[Numpy-discussion] numpy : your experiences?
Sat Nov 17 09:28:05 CST 2007
> a) Can you guys tell me briefly about the kind of problems you are
> tackling with numpy and scipy?
I'm a grad student "doing" computational biology. I primarily use the
NumPy/SciPy/matplotlib triumvirate as a post processing tool to
analyze what the heck happened after we run some learning algorithms
we develop (or canned ones, like libsvm (for example)) to look for
some sense in the results.
I've been working w/ analyzing interaction networks/graphs, so I also
use NetworkX quite a bit as well (it's also a nice package w/
Many of the folks (in my lab, and collaborators) like to use MATLAB,
so I've found scipy's io.loadmat invaluable for making this a bit more
So, in general, for me (so far) numpy/scipy are generally used to
integrate various datasets together and see if things "look
kosher" (before runs and after runs).
> b) Have you ever felt that numpy/scipy was slow and had to switch to
Yes, for things like boosting, svm, graph mining, etc ... but that's
no real surprise since their iterative and need to run on large
You should also note that there are python interfaces to these things
out there as well, but I (thus far) haven't taken much of advantage of
those and usually pipe out data into the expected text input formats
and pull them back in when the algo is done.
> c) Do you use any form of parallel processing? Multicores? SMPs?
> Clusters? If yes how did u utilize them?
I'd really like to (not just for Python), but I haven't.
 NetworkX: https://networkx.lanl.gov/wiki
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