sklearn/doc/modules/impute.rst

.. _impute:

============================
Imputation of missing values
============================

.. currentmodule:: sklearn.impute

For various reasons, many real world datasets contain missing values, often
encoded as blanks, NaNs or other placeholders. Such datasets however are
incompatible with scikit-learn estimators which assume that all values in an
array are numerical, and that all have and hold meaning. A basic strategy to
use incomplete datasets is to discard entire rows and/or columns containing
missing values. However, this comes at the price of losing data which may be
valuable (even though incomplete). A better strategy is to impute the missing
values, i.e., to infer them from the known part of the data. See the
glossary entry on :term:`imputation`.


Univariate vs. Multivariate Imputation
======================================

One type of imputation algorithm is univariate, which imputes values in the
i-th feature dimension using only non-missing values in that feature dimension
(e.g. :class:`SimpleImputer`). By contrast, multivariate imputation
algorithms use the entire set of available feature dimensions to estimate the
missing values (e.g. :class:`IterativeImputer`).


.. _single_imputer:

Univariate feature imputation
=============================

The :class:`SimpleImputer` class provides basic strategies for imputing missing
values. Missing values can be imputed with a provided constant value, or using
the statistics (mean, median or most frequent) of each column in which the
missing values are located. This class also allows for different missing values
encodings.

The following snippet demonstrates how to replace missing values,
encoded as ``np.nan``, using the mean value of the columns (axis 0)
that contain the missing values::

    >>> import numpy as np
    >>> from sklearn.impute import SimpleImputer
    >>> imp = SimpleImputer(missing_values=np.nan, strategy='mean')
    >>> imp.fit([[1, 2], [np.nan, 3], [7, 6]])
    SimpleImputer()
    >>> X = [[np.nan, 2], [6, np.nan], [7, 6]]
    >>> print(imp.transform(X))
    [[4.          2.        ]
     [6.          3.666...]
     [7.          6.        ]]

The :class:`SimpleImputer` class also supports sparse matrices::

    >>> import scipy.sparse as sp
    >>> X = sp.csc_matrix([[1, 2], [0, -1], [8, 4]])
    >>> imp = SimpleImputer(missing_values=-1, strategy='mean')
    >>> imp.fit(X)
    SimpleImputer(missing_values=-1)
    >>> X_test = sp.csc_matrix([[-1, 2], [6, -1], [7, 6]])
    >>> print(imp.transform(X_test).toarray())
    [[3. 2.]
     [6. 3.]
     [7. 6.]]

Note that this format is not meant to be used to implicitly store missing
values in the matrix because it would densify it at transform time. Missing
values encoded by 0 must be used with dense input.

The :class:`SimpleImputer` class also supports categorical data represented as
string values or pandas categoricals when using the ``'most_frequent'`` or
``'constant'`` strategy::

    >>> import pandas as pd
    >>> df = pd.DataFrame([["a", "x"],
    ...                    [np.nan, "y"],
    ...                    ["a", np.nan],
    ...                    ["b", "y"]], dtype="category")
    ...
    >>> imp = SimpleImputer(strategy="most_frequent")
    >>> print(imp.fit_transform(df))
    [['a' 'x']
     ['a' 'y']
     ['a' 'y']
     ['b' 'y']]

For another example on usage, see :ref:`sphx_glr_auto_examples_impute_plot_missing_values.py`.

.. _iterative_imputer:


Multivariate feature imputation
===============================

A more sophisticated approach is to use the :class:`IterativeImputer` class,
which models each feature with missing values as a function of other features,
and uses that estimate for imputation. It does so in an iterated round-robin
fashion: at each step, a feature column is designated as output ``y`` and the
other feature columns are treated as inputs ``X``. A regressor is fit on ``(X,
y)`` for known ``y``. Then, the regressor is used to predict the missing values
of ``y``.  This is done for each feature in an iterative fashion, and then is
repeated for ``max_iter`` imputation rounds. The results of the final
imputation round are returned.

.. note::

   This estimator is still **experimental** for now: default parameters or
   details of behaviour might change without any deprecation cycle. Resolving
   the following issues would help stabilize :class:`IterativeImputer`:
   convergence criteria (:issue:`14338`), default estimators (:issue:`13286`),
   and use of random state (:issue:`15611`). To use it, you need to explicitly
   import ``enable_iterative_imputer``.

::

    >>> import numpy as np
    >>> from sklearn.experimental import enable_iterative_imputer
    >>> from sklearn.impute import IterativeImputer
    >>> imp = IterativeImputer(max_iter=10, random_state=0)
    >>> imp.fit([[1, 2], [3, 6], [4, 8], [np.nan, 3], [7, np.nan]])
    IterativeImputer(random_state=0)
    >>> X_test = [[np.nan, 2], [6, np.nan], [np.nan, 6]]
    >>> # the model learns that the second feature is double the first
    >>> print(np.round(imp.transform(X_test)))
    [[ 1.  2.]
     [ 6. 12.]
     [ 3.  6.]]

