[pymvpa] Sensitivity map with RFE?

[Roberto Guidotti]

Dear Marco,

>From your snippet I notice that you get the sensitivity analyzer without
run any CrossValidation/Classification.

So try to run
-------
err = fclfsvm(fds) #That let you to cross validate/classify/select features
on your dataset
-------
This let you to train your object and then you can get the sensitivity of
your classifier.

I've never used RFE, but this is what I get by your snippet.

Ciao
Roberto


On 12 July 2013 11:04, marco tettamanti <tettamanti.marco at hsr.it> wrote:

> Dear all,
> is there any manner to obtain a sensitivity map with RFE, similar to what
> can be done with feature selection?
>
> I am trying to use the following code:
>
> #-----------------------------**--------------------
> clfsvm = LinearCSVMC()
>
> rfesvm = RFE(clfsvm.get_sensitivity_**analyzer(postproc=maxofabs_**sample()),
> CrossValidation(clfsvm, NFoldPartitioner(), errorfx=mean_mismatch_error,
> postproc=mean_sample()), Repeater(2), fselector=**FractionTailSelector(0.30,
> mode='select', tail='upper'), stopping_criterion=**NBackHistoryStopCrit(**BestDetector(),
> 10), update_sensitivity=True)
>
> fclfsvm = FeatureSelectionClassifier(**clfsvm, rfesvm)
>
> sensanasvm = fclfsvm.get_sensitivity_**analyzer(postproc=maxofabs_**
> sample())
>
> cv_sensana_svm = RepeatedMeasure(sensanasvm, NFoldPartitioner())
>
> senssvm = cv_sensana_svm(fds)
> #-----------------------------**--------------------
>
> However, after a while I get the following error:
>
> RuntimeError: Cannot reverse-map data since the original data shape is
> unknown. Either set `dshape` in the constructor, or call train().
>
>
> Thank you in advance for any help!
> Best wishes,
> Marco
>
> --
> Marco Tettamanti, Ph.D.
> Nuclear Medicine Department & Division of Neuroscience
> San Raffaele Scientific Institute
> Via Olgettina 58
> I-20132 Milano, Italy
> Phone ++39-02-26434888
> Fax ++39-02-26434892
> Email: tettamanti.marco at hsr.it
> Skype: mtettamanti
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