[pymvpa] Train and test on different datasets using searchlights

[Michael W. Cole]

Hi Yaroslav,

Thanks for the tips! The first one worked quite well (with a few minor
tweaks).

All the best,
Michael

On Thu, Oct 28, 2010 at 7:18 PM, Yaroslav Halchenko
<debian at onerussian.com>wrote:

> Hi Michael,
>
> Although your use case seems to be quite "reasonable to be common",
> apparently
> we do not have an interface for efficient "1 liner"  solution for it...
> thanks for bringing it up...
>
> As for how to implement with PyMVPA 0.4 series, which I guess you are
> using:
>
> 1. the easiest, but least efficient memory (and cpu) -wise
>
>  join both datasets into a single one with two distinct chunk ids
>  and then use CustomSplitter with a conventional flow of things for
>  searchlight, i.e. something like (not tested -- be warned ;) )
>
>  cv = CrossValidatedTransferError(
>         TransferError(LinearCSVMC()),
>         CustomSplitter([(0, 1)])) # 0 for training, 1 for testing
>
>  sl = Searchlight(cv, radius=5)
>
>  # assuming you have dstrain and dstest
>  dstrain.chunks[:] = 0
>  dstest.chunks[:] = 1
>
>  sl_map = sl(dstrain + dstest)
>
> 2. Searchlight is just a simple loop (see mvpa/measures/searchlight.py),
>   which you could simply embed in your code and there do
>   .selectFeatures on both datasets and providing them to TransferError
> instance
>   call.
> 3.
> 4. ...  well -- lets see first what you think about 1 (and 2) ;-)
>
> Cheers,
>
> On Thu, 28 Oct 2010, Michael W. Cole wrote:
>
> >    Hello PyMVPAers,
>
> >    I'm attempting to use the searchlight class to train with one dataset
> >    and test the resulting classifiers on another dataset. Is there a
> >    straightforward way to do this? The searchlight class seems to want a
> >    splitter object, yet it doesn't appear that there is a splitter class
> >    that can take two datasets and designate one as the
> >    training dataset and the other as the testing dataset.
>
> >    Thanks,
>
> >    Michael
>
> > _______________________________________________
> > Pkg-ExpPsy-PyMVPA mailing list
> > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
>
>
> --
>                                  .-.
> =------------------------------   /v\  ----------------------------=
> Keep in touch                    // \\     (yoh@|www.)onerussian.com
> Yaroslav Halchenko              /(   )\               ICQ#: 60653192
>                   Linux User    ^^-^^    [175555]
>
>
>
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-- 
Michael W. Cole, Ph.D.
Post-doctoral researcher
Cognitive Control & Psychopathology Lab
Washington University in St. Louis
http://www.mwcole.net
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