Both :class:`SimpleImputer` and :class:`IterativeImputer` can be used in a
Pipeline as a way to build a composite estimator that supports imputation.
See :ref:`sphx_glr_auto_examples_impute_plot_missing_values.py`.

Flexibility of IterativeImputer
-------------------------------

There are many well-established imputation packages in the R data science
ecosystem: Amelia, mi, mice, missForest, etc. missForest is popular, and turns
out to be a particular instance of different sequential imputation algorithms
that can all be implemented with :class:`IterativeImputer` by passing in
different regressors to be used for predicting missing feature values. In the
case of missForest, this regressor is a Random Forest.
See :ref:`sphx_glr_auto_examples_impute_plot_iterative_imputer_variants_comparison.py`.


.. _multiple_imputation:

Multiple vs. Single Imputation
------------------------------

In the statistics community, it is common practice to perform multiple
imputations, generating, for example, ``m`` separate imputations for a single
feature matrix. Each of these ``m`` imputations is then put through the
subsequent analysis pipeline (e.g. feature engineering, clustering, regression,
classification). The ``m`` final analysis results (e.g. held-out validation
errors) allow the data scientist to obtain understanding of how analytic
results may differ as a consequence of the inherent uncertainty caused by the
missing values. The above practice is called multiple imputation.

Our implementation of :class:`IterativeImputer` was inspired by the R MICE
package (Multivariate Imputation by Chained Equations) [1]_, but differs from
it by returning a single imputation instead of multiple imputations.  However,
:class:`IterativeImputer` can also be used for multiple imputations by applying
it repeatedly to the same dataset with different random seeds when
``sample_posterior=True``. See [2]_, chapter 4 for more discussion on multiple
vs. single imputations.

It is still an open problem as to how useful single vs. multiple imputation is
in the context of prediction and classification when the user is not
interested in measuring uncertainty due to missing values.

Note that a call to the ``transform`` method of :class:`IterativeImputer` is
not allowed to change the number of samples. Therefore multiple imputations
cannot be achieved by a single call to ``transform``.

References
----------

.. [1] `Stef van Buuren, Karin Groothuis-Oudshoorn (2011). "mice: Multivariate
   Imputation by Chained Equations in R". Journal of Statistical Software 45:
   1-67. <https://www.jstatsoft.org/article/view/v045i03>`_

.. [2] Roderick J A Little and Donald B Rubin (1986). "Statistical Analysis
   with Missing Data". John Wiley & Sons, Inc., New York, NY, USA.

.. _knnimpute:

Nearest neighbors imputation
============================

The :class:`KNNImputer` class provides imputation for filling in missing values
using the k-Nearest Neighbors approach. By default, a euclidean distance metric
that supports missing values,
:func:`~sklearn.metrics.pairwise.nan_euclidean_distances`, is used to find the
nearest neighbors. Each missing feature is imputed using values from
``n_neighbors`` nearest neighbors that have a value for the feature. The
feature of the neighbors are averaged uniformly or weighted by distance to each
neighbor. If a sample has more than one feature missing, then the neighbors for
that sample can be different depending on the particular feature being imputed.
When the number of available neighbors is less than `n_neighbors` and there are
no defined distances to the training set, the training set average for that
feature is used during imputation. If there is at least one neighbor with a
defined distance, the weighted or unweighted average of the remaining neighbors
will be used during imputation. If a feature is always missing in training, it
is removed during `transform`. For more information on the methodology, see
ref. [OL2001]_.

The following snippet demonstrates how to replace missing values,
encoded as ``np.nan``, using the mean feature value of the two nearest
neighbors of samples with missing values::

    >>> import numpy as np
    >>> from sklearn.impute import KNNImputer
    >>> nan = np.nan
    >>> X = [[1, 2, nan], [3, 4, 3], [nan, 6, 5], [8, 8, 7]]
    >>> imputer = KNNImputer(n_neighbors=2, weights="uniform")
    >>> imputer.fit_transform(X)
    array([[1. , 2. , 4. ],
           [3. , 4. , 3. ],
           [5.5, 6. , 5. ],
           [8. , 8. , 7. ]])

For another example on usage, see :ref:`sphx_glr_auto_examples_impute_plot_missing_values.py`.

.. rubric:: References

.. [OL2001] `Olga Troyanskaya, Michael Cantor, Gavin Sherlock, Pat Brown,
    Trevor Hastie, Robert Tibshirani, David Botstein and Russ B. Altman,
    Missing value estimation methods for DNA microarrays, BIOINFORMATICS
    Vol. 17 no. 6, 2001 Pages 520-525.
    <https://academic.oup.com/bioinformatics/article/17/6/520/272365>`_

Keeping the number of features constant
=======================================

By default, the scikit-learn imputers will drop fully empty features, i.e.
columns containing only missing values. For instance::

  >>> imputer = SimpleImputer()
  >>> X = np.array([[np.nan, 1], [np.nan, 2], [np.nan, 3]])
  >>> imputer.fit_transform(X)
  array([[1.],
         [2.],
         [3.]])

