.. _combining_estimators:

==================================
Pipelines and composite estimators
==================================

Transformers are usually combined with classifiers, regressors or other
estimators to build a composite estimator.  The most common tool is a
:ref:`Pipeline <pipeline>`. Pipeline is often used in combination with
:ref:`FeatureUnion <feature_union>` which concatenates the output of
transformers into a composite feature space.  :ref:`TransformedTargetRegressor
<transformed_target_regressor>` deals with transforming the :term:`target`
(i.e. log-transform :term:`y`). In contrast, Pipelines only transform the
observed data (:term:`X`).

.. _pipeline:

Pipeline: chaining estimators
=============================

.. currentmodule:: sklearn.pipeline

:class:`Pipeline` can be used to chain multiple estimators
into one. This is useful as there is often a fixed sequence
of steps in processing the data, for example feature selection, normalization
and classification. :class:`Pipeline` serves multiple purposes here:

Convenience and encapsulation
    You only have to call ``fit`` and ``predict`` once on your
    data to fit a whole sequence of estimators.
Joint parameter selection
    You can :ref:`grid search <grid_search>`
    over parameters of all estimators in the pipeline at once.
Safety
    Pipelines help avoid leaking statistics from your test data into the
    trained model in cross-validation, by ensuring that the same samples are
    used to train the transformers and predictors.

All estimators in a pipeline, except the last one, must be transformers
(i.e. must have a ``transform`` method).
The last estimator may be any type (transformer, classifier, etc.).


Usage
-----

The :class:`Pipeline` is built using a list of ``(key, value)`` pairs, where
the ``key`` is a string containing the name you want to give this step and ``value``
is an estimator object::

    >>> from sklearn.pipeline import Pipeline
    >>> from sklearn.svm import SVC
    >>> from sklearn.decomposition import PCA
    >>> estimators = [('reduce_dim', PCA()), ('clf', SVC())]
    >>> pipe = Pipeline(estimators)
    >>> pipe # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
    Pipeline(memory=None,
             steps=[('reduce_dim', PCA(copy=True,...)),
                    ('clf', SVC(C=1.0,...))])

The utility function :func:`make_pipeline` is a shorthand
for constructing pipelines;
it takes a variable number of estimators and returns a pipeline,
filling in the names automatically::

    >>> from sklearn.pipeline import make_pipeline
    >>> from sklearn.naive_bayes import MultinomialNB
    >>> from sklearn.preprocessing import Binarizer
    >>> make_pipeline(Binarizer(), MultinomialNB()) # doctest: +NORMALIZE_WHITESPACE
    Pipeline(memory=None,
             steps=[('binarizer', Binarizer(copy=True, threshold=0.0)),
                    ('multinomialnb', MultinomialNB(alpha=1.0,
                                                    class_prior=None,
                                                    fit_prior=True))])

The estimators of a pipeline are stored as a list in the ``steps`` attribute::

    >>> pipe.steps[0]
    ('reduce_dim', PCA(copy=True, iterated_power='auto', n_components=None, random_state=None,
      svd_solver='auto', tol=0.0, whiten=False))

and as a ``dict`` in ``named_steps``::

    >>> pipe.named_steps['reduce_dim']
    PCA(copy=True, iterated_power='auto', n_components=None, random_state=None,
      svd_solver='auto', tol=0.0, whiten=False)

Parameters of the estimators in the pipeline can be accessed using the
``<estimator>__<parameter>`` syntax::

    >>> pipe.set_params(clf__C=10) # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
    Pipeline(memory=None,
             steps=[('reduce_dim', PCA(copy=True, iterated_power='auto',...)),
                    ('clf', SVC(C=10, cache_size=200, class_weight=None,...))])

