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.
Another alternative to avoid double-counting structure and increase the discriminative power of the kernel is to use a decomposition into . A path is a sequence of edges such that no vertex is repeated in the path. The All-Paths (AP) kernel was proposed by Borgwardt and Kriegel @cite_0 : where @math is the set of all paths in a graph and @math is a base kernel for paths, typically the delta-function kernel. Borgwardt and Kriegel define a path to be an edge path, one which may not repeat edges but may repeat vertices, which is different from our definition but this has little practical impact. They note that computing all the paths is NP-hard in principle and difficult in practice, making this kernel impractical. Instead they adopt the kernel, where @math only contains the paths which are geodesically the shortest between any pair of vertices. Paths are labelled by their end-point labels. The shortest-path kernel is efficiently computable and practical to implement but ignores most of the paths present in a graph.
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Kernels are typically applied to linear algorithms whose weight vector is a linear combination of the feature vectors of the examples. On-line versions of these algorithms are sometimes called "additive updates" because they add a multiple of the last feature vector to the current weight vector.In this paper we have found a way to use special convolution kernels to efficiently implement "multiplicative" updates. The kernels are defined by a directed graph. Each edge contributes an input. The inputs along a path form a product feature and all such products build the feature vector associated with the inputs.We also have a set of probabilities on the edges so that the outflow from each vertex is one. We then discuss multiplicative updates on these graphs where the prediction is essentially a kernel computation and the update contributes a factor to each edge. After adding the factors to the edges, the total outflow out of each vertex is not one any more. However some clever algorithms re-normalize the weights on the paths so that the total outflow out of each vertex is one again. Finally, we show that if the digraph is built from a regular expressions, then this can be used for speeding up the kernel and re-normalization computations.We reformulate a large number of multiplicative update algorithms using path kernels and characterize the applicability of our method. The examples include efficient algorithms for learning disjunctions and a recent algorithm that predicts as well as the best pruning of a series parallel digraphs. 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. 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 present a geometric formulation of the Multiple Kernel Learning (MKL) problem. To do so, we reinterpret the problem of learning kernel weights as searching for a kernel that maximizes the minimum (kernel) distance between two convex polytopes. This interpretation combined with novel structural insights from our geometric formulation allows us to reduce the MKL problem to a simple optimization routine that yields provable convergence as well as quality guarantees. As a result our method scales efficiently to much larger data sets than most prior methods can handle. Empirical evaluation on eleven datasets shows that we are significantly faster and even compare favorably with a uniform unweighted combination of kernels.