sklearn/doc/whats_new/v0.14.rst

.. include:: _contributors.rst

.. currentmodule:: sklearn

============
Version 0.14
============

.. _changes_0_14:

Version 0.14
===============

**August 7, 2013**

Changelog
---------

- Missing values with sparse and dense matrices can be imputed with the
  transformer `preprocessing.Imputer` by `Nicolas Trésegnie`_.

- The core implementation of decisions trees has been rewritten from
  scratch, allowing for faster tree induction and lower memory
  consumption in all tree-based estimators. By `Gilles Louppe`_.

- Added :class:`ensemble.AdaBoostClassifier` and
  :class:`ensemble.AdaBoostRegressor`, by `Noel Dawe`_  and
  `Gilles Louppe`_. See the :ref:`AdaBoost <adaboost>` section of the user
  guide for details and examples.

- Added `grid_search.RandomizedSearchCV` and
  `grid_search.ParameterSampler` for randomized hyperparameter
  optimization. By `Andreas Müller`_.

- Added :ref:`biclustering <biclustering>` algorithms
  (`sklearn.cluster.bicluster.SpectralCoclustering` and
  `sklearn.cluster.bicluster.SpectralBiclustering`), data
  generation methods (:func:`sklearn.datasets.make_biclusters` and
  :func:`sklearn.datasets.make_checkerboard`), and scoring metrics
  (:func:`sklearn.metrics.consensus_score`). By `Kemal Eren`_.

- Added :ref:`Restricted Boltzmann Machines<rbm>`
  (:class:`neural_network.BernoulliRBM`). By `Yann Dauphin`_.

- Python 3 support by :user:`Justin Vincent <justinvf>`, `Lars Buitinck`_,
  :user:`Subhodeep Moitra <smoitra87>` and `Olivier Grisel`_. All tests now pass under
  Python 3.3.

- Ability to pass one penalty (alpha value) per target in
  :class:`linear_model.Ridge`, by @eickenberg and `Mathieu Blondel`_.

- Fixed `sklearn.linear_model.stochastic_gradient.py` L2 regularization
  issue (minor practical significance).
  By :user:`Norbert Crombach <norbert>` and `Mathieu Blondel`_ .

- Added an interactive version of `Andreas Müller`_'s
  `Machine Learning Cheat Sheet (for scikit-learn)
  <https://peekaboo-vision.blogspot.de/2013/01/machine-learning-cheat-sheet-for-scikit.html>`_
  to the documentation. See :ref:`Choosing the right estimator <ml_map>`.
  By `Jaques Grobler`_.

- `grid_search.GridSearchCV` and
  `cross_validation.cross_val_score` now support the use of advanced
  scoring function such as area under the ROC curve and f-beta scores.
  See :ref:`scoring_parameter` for details. By `Andreas Müller`_
  and `Lars Buitinck`_.
  Passing a function from :mod:`sklearn.metrics` as ``score_func`` is
  deprecated.

- Multi-label classification output is now supported by
  :func:`metrics.accuracy_score`, :func:`metrics.zero_one_loss`,
  :func:`metrics.f1_score`, :func:`metrics.fbeta_score`,
  :func:`metrics.classification_report`,
  :func:`metrics.precision_score` and :func:`metrics.recall_score`
  by `Arnaud Joly`_.

- Two new metrics :func:`metrics.hamming_loss` and
  `metrics.jaccard_similarity_score`
  are added with multi-label support by `Arnaud Joly`_.

- Speed and memory usage improvements in
  :class:`feature_extraction.text.CountVectorizer` and
  :class:`feature_extraction.text.TfidfVectorizer`,
  by Jochen Wersdörfer and Roman Sinayev.

- The ``min_df`` parameter in
  :class:`feature_extraction.text.CountVectorizer` and
  :class:`feature_extraction.text.TfidfVectorizer`, which used to be 2,
  has been reset to 1 to avoid unpleasant surprises (empty vocabularies)
  for novice users who try it out on tiny document collections.
  A value of at least 2 is still recommended for practical use.