The first feature in `X` containing only `np.nan` was dropped after the
imputation. While this feature will not help in predictive setting, dropping
the columns will change the shape of `X` which could be problematic when using
imputers in a more complex machine-learning pipeline. The parameter
`keep_empty_features` offers the option to keep the empty features by imputing
with a constant values. In most of the cases, this constant value is zero::

  >>> imputer.set_params(keep_empty_features=True)
  SimpleImputer(keep_empty_features=True)
  >>> imputer.fit_transform(X)
  array([[0., 1.],
         [0., 2.],
         [0., 3.]])

.. _missing_indicator:

Marking imputed values
======================

The :class:`MissingIndicator` transformer is useful to transform a dataset into
corresponding binary matrix indicating the presence of missing values in the
dataset. This transformation is useful in conjunction with imputation. When
using imputation, preserving the information about which values had been
missing can be informative. Note that both the :class:`SimpleImputer` and
:class:`IterativeImputer` have the boolean parameter ``add_indicator``
(``False`` by default) which when set to ``True`` provides a convenient way of
stacking the output of the :class:`MissingIndicator` transformer with the
output of the imputer.

``NaN`` is usually used as the placeholder for missing values. However, it
enforces the data type to be float. The parameter ``missing_values`` allows to
specify other placeholder such as integer. In the following example, we will
use ``-1`` as missing values::

  >>> from sklearn.impute import MissingIndicator
  >>> X = np.array([[-1, -1, 1, 3],
  ...               [4, -1, 0, -1],
  ...               [8, -1, 1, 0]])
  >>> indicator = MissingIndicator(missing_values=-1)
  >>> mask_missing_values_only = indicator.fit_transform(X)
  >>> mask_missing_values_only
  array([[ True,  True, False],
         [False,  True,  True],
         [False,  True, False]])

The ``features`` parameter is used to choose the features for which the mask is
constructed. By default, it is ``'missing-only'`` which returns the imputer
mask of the features containing missing values at ``fit`` time::

  >>> indicator.features_
  array([0, 1, 3])

The ``features`` parameter can be set to ``'all'`` to return all features
whether or not they contain missing values::

  >>> indicator = MissingIndicator(missing_values=-1, features="all")
  >>> mask_all = indicator.fit_transform(X)
  >>> mask_all
  array([[ True,  True, False, False],
         [False,  True, False,  True],
         [False,  True, False, False]])
  >>> indicator.features_
  array([0, 1, 2, 3])

When using the :class:`MissingIndicator` in a
:class:`~sklearn.pipeline.Pipeline`, be sure to use the
:class:`~sklearn.pipeline.FeatureUnion` or
:class:`~sklearn.compose.ColumnTransformer` to add the indicator features to
the regular features. First we obtain the `iris` dataset, and add some missing
values to it.

  >>> from sklearn.datasets import load_iris
  >>> from sklearn.impute import SimpleImputer, MissingIndicator
  >>> from sklearn.model_selection import train_test_split
  >>> from sklearn.pipeline import FeatureUnion, make_pipeline
  >>> from sklearn.tree import DecisionTreeClassifier
  >>> X, y = load_iris(return_X_y=True)
  >>> mask = np.random.randint(0, 2, size=X.shape).astype(bool)
  >>> X[mask] = np.nan
  >>> X_train, X_test, y_train, _ = train_test_split(X, y, test_size=100,
  ...                                                random_state=0)

Now we create a :class:`~sklearn.pipeline.FeatureUnion`. All features will be
imputed using :class:`SimpleImputer`, in order to enable classifiers to work
with this data. Additionally, it adds the indicator variables from
:class:`MissingIndicator`.

  >>> transformer = FeatureUnion(
  ...     transformer_list=[
  ...         ('features', SimpleImputer(strategy='mean')),
  ...         ('indicators', MissingIndicator())])
  >>> transformer = transformer.fit(X_train, y_train)
  >>> results = transformer.transform(X_test)
  >>> results.shape
  (100, 8)

Of course, we cannot use the transformer to make any predictions. We should
wrap this in a :class:`~sklearn.pipeline.Pipeline` with a classifier (e.g., a
:class:`~sklearn.tree.DecisionTreeClassifier`) to be able to make predictions.

  >>> clf = make_pipeline(transformer, DecisionTreeClassifier())
  >>> clf = clf.fit(X_train, y_train)
  >>> results = clf.predict(X_test)
  >>> results.shape
  (100,)

Estimators that handle NaN values
=================================

Some estimators are designed to handle NaN values without preprocessing.
Below is the list of these estimators, classified by type
(cluster, regressor, classifier, transform):

.. allow_nan_estimators::