Package mvpa :: Package clfs :: Module enet :: Class ENET
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Class ENET

source code


Elastic-Net regression (ENET) `Classifier`.

Elastic-Net is the model selection algorithm from:

:ref:`Zou and Hastie (2005) <ZH05>` 'Regularization and Variable
Selection via the Elastic Net' Journal of the Royal Statistical
Society, Series B, 67, 301-320.

Similar to SMLR, it performs a feature selection while performing
classification, but instead of starting with all features, it
starts with none and adds them in, which is similar to boosting.

Unlike LARS it has both L1 and L2 regularization (instead of just
L1).  This means that while it tries to sparsify the features it
also tries to keep redundant features, which may be very very good
for fMRI classification.

In the true nature of the PyMVPA framework, this algorithm was
actually implemented in R by Zou and Hastie and wrapped via RPy.
To make use of ENET, you must have R and RPy installed as well as
both the lars and elasticnet contributed package. You can install
the R and RPy with the following command on Debian-based machines:

sudo aptitude install python-rpy python-rpy-doc r-base-dev

You can then install the lars and elasticnet package by running R
as root and calling:

install.packages()

Nested Classes [hide private]

Inherited from misc.state.ClassWithCollections: __metaclass__

Instance Methods [hide private]
 
__init__(self, lm=1.0, trace=False, normalize=True, intercept=True, max_steps=None, **kwargs)
Initialize ENET.
source code
 
__repr__(self)
String summary of the object
source code
 
_train(self, data)
Train the classifier using data (Dataset).
source code
 
_predict(self, data)
Predict the output for the provided data.
source code
 
_getFeatureIds(self)
Return ids of the used features
source code
 
getSensitivityAnalyzer(self, **kwargs)
Returns a sensitivity analyzer for ENET.
source code

Inherited from base.Classifier: __str__, clone, isTrained, predict, repredict, retrain, summary, train, trained, untrain

Inherited from base.Classifier (private): _postpredict, _posttrain, _prepredict, _pretrain, _regressionIsBogus, _setRetrainable

Inherited from misc.state.ClassWithCollections: __getattribute__, __new__, __setattr__, reset

Inherited from object: __delattr__, __format__, __hash__, __reduce__, __reduce_ex__, __sizeof__, __subclasshook__

Class Variables [hide private]
  _clf_internals = ['enet', 'regression', 'linear', 'has_sensiti...
Describes some specifics about the classifier -- is that it is doing regression for instance....
  weights = property(lambda self: self.__weights)

Inherited from base.Classifier: _DEV__doc__, feature_ids, predicting_time, predictions, regression, retrainable, trained_dataset, trained_labels, trained_nsamples, training_confusion, training_time, values

Inherited from misc.state.ClassWithCollections: descr

Instance Variables [hide private]
  __weights
The beta weights for each feature.
  __trained_model
The model object after training that will be used for predictions.
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, lm=1.0, trace=False, normalize=True, intercept=True, max_steps=None, **kwargs)
(Constructor)

source code 

Initialize ENET.

See the help in R for further details on the following parameters:

Parameters:
  • lm (float) - Penalty parameter. 0 will perform LARS with no ridge regression. Default is 1.0.
  • trace (boolean) - Whether to print progress in R as it works.
  • normalize (boolean) - Whether to normalize the L2 Norm.
  • intercept (boolean) - Whether to add a non-penalized intercept to the model.
  • max_steps (None or int) - If not None, specify the total number of iterations to run. Each iteration adds a feature, but leaving it none will add until convergence.
Overrides: object.__init__

__repr__(self)
(Representation operator)

source code 
String summary of the object
Parameters:
  • fullname - Either to include full name of the module
  • prefixes - What other prefixes to prepend to list of arguments
Overrides: object.__repr__

_train(self, data)

source code 
Train the classifier using data (Dataset).
Overrides: base.Classifier._train

_predict(self, data)

source code 
Predict the output for the provided data.
Overrides: base.Classifier._predict

_getFeatureIds(self)

source code 
Return ids of the used features
Overrides: base.Classifier._getFeatureIds

getSensitivityAnalyzer(self, **kwargs)

source code 
Returns a sensitivity analyzer for ENET.
Overrides: base.Classifier.getSensitivityAnalyzer

Class Variable Details [hide private]

_clf_internals

Describes some specifics about the classifier -- is that it is doing regression for instance....
Value:
['enet', 'regression', 'linear', 'has_sensitivity', 'does_feature_sele\
ction']