With the recent rise in the amount of structured data available, there has been considerable interest in methods for machine learning with graphs. Many of these approaches have been kernel methods, which focus on measuring the similarity between graphs. These generally involving measuring the similarity of structural elements such as walks or paths. Borgwardt and Kriegel proposed the all-paths kernel but emphasized that it is NP-hard to compute and infeasible in practice, favouring instead the shortest-path kernel. In this paper, we introduce a new algorithm for computing the all-paths kernel which is very efficient and enrich it further by including the simple cycles as well. We demonstrate how it is feasible even on large datasets to compute all the paths and simple cycles up to a moderate length. We show how to count labelled paths simple cycles between vertices of a graph and evaluate a labelled path and simple cycles kernel. Extensive evaluations on a variety of graph datasets demonstrate that the all-paths and cycles kernel has superior performance to the shortest-path kernel and state-of-the-art performance overall.
Graph kernels based on walks have also been proposed, the simplest example of which is the random walk kernel @cite_13 which counts the number of matching walks between two graphs where @math is the set of all walks in a graph, @math is the delta function kernel, i.e. 1 when the walks match and 0 otherwise, and @math is a weighting function dependent on the length of the walk. Two walks match if they are the same length or in the case of labelled graphs, if they have the same label sequence. This kernel is of interest because it can be efficiently evaluated in cubic time from the adjacency matrix of the product graph, i.e. @math . A number of suggestions have been made to improve the performance of the random walk kernel, for example to remove backtracking steps from the walk @cite_14 @cite_1 since this eliminates double-counting of structure.
@cite_1 @cite_14 @cite_13
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Positive definite kernels between labeled graphs have recently been proposed. They enable the application of kernel methods, such as support vector machines, to the analysis and classification of graphs, for example, chemical compounds. These graph kernels are obtained by marginalizing a kernel between paths with respect to a random walk model on the graph vertices along the edges. We propose two extensions of these graph kernels, with the double goal to reduce their computation time and increase their relevance as measure of similarity between graphs. First, we propose to modify the label of each vertex by automatically adding information about its environment with the use of the Morgan algorithm. Second, we suggest a modification of the random walk model to prevent the walk from coming back to a vertex that was just visited. These extensions are then tested on benchmark experiments of chemical compounds classification, with promising results. We study properties of multiple random walks on a graph under various assumptions of interaction between the particles. To give precise results, we make the analysis for random regular graphs. The cover time of a random walk on a random @math -regular graph was studied in [C. Cooper and A. Frieze, SIAM J. Discrete Math., 18 (2005), pp. 728-740], where it was shown with high probability (whp) that for @math the cover time is asymptotic to @math , where @math . In this paper we prove the following (whp) results, arising from the study of multiple random walks on a random regular graph @math . For @math independent walks on @math , the cover time @math is asymptotic to @math , where @math is the cover time of a single walk. For most starting positions, the expected number of steps before any of the walks meet is @math . If the walks can communicate when meeting at a vertex, we show that, for most starting positions, the expected time for @math walks to broadcast a single piece of information to each other is asymptotic to @math as @math . We also establish properties of walks where there are two types of particles, predator and prey, or where particles interact when they meet at a vertex by coalescing or by annihilating each other. For example, the expected extinction time of @math explosive particles ( @math even) tends to @math as @math . The case of @math coalescing particles, where one particle is initially located at each vertex, corresponds to a voter model defined as follows: Initially each vertex has a distinct opinion, and at each step each vertex changes its opinion to that of a random neighbor. The expected time for a unique opinion to emerge is the same as the expected time for all the particles to coalesce, which is asymptotic to @math . Combining results from the predator-prey and multiple random walk models allows us to compare expected detection times of all prey in the following scenarios: Both the predator and the prey move randomly, the prey moves randomly and the predators stay fixed, and the predators move randomly and the prey stays fixed. In all cases, with @math predators and @math prey the expected detection time is @math , where @math is the @math th harmonic number. Given a discrete random walk on a finite graph @math , the vacant set and vacant net are, respectively, the sets of vertices and edges which remain unvisited by the walk at a given step @math . These sets induce subgraphs of the underlying graph. Let @math be the subgraph of @math induced by the vacant set of the walk at step @math . Similarly, let @math be the subgraph of @math induced by the edges of the vacant net. For random @math -regular graphs @math , it was previously established that for a simple random walk, the graph @math of the vacant set undergoes a phase transition in the sense of the phase transition on Erd os -Renyi graphs @math . Thus, for @math there is an explicit value @math of the walk, such that for @math , @math has a unique giant component, plus components of size @math , whereas for @math all the components of @math are of size @math . We establish the threshold value @math for a phase transition in the graph @math of the vacant net of a simple random walk on a random @math -regular graph. We obtain the corresponding threshold results for the vacant set and vacant net of two modified random walks. These are a non-backtracking random walk, and, for @math even, a random walk which chooses unvisited edges whenever available. This allows a direct comparison of thresholds between simple and modified walks on random @math -regular graphs. The main findings are the following: As @math increases the threshold for the vacant set converges to @math in all three walks. For the vacant net, the threshold converges to @math for both the simple random walk and non-backtracking random walk. When @math is even, the threshold for the vacant net of the unvisited edge process converges to @math , which is also the vertex cover time of the process. 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.