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

Generalized Shortest Path Kernel on Graphs

We consider the problem of classifying graphs using graph kernels. We define a new graph kernel, called the generalized shortest path kernel, based on the number and length of shortest paths between nodes. For our example classification problem, we consider the task of classifying random graphs from two well-known families, by the number of clusters they contain. We verify empirically that the generalized shortest path kernel outperforms the original shortest path kernel on a number of datasets. We give a theoretical analysis for explaining our experimental results. In particular, we estimate distributions of the expected feature vectors for the shortest path kernel and the generalized shortest path kernel, and we show some evidence explaining why our graph kernel outperforms the shortest path kernel for our graph classification problem.Comment: Short version presented at Discovery Science 2015 in Banf

A Labeled Graph Kernel for Relationship Extraction

In this paper, we propose an approach for Relationship Extraction (RE) based on labeled graph kernels. The kernel we propose is a particularization of a random walk kernel that exploits two properties previously studied in the RE literature: (i) the words between the candidate entities or connecting them in a syntactic representation are particularly likely to carry information regarding the relationship; and (ii) combining information from distinct sources in a kernel may help the RE system make better decisions. We performed experiments on a dataset of protein-protein interactions and the results show that our approach obtains effectiveness values that are comparable with the state-of-the art kernel methods. Moreover, our approach is able to outperform the state-of-the-art kernels when combined with other kernel methods

A tree-based kernel for graphs with continuous attributes

The availability of graph data with node attributes that can be either discrete or real-valued is constantly increasing. While existing kernel methods are effective techniques for dealing with graphs having discrete node labels, their adaptation to non-discrete or continuous node attributes has been limited, mainly for computational issues. Recently, a few kernels especially tailored for this domain, and that trade predictive performance for computational efficiency, have been proposed. In this paper, we propose a graph kernel for complex and continuous nodes' attributes, whose features are tree structures extracted from specific graph visits. The kernel manages to keep the same complexity of state-of-the-art kernels while implicitly using a larger feature space. We further present an approximated variant of the kernel which reduces its complexity significantly. Experimental results obtained on six real-world datasets show that the kernel is the best performing one on most of them. Moreover, in most cases the approximated version reaches comparable performances to current state-of-the-art kernels in terms of classification accuracy while greatly shortening the running times.Comment: This work has been submitted to the IEEE Transactions on Neural Networks and Learning Systems for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessibl

Data Reduction for Graph Coloring Problems

This paper studies the kernelization complexity of graph coloring problems with respect to certain structural parameterizations of the input instances. We are interested in how well polynomial-time data reduction can provably shrink instances of coloring problems, in terms of the chosen parameter. It is well known that deciding 3-colorability is already NP-complete, hence parameterizing by the requested number of colors is not fruitful. Instead, we pick up on a research thread initiated by Cai (DAM, 2003) who studied coloring problems parameterized by the modification distance of the input graph to a graph class on which coloring is polynomial-time solvable; for example parameterizing by the number k of vertex-deletions needed to make the graph chordal. We obtain various upper and lower bounds for kernels of such parameterizations of q-Coloring, complementing Cai's study of the time complexity with respect to these parameters. Our results show that the existence of polynomial kernels for q-Coloring parameterized by the vertex-deletion distance to a graph class F is strongly related to the existence of a function f(q) which bounds the number of vertices which are needed to preserve the NO-answer to an instance of q-List-Coloring on F.Comment: Author-accepted manuscript of the article that will appear in the FCT 2011 special issue of Information & Computatio