Code to reproduce the experiments in the paper "The Kendall and Mallows Kernels for Permutations"
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APA
eurovision
geneexpr
README.md

README.md

kendallkernel

This repo contains R code for reproducing results and more experiments from

Yunlong Jiao, Jean-Philippe Vert. "The Kendall and Mallows Kernels for Permutations." IEEE Transactions on Pattern Analysis and Machine Intelligence(TPAMI), 2017. DOI: 10.1109/TPAMI.2017.2719680

Cluster full rankings (APA)

setwd("[somepath]/kendallkernel_demo/APA/")
install.packages(c("rmarkdown", "combinat", "caret", "mvtnorm", "reshape2", "ggplot2", "gplots", "flexclust", "Rankcluster", "devtools"))
devtools::install_github("YunlongJiao/kernrank")
rmarkdown::render("analysis.Rmd")

Cluster multivariate partial rankings (eurovision)

setwd("[somepath]/kendallkernel_demo/eurovision/")
install.packages(c("rmarkdown", "combinat", "reshape2", "ggplot2", "gplots", "kernlab", "Rankcluster", "cluster", "devtools"))
devtools::install_github("YunlongJiao/kernrank")
rmarkdown::render("analysis.Rmd")

Classify gene expression data (geneexpr)

setwd("[somepath]/kendallkernel_demo/geneexpr/")
install.packages(c("rmarkdown", "kernlab", "pcaPP", "caret"))
system("R CMD SHLIB src/utiles.c", intern = TRUE)
system("R CMD SHLIB src/tsp.c", intern = TRUE)
rmarkdown::render("analysis.Rmd")

Notes

  • Some implementations depend on parallel::mclapply which may be inconvenient for MS Windows users. See here for an easy solution, or manually revert all mclapply to lapply.