Fast Computation of Graph Kernels

Part of Advances in Neural Information Processing Systems 19 (NIPS 2006)

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Karsten Borgwardt, Nicol Schraudolph, S.v.n. Vishwanathan


Using extensions of linear algebra concepts to Reproducing Kernel Hilbert Spaces (RKHS), we define a unifying framework for random walk kernels on graphs. Re- duction to a Sylvester equation allows us to compute many of these kernels in O(n3) worst-case time. This includes kernels whose previous worst-case time complexity was O(n6), such as the geometric kernels of G¨artner et al. [1] and the marginal graph kernels of Kashima et al. [2]. Our algebra in RKHS allow us to exploit sparsity in directed and undirected graphs more effectively than previ- ous methods, yielding sub-cubic computational complexity when combined with conjugate gradient solvers or fixed-point iterations. Experiments on graphs from bioinformatics and other application domains show that our algorithms are often more than 1000 times faster than existing approaches.