Edge distance graph kernel and its application to small molecule classification

Abstract

Graph classification is an important problem in graph mining with various applications in different fields. Kernel methods have been successfully applied to this problem, recently producing promising results. A graph kernel that mostly specifies classification performance has to be defined in order to apply kernel methods to a graph classification problem. Although there are various previously proposed graph kernels, the problem is still worth investigating, as the available kernels are far from perfect. In this paper, we propose a new graph kernel based on a recently proposed concept called edge distance-k graphs. These new graphs are derived from the original graph and have the potential to be used as novel graph descriptors. We propose a method to convert these graphs into a multiset of strings that is further used to compute a kernel for graphs. The proposed graph kernel is then evaluated on various data sets in comparison to a recently proposed group of graph kernels. The results are promising, both in terms of performance and computational requirements.