[SciPy-User] Sparse Matricies and NNLS

Calvin Morrison mutantturkey@gmail....
Thu Mar 28 16:33:07 CDT 2013


Paul,

It seems nobody wants to touch the nnls algorithm because the only
implementation that is floating around is the one from the original
publication or automatic conversions of it.

Calvin
On Mar 28, 2013 4:48 PM, "Pauli Virtanen" <pav@iki.fi> wrote:

> 28.03.2013 21:46, Calvin Morrison kirjoitti:
> [clip]
> > I was thinking about using a sparse matrix since it is relatively
> > sparse, but the problem is that even if I was to use the sparse
> > matricies, the nnls function only accepts a ndarray, not a sparse
> > matrix. (when I try and throw a sparse matrix at it I get an error.)
>
> The nnls algorithm in Scipy relies on dense matrix algebra, and is
> moreover written in Fortran. So, there is no way to tell it to use
> sparse matrices.
>
> You'll need to find an implementation of NNLS algorithm that either is
> matrix-free or works for sparse problems. If you find such code, be sure
> to reply to this list --- it might be useful to include it in Scipy,
> provided the license is compatible.
>
> --
> Pauli Virtanen
>
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