Attributes of named_steps map to keys, enabling tab completion in interactive environments::

    >>> pipe.named_steps.reduce_dim is pipe.named_steps['reduce_dim']
    True

This is particularly important for doing grid searches::

    >>> from sklearn.model_selection import GridSearchCV
    >>> param_grid = dict(reduce_dim__n_components=[2, 5, 10],
    ...                   clf__C=[0.1, 10, 100])
    >>> grid_search = GridSearchCV(pipe, param_grid=param_grid)

Individual steps may also be replaced as parameters, and non-final steps may be
ignored by setting them to ``None``::

    >>> from sklearn.linear_model import LogisticRegression
    >>> param_grid = dict(reduce_dim=[None, PCA(5), PCA(10)],
    ...                   clf=[SVC(), LogisticRegression()],
    ...                   clf__C=[0.1, 10, 100])
    >>> grid_search = GridSearchCV(pipe, param_grid=param_grid)

.. topic:: Examples:

 * :ref:`sphx_glr_auto_examples_feature_selection_plot_feature_selection_pipeline.py`
 * :ref:`sphx_glr_auto_examples_model_selection_grid_search_text_feature_extraction.py`
 * :ref:`sphx_glr_auto_examples_compose_plot_digits_pipe.py`
 * :ref:`sphx_glr_auto_examples_plot_kernel_approximation.py`
 * :ref:`sphx_glr_auto_examples_svm_plot_svm_anova.py`
 * :ref:`sphx_glr_auto_examples_compose_plot_compare_reduction.py`

.. topic:: See also:

 * :ref:`grid_search`


Notes
-----

Calling ``fit`` on the pipeline is the same as calling ``fit`` on
each estimator in turn, ``transform`` the input and pass it on to the next step.
The pipeline has all the methods that the last estimator in the pipeline has,
i.e. if the last estimator is a classifier, the :class:`Pipeline` can be used
as a classifier. If the last estimator is a transformer, again, so is the
pipeline.

.. _pipeline_cache:

Caching transformers: avoid repeated computation
-------------------------------------------------

.. currentmodule:: sklearn.pipeline

Fitting transformers may be computationally expensive. With its
``memory`` parameter set, :class:`Pipeline` will cache each transformer
after calling ``fit``.
This feature is used to avoid computing the fit transformers within a pipeline
if the parameters and input data are identical. A typical example is the case of
a grid search in which the transformers can be fitted only once and reused for
each configuration.

The parameter ``memory`` is needed in order to cache the transformers.
``memory`` can be either a string containing the directory where to cache the
transformers or a `joblib.Memory <https://pythonhosted.org/joblib/memory.html>`_
object::

    >>> from tempfile import mkdtemp
    >>> from shutil import rmtree
    >>> from sklearn.decomposition import PCA
    >>> from sklearn.svm import SVC
    >>> from sklearn.pipeline import Pipeline
    >>> estimators = [('reduce_dim', PCA()), ('clf', SVC())]
    >>> cachedir = mkdtemp()
    >>> pipe = Pipeline(estimators, memory=cachedir)
    >>> pipe # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
    Pipeline(...,
             steps=[('reduce_dim', PCA(copy=True,...)),
                    ('clf', SVC(C=1.0,...))])
    >>> # Clear the cache directory when you don't need it anymore
    >>> rmtree(cachedir)

.. warning:: **Side effect of caching transformers**

   Using a :class:`Pipeline` without cache enabled, it is possible to
   inspect the original instance such as::

     >>> from sklearn.datasets import load_digits
     >>> digits = load_digits()
     >>> pca1 = PCA()
     >>> svm1 = SVC(gamma='scale')
     >>> pipe = Pipeline([('reduce_dim', pca1), ('clf', svm1)])
     >>> pipe.fit(digits.data, digits.target)
     ... # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
     Pipeline(memory=None,
              steps=[('reduce_dim', PCA(...)), ('clf', SVC(...))])
     >>> # The pca instance can be inspected directly
     >>> print(pca1.components_) # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
         [[-1.77484909e-19  ... 4.07058917e-18]]

   Enabling caching triggers a clone of the transformers before fitting.
   Therefore, the transformer instance given to the pipeline cannot be
   inspected directly.
   In following example, accessing the :class:`PCA` instance ``pca2``
   will raise an ``AttributeError`` since ``pca2`` will be an unfitted
   transformer.
   Instead, use the attribute ``named_steps`` to inspect estimators within
   the pipeline::

