Github user rezazadeh commented on the pull request: https://github.com/apache/incubator-spark/pull/564#issuecomment-34585044 Yes I agree, densifying the matrix for sake of centering is a problem for sparse matrices. I can solve it, but with appropriate sparse vector support. Once we have the sparse vector primitives in mllib I will change this to use those and avoid densifying. It can be done by constructing A^TA and centering A all in one step (A^TA is n x n and small, assuming n is small). Mentioned before, sparse vector primitives are tracked by https://spark-project.atlassian.net/browse/MLLIB-18
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