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10.1093/bioinformatics/btx602

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suck abstract from ncbi


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pmid29028902
      Bioinformatics 2018 ; 34 (3 ): 530-532
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  • graphkernels: R and Python packages for graph comparison #MMPMID29028902
  • Sugiyama M ; Ghisu ME ; Llinares-López F ; Borgwardt K
  • Bioinformatics 2018[Feb]; 34 (3 ): 530-532 PMID29028902 show ga
  • SUMMARY: Measuring the similarity of graphs is a fundamental step in the analysis of graph-structured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, classic graph kernels such as random walk based kernels, and the state-of-the-art Weisfeiler-Lehman graph kernel. The core of all graph kernels is implemented in C?++ for efficiency. Using the kernel matrices computed by the package, we can easily perform tasks such as classification, regression and clustering on graph-structured samples. AVAILABILITY AND IMPLEMENTATION: The R and Python packages including source code are available at https://CRAN.R-project.org/package=graphkernels and https://pypi.python.org/pypi/graphkernels. CONTACT: mahito@nii.ac.jp or elisabetta.ghisu@bsse.ethz.ch. SUPPLEMENTARY INFORMATION: Supplementary data are available online at Bioinformatics.
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