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doc/modules/mixture.rst
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Yao Xiao
DOC fix wrong indentations in the documentation that lead to undesired blockquotes (#28107)
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.. _mixture:

.. _gmm:

=======================
Gaussian mixture models
=======================

.. currentmodule:: sklearn.mixture

``sklearn.mixture`` is a package which enables one to learn
Gaussian Mixture Models (diagonal, spherical, tied and full covariance
matrices supported), sample them, and estimate them from
data. Facilities to help determine the appropriate number of
components are also provided.

.. figure:: ../auto_examples/mixture/images/sphx_glr_plot_gmm_pdf_001.png
  :target: ../auto_examples/mixture/plot_gmm_pdf.html
  :align: center
  :scale: 50%

  **Two-component Gaussian mixture model:** *data points, and equi-probability
  surfaces of the model.*

A Gaussian mixture model is a probabilistic model that assumes all the
data points are generated from a mixture of a finite number of
Gaussian distributions with unknown parameters. One can think of
mixture models as generalizing k-means clustering to incorporate
information about the covariance structure of the data as well as the
centers of the latent Gaussians.

Scikit-learn implements different classes to estimate Gaussian
mixture models, that correspond to different estimation strategies,
detailed below.

Gaussian Mixture
================

The :class:`GaussianMixture` object implements the
:ref:`expectation-maximization <expectation_maximization>` (EM)
algorithm for fitting mixture-of-Gaussian models. It can also draw
confidence ellipsoids for multivariate models, and compute the
Bayesian Information Criterion to assess the number of clusters in the
data. A :meth:`GaussianMixture.fit` method is provided that learns a Gaussian
Mixture Model from train data. Given test data, it can assign to each
sample the Gaussian it most probably belongs to using
the :meth:`GaussianMixture.predict` method.

..
    Alternatively, the probability of each
    sample belonging to the various Gaussians may be retrieved using the
    :meth:`GaussianMixture.predict_proba` method.

The :class:`GaussianMixture` comes with different options to constrain the
covariance of the difference classes estimated: spherical, diagonal, tied or
full covariance.

.. figure:: ../auto_examples/mixture/images/sphx_glr_plot_gmm_covariances_001.png
   :target: ../auto_examples/mixture/plot_gmm_covariances.html
   :align: center
   :scale: 75%

.. topic:: Examples:

    * See :ref:`sphx_glr_auto_examples_mixture_plot_gmm_covariances.py` for an example of
      using the Gaussian mixture as clustering on the iris dataset.

    * See :ref:`sphx_glr_auto_examples_mixture_plot_gmm_pdf.py` for an example on plotting the
      density estimation.

|details-start|
**Pros and cons of class GaussianMixture**
|details-split|

.. topic:: Pros:

    :Speed: It is the fastest algorithm for learning mixture models

    :Agnostic: As this algorithm maximizes only the likelihood, it
      will not bias the means towards zero, or bias the cluster sizes to
      have specific structures that might or might not apply.

.. topic:: Cons:

    :Singularities: When one has insufficiently many points per
      mixture, estimating the covariance matrices becomes difficult,
      and the algorithm is known to diverge and find solutions with
      infinite likelihood unless one regularizes the covariances artificially.

    :Number of components: This algorithm will always use all the
      components it has access to, needing held-out data
      or information theoretical criteria to decide how many components to use
      in the absence of external cues.

|details-end|


|details-start|
**Selecting the number of components in a classical Gaussian Mixture model**
|details-split|

The BIC criterion can be used to select the number of components in a Gaussian
Mixture in an efficient way. In theory, it recovers the true number of
components only in the asymptotic regime (i.e. if much data is available and
assuming that the data was actually generated i.i.d. from a mixture of Gaussian
distribution). Note that using a :ref:`Variational Bayesian Gaussian mixture <bgmm>`
avoids the specification of the number of components for a Gaussian mixture
model.

.. figure:: ../auto_examples/mixture/images/sphx_glr_plot_gmm_selection_002.png
   :target: ../auto_examples/mixture/plot_gmm_selection.html
   :align: center
   :scale: 50%

.. topic:: Examples:

    * See :ref:`sphx_glr_auto_examples_mixture_plot_gmm_selection.py` for an example
      of model selection performed with classical Gaussian mixture.

|details-end|

.. _expectation_maximization:

|details-start|
**Estimation algorithm expectation-maximization**
|details-split|

