[pymvpa] nperlabel question
Arteaga, Dan (NIH/NINDS) [F]
dan.arteaga at nih.gov
Wed Jun 15 17:51:28 UTC 2011
I was wondering - is it possible to have an equal number of training labels per fold without balancing the number of testing labels? nperlabel='equal' seems to balance both the number of training and testing labels across entire folds (not on a per chunk basis).
Thanks.
Dan
-----Original Message-----
From: Yaroslav Halchenko [mailto:debian at onerussian.com]
Sent: Tuesday, June 14, 2011 5:34 PM
To: Development and support pf PyMVPA
Subject: Re: [pymvpa] RFE confusion_state
sorry... didn't have change to look in detail -- I guess that doc page
of ours got outdated since it reflects how you would do RFE using 0.4.x
version of PyMVPA. So you could do it that way if you used 0.4.7.
Sorry about the confusion.
For 0.6.x -- here is an example from our unittests which I hope would be of
help help. It does pretty much the same ;-)
def test_james_problem(self):
percent = 80
dataset = datasets['uni2small']
rfesvm_split = LinearCSVMC()
fs = \
RFE(rfesvm_split.get_sensitivity_analyzer(),
ProxyMeasure(rfesvm_split,
postproc=BinaryFxNode(mean_mismatch_error,
'targets')),
Splitter('train'),
fselector=FractionTailSelector(
percent / 100.0,
mode='select', tail='upper'), update_sensitivity=True)
clf = FeatureSelectionClassifier(
LinearCSVMC(),
# on features selected via RFE
fs)
# update sensitivity at each step (since we're not using the
# same CLF as sensitivity analyzer)
cv = CrossValidation(clf, NFoldPartitioner(), postproc=mean_sample(),
enable_ca=['confusion'])
if you want to see the progress of RFE -- just enable debug variables
RFEC and RFEC_ for more verbosity... eg. in the environment
export MVPA_DEBUG=RFEC,RFEC_
before running your python script
On Tue, 14 Jun 2011, Kimberly Zhou wrote:
> Hi all,
> I'm still trying to get recursive feature selection to work with the
> example from
> [1]http://dev.pymvpa.org/featsel.html#recursive-feature-elimination,
> however I can't get past an error from the line with
> confusion_state="confusion".
> Here's the code:
--
=------------------------------------------------------------------=
Keep in touch www.onerussian.com
Yaroslav Halchenko www.ohloh.net/accounts/yarikoptic
_______________________________________________
Pkg-ExpPsy-PyMVPA mailing list
Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
More information about the Pkg-ExpPsy-PyMVPA
mailing list