     >>> cachedir = mkdtemp()
     >>> pca2 = PCA()
     >>> svm2 = SVC(gamma='scale')
     >>> cached_pipe = Pipeline([('reduce_dim', pca2), ('clf', svm2)],
     ...                        memory=cachedir)
     >>> cached_pipe.fit(digits.data, digits.target)
     ... # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
      Pipeline(memory=...,
               steps=[('reduce_dim', PCA(...)), ('clf', SVC(...))])
     >>> print(cached_pipe.named_steps['reduce_dim'].components_)
     ... # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
         [[-1.77484909e-19  ... 4.07058917e-18]]
     >>> # Remove the cache directory
     >>> rmtree(cachedir)

.. topic:: Examples:

 * :ref:`sphx_glr_auto_examples_compose_plot_compare_reduction.py`

.. _transformed_target_regressor:

Transforming target in regression
=================================

:class:`TransformedTargetRegressor` transforms the targets ``y`` before fitting
a regression model. The predictions are mapped back to the original space via
an inverse transform. It takes as an argument the regressor that will be used
for prediction, and the transformer that will be applied to the target
variable::

  >>> import numpy as np
  >>> from sklearn.datasets import load_boston
  >>> from sklearn.compose import TransformedTargetRegressor
  >>> from sklearn.preprocessing import QuantileTransformer
  >>> from sklearn.linear_model import LinearRegression
  >>> from sklearn.model_selection import train_test_split
  >>> boston = load_boston()
  >>> X = boston.data
  >>> y = boston.target
  >>> transformer = QuantileTransformer(output_distribution='normal')
  >>> regressor = LinearRegression()
  >>> regr = TransformedTargetRegressor(regressor=regressor,
  ...                                   transformer=transformer)
  >>> X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
  >>> regr.fit(X_train, y_train) # doctest: +ELLIPSIS
  TransformedTargetRegressor(...)
  >>> print('R2 score: {0:.2f}'.format(regr.score(X_test, y_test)))
  R2 score: 0.67
  >>> raw_target_regr = LinearRegression().fit(X_train, y_train)
  >>> print('R2 score: {0:.2f}'.format(raw_target_regr.score(X_test, y_test)))
  R2 score: 0.64

For simple transformations, instead of a Transformer object, a pair of
functions can be passed, defining the transformation and its inverse mapping::

  >>> from __future__ import division
  >>> def func(x):
  ...     return np.log(x)
  >>> def inverse_func(x):
  ...     return np.exp(x)

Subsequently, the object is created as::

  >>> regr = TransformedTargetRegressor(regressor=regressor,
  ...                                   func=func,
  ...                                   inverse_func=inverse_func)
  >>> regr.fit(X_train, y_train) # doctest: +ELLIPSIS
  TransformedTargetRegressor(...)
  >>> print('R2 score: {0:.2f}'.format(regr.score(X_test, y_test)))
  R2 score: 0.65

By default, the provided functions are checked at each fit to be the inverse of
each other. However, it is possible to bypass this checking by setting
``check_inverse`` to ``False``::

  >>> def inverse_func(x):
  ...     return x
  >>> regr = TransformedTargetRegressor(regressor=regressor,
  ...                                   func=func,
  ...                                   inverse_func=inverse_func,
  ...                                   check_inverse=False)
  >>> regr.fit(X_train, y_train) # doctest: +ELLIPSIS
  TransformedTargetRegressor(...)
  >>> print('R2 score: {0:.2f}'.format(regr.score(X_test, y_test)))
  R2 score: -4.50

.. note::

   The transformation can be triggered by setting either ``transformer`` or the
   pair of functions ``func`` and ``inverse_func``. However, setting both
   options will raise an error.

.. topic:: Examples:

 * :ref:`sphx_glr_auto_examples_compose_plot_transformed_target.py`


.. _feature_union:

FeatureUnion: composite feature spaces
======================================

.. currentmodule:: sklearn.pipeline

:class:`FeatureUnion` combines several transformer objects into a new
transformer that combines their output. A :class:`FeatureUnion` takes
a list of transformer objects. During fitting, each of these
is fit to the data independently. The transformers are applied in parallel,
and the feature matrices they output are concatenated side-by-side into a
larger matrix.

