[pymvpa] Repost: RFE error with CustomPartitioner
marco tettamanti
mrctttmnt at gmail.com
Thu Dec 12 11:22:25 UTC 2013
Dear all,
sorry for the repost: I am just giving my question a second chance, it would be
enormously helpful if somebody came up with a solution!
I am trying to understand why a RFE will not work with a CustomPartitioner of mine.
The RFE snippet is:
--------------------------------------------------------------------------------
## Define RFE FractionTailSelector:
clf = LinearCSVMC()
rfe = RFE(clf.get_sensitivity_analyzer(postproc=maxofabs_sample()),
CrossValidation(clf, partitioner, errorfx=mean_mismatch_error,
postproc=mean_sample()), Repeater(2), fselector=FractionTailSelector(0.50,
mode='select', tail='upper'),
stopping_criterion=NBackHistoryStopCrit(BestDetector(), 10),
train_pmeasure=False, update_sensitivity=True)
## Run crossvalidation:
fclf = FeatureSelectionClassifier(clf, rfe)
rfecvte = CrossValidation(fclf, partitioner, errorfx=lambda p, t:np.mean(p ==
t), postproc=mean_sample(), enable_ca=['confusion', 'stats'])
rfe_res=rfecvte(fds)
--------------------------------------------------------------------------------
The snippet works smoothly if:
partitioner=NFoldPartitioner()
If however:
partitioner =
CustomPartitioner(([([0,1,2,3,4],[5]),([0,1,2,3,5],[4]),([0,1,2,4,5],[3]),([0,1,3,4,5],[2]),([0,2,3,4,5],[1]),([1,2,3,4,5],[0])]),
attr='chunks') ## Note: fds contains 6 chunks
I get the error message:
"ValueError: Got empty testing dataset from splitting in TransferMeasure. Unique
values of input split attribute are: [1])"
Originally, I wanted to use different custom parititions, but I ended up
implementing the above CustomPartitioner, which in my intentions should be
equivalent to NFoldPartitioner (leave-one-chunk-out). Apparently, no matter how
CustomPartitioner is defined, rfe will terminate with an error.
With a larger dataset, I also seem to get an error using:
partitioner=HalfPartitioner()
but again not using:
partitioner=NFoldPartitioner()
Below is the output of my mvpa2.wtf().
Thank you a lot for any help!
Marco
In [17]: mvpa2.wtf()
Out[17]:
Current date: 2013-11-20 16:48
PyMVPA:
Version: 2.2.0
Hash: $Format:%H$
Path: /usr/local/PyMVPA/mvpa2/__init__.pyc
Version control (GIT):
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# modified: mvpa2/tests/test_eeglab.py
# modified: mvpa2/tests/test_eepdataset.py
# modified: mvpa2/tests/test_emp_null.py
# modified: mvpa2/tests/test_enet.py
# modified: mvpa2/tests/test_erdataset.py
# modified: mvpa2/tests/test_errorfx.py
# modified: mvpa2/tests/test_externals.py
# modified: mvpa2/tests/test_filters.py
# modified: mvpa2/tests/test_fxmapper.py
# modified: mvpa2/tests/test_generators.py
# modified: mvpa2/tests/test_glmnet.py
# modified: mvpa2/tests/test_gnb.py
# modified: mvpa2/tests/test_gpr.py
# modified: mvpa2/tests/test_hamster.py
# modified: mvpa2/tests/test_hdf5.py
# modified: mvpa2/tests/test_hdf5_clf.py
# modified: mvpa2/tests/test_hyperalignment.py
# modified: mvpa2/tests/test_ifs.py
# modified: mvpa2/tests/test_iohelpers.py
# modified: mvpa2/tests/test_kernel.py
# modified: mvpa2/tests/test_knn.py
# modified: mvpa2/tests/test_lars.py
# modified: mvpa2/tests/test_mapper.py
# modified: mvpa2/tests/test_mapper_sp.py
# modified: mvpa2/tests/test_mdp.py
# modified: mvpa2/tests/test_meg.py
# modified: mvpa2/tests/test_misc.py
# modified: mvpa2/tests/test_multiclf.py
# modified: mvpa2/tests/test_neighborhood.py
# modified: mvpa2/tests/test_niftidataset.py
# modified: mvpa2/tests/test_params.py
# modified: mvpa2/tests/test_perturbsensana.py
# modified: mvpa2/tests/test_plr.py
# modified: mvpa2/tests/test_procrust.py
# modified: mvpa2/tests/test_prototypemapper.py
# modified: mvpa2/tests/test_regr.py
# modified: mvpa2/tests/test_report.py
# modified: mvpa2/tests/test_rfe.py
# modified: mvpa2/tests/test_ridge.py
# modified: mvpa2/tests/test_searchlight.py
# modified: mvpa2/tests/test_senses.py
# modified: mvpa2/tests/test_smlr.py
# modified: mvpa2/tests/test_som.py
# modified: mvpa2/tests/test_spam.py
# modified: mvpa2/tests/test_splitter.py
# modified: mvpa2/tests/test_state.py
# modified: mvpa2/tests/test_staticprojection.py
# modified: mvpa2/tests/test_stats.py
# modified: mvpa2/tests/test_stats_sp.py
# modified: mvpa2/tests/test_suite.py
# modified: mvpa2/tests/test_support.py
# modified: mvpa2/tests/test_surfing.py
# modified: mvpa2/tests/test_surfing_afni.py
# modified: mvpa2/tests/test_surfing_voxelselection.py
# modified: mvpa2/tests/test_svdmapper.py
# modified: mvpa2/tests/test_svm.py
# modified: mvpa2/tests/test_svmkernels.py
# modified: mvpa2/tests/test_testing.py
# modified: mvpa2/tests/test_transerror.py
# modified: mvpa2/tests/test_transformers.py
# modified: mvpa2/tests/test_usecases.py
# modified: mvpa2/tests/test_verbosity.py
# modified: mvpa2/tests/test_waveletmapper.py
# modified: mvpa2/tests/test_winner.py
# modified: mvpa2/tests/test_zscoremapper.py
# modified: py3tool.py
# modified: setup.cfg.win
# modified: tools/Makefile
# modified: tools/apigen.py
# modified: tools/mpkg_wrapper.py
# modified: tools/pdfbook.c
# modified: tools/valgrind-python.supp
#
no changes added to commit (use "git add" and/or "git commit -a")
