publication . Article . Preprint . 2018

GraKeL: A Graph Kernel Library in Python

Siglidis, Giannis; Nikolentzos, Giannis; Limnios, Stratis; Giatsidis, Christos; Skianis, Konstantinos; Vazirgiannis, Michalis;
Open Access English
  • Published: 06 Jun 2018
  • Publisher: HAL CCSD
  • Country: France
Abstract
International audience; The problem of accurately measuring the similarity between graphs is at the core of many applications in a variety of disciplines. Graph kernels have recently emerged as a promising approach to this problem. There are now many kernels, each focusing on different structural aspects of graphs. Here, we present GraKeL, a library that unifies several graph kernels into a common framework. The library is written in Python and adheres to the scikit-learn interface. It is simple to use and can be naturally combined with scikit-learn's modules to build a complete machine learning pipeline for tasks such as graph classification and clustering. The...
Subjects
free text keywords: Python, graph similarity, graph kernels, scikit-learn, [INFO]Computer Science [cs], Statistics - Machine Learning, Computer Science - Machine Learning

Martin S Andersen, Joachim Dahl, and Lieven Vandenberghe. CVXOPT: A Python package for convex optimization. Available at cvxopt. org, 2013.

Stefan Behnel, Robert Bradshaw, Craig Citro, Lisandro Dalcin, Dag Sverre Seljebotn, and Kurt Smith. Cython: The Best of Both Worlds. Computing in Science & Engineering, 13(2):31{39, 2011.

Tommi Junttila and Petteri Kaski. Engineering an E cient Canonical Labeling Toolfor Large and Sparse Graphs. In Proceedings of the 9th Workshop on Algorithm Engineering and Experiments and the 4th Workshop on Analytic Algorithms and Combinatorics, pages 135{149, 2007.

Kristian Kersting, Nils M. Kriege, Christopher Morris, Petra Mutzel, and Marion Neumann. Benchmark Data Sets for Graph Kernels, 2016. URL http://graphkernels.cs. tu-dortmund.de.

Fabian Pedregosa, Gael Varoquaux, Alexandre Gramfort, Vincent Michel, Bertrand Thirion, Olivier Grisel, Mathieu Blondel, Peter Prettenhofer, Ron Weiss, Vincent Dubourg, Jake Vanderplas, Alexandre Passos, and David Cournapeau. Scikit-learn: Machine Learning in Python. Journal of Machine Learning Research, 12(Oct):2825{2830, 2011. [OpenAIRE]

Nino Shervashidze, Pascal Schweitzer, Erik Jan van Leeuwen, Kurt Mehlhorn, and Karsten M Borgwardt. Weisfeiler-Lehman Graph Kernels. Journal of Machine Learning Research, 12(Sep):2539{2561, 2011.

Mahito Sugiyama, M Elisabetta Ghisu, Felipe Llinares-Lopez, and Karsten Borgwardt. graphkernels: R and Python packages for graph comparison. Bioinformatics, 34(3):530{ 532, 2017. [OpenAIRE]

Pauli Virtanen, Ralf Gommers, Travis E Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, et al. SciPy 1.0: fundamental algorithms for scienti c computing in Python. Nature Methods, pages 1{12, 2020.

Stefan van der Walt, S Chris Colbert, and Gael Varoquaux. The NumPy array: a structure for e cient numerical computation. Computing in Science & Engineering, 13(2):22{30, 2011.

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Abstract
International audience; The problem of accurately measuring the similarity between graphs is at the core of many applications in a variety of disciplines. Graph kernels have recently emerged as a promising approach to this problem. There are now many kernels, each focusing on different structural aspects of graphs. Here, we present GraKeL, a library that unifies several graph kernels into a common framework. The library is written in Python and adheres to the scikit-learn interface. It is simple to use and can be naturally combined with scikit-learn's modules to build a complete machine learning pipeline for tasks such as graph classification and clustering. The...
Subjects
free text keywords: Python, graph similarity, graph kernels, scikit-learn, [INFO]Computer Science [cs], Statistics - Machine Learning, Computer Science - Machine Learning

Martin S Andersen, Joachim Dahl, and Lieven Vandenberghe. CVXOPT: A Python package for convex optimization. Available at cvxopt. org, 2013.

Stefan Behnel, Robert Bradshaw, Craig Citro, Lisandro Dalcin, Dag Sverre Seljebotn, and Kurt Smith. Cython: The Best of Both Worlds. Computing in Science & Engineering, 13(2):31{39, 2011.

Tommi Junttila and Petteri Kaski. Engineering an E cient Canonical Labeling Toolfor Large and Sparse Graphs. In Proceedings of the 9th Workshop on Algorithm Engineering and Experiments and the 4th Workshop on Analytic Algorithms and Combinatorics, pages 135{149, 2007.

Kristian Kersting, Nils M. Kriege, Christopher Morris, Petra Mutzel, and Marion Neumann. Benchmark Data Sets for Graph Kernels, 2016. URL http://graphkernels.cs. tu-dortmund.de.

Fabian Pedregosa, Gael Varoquaux, Alexandre Gramfort, Vincent Michel, Bertrand Thirion, Olivier Grisel, Mathieu Blondel, Peter Prettenhofer, Ron Weiss, Vincent Dubourg, Jake Vanderplas, Alexandre Passos, and David Cournapeau. Scikit-learn: Machine Learning in Python. Journal of Machine Learning Research, 12(Oct):2825{2830, 2011. [OpenAIRE]

Nino Shervashidze, Pascal Schweitzer, Erik Jan van Leeuwen, Kurt Mehlhorn, and Karsten M Borgwardt. Weisfeiler-Lehman Graph Kernels. Journal of Machine Learning Research, 12(Sep):2539{2561, 2011.

Mahito Sugiyama, M Elisabetta Ghisu, Felipe Llinares-Lopez, and Karsten Borgwardt. graphkernels: R and Python packages for graph comparison. Bioinformatics, 34(3):530{ 532, 2017. [OpenAIRE]

Pauli Virtanen, Ralf Gommers, Travis E Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, et al. SciPy 1.0: fundamental algorithms for scienti c computing in Python. Nature Methods, pages 1{12, 2020.

Stefan van der Walt, S Chris Colbert, and Gael Varoquaux. The NumPy array: a structure for e cient numerical computation. Computing in Science & Engineering, 13(2):22{30, 2011.

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publication . Article . Preprint . 2018

GraKeL: A Graph Kernel Library in Python

Siglidis, Giannis; Nikolentzos, Giannis; Limnios, Stratis; Giatsidis, Christos; Skianis, Konstantinos; Vazirgiannis, Michalis;