[SciPy-User] Graph connect components and sparse matrices

Gael Varoquaux gael.varoquaux@normalesup....
Wed Nov 18 08:31:19 CST 2009


On Wed, Nov 18, 2009 at 03:24:37PM +0100, Robert Cimrman wrote:
> > Well, getting the largest eigenvector of the transition matrix is in
> > o(n), using arpack, AFAIK. So the cost is similar, and on one side we
> > have optimized C code, and on the other side I only had Python code (or C
> > code that I don't want to maintain). In addition, as I am doing diffusion
> > maps, I needed to call arpack anyhow.

> I see. BTW. putting a code into scipy somewhat alleviates the
> maintenance burden ;)

I'd love to, but the code I am talking about is not something you want to
see. I inherited it from the lab, and its been a horrible burden. Not
that there are not good part in it (there are a lot of excellent
alogrithms), but the problem is that it uses home grown vector
abstractions, and graph structures, which makes it really hard to split
out the good part. In the long run, I hope I will be able to trim out the
bad parts and the vector library, and replace this by scipy components,
and the work that David Cournapeau has been doing to expose numpy
internals to C libraries. Once this is doing, we can think of moving
things out to other libraries: scipy, networkx, or the machine learning
scikit (we have an engineer hired to work on that, beginning in January).

Gaël


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