The main difficulty in learning Gaussian mixture models from unlabeled
data is that one usually doesn't know which points came from
which latent component (if one has access to this information it gets
very easy to fit a separate Gaussian distribution to each set of
points). `Expectation-maximization
<https://en.wikipedia.org/wiki/Expectation%E2%80%93maximization_algorithm>`_
is a well-founded statistical
algorithm to get around this problem by an iterative process. First
one assumes random components (randomly centered on data points,
learned from k-means, or even just normally distributed around the
origin) and computes for each point a probability of being generated by
each component of the model. Then, one tweaks the
parameters to maximize the likelihood of the data given those
assignments. Repeating this process is guaranteed to always converge
to a local optimum.

|details-end|

|details-start|
**Choice of the Initialization method**
|details-split|

There is a choice of four initialization methods (as well as inputting user defined
initial means) to generate the initial centers for the model components:

k-means (default)
  This applies a traditional k-means clustering algorithm.
  This can be computationally expensive compared to other initialization methods.

k-means++
  This uses the initialization method of k-means clustering: k-means++.
  This will pick the first center at random from the data. Subsequent centers will be
  chosen from a weighted distribution of the data favouring points further away from
  existing centers. k-means++ is the default initialization for k-means so will be
  quicker than running a full k-means but can still take a significant amount of
  time for large data sets with many components.

random_from_data
  This will pick random data points from the input data as the initial
  centers. This is a very fast method of initialization but can produce non-convergent
  results if the chosen points are too close to each other.

random
  Centers are chosen as a small perturbation away from the mean of all data.
  This method is simple but can lead to the model taking longer to converge.

.. figure:: ../auto_examples/mixture/images/sphx_glr_plot_gmm_init_001.png
   :target: ../auto_examples/mixture/plot_gmm_init.html
   :align: center
   :scale: 50%

.. topic:: Examples:

    * See :ref:`sphx_glr_auto_examples_mixture_plot_gmm_init.py` for an example of
      using different initializations in Gaussian Mixture.

|details-end|

.. _bgmm:

Variational Bayesian Gaussian Mixture
=====================================

The :class:`BayesianGaussianMixture` object implements a variant of the
Gaussian mixture model with variational inference algorithms. The API is
similar to the one defined by :class:`GaussianMixture`.

.. _variational_inference:

**Estimation algorithm: variational inference**

Variational inference is an extension of expectation-maximization that
maximizes a lower bound on model evidence (including
priors) instead of data likelihood. The principle behind
variational methods is the same as expectation-maximization (that is
both are iterative algorithms that alternate between finding the
probabilities for each point to be generated by each mixture and
fitting the mixture to these assigned points), but variational
methods add regularization by integrating information from prior
distributions. This avoids the singularities often found in
expectation-maximization solutions but introduces some subtle biases
to the model. Inference is often notably slower, but not usually as
much so as to render usage unpractical.

Due to its Bayesian nature, the variational algorithm needs more hyperparameters
than expectation-maximization, the most important of these being the
concentration parameter ``weight_concentration_prior``. Specifying a low value
for the concentration prior will make the model put most of the weight on a few
components and set the remaining components' weights very close to zero. High
values of the concentration prior will allow a larger number of components to
be active in the mixture.

The parameters implementation of the :class:`BayesianGaussianMixture` class
proposes two types of prior for the weights distribution: a finite mixture model
with Dirichlet distribution and an infinite mixture model with the Dirichlet
Process. In practice Dirichlet Process inference algorithm is approximated and
uses a truncated distribution with a fixed maximum number of components (called
the Stick-breaking representation). The number of components actually used
almost always depends on the data.

The next figure compares the results obtained for the different type of the
weight concentration prior (parameter ``weight_concentration_prior_type``)
for different values of ``weight_concentration_prior``.
Here, we can see the value of the ``weight_concentration_prior`` parameter
has a strong impact on the effective number of active components obtained. We
can also notice that large values for the concentration weight prior lead to
more uniform weights when the type of prior is 'dirichlet_distribution' while
this is not necessarily the case for the 'dirichlet_process' type (used by
default).

.. |plot_bgmm| image:: ../auto_examples/mixture/images/sphx_glr_plot_concentration_prior_001.png
   :target: ../auto_examples/mixture/plot_concentration_prior.html
   :scale: 48%

.. |plot_dpgmm| image:: ../auto_examples/mixture/images/sphx_glr_plot_concentration_prior_002.png
   :target: ../auto_examples/mixture/plot_concentration_prior.html
   :scale: 48%

.. centered:: |plot_bgmm| |plot_dpgmm|

The examples below compare Gaussian mixture models with a fixed number of
components, to the variational Gaussian mixture models with a Dirichlet process
prior. Here, a classical Gaussian mixture is fitted with 5 components on a
dataset composed of 2 clusters. We can see that the variational Gaussian mixture
with a Dirichlet process prior is able to limit itself to only 2 components
whereas the Gaussian mixture fits the data with a fixed number of components
that has to be set a priori by the user. In this case the user has selected
``n_components=5`` which does not match the true generative distribution of this
toy dataset. Note that with very little observations, the variational Gaussian
mixture models with a Dirichlet process prior can take a conservative stand, and
fit only one component.