Reference:
c67827abe179baf19bf2bd6040a2b8711871e478 HEAD
c67827abe179baf19bf2bd6040a2b8711871e478 refs/remotes/origin/HEAD
Difference from last release 2.2.0:
160 files changed, 18050 insertions(+), 882 deletions(-)
SYSTEM:
OS: posix Linux 3.10-3-amd64 #1 SMP Debian 3.10.11-1 (2013-09-10)
Distribution: debian/jessie/sid
EXTERNALS:
Present: atlas_fsl, cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_continuous._reduce_func(floc,fscale), good
scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, ipython, liblapack.so,
libsvm, libsvm verbosity control, lxml, matplotlib, mdp, mdp ge 2.4, nibabel,
nose, numpy, numpy_correct_unique, pprocess, pylab, pylab plottable, pywt, pywt
wp reconstruct, reportlab, running ipython env, scipy, skl, weave
Absent: atlas_pymvpa, cran-energy, elasticnet, glmnet, hcluster, lars,
mass, nipy, nipy.neurospin, numpydoc, openopt, pywt wp reconstruct fixed, rpy2,
sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr,
shogun.lightsvm, shogun.mpd, shogun.svmocas, shogun.svrlight, statsmodels
Versions of critical externals:
ctypes : 1.1.0
h5py : 2.0.1
ipython : 0.13.2
lxml : 3.2.0
matplotlib : 1.3.1
mdp : 3.4
nibabel : 1.3.0
numpy : 1.7.1
pprocess : 0.5
reportlab : 2.5
scipy : 0.12.0
skl : 0.14.1
Matplotlib backend: TkAgg
RUNTIME:
PyMVPA Environment Variables:
PYTHONPATH :
":/usr/lib/python2.7/lib-old:/usr/local/lib/python2.7/dist-packages:/usr/local/PyMVPA:/usr/lib/python2.7/plat-x86_64-linux-gnu:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-dynload:/home/marco/data/bll/abstrasomat_pymvpa/negsomloc6s_abssom6s_pymvpa:/usr/bin:/usr/local/PyMVPA/:/usr/lib/python2.7/dist-packages:/usr/lib/pymodules/python2.7:/usr/lib/python2.7/dist-packages/IPython/extensions:/usr/lib/python2.7:/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode:/home/marco/.python27_compiled:/usr/lib/python2.7/dist-packages/gtk-2.0:/usr/lib/python2.7/dist-packages/PIL"
PyMVPA Runtime Configuration:
[general]
verbose = 1
[externals]
have running ipython env = yes
have ipython = yes
have numpy = yes
have scipy = yes
have matplotlib = yes
have h5py = yes
have reportlab = yes
have weave = yes
have good scipy.stats.rdist = yes
have good scipy.stats.rv_discrete.ppf = yes
have good scipy.stats.rv_continuous._reduce_func(floc,fscale) = yes
have pylab = yes
have lars = no
have elasticnet = no
have glmnet = no
have skl = yes
have ctypes = yes
have libsvm = yes
have shogun = no
have openopt = no
have nibabel = yes
have mdp = yes
have mdp ge 2.4 = yes
have statsmodels = no
have pywt = yes
have cpickle = yes
have gzip = yes
have cran-energy = no
have griddata = yes
have nipy.neurospin = no
have lxml = yes
have atlas_fsl = yes
have atlas_pymvpa = no
have hcluster = no
have liblapack.so = yes
have libsvm verbosity control = yes
have mass = no
have nipy = no
have nose = yes
have numpy_correct_unique = yes
have numpydoc = no
have pprocess = yes
have pylab plottable = yes
have pywt wp reconstruct = yes
have pywt wp reconstruct fixed = no
have rpy2 = no
have sg ge 0.6.4 = no
have sg ge 0.6.5 = no
have sg_fixedcachesize = no
have shogun.krr = no
have shogun.lightsvm = no
have shogun.mpd = no
have shogun.svmocas = no
have shogun.svrlight = no
Process Information:
Name: ipython
State: R (running)
Tgid: 7966
Pid: 7966
PPid: 4220
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 256
Groups: 6 7 20 24 25 27 29 30 44 46 100 104 113 114 116 999 1000
VmPeak: 1156192 kB
VmSize: 786244 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 538160 kB
VmRSS: 165008 kB
VmData: 296740 kB
VmStk: 136 kB
VmExe: 2792 kB
VmLib: 55308 kB
VmPTE: 1232 kB
VmSwap: 0 kB
Threads: 3
SigQ: 0/254507
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000001001000
SigCgt: 0000000180000002
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: 0000001fffffffff
Seccomp: 0
Cpus_allowed: ff
Cpus_allowed_list: 0-7
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 62667
nonvoluntary_ctxt_switches: 788
--
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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