“Choosing a good k for your data” refers to the problem of choosing the right number of clusters. Since the k-means algorithm works with a given number of cluster centers, their number must be selected first. Choosing the wrong number can make it difficult to split data points into clusters, or clusters can become small and meaningless.
I cannot give you an answer on whether to ignore empty clusters. If you do this, you may encounter fewer clusters than you identified at the beginning. This will confuse people who expect k to work in a certain way, but this is not necessarily a bad idea.
If you reinstall all empty cluster centers, your algorithm will probably converge if this happens a limited number of times. However, if you have to move too often, it may happen that your algorithm does not complete.
Konstantin schubert
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