.. figure:: ../auto_examples/mixture/images/sphx_glr_plot_gmm_001.png
   :target: ../auto_examples/mixture/plot_gmm.html
   :align: center
   :scale: 70%


On the following figure we are fitting a dataset not well-depicted by a
Gaussian mixture. Adjusting the ``weight_concentration_prior``, parameter of the
:class:`BayesianGaussianMixture` controls the number of components used to fit
this data. We also present on the last two plots a random sampling generated
from the two resulting mixtures.

.. figure:: ../auto_examples/mixture/images/sphx_glr_plot_gmm_sin_001.png
   :target: ../auto_examples/mixture/plot_gmm_sin.html
   :align: center
   :scale: 65%



.. topic:: Examples:

    * See :ref:`sphx_glr_auto_examples_mixture_plot_gmm.py` for an example on
      plotting the confidence ellipsoids for both :class:`GaussianMixture`
      and :class:`BayesianGaussianMixture`.

    * :ref:`sphx_glr_auto_examples_mixture_plot_gmm_sin.py` shows using
      :class:`GaussianMixture` and :class:`BayesianGaussianMixture` to fit a
      sine wave.

    * See :ref:`sphx_glr_auto_examples_mixture_plot_concentration_prior.py`
      for an example plotting the confidence ellipsoids for the
      :class:`BayesianGaussianMixture` with different
      ``weight_concentration_prior_type`` for different values of the parameter
      ``weight_concentration_prior``.

|details-start|
**Pros and cons of variational inference with BayesianGaussianMixture**
|details-split|

.. topic:: Pros:

    :Automatic selection: when ``weight_concentration_prior`` is small enough and
      ``n_components`` is larger than what is found necessary by the model, the
      Variational Bayesian mixture model has a natural tendency to set some mixture
      weights values close to zero. This makes it possible to let the model choose
      a suitable number of effective components automatically. Only an upper bound
      of this number needs to be provided. Note however that the "ideal" number of
      active components is very application specific and is typically ill-defined
      in a data exploration setting.

    :Less sensitivity to the number of parameters: unlike finite models, which will
      almost always use all components as much as they can, and hence will produce
      wildly different solutions for different numbers of components, the
      variational inference with a Dirichlet process prior
      (``weight_concentration_prior_type='dirichlet_process'``) won't change much
      with changes to the parameters, leading to more stability and less tuning.

    :Regularization: due to the incorporation of prior information,
      variational solutions have less pathological special cases than
      expectation-maximization solutions.


.. topic:: Cons:

    :Speed: the extra parametrization necessary for variational inference makes
      inference slower, although not by much.

    :Hyperparameters: this algorithm needs an extra hyperparameter
      that might need experimental tuning via cross-validation.

    :Bias: there are many implicit biases in the inference algorithms (and also in
      the Dirichlet process if used), and whenever there is a mismatch between
      these biases and the data it might be possible to fit better models using a
      finite mixture.

|details-end|

.. _dirichlet_process:

The Dirichlet Process
---------------------

Here we describe variational inference algorithms on Dirichlet process
mixture. The Dirichlet process is a prior probability distribution on
*clusterings with an infinite, unbounded, number of partitions*.
Variational techniques let us incorporate this prior structure on
Gaussian mixture models at almost no penalty in inference time, comparing
with a finite Gaussian mixture model.

An important question is how can the Dirichlet process use an infinite,
unbounded number of clusters and still be consistent. While a full explanation
doesn't fit this manual, one can think of its `stick breaking process
<https://en.wikipedia.org/wiki/Dirichlet_process#The_stick-breaking_process>`_
analogy to help understanding it. The stick breaking process is a generative
story for the Dirichlet process. We start with a unit-length stick and in each
step we break off a portion of the remaining stick. Each time, we associate the
length of the piece of the stick to the proportion of points that falls into a
group of the mixture. At the end, to represent the infinite mixture, we
associate the last remaining piece of the stick to the proportion of points
that don't fall into all the other groups. The length of each piece is a random
variable with probability proportional to the concentration parameter. Smaller
values of the concentration will divide the unit-length into larger pieces of
the stick (defining more concentrated distribution). Larger concentration
values will create smaller pieces of the stick (increasing the number of
components with non zero weights).

Variational inference techniques for the Dirichlet process still work
with a finite approximation to this infinite mixture model, but
instead of having to specify a priori how many components one wants to
use, one just specifies the concentration parameter and an upper bound
on the number of mixture components (this upper bound, assuming it is
higher than the "true" number of components, affects only algorithmic
complexity, not the actual number of components used).