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This is a short post on how to quickly calculate the Fiedler vector
for large graphs with the igraph package.
#used libraries library(igraph) # for network data structures and tools library(microbenchmark) # for benchmark results
Fiedler Vector with eigen
My goto approach at the start was using the eigen() function to compute the
whole spectrum of the Laplacian Matrix.
g <- sample_gnp(n = 100,p = 0.1,directed = FALSE,loops = FALSE) M <- laplacian_matrix(g,sparse = FALSE) spec <- eigen(M) comps <- sum(round(spec$values,8)==0) fiedler <- spec$vectors[,comps-1]
While this is easy to implement, it comes with the huge drawback of computing many unnecessary eigenvectors. We just need one, but we calculate all 100 in the example. The bigger the graph, the bigger the overheat from computing all eigenvectors.
# 100 nodes g <- sample_gnp(n = 100,p = 0.1,directed = FALSE,loops = FALSE) M <- laplacian_matrix(g,sparse = FALSE) system.time(eigen(M)) ## user system elapsed ## 0.003 0.000 0.004 # 1000 nodes g <- sample_gnp(n = 1000,p = 0.02,directed = FALSE,loops = FALSE) M <- laplacian_matrix(g,sparse = FALSE) system.time(eigen(M)) ## user system elapsed ## 1.659 0.011 1.672 # 2500 nodes g <- sample_gnp(n = 2500,p = 0.01,directed = FALSE,loops = FALSE) M <- laplacian_matrix(g,sparse = FALSE) system.time(eigen(M)) ## user system elapsed ## 21.153 0.119 21.276
It would thus be useful to have a function that computes only a small number of eigenvectors, which should speed up the calculations considerably.
Fiedler Vector with arpack
What I found after some digging is that igraph provides an interface to the ARPACK
library for calculating eigenvectors of sparse matrices via the function arpack().
The function below is an implementation to calculate the Fiedler vector for connected graphs.
fiedler_vector <- function(g){
M <- laplacian_matrix(g, sparse = TRUE)
f <- function(x,extra = NULL){
as.vector(M%*%x)
}
fvec <- arpack(f,sym = TRUE,options=list(n = vcount(g),nev = 2,ncv = 8,
which = "SM",maxiter = 2000))
return(fvec$vectors[,2])
}
The parameters n and maxiter should be self explanatory. nev specifies the number of eigenvectors
to return and which if it should be the largest (“LM”) or smallest (“SM”) one’s.
Since the Fiedler vector of connected graphs is the second smallest, we need to return the
two smallest eigenvalues.
Let’s see how much we gain.
g <- sample_gnp(n = 2500,p = 0.01,directed = FALSE,loops = FALSE) system.time(fiedler_vector(g)) ## user system elapsed ## 0.790 0.016 0.812
The speed up is enormous (20x) and a nice feature of the arpack() function is that its
performance mostly depends on the sparsity of the graph.
g <- sample_gnp(n = 10000,p = 0.005,directed = FALSE,loops = FALSE) system.time(fiedler_vector(g)) ## user system elapsed ## 0.600 0.004 0.603
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