Global graph kernels using geometric embeddings

Applications of machine learning methods increasingly deal with graph structured data through kernels. Most existing graph kernels compare graphs in terms of features defined on small subgraphs such as walks, paths or graphlets, adopting an inherently local perspective. However, several interesting properties such as girth or chromatic number are global properties of the graph, and are not captured in local substructures. This paper presents two graph kernels defined on unlabeled graphs which capture global properties of graphs using the celebrated Lovasz number and its associated orthonormal representation. We make progress towards theoretical results aiding kernel choice, proving a result about the separation margin of our kernel for classes of graphs. We give empirical results on classification of synthesized graphs with important global properties as well as established benchmark graph datasets, showing that the accuracy of our kernels is better than or competitive to existing graph kernels.

[1]  P. Erdös,et al.  Graph Theory and Probability , 1959 .

[2]  László Lovász,et al.  On the Shannon capacity of a graph , 1979, IEEE Trans. Inf. Theory.

[3]  Emo Welzl,et al.  Smallest enclosing disks (balls and ellipsoids) , 1991, New Results and New Trends in Computer Science.

[4]  A. Debnath,et al.  Structure-activity relationship of mutagenic aromatic and heteroaromatic nitro compounds. Correlation with molecular orbital energies and hydrophobicity. , 1991, Journal of medicinal chemistry.

[5]  Noga Alon,et al.  The Probabilistic Method , 2015, Fundamentals of Ramsey Theory.

[6]  Donald E. Knuth The Sandwich Theorem , 1994, Electron. J. Comb..

[7]  Alan M. Frieze,et al.  Improved Approximation Algorithms for MAX k-CUT and MAX BISECTION , 1995, IPCO.

[8]  Michel X. Goemans,et al.  Semideenite Programming in Combinatorial Optimization , 1999 .

[9]  Ari Juels,et al.  Hiding Cliques for Cryptographic Security , 1998, SODA '98.

[10]  David R. Karger,et al.  Approximate graph coloring by semidefinite programming , 1998, JACM.

[11]  Noga Alon,et al.  Finding a large hidden clique in a random graph , 1998, SODA '98.

[12]  David Haussler,et al.  Convolution kernels on discrete structures , 1999 .

[13]  U. Feige,et al.  Finding and certifying a large hidden clique in a semirandom graph , 2000 .

[14]  Leonidas D. Iasemidis,et al.  Quadratic Binary Programming and Dynamical System Approach to Determine the Predictability of Epileptic Seizures , 2001, J. Comb. Optim..

[15]  Ashwin Srinivasan,et al.  The Predictive Toxicology Challenge 2000-2001 , 2001, Bioinform..

[16]  Thomas Gärtner,et al.  On Graph Kernels: Hardness Results and Efficient Alternatives , 2003, COLT.

[17]  Jan Ramon,et al.  Expressivity versus efficiency of graph kernels , 2003 .

[18]  Bernhard Schölkopf,et al.  Kernel Methods in Computational Biology , 2005 .

[19]  Alexander Schrijver,et al.  A Convex Quadratic Characterization of the Lovász Theta Number , 2005, SIAM J. Discret. Math..

[20]  Hans-Peter Kriegel,et al.  Shortest-path kernels on graphs , 2005, Fifth IEEE International Conference on Data Mining (ICDM'05).

[21]  Hans-Peter Kriegel,et al.  Protein function prediction via graph kernels , 2005, ISMB.

[22]  George Karypis,et al.  Comparison of descriptor spaces for chemical compound retrieval and classification , 2006, Sixth International Conference on Data Mining (ICDM'06).

[23]  Don R. Hush,et al.  QP Algorithms with Guaranteed Accuracy and Run Time for Support Vector Machines , 2006, J. Mach. Learn. Res..

[24]  S. V. N. Vishwanathan,et al.  Graph kernels , 2007 .

[25]  Jean-Philippe Vert,et al.  Graph kernels based on tree patterns for molecules , 2006, Machine Learning.

[26]  Franz Rendl,et al.  A semidefinite programming-based heuristic for graph coloring , 2008, Discret. Appl. Math..

[27]  Rüdiger L. Urbanke,et al.  Modern Coding Theory , 2008 .

[28]  Karsten M. Borgwardt,et al.  Fast subtree kernels on graphs , 2009, NIPS.

[29]  Andrea Montanari,et al.  Generating random graphs with large girth , 2008, SODA.

[30]  Kurt Mehlhorn,et al.  Efficient graphlet kernels for large graph comparison , 2009, AISTATS.

[31]  Rajiv Raman,et al.  An SDP primal-dual algorithm for approximating the Lovász-theta function , 2009, ISIT.

[32]  Chih-Jen Lin,et al.  LIBSVM: A library for support vector machines , 2011, TIST.

[33]  G. Lugosi,et al.  High-dimensional random geometric graphs and their clique number , 2011 .

[34]  Clifford Stein,et al.  Approximating Semidefinite Packing Programs , 2011, SIAM J. Optim..

[35]  Kurt Mehlhorn,et al.  Weisfeiler-Lehman Graph Kernels , 2011, J. Mach. Learn. Res..

[36]  Devdatt P. Dubhashi,et al.  Lovász ϑ function, SVMs and finding dense subgraphs , 2013, J. Mach. Learn. Res..

[37]  Carey E. Priebe,et al.  Graph Classification Using Signal-Subgraphs: Applications in Statistical Connectomics , 2013, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[38]  Marleen de Bruijne,et al.  Scalable kernels for graphs with continuous attributes , 2013, NIPS.

[39]  Devdatt P. Dubhashi,et al.  Entity disambiguation in anonymized graphs using graph kernels , 2013, CIKM.