I am have a data set with 52 variables. Most of them have zeros, it resembles a sparse matrix. How can I cluster this kind of data and are there any special types of clustering? I am attaching pca plot

enter image description here

  • 4
    $\begingroup$ Have you seen the following posts, 1, 2, 3 and 4? $\endgroup$
    – mnm
    Sep 27, 2017 at 13:28
  • $\begingroup$ Apparent duplicate of datascience.stackexchange.com/questions/23349/… $\endgroup$ Sep 27, 2017 at 17:52
  • $\begingroup$ Do you close duplicate questions? $\endgroup$ Oct 24, 2017 at 14:23
  • $\begingroup$ What about using some dimensionality reduction, like PCA? $\endgroup$
    – Jirka
    Apr 23, 2019 at 21:31

1 Answer 1


It doesn't require any special method. The algorithm of choice depends on your data if for instance Euclidean distance works for your data or not.

Generally, you can try Kmeans or other methods on your X or PCAs; but Hierarchical Clustering may be a good choice for visualizing the clusters for high dimensional data.

enter image description here

Please check here if you can read/write python code.

  • $\begingroup$ I guess the problem of the poster that it is a high dimensional sparse data. Traditional distance metrics will not work well in this case. $\endgroup$
    – Viktor
    Jan 15, 2020 at 11:26

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