- :class:`svm.LinearSVC`, :class:`linear_model.SGDClassifier` and
  :class:`linear_model.SGDRegressor` now have a ``sparsify`` method that
  converts their ``coef_`` into a sparse matrix, meaning stored models
  trained using these estimators can be made much more compact.

- :class:`linear_model.SGDClassifier` now produces multiclass probability
  estimates when trained under log loss or modified Huber loss.

- Hyperlinks to documentation in example code on the website by
  :user:`Martin Luessi <mluessi>`.

- Fixed bug in :class:`preprocessing.MinMaxScaler` causing incorrect scaling
  of the features for non-default ``feature_range`` settings. By `Andreas
  Müller`_.

- ``max_features`` in :class:`tree.DecisionTreeClassifier`,
  :class:`tree.DecisionTreeRegressor` and all derived ensemble estimators
  now supports percentage values. By `Gilles Louppe`_.

- Performance improvements in :class:`isotonic.IsotonicRegression` by
  `Nelle Varoquaux`_.

- :func:`metrics.accuracy_score` has an option normalize to return
  the fraction or the number of correctly classified sample
  by `Arnaud Joly`_.

- Added :func:`metrics.log_loss` that computes log loss, aka cross-entropy
  loss. By Jochen Wersdörfer and `Lars Buitinck`_.

- A bug that caused :class:`ensemble.AdaBoostClassifier`'s to output
  incorrect probabilities has been fixed.

- Feature selectors now share a mixin providing consistent ``transform``,
  ``inverse_transform`` and ``get_support`` methods. By `Joel Nothman`_.

- A fitted `grid_search.GridSearchCV` or
  `grid_search.RandomizedSearchCV` can now generally be pickled.
  By `Joel Nothman`_.

- Refactored and vectorized implementation of :func:`metrics.roc_curve`
  and :func:`metrics.precision_recall_curve`. By `Joel Nothman`_.

- The new estimator :class:`sklearn.decomposition.TruncatedSVD`
  performs dimensionality reduction using SVD on sparse matrices,
  and can be used for latent semantic analysis (LSA).
  By `Lars Buitinck`_.

- Added self-contained example of out-of-core learning on text data
  :ref:`sphx_glr_auto_examples_applications_plot_out_of_core_classification.py`.
  By :user:`Eustache Diemert <oddskool>`.

- The default number of components for
  `sklearn.decomposition.RandomizedPCA` is now correctly documented
  to be ``n_features``. This was the default behavior, so programs using it
  will continue to work as they did.

- :class:`sklearn.cluster.KMeans` now fits several orders of magnitude
  faster on sparse data (the speedup depends on the sparsity). By
  `Lars Buitinck`_.

- Reduce memory footprint of FastICA by `Denis Engemann`_ and
  `Alexandre Gramfort`_.

- Verbose output in `sklearn.ensemble.gradient_boosting` now uses
  a column format and prints progress in decreasing frequency.
  It also shows the remaining time. By `Peter Prettenhofer`_.

- `sklearn.ensemble.gradient_boosting` provides out-of-bag improvement
  `oob_improvement_`
  rather than the OOB score for model selection. An example that shows
  how to use OOB estimates to select the number of trees was added.
  By `Peter Prettenhofer`_.

- Most metrics now support string labels for multiclass classification
  by `Arnaud Joly`_ and `Lars Buitinck`_.

- New OrthogonalMatchingPursuitCV class by `Alexandre Gramfort`_
  and `Vlad Niculae`_.

- Fixed a bug in `sklearn.covariance.GraphLassoCV`: the
  'alphas' parameter now works as expected when given a list of
  values. By Philippe Gervais.

- Fixed an important bug in `sklearn.covariance.GraphLassoCV`
  that prevented all folds provided by a CV object to be used (only
  the first 3 were used). When providing a CV object, execution
  time may thus increase significantly compared to the previous
  version (bug results are correct now). By Philippe Gervais.

- `cross_validation.cross_val_score` and the `grid_search`
  module is now tested with multi-output data by `Arnaud Joly`_.

- :func:`datasets.make_multilabel_classification` can now return
  the output in label indicator multilabel format  by `Arnaud Joly`_.

