bigkmeans {biganalytics}R Documentation

Memory-efficient k-means cluster analysis

Description

k-means cluster analysis without the memory overhead, and possibly in parallel using shared memory.

Usage

bigkmeans(x, centers, iter.max = 10, nstart = 1, dist = "euclid")

Arguments

x

a big.matrix object.

centers

a scalar denoting the number of clusters, or for k clusters, a k by ncol(x) matrix.

iter.max

the maximum number of iterations.

nstart

number of random starts, to be done in parallel if there is a registered backend (see below).

dist

the distance function. Can be "euclid" or "cosine".

Details

The real benefit is the lack of memory overhead compared to the standard kmeans function. Part of the overhead from kmeans() stems from the way it looks for unique starting centers, and could be improved upon. The bigkmeans() function works on either regular R matrix objects, or on big.matrix objects. In either case, it requires no extra memory (beyond the data, other than recording the cluster memberships), whereas kmeans() makes at least two extra copies of the data. And kmeans() is even worse if multiple starts (nstart>1) are used. If nstart>1 and you are using bigkmeans() in parallel, a vector of cluster memberships will need to be stored for each worker, which could be memory-intensive for large data. This isn't a problem if you use are running the multiple starts sequentially.

Unless you have a really big data set (where a single run of kmeans not only burns memory but takes more than a few seconds), use of parallel computing for multiple random starts is unlikely to be much faster than running iteratively.

Only the algorithm by MacQueen is used here.

Value

An object of class kmeans, just as produced by kmeans.

Note

A comment should be made about the excellent package foreach. By default, it provides foreach, which is used much like a for loop, here over the nstart and doing a final comparison of all results).

When a parallel backend has been registered (see packages doSNOW, doMC, and doMPI, for example), bigkmeans() automatically distributes the nstart random starting points across the available workers. This is done in shared memory on an SMP, but is distributed on a cluster *IF* the big.matrix is file-backed. If used on a cluster with an in-RAM big.matrix, it will fail horribly. We're considering an extra option as an alternative to the current behavior.


[Package biganalytics version 1.1.21 Index]