Block graph

Abstract: In this article, we propose a family of efficient kernels for large graphs with discrete node labels. Key to our method is a rapid feature extraction scheme based on the Weisfeiler-Lehman test of isomorphism on graphs. It maps the original graph to a sequence of graphs, whose node attributes capture topological and label information. A family of kernels can be defined based on this Weisfeiler-Lehman sequence of graphs, including a highly efficient kernel comparing subtree-like patterns. Its runtime scales only linearly in the number of edges of the graphs and the length of the Weisfeiler-Lehman graph sequence. In our experimental evaluation, our kernels outperform state-of-the-art graph kernels on several graph classification benchmark data sets in terms of accuracy and runtime. Our kernels open the door to large-scale applications of graph kernels in various disciplines such as computational biology and social network analysis.

Abstract: Data mining algorithms are facing the challenge to deal with an increasing number of complex objects. For graph data, a whole toolbox of data mining algorithms becomes available by defining a kernel function on instances of graphs. Graph kernels based on walks, subtrees and cycles in graphs have been proposed so far. As a general problem, these kernels are either computationally expensive or limited in their expressiveness. We try to overcome this problem by defining expressive graph kernels which are based on paths. As the computation of all paths and longest paths in a graph is NP-hard, we propose graph kernels based on shortest paths. These kernels are computable in polynomial time, retain expressivity and are still positive definite. In experiments on classification of graph models of proteins, our shortest-path kernels show significantly higher classification accuracy than walk-based kernels.

Abstract: As most ‘real-world’ data is structured, research in kernel methods has begun investigating kernels for various kinds of structured data. One of the most widely used tools for modeling structured data are graphs. An interesting and important challenge is thus to investigate kernels on instances that are represented by graphs. So far, only very specific graphs such as trees and strings have been considered.