- K-nearest neighbors, :class:`neighbors.KNeighborsRegressor`
  and :class:`neighbors.RadiusNeighborsRegressor`,
  and radius neighbors, :class:`neighbors.RadiusNeighborsRegressor` and
  :class:`neighbors.RadiusNeighborsClassifier` support multioutput data
  by `Arnaud Joly`_.

- Random state in LibSVM-based estimators (:class:`svm.SVC`, :class:`svm.NuSVC`,
  :class:`svm.OneClassSVM`, :class:`svm.SVR`, :class:`svm.NuSVR`) can now be
  controlled.  This is useful to ensure consistency in the probability
  estimates for the classifiers trained with ``probability=True``. By
  `Vlad Niculae`_.

- Out-of-core learning support for discrete naive Bayes classifiers
  :class:`sklearn.naive_bayes.MultinomialNB` and
  :class:`sklearn.naive_bayes.BernoulliNB` by adding the ``partial_fit``
  method by `Olivier Grisel`_.

- New website design and navigation by `Gilles Louppe`_, `Nelle Varoquaux`_,
  Vincent Michel and `Andreas Müller`_.

- Improved documentation on :ref:`multi-class, multi-label and multi-output
  classification <multiclass>` by `Yannick Schwartz`_ and `Arnaud Joly`_.

- Better input and error handling in the :mod:`sklearn.metrics` module by
  `Arnaud Joly`_ and `Joel Nothman`_.

- Speed optimization of the `hmm` module by :user:`Mikhail Korobov <kmike>`

- Significant speed improvements for :class:`sklearn.cluster.DBSCAN`
  by `cleverless <https://github.com/cleverless>`_


API changes summary
-------------------

- The `auc_score` was renamed :func:`metrics.roc_auc_score`.

- Testing scikit-learn with ``sklearn.test()`` is deprecated. Use
  ``nosetests sklearn`` from the command line.

- Feature importances in :class:`tree.DecisionTreeClassifier`,
  :class:`tree.DecisionTreeRegressor` and all derived ensemble estimators
  are now computed on the fly when accessing  the ``feature_importances_``
  attribute. Setting ``compute_importances=True`` is no longer required.
  By `Gilles Louppe`_.

- :class:`linear_model.lasso_path` and
  :class:`linear_model.enet_path` can return its results in the same
  format as that of :class:`linear_model.lars_path`. This is done by
  setting the ``return_models`` parameter to ``False``. By
  `Jaques Grobler`_ and `Alexandre Gramfort`_

- `grid_search.IterGrid` was renamed to `grid_search.ParameterGrid`.

- Fixed bug in `KFold` causing imperfect class balance in some
  cases. By `Alexandre Gramfort`_ and Tadej Janež.

- :class:`sklearn.neighbors.BallTree` has been refactored, and a
  :class:`sklearn.neighbors.KDTree` has been
  added which shares the same interface.  The Ball Tree now works with
  a wide variety of distance metrics.  Both classes have many new
  methods, including single-tree and dual-tree queries, breadth-first
  and depth-first searching, and more advanced queries such as
  kernel density estimation and 2-point correlation functions.
  By `Jake Vanderplas`_

- Support for scipy.spatial.cKDTree within neighbors queries has been
  removed, and the functionality replaced with the new
  :class:`sklearn.neighbors.KDTree` class.

- :class:`sklearn.neighbors.KernelDensity` has been added, which performs
  efficient kernel density estimation with a variety of kernels.

- :class:`sklearn.decomposition.KernelPCA` now always returns output with
  ``n_components`` components, unless the new parameter ``remove_zero_eig``
  is set to ``True``. This new behavior is consistent with the way
  kernel PCA was always documented; previously, the removal of components
  with zero eigenvalues was tacitly performed on all data.

- ``gcv_mode="auto"`` no longer tries to perform SVD on a densified
  sparse matrix in :class:`sklearn.linear_model.RidgeCV`.

- Sparse matrix support in `sklearn.decomposition.RandomizedPCA`
  is now deprecated in favor of the new ``TruncatedSVD``.

