README.md

In youngser/gmmase: Graph Spectral Clustering

Graph Spectral Clustering

Department of Applied Mathematics and Statistics Johns Hopkins University r date()

Codes and Demos

This is an R package that does

1. generate or read a graph,
2. do a pass-to-rank for a weighted graph (PTR, no-op for an unweighted graph),
3. do a graph spectral embedding (ASE or LSE) with a diagonal augmentation,
4. do a dimension reduction (ZG) and merge left and right vectors (no-op for an undirected graph),
5. cluster vertices (GMM or Kmeans).

R Package

The latest R source package can be installed via github as

require(devtools)
devtools::install_github("youngser/gmmase")

Demos

Example codes are in the demo folder at github, which can be run via

library(gmmase)

# a toy graph with 100 vertices
demo(toygraph)

# a larger graph with 10,000 vertices: may take a few minutes, depending on the system
demo(usergraph)

The outputs of the demos are here:

• toygraph
• usergraph

User data

To use a user graph, please try this (as shown in the code in demo/usergraph.R):

fname <- readline(prompt="Enter a file name (e.g., /path/edgelist.txt): ")
g <- read_graph(fname, format="edgelist") 
E(g)$weight <- runif(ecount(g), 1, 5) # add random edge weights
Y <- gmmase(g, dmax=20, use.ptr=TRUE, embed="ASE", clustering="GMM")

where

• embed can be either "ASE" or "LSE", and
• clustering can be either "GMM" or "Kmeans", where
  • "GMM" yields BIC curve, and
  • "Kmeans" yields ASW curve.

The output of gmmase function is a clustering label vector.

Also, please refer to the igraph's manual page for details about other graph formats it can handle.

Software and Hardware Information

library(help='gmmase')
sessionInfo()

## R version 3.3.3 (2017-03-06)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: macOS Sierra 10.12.4
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] backports_1.0.5 magrittr_1.5    rprojroot_1.2   tools_3.3.3    
##  [5] htmltools_0.3.6 yaml_2.1.14     Rcpp_0.12.11    stringi_1.1.5  
##  [9] rmarkdown_1.6   knitr_1.16      stringr_1.2.0   digest_0.6.12  
## [13] evaluate_0.10

prepared by [e-mail] on Wed Aug 9 12:04:48 2017

youngser/gmmase documentation built on May 30, 2019, 7:19 p.m.