical analyses have been conducted to study the expressivity and trainability of deep GCNs. In this work, we demonstrate these characterizations by studying the Gaussian Process Kernel (GPK) and Graph Neural Tangent Kernel (GNTK) of an infinitely-wide GCN, corresponding to the analysis on expressivity and trainability, respectively. We first prove the expressivity of infinitely-wide GCNs decaying at an exponential rate by applying the mean-field theory on GPK. Besides, we formulate the asymptotic behaviors of GNTK in the large depth, which enables us to reveal the dropping trainability of wide and deep GCNs at an exponential rate. Additionally, we extend our theoretical framework to analyze residual connection-resemble techniques. We found that these techniques can mildly mitigate exponential decay, but they failed to overcome it fundamentally. Finally, all theoretical results in this work are corroborated experimentally on a variety of graph-structured datasets.Comment: 23 pages, 4 figure

Measuring the expressivity of graph kernels through the rademacher complexity

Graph kernels are widely adopted in real-world applications that involve learning on graph data. Different graph kernels have been proposed in literature, but no theoretical comparison among them is present. In this paper we provide a formal definition for the expressiveness of a graph kernel by means of the Rademacher Complexity, and analyze the differences among some state-of-the-art graph kernels. Results on real world datasets confirm some known properties of graph kernels, showing that the Rademacher Complexity is indeed a suitable measure for this analysis

Labeled Subgraph Entropy Kernel

In recent years, kernel methods are widespread in tasks of similarity measuring. Specifically, graph kernels are widely used in fields of bioinformatics, chemistry and financial data analysis. However, existing methods, especially entropy based graph kernels are subject to large computational complexity and the negligence of node-level information. In this paper, we propose a novel labeled subgraph entropy graph kernel, which performs well in structural similarity assessment. We design a dynamic programming subgraph enumeration algorithm, which effectively reduces the time complexity. Specially, we propose labeled subgraph, which enriches substructure topology with semantic information. Analogizing the cluster expansion process of gas cluster in statistical mechanics, we re-derive the partition function and calculate the global graph entropy to characterize the network. In order to test our method, we apply several real-world datasets and assess the effects in different tasks. To capture more experiment details, we quantitatively and qualitatively analyze the contribution of different topology structures. Experimental results successfully demonstrate the effectiveness of our method which outperforms several state-of-the-art methods.Comment: 9 pages,5 figure