- `cross_validation.KFold` and
  `cross_validation.StratifiedKFold` now enforce `n_folds >= 2`
  otherwise a ``ValueError`` is raised. By `Olivier Grisel`_.

- :func:`datasets.load_files`'s ``charset`` and ``charset_errors``
  parameters were renamed ``encoding`` and ``decode_errors``.

- Attribute ``oob_score_`` in :class:`sklearn.ensemble.GradientBoostingRegressor`
  and :class:`sklearn.ensemble.GradientBoostingClassifier`
  is deprecated and has been replaced by ``oob_improvement_`` .

- Attributes in OrthogonalMatchingPursuit have been deprecated
  (copy_X, Gram, ...) and precompute_gram renamed precompute
  for consistency. See #2224.

- :class:`sklearn.preprocessing.StandardScaler` now converts integer input
  to float, and raises a warning. Previously it rounded for dense integer
  input.

- :class:`sklearn.multiclass.OneVsRestClassifier` now has a
  ``decision_function`` method. This will return the distance of each
  sample from the decision boundary for each class, as long as the
  underlying estimators implement the ``decision_function`` method.
  By `Kyle Kastner`_.

- Better input validation, warning on unexpected shapes for y.

People
------
List of contributors for release 0.14 by number of commits.

* 277  Gilles Louppe
* 245  Lars Buitinck
* 187  Andreas Mueller
* 124  Arnaud Joly
* 112  Jaques Grobler
* 109  Gael Varoquaux
* 107  Olivier Grisel
* 102  Noel Dawe
*  99  Kemal Eren
*  79  Joel Nothman
*  75  Jake VanderPlas
*  73  Nelle Varoquaux
*  71  Vlad Niculae
*  65  Peter Prettenhofer
*  64  Alexandre Gramfort
*  54  Mathieu Blondel
*  38  Nicolas Trésegnie
*  35  eustache
*  27  Denis Engemann
*  25  Yann N. Dauphin
*  19  Justin Vincent
*  17  Robert Layton
*  15  Doug Coleman
*  14  Michael Eickenberg
*  13  Robert Marchman
*  11  Fabian Pedregosa
*  11  Philippe Gervais
*  10  Jim Holmström
*  10  Tadej Janež
*  10  syhw
*   9  Mikhail Korobov
*   9  Steven De Gryze
*   8  sergeyf
*   7  Ben Root
*   7  Hrishikesh Huilgolkar
*   6  Kyle Kastner
*   6  Martin Luessi
*   6  Rob Speer
*   5  Federico Vaggi
*   5  Raul Garreta
*   5  Rob Zinkov
*   4  Ken Geis
*   3  A. Flaxman
*   3  Denton Cockburn
*   3  Dougal Sutherland
*   3  Ian Ozsvald
*   3  Johannes Schönberger
*   3  Robert McGibbon
*   3  Roman Sinayev
*   3  Szabo Roland
*   2  Diego Molla
*   2  Imran Haque
*   2  Jochen Wersdörfer
*   2  Sergey Karayev
*   2  Yannick Schwartz
*   2  jamestwebber
*   1  Abhijeet Kolhe
*   1  Alexander Fabisch
*   1  Bastiaan van den Berg
*   1  Benjamin Peterson
*   1  Daniel Velkov
*   1  Fazlul Shahriar
*   1  Felix Brockherde
*   1  Félix-Antoine Fortin
*   1  Harikrishnan S
*   1  Jack Hale
*   1  JakeMick
*   1  James McDermott
*   1  John Benediktsson
*   1  John Zwinck
*   1  Joshua Vredevoogd
*   1  Justin Pati
*   1  Kevin Hughes
*   1  Kyle Kelley
*   1  Matthias Ekman
*   1  Miroslav Shubernetskiy
*   1  Naoki Orii
*   1  Norbert Crombach
*   1  Rafael Cunha de Almeida
*   1  Rolando Espinoza La fuente
*   1  Seamus Abshere
*   1  Sergey Feldman
*   1  Sergio Medina
*   1  Stefano Lattarini
*   1  Steve Koch
*   1  Sturla Molden
*   1  Thomas Jarosch
*   1  Yaroslav Halchenko