[Numpy-discussion] Faster
Keith Goodman
kwgoodman@gmail....
Sat May 3 08:48:34 CDT 2008
On Fri, May 2, 2008 at 11:51 PM, Hoyt Koepke <hoytak@gmail.com> wrote:
> You know, for linkage clustering and BHC, I've found it a lot easier
> to work with an intermediate 1d map of indices and never resize the
> distance matrix. I then just remove one element from this map at each
> iteration, which is a LOT faster than removing a column and a row from
> a matrix. if idxmap were the map, you would be working with
> X[idxmap[i], idxmap[j] ] instead of X[i, j]. Also, you could even use
> a python list in this case, as they are a lot better for deletions
> than an array.
I thought of replacing the row and column with 1e10 instead of
deleting it. But your idea is better. If I use lists then I bet Psyco
will speed things up. Thanks for the tip.
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