Simplifying Graph Kernels for Efficient

TL;DR

This paper introduces simplified graph kernels that replace deep stacking with efficient message aggregation and leverage Gaussian Process theory, achieving competitive accuracy with reduced computational complexity for large-scale graph learning.

Contribution

It presents novel simplified graph kernels that improve efficiency by avoiding deep layer stacking and using analytical computation based on Gaussian Process theory.

Findings

Achieved competitive accuracy on standard benchmarks

Reduced runtime significantly compared to traditional methods

Maintained expressive power with streamlined kernel formulations

Abstract

While kernel methods and Graph Neural Networks offer complementary strengths, integrating the two has posed challenges in efficiency and scalability. The Graph Neural Tangent Kernel provides a theoretical bridge by interpreting GNNs through the lens of neural tangent kernels. However, its reliance on deep, stacked layers introduces repeated computations that hinder performance. In this work, we introduce a new perspective by designing the simplified graph kernel, which replaces deep layer stacking with a streamlined $K$-step message aggregation process. This formulation avoids iterative layer-wise propagation altogether, leading to a more concise and computationally efficient framework without sacrificing the expressive power needed for graph tasks. Beyond this simplification, we propose another Simplified Graph Kernel, which draws from Gaussian Process theory to model infinite-width GNNs. Rather than simulating network depth, this kernel analytically computes kernel values based on the statistical behavior of nonlinear activations in the infinite limit. This eliminates the need for explicit architecture simulation, further reducing complexity. Our experiments on standard graph and node classification benchmarks show that our methods achieve competitive accuracy while reducing runtime. This makes them practical alternatives for learning on graphs at scale. Full implementation and reproducibility materials are provided at: https://anonymous.4open.science/r/SGNK-1CE4/.