twkm: Two-level variable weighting clustering
In wskm: Weighted k-Means Clustering

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/twkm.R

Two-level variable weighting clustering.

1 2	twkm(x, centers, groups, lambda, eta, maxiter=100, delta=0.000001, maxrestart=10,seed=-1)

`x`	numeric matrix of observations and features.
`centers`	target number of clusters or the initial centers for clustering.
`groups`	a string give the group information, formatted as `"0,1,2,4;3,5;6,7,8"` or `"0-2,4;3,5;6-8"`, where `";"` defines a group; or a vector of length of features, each element of the vector indicates the group of the feature. For example, `c(1,1,1,2,1,2,3,3,3)` is the same as `"0-2,4;3,5;6-8"`, or even `c("a","a","a","b","a","b","c","c","c")`.
`lambda`	parameter of feature weight distribution.
`eta`	parameter of group weight distribution.
`delta`	maximum change allowed between iterations for convergence.
`maxiter`	maximum number of iterations.
`maxrestart`	maximum number of restarts. Default is 10 so that we stand a good chance of getting a full set of clusters. Normally, any empty clusters that result are removed from the result, and so we may obtain fewer than k clusters if we don't allow restarts(i.e., maxrestart=0). If < 0, then there is no limit on the number of restarts and we are much likely to get a full set of k clusters.
`seed`	random seed. If it was set below 0, then a randomly generated number will be assigned.

The two-level variable weighting clustering algorithm is a extension to ewkm, which itself is a soft subspace clustering method.

The algorithm weights subspaces in both feature groups and individual features.

Always check the number of iterations, the number of restarts, and the total number of iterations as they give a good indication of whether the algorithm converged.

As with any distance based algorithm, be sure to rescale your numeric data so that large values do not bias the clustering. A quick rescaling method to use is scale.

Return an object of class "kmeans" and "twkm", compatible with other function that work with kmeans objects, such as the 'print' method. The object is a list with the following components in addition to the components of the kmeans object:

`cluster`	A vector of integer (from 1:k) indicating the cluster to which each point is allocated.
`centers`	A matrix of cluster centers.
`featureWeight`	A vector of weights recording the relative importance of each feature.
`groupWeight`	A vector of group weights recording the relative importance of each feature group.
`iterations`	This report on the number of iterations before termination. Check this to see whether the maxiters was reached. If so then teh algorithm may not be converging, and thus the resulting clustering may not be particularly good.
`restarts`	The number of times the clustering restarted because of a disappearing cluster resulting from one or more k-means having no observations associated with it. An number here greater than zero indicates that the algorithm is not converging on a clustering for the given k. It is recommended that k be reduced.
`totalIterations`	The total number of iterations over all restarts.
`totolCost`	The total cost calculated in the cost function.

Xiaojun Chen xjchen.hitsz@gmail.com

Xiaojun Chen, Xiaofei Xu, Joshua Zhexue Huang and Yunming Ye (2013). TW-k-Means: Automated Two-level Variable Weighting Clustering Algorithm for Multiview Data. IEEE Transactions on Knowledge and Data Engineering, 25(4), 932–944.

kmeans ewkm fgkm

# The data twkm.sample has 2000 objects and 410 variables.
# Scale the data before clustering
x <- scale(twkm.sample[,1:409])

# Group information is formated as below.
# Each group is separated by ';'.
strGroup <- "0-75;76-291;292-355;356-402;403-408"
groups <- c(rep(0, abs(0-75-1)), rep(1, abs(76-291-1)), rep(2, abs(292-355-1)),
            rep(3, abs(356-402-1)), rep(4, abs(403-408-1)))


# Use the twkm algorithm.
mytwkm <- twkm(x, 10, strGroup, 3, 1, seed=19)
mytwkm2 <- twkm(x, 10, groups, 3, 1, seed=19)
all.equal(mytwkm, mytwkm2)

# You can print the clustering result now.
mytwkm$cluster
mytwkm$featureWeight
mytwkm$groupWeight
mytwkm$iterations
mytwkm$restarts
mytwkm$totiters
mytwkm$totss

# Use a cluster validation method from package 'fpc'.

# real.cluster is the real class label of the data 'twkm.sample'.
real.cluster <- twkm.sample[,410]

# cluster.stats() computes several distance based statistics.
kmstats <- cluster.stats(d=dist(x), as.integer(mytwkm$cluster), real.cluster)

# corrected Rand index
kmstats$corrected.rand

# variation of information (VI) index
kmstats$vi