[pymvpa] Alternatives to Cross-validation

Yaroslav Halchenko debian at onerussian.com
Wed Oct 24 13:48:47 UTC 2012

Thanks everyone and sorry I haven't managed to understand the goal

Here is the ultimate example:

    est = clf.predict(ds_test)
    # now you can get the error
    print mean_mismatch_error(est, ds_test.targets)
    # or if you like a full ConfusionMatrix beast
    cm = ConfusionMatrix(targets=ds_test.targets,
    print cm

This, and more of trickeries you can discover if you go through the
tutorial, e.g. in this particular case it was pretty much the beginning:




On Wed, 24 Oct 2012, Jacob Itzhacki wrote:

>    Thank you for your prompt response.
>    "not sure why cross-validation doesn't fit your needs here. �Could you
>    elaborate a bit more on what you are trying to achieve."
>    I'll put it bluntly. I am trying to script a way for the algorithm to
>    create a comparison pattern based on one set of training-stimuli, then
>    disregard this set of stimuli and compare the pattern formed to a
>    different set of test-stimuli, which will also be of different kind, but
>    should produce similar activation patterns in the ROIs scrutinized.
>    "Do you mean that you want to train with all examples from one dataset,
>    then test with all examples from a different dataset?"
>    This is exactly it.
>    "You could always combine the two datasets as the two cross-validation
>    folds and get per-fold results, no?"
>    This is an option we have considered (and will take upon if we find no
>    better solution), to have all the stimuli fall under the same dataset to
>    make cross-validation viable. However we believe that the predictions
>    given on the confusion tables would not be as ideal as if the comparison
>    could be performed as described above.
>    Thanks again for any help you can offer us.
>    J.

>    On Wed, Oct 24, 2012 at 3:16 PM, Francisco Pereira
>    <[1]francisco.pereira at gmail.com> wrote:

>      You could always combine the two datasets as the two cross-validation
>      folds and get per-fold results, no?
>      Francisco
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Yaroslav O. Halchenko
Postdoctoral Fellow,   Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        

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