k-means clustering in R on very large, sparse matrix?

Posted by movingabout on Stack Overflow See other posts from Stack Overflow or by movingabout
Published on 2010-06-14T18:03:36Z Indexed on 2010/06/14 18:12 UTC
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r

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clustering

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large

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sparse-matrix

Hello,

I am trying to do some k-means clustering on a very large matrix.

The matrix is approximately 500000 rows x 4000 cols yet very sparse (only a couple of "1" values per row).

The whole thing does not fit into memory, so I converted it into a sparse ARFF file. But R obviously can't read the sparse ARFF file format. I also have the data as a plain CSV file.

Is there any package available in R for loading such sparse matrices efficiently? I'd then use the regular k-means algorithm from the cluster package to proceed.

Many thanks

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