T4cluster (version 0.1.2)

scUL: Spectral Clustering with Unnormalized Laplacian

Description

The version of Shi and Malik first constructs the affinity matrix $$A_{ij}=\exp (-d(x_i,d_j{)}^2/{\sigma }^2)$$ where $\sigma$ is a common bandwidth parameter and performs k-means (or possibly, GMM) clustering on the row-space of eigenvectors for the unnormalized graph laplacian matrix $$L=D-A$$.

Usage

scUL(data, k = 2, sigma = 1, ...)

Arguments

data

an $(n\times p)$ matrix of row-stacked observations or S3 dist object of $n$ observations.

k

the number of clusters (default: 2).

sigma

bandwidth parameter (default: 1).

...

extra parameters including

algclust

method to perform clustering on embedded data; either "kmeans" (default) or "GMM".

maxiter

the maximum number of iterations (default: 10).

Value

a named list of S3 class T4cluster containing

cluster

a length-$n$ vector of class labels (from $1:k$).

eigval

eigenvalues of the graph laplacian's spectral decomposition.

embeds

an $(n\times k)$ low-dimensional embedding.

algorithm

name of the algorithm.

References

von_luxburg_tutorial_2007T4cluster

Examples

# NOT RUN {
# -------------------------------------------------------------
#            clustering with 'iris' dataset
# -------------------------------------------------------------
## PREPARE
data(iris)
X   = as.matrix(iris[,1:4])
lab = as.integer(as.factor(iris[,5]))

## EMBEDDING WITH PCA
X2d = Rdimtools::do.pca(X, ndim=2)$Y

## CLUSTERING WITH DIFFERENT K VALUES
cl2 = scUL(X, k=2)$cluster
cl3 = scUL(X, k=3)$cluster
cl4 = scUL(X, k=4)$cluster

## VISUALIZATION
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,4), pty="s")
plot(X2d, col=lab, pch=19, main="true label")
plot(X2d, col=cl2, pch=19, main="scUL: k=2")
plot(X2d, col=cl3, pch=19, main="scUL: k=3")
plot(X2d, col=cl4, pch=19, main="scUL: k=4")
par(opar)

# }