Improve efficiency of kopt implementation

Open FarnazH opened this issue 5 years ago • 1 comments

Actually, why make a permutation matrix (mostly zeros and ones) and multiply by A (cost of O(n^3)). You can directly compute A with permuted rows/columns, then compute the error in (permuted) A. This has cost O(n^2) (computing the error) instead of O(n^3). IF the error is reduced, you can return the permutation, or even the permutation matrix (which can be constructed at the very end).

Originally posted by @PaulWAyers in https://github.com/theochem/procrustes/pull/62#discussion_r588938851

Mar 07 '21 02:03 FarnazH

This supersedes https://github.com/theochem/procrustes/issues/79 which I closed.

Mar 14 '21 04:03 PaulWAyers