When you want to apply different transformations to each field of the data,
see the related class :class:`sklearn.compose.ColumnTransformer`
(see :ref:`user guide <column_transformer>`).

:class:`FeatureUnion` serves the same purposes as :class:`Pipeline` -
convenience and joint parameter estimation and validation.

:class:`FeatureUnion` and :class:`Pipeline` can be combined to
create complex models.

(A :class:`FeatureUnion` has no way of checking whether two transformers
might produce identical features. It only produces a union when the
feature sets are disjoint, and making sure they are the caller's
responsibility.)


Usage
-----

A :class:`FeatureUnion` is built using a list of ``(key, value)`` pairs,
where the ``key`` is the name you want to give to a given transformation
(an arbitrary string; it only serves as an identifier)
and ``value`` is an estimator object::

    >>> from sklearn.pipeline import FeatureUnion
    >>> from sklearn.decomposition import PCA
    >>> from sklearn.decomposition import KernelPCA
    >>> estimators = [('linear_pca', PCA()), ('kernel_pca', KernelPCA())]
    >>> combined = FeatureUnion(estimators)
    >>> combined # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
    FeatureUnion(n_jobs=None,
                 transformer_list=[('linear_pca', PCA(copy=True,...)),
                                   ('kernel_pca', KernelPCA(alpha=1.0,...))],
                 transformer_weights=None)


Like pipelines, feature unions have a shorthand constructor called
:func:`make_union` that does not require explicit naming of the components.


Like ``Pipeline``, individual steps may be replaced using ``set_params``,
and ignored by setting to ``'drop'``::

    >>> combined.set_params(kernel_pca='drop')
    ... # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
    FeatureUnion(n_jobs=None,
                 transformer_list=[('linear_pca', PCA(copy=True,...)),
                                   ('kernel_pca', 'drop')],
                 transformer_weights=None)

.. topic:: Examples:

 * :ref:`sphx_glr_auto_examples_compose_plot_feature_union.py`


.. _column_transformer:

ColumnTransformer for heterogeneous data
========================================

.. warning::

    The :class:`compose.ColumnTransformer <sklearn.compose.ColumnTransformer>`
    class is experimental and the API is subject to change.

Many datasets contain features of different types, say text, floats, and dates,
where each type of feature requires separate preprocessing or feature
extraction steps.  Often it is easiest to preprocess data before applying
scikit-learn methods, for example using `pandas <http://pandas.pydata.org/>`__.
Processing your data before passing it to scikit-learn might be problematic for
one of the following reasons:

1. Incorporating statistics from test data into the preprocessors makes
   cross-validation scores unreliable (known as *data leakage*),
   for example in the case of scalers or imputing missing values.
2. You may want to include the parameters of the preprocessors in a
   :ref:`parameter search <grid_search>`.

The :class:`~sklearn.compose.ColumnTransformer` helps performing different
transformations for different columns of the data, within a
:class:`~sklearn.pipeline.Pipeline` that is safe from data leakage and that can
be parametrized. :class:`~sklearn.compose.ColumnTransformer` works on
arrays, sparse matrices, and
`pandas DataFrames <http://pandas.pydata.org/pandas-docs/stable/>`__.

To each column, a different transformation can be applied, such as
preprocessing or a specific feature extraction method::

  >>> import pandas as pd
  >>> X = pd.DataFrame(
  ...     {'city': ['London', 'London', 'Paris', 'Sallisaw'],
  ...      'title': ["His Last Bow", "How Watson Learned the Trick",
  ...                "A Moveable Feast", "The Grapes of Wrath"],
  ...      'expert_rating': [5, 3, 4, 5],
  ...      'user_rating': [4, 5, 4, 3]})

