Fast depth-based subgraph kernels for unattributed graphs

In this paper, we investigate two fast subgraph kernels based on a depth-based representation of graph-structure. Both methods gauge depth information through a family of K-layer expansion subgraphs rooted at a vertex [1]. The first method commences by computing a centroid-based complexity trace for each graph, using a depth-based representation rooted at the centroid vertex that has minimum shortest path length variance to the remaining vertices [2]. This subgraph kernel is computed by measuring the Jensen-Shannon divergence between centroid-based complexity entropy traces. The second method, on the other hand, computes a depth-based representation around each vertex in turn. The corresponding subgraph kernel is computed using isomorphisms tests to compare the depth-based representation rooted at each vertex in turn. For graphs with n vertices, the time complexities for the two new kernels are O(n 2) and O(n 3), in contrast to O(n 6) for the classic Gärtner graph kernel [3]. Key to achieving this efficiency is that we compute the required Shannon entropy of the random walk for our kernels with O(n 2) operations. This computational strategy enables our subgraph kernels to easily scale up to graphs of reasonably large sizes and thus overcome the size limits arising in state-of-the-art graph kernels. Experiments on standard bioinformatics and computer vision graph datasets demonstrate the effectiveness and efficiency of our new subgraph kernels

Information Theoretic Graph Kernels

This thesis addresses the problems that arise in state-of-the-art structural learning methods for (hyper)graph classification or clustering, particularly focusing on developing novel information theoretic kernels for graphs. To this end, we commence in Chapter 3 by defining a family of Jensen-Shannon diffusion kernels, i.e., the information theoretic kernels, for (un)attributed graphs. We show that our kernels overcome the shortcomings of inefficiency (for the unattributed diffusion kernel) and discarding un-isomorphic substructures (for the attributed diffusion kernel) that arise in the R-convolution kernels. In Chapter 4, we present a novel framework of computing depth-based complexity traces rooted at the centroid vertices for graphs, which can be efficiently computed for graphs with large sizes. We show that our methods can characterize a graph in a higher dimensional complexity feature space than state-of-the-art complexity measures. In Chapter 5, we develop a novel unattributed graph kernel by matching the depth-based substructures in graphs, based on the contribution in Chapter 4. Unlike most existing graph kernels in the literature which merely enumerate similar substructure pairs of limited sizes, our method incorporates explicit local substructure correspondence into the process of kernelization. The new kernel thus overcomes the shortcoming of neglecting structural correspondence that arises in most state-of-the-art graph kernels. The novel methods developed in Chapters 3, 4, and 5 are only restricted to graphs. However, real-world data usually tends to be represented by higher order relationships (i.e., hypergraphs). To overcome the shortcoming, in Chapter 6 we present a new hypergraph kernel using substructure isomorphism tests. We show that our kernel limits tottering that arises in the existing walk and subtree based (hyper)graph kernels. In Chapter 7, we summarize the contributions of this thesis. Furthermore, we analyze the proposed methods. Finally, we give some suggestions for the future work