Hi Dominic,

Did you get the pull request of the MLP? It seems you have installed scikit from the main repository, where MLP haven't been pushed onto yet.

You can double check if MLP is there by going to the installation directory 'site-packages' of python, and see if the `neural network` folder is present

A subset of the path is something like this 'sklearn\neural_network'

~Issam



On 7/11/2013 4:37 PM, Dominic Steinitz wrote:
Many thanks for all the help so far. I am running the tests after installation. I get the output below. Should I be worried?

Also my python doesn't seem to be able to find the neural network module but it seemed to install ok. I can send the output from the install if necessary.

~/Dropbox/Private/Machine Learning $ python
Python 2.7.3 (v2.7.3:70274d53c1dd, Apr  9 2012, 20:52:43)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from sklearn.neural_network import MLPClassifier
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named neural_network


Dominics-MacBook-Pro:Machine Learning dom$ nosetests --exe sklearn
....................S........................................../Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/manifold/spectral_embedding.py:225: UserWarning: Graph is not fully connected, spectral embedding may not works as expected.
  warnings.warn("Graph is not fully connected, spectral embedding"
......./Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/covariance/graph_lasso_.py:45: RuntimeWarning: invalid value encountered in absolute
  gap += alpha * (np.abs(precision_).sum()
/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/covariance/graph_lasso_.py:46: RuntimeWarning: invalid value encountered in absolute
  - np.abs(np.diag(precision_)).sum())
/Library/Python/2.7/site-packages/numpy-1.8.0.dev_4600b2f_20130131-py2.7-macosx-10.8-intel.egg/numpy/linalg/linalg.py:1664: RuntimeWarning: invalid value encountered in absolute
  absd = absolute(d)
/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/covariance/graph_lasso_.py:32: RuntimeWarning: invalid value encountered in absolute
  cost += alpha * (np.abs(precision_).sum()
/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/covariance/graph_lasso_.py:33: RuntimeWarning: invalid value encountered in absolute
  - np.abs(np.diag(precision_)).sum())
/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/covariance/graph_lasso_.py:195: RuntimeWarning: invalid value encountered in absolute
  if np.abs(d_gap) < tol:
....SS....../Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/datasets/tests/test_base.py:124: UserWarning: Could not load sample images, PIL is not available.
  warnings.warn("Could not load sample images, PIL is not available.")
.../Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/datasets/tests/test_base.py:145: UserWarning: Could not load sample images, PIL is not available.
  warnings.warn("Could not load sample images, PIL is not available.")
./Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/datasets/tests/test_base.py:161: UserWarning: Could not load sample images, PIL is not available.
  warnings.warn("Could not load sample images, PIL is not available.")
.....S..............................................E.S.........................................................S.........................................SSS....................../Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/externals/joblib/test/test_func_inspect.py:122: UserWarning: Cannot inspect object <functools.partial object at 0x108bd3998>, ignore list will not work.
  nose.tools.assert_equal(filter_args(ff, ['y'], (1, )),
.....................................................................................................................................................................................................................................................................................................................................................................................S.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSS....S....S..................................................................................................................................
======================================================================
ERROR: sklearn.decomposition.tests.test_dict_learning.test_dict_learning_online_overcomplete
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/nose-1.2.1-py2.7.egg/nose/case.py", line 197, in runTest
    self.test(*self.arg)
File "/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/decomposition/tests/test_dict_learning.py", line 117, in test_dict_learning_online_overcomplete
    dico = MiniBatchDictionaryLearning(n_components, n_iter=20).fit(X)
File "/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/decomposition/dict_learning.py", line 1098, in fit
    random_state=self.random_state)
File "/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/decomposition/dict_learning.py", line 624, in dict_learning_online
    alpha=alpha).T
File "/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/decomposition/dict_learning.py", line 238, in sparse_encode
    init=init, max_iter=max_iter)
File "/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/decomposition/dict_learning.py", line 99, in _sparse_encode
    lasso_lars.fit(dictionary.T, X.T, Xy=cov)
File "/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/linear_model/least_angle.py", line 576, in fit
    eps=self.eps, return_path=False)
File "/Library/Python/2.7/site-packages/scikit_learn-0.14_git-py2.7-macosx-10.8-intel.egg/sklearn/linear_model/least_angle.py", line 233, in lars_path
    % (n_iter, alphas[n_iter], n_active, diag))
UnboundLocalError: local variable 'alphas' referenced before assignment

----------------------------------------------------------------------
Ran 1332 tests in 63.817s

FAILED (SKIP=15, errors=1)


Dominic Steinitz
domi...@steinitz.org <mailto:domi...@steinitz.org>
http://idontgetoutmuch.wordpress.com

On 11 Jul 2013, at 10:09, Dominic Steinitz <domi...@steinitz.org <mailto:domi...@steinitz.org>> wrote:

Perhaps my googling skills are failing me but all I could find on the subject was:

Module ann (Artificial Neural Networks) has been removed from the distribution. Users wanting this sort of algorithms should take a look into pybrain

This was part of the release notes for Scikit-learn 0.5 so possibly out of date.

Why is there no neural network module in Scikit-learn? Is pybrain still my best bet? Should I investigate e.g. neurolab?

Many thanks.

Dominic Steinitz
domi...@steinitz.org <mailto:domi...@steinitz.org>
http://idontgetoutmuch.wordpress.com <http://idontgetoutmuch.wordpress.com/>




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