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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.