How do I determine k when using k-means clustering?

Question

I've been studying about k-means clustering, and one thing that's not clear is how you choose the value of k. Is it just a matter of trial and error, or is there more to it?

Answer 1

Basically, you want to find a balance between two variables: the number of clusters (k) and the average variance of the clusters. You want to minimize the former while also minimizing the latter. Of course, as the number of clusters increases, the average variance decreases (up to the trivial case of k=n and variance=0).

As always in data analysis, there is no one true approach that works better than all others in all cases. In the end, you have to use your own best judgement. For that, it helps to plot the number of clusters against the average variance (which assumes that you have already run the algorithm for several values of k). Then you can use the number of clusters at the knee of the curve.

Answer 2

Try 10. Then try 3.

Answer 3

You can maximize the Bayesian Information Criterion (BIC):

BIC(C | X) = L(X | C) - (p / 2) * log n

where L(X | C) is the log-likelihood of the dataset X according to model C, p is the number of parameters in the model C, and n is the number of points in the dataset. See "X-means: extending K-means with efficient estimation of the number of clusters" by Dan Pelleg and Andrew Moore in ICML 2000.

Another approach is to start with a large value for k and keep removing centroids (reducing k) until it no longer reduces the description length. See "MDL principle for robust vector quantisation" by Horst Bischof, Ales Leonardis, and Alexander Selb in Pattern Analysis and Applications vol. 2, p. 59-72, 1999.

Finally, you can start with one cluster, then keep splitting clusters until the points assigned to each cluster have a Gaussian distribution. In "Learning the k in k-means" (NIPS 2003), Greg Hamerly and Charles Elkan show some evidence that this works better than BIC, and that BIC does not penalize the model's complexity strongly enough.

Answer 4

First build a minimum spanning tree of your data. Removing the K-1 most expensive edges splits the tree into K clusters,
so you can build the MST once, look at cluster spacings / metrics for various K, and take the knee of the curve.

This works only for Single-linkage_clustering, but for that it's fast and easy. Plus, MSTs make good visuals.