For this data, we might want to encode the ``'city'`` column as a categorical
variable, but apply a :class:`feature_extraction.text.CountVectorizer
<sklearn.feature_extraction.text.CountVectorizer>` to the ``'title'`` column.
As we might use multiple feature extraction methods on the same column, we give
each transformer a unique name, say ``'city_category'`` and ``'title_bow'``.
By default, the remaining rating columns are ignored (``remainder='drop'``)::

  >>> from sklearn.compose import ColumnTransformer
  >>> from sklearn.feature_extraction.text import CountVectorizer
  >>> column_trans = ColumnTransformer(
  ...     [('city_category', CountVectorizer(analyzer=lambda x: [x]), 'city'),
  ...      ('title_bow', CountVectorizer(), 'title')],
  ...     remainder='drop')

  >>> column_trans.fit(X) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS
  ColumnTransformer(n_jobs=None, remainder='drop', sparse_threshold=0.3,
      transformer_weights=None,
      transformers=...)

  >>> column_trans.get_feature_names()
  ... # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS
  ['city_category__London', 'city_category__Paris', 'city_category__Sallisaw',
  'title_bow__bow', 'title_bow__feast', 'title_bow__grapes', 'title_bow__his',
  'title_bow__how', 'title_bow__last', 'title_bow__learned', 'title_bow__moveable',
  'title_bow__of', 'title_bow__the', 'title_bow__trick', 'title_bow__watson',
  'title_bow__wrath']

  >>> column_trans.transform(X).toarray()
  ... # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS
  array([[1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0],
         [1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0],
         [0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
         [0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1]]...)

In the above example, the
:class:`~sklearn.feature_extraction.text.CountVectorizer` expects a 1D array as
input and therefore the columns were specified as a string (``'city'``).
However, other transformers generally expect 2D data, and in that case you need
to specify the column as a list of strings (``['city']``).

Apart from a scalar or a single item list, the column selection can be specified
as a list of multiple items, an integer array, a slice, or a boolean mask.
Strings can reference columns if the input is a DataFrame, integers are always
interpreted as the positional columns.

We can keep the remaining rating columns by setting
``remainder='passthrough'``. The values are appended to the end of the
transformation::

  >>> column_trans = ColumnTransformer(
  ...     [('city_category', CountVectorizer(analyzer=lambda x: [x]), 'city'),
  ...      ('title_bow', CountVectorizer(), 'title')],
  ...     remainder='passthrough')

  >>> column_trans.fit_transform(X)
  ... # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS
  array([[1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 5, 4],
         [1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 3, 5],
         [0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 4, 4],
         [0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 5, 3]]...)

The ``remainder`` parameter can be set to an estimator to transform the
remaining rating columns. The transformed values are appended to the end of
the transformation::

  >>> from sklearn.preprocessing import MinMaxScaler
  >>> column_trans = ColumnTransformer(
  ...     [('city_category', CountVectorizer(analyzer=lambda x: [x]), 'city'),
  ...      ('title_bow', CountVectorizer(), 'title')],
  ...     remainder=MinMaxScaler())

  >>> column_trans.fit_transform(X)[:, -2:]
  ... # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS
  array([[1. , 0.5],
         [0. , 1. ],
         [0.5, 0.5],
         [1. , 0. ]])

The :func:`~sklearn.compose.make_column_transformer` function is available
to more easily create a :class:`~sklearn.compose.ColumnTransformer` object.
Specifically, the names will be given automatically. The equivalent for the
above example would be::

  >>> from sklearn.compose import make_column_transformer
  >>> column_trans = make_column_transformer(
  ...     (CountVectorizer(analyzer=lambda x: [x]), 'city'),
  ...     (CountVectorizer(), 'title'),
  ...     remainder=MinMaxScaler())
  >>> column_trans # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS
  ColumnTransformer(n_jobs=None, remainder=MinMaxScaler(copy=True, ...),
           sparse_threshold=0.3,
           transformer_weights=None,
           transformers=[('countvectorizer-1', ...)

.. topic:: Examples:

 * :ref:`sphx_glr_auto_examples_compose_plot_column_transformer.py`
 * :ref:`sphx_glr_auto_examples_compose_plot_column_transformer_mixed_types.py`