.. _supervised_learning_tut:
=======================================================================================
Supervised learning: predicting an output variable from high-dimensional observations
=======================================================================================
.. topic:: The problem solved in supervised learning
:ref:`Supervised learning <supervised-learning>`
consists in learning the link between two
datasets: the observed data ``X`` and an external variable ``y`` that we
are trying to predict, usually called "target" or "labels". Most often,
``y`` is a 1D array of length ``n_samples``.
All supervised `estimators <https://en.wikipedia.org/wiki/Estimator>`_
in scikit-learn implement a ``fit(X, y)`` method to fit the model
and a ``predict(X)`` method that, given unlabeled observations ``X``,
returns the predicted labels ``y``.
.. topic:: Vocabulary: classification and regression
If the prediction task is to classify the observations in a set of
finite labels, in other words to "name" the objects observed, the task
is said to be a **classification** task. On the other hand, if the goal
is to predict a continuous target variable, it is said to be a
**regression** task.
When doing classification in scikit-learn, ``y`` is a vector of integers
or strings.
Note: See the :ref:`Introduction to machine learning with scikit-learn
Tutorial <introduction>` for a quick run-through on the basic machine
learning vocabulary used within scikit-learn.
Nearest neighbor and the curse of dimensionality
=================================================
.. topic:: Classifying irises:
The iris dataset is a classification task consisting in identifying 3
different types of irises (Setosa, Versicolour, and Virginica) from
their petal and sepal length and width::
>>> import numpy as np
>>> from sklearn import datasets
>>> iris_X, iris_y = datasets.load_iris(return_X_y=True)
>>> np.unique(iris_y)
array([0, 1, 2])
.. image:: /auto_examples/datasets/images/sphx_glr_plot_iris_dataset_001.png
:target: ../../auto_examples/datasets/plot_iris_dataset.html
:align: center
:scale: 50
k-Nearest neighbors classifier
-------------------------------
The simplest possible classifier is the
`nearest neighbor <https://en.wikipedia.org/wiki/K-nearest_neighbor_algorithm>`_:
given a new observation ``X_test``, find in the training set (i.e. the data
used to train the estimator) the observation with the closest feature vector.
(Please see the :ref:`Nearest Neighbors section<neighbors>` of the online
Scikit-learn documentation for more information about this type of classifier.)
.. topic:: Training set and testing set
While experimenting with any learning algorithm, it is important not to
test the prediction of an estimator on the data used to fit the
estimator as this would not be evaluating the performance of the
estimator on **new data**. This is why datasets are often split into
*train* and *test* data.
**KNN (k nearest neighbors) classification example**:
.. image:: /auto_examples/neighbors/images/sphx_glr_plot_classification_001.png
:target: ../../auto_examples/neighbors/plot_classification.html
:align: center
:scale: 70
::
>>> # Split iris data in train and test data
>>> # A random permutation, to split the data randomly
>>> np.random.seed(0)
>>> indices = np.random.permutation(len(iris_X))
>>> iris_X_train = iris_X[indices[:-10]]
>>> iris_y_train = iris_y[indices[:-10]]
>>> iris_X_test = iris_X[indices[-10:]]
>>> iris_y_test = iris_y[indices[-10:]]
>>> # Create and fit a nearest-neighbor classifier
>>> from sklearn.neighbors import KNeighborsClassifier
>>> knn = KNeighborsClassifier()
>>> knn.fit(iris_X_train, iris_y_train)
KNeighborsClassifier()
>>> knn.predict(iris_X_test)
array([1, 2, 1, 0, 0, 0, 2, 1, 2, 0])
>>> iris_y_test
array([1, 1, 1, 0, 0, 0, 2, 1, 2, 0])
.. _curse_of_dimensionality:
The curse of dimensionality
-------------------------------
For an estimator to be effective, you need the distance between neighboring
points to be less than some value :math:`d`, which depends on the problem.
In one dimension, this requires on average :math:`n \sim 1/d` points.
In the context of the above :math:`k`-NN example, if the data is described by
just one feature with values ranging from 0 to 1 and with :math:`n` training
observations, then new data will be no further away than :math:`1/n`.
Therefore, the nearest neighbor decision rule will be efficient as soon as
:math:`1/n` is small compared to the scale of between-class feature variations.
If the number of features is :math:`p`, you now require :math:`n \sim 1/d^p`
points. Let's say that we require 10 points in one dimension: now :math:`10^p`
points are required in :math:`p` dimensions to pave the :math:`[0, 1]` space.
As :math:`p` becomes large, the number of training points required for a good
estimator grows exponentially.
For example, if each point is just a single number (8 bytes), then an
effective :math:`k`-NN estimator in a paltry :math:`p \sim 20` dimensions would
require more training data than the current estimated size of the entire
internet (±1000 Exabytes or so).
This is called the
`curse of dimensionality <https://en.wikipedia.org/wiki/Curse_of_dimensionality>`_
and is a core problem that machine learning addresses.
Linear model: from regression to sparsity
==========================================
.. topic:: Diabetes dataset
The diabetes dataset consists of 10 physiological variables (age,
sex, weight, blood pressure) measured on 442 patients, and an
indication of disease progression after one year::
>>> diabetes_X, diabetes_y = datasets.load_diabetes(return_X_y=True)
>>> diabetes_X_train = diabetes_X[:-20]
>>> diabetes_X_test = diabetes_X[-20:]
>>> diabetes_y_train = diabetes_y[:-20]
>>> diabetes_y_test = diabetes_y[-20:]
The task at hand is to predict disease progression from physiological
variables.
Linear regression
------------------
.. currentmodule:: sklearn.linear_model
:class:`LinearRegression`,
in its simplest form, fits a linear model to the data set by adjusting
a set of parameters in order to make the sum of the squared residuals
of the model as small as possible.
Linear models: :math:`y = X\beta + \epsilon`
* :math:`X`: data
* :math:`y`: target variable
* :math:`\beta`: Coefficients
* :math:`\epsilon`: Observation noise
.. image:: /auto_examples/linear_model/images/sphx_glr_plot_ols_001.png
:target: ../../auto_examples/linear_model/plot_ols.html
:scale: 50
:align: center
::
>>> from sklearn import linear_model
>>> regr = linear_model.LinearRegression()
>>> regr.fit(diabetes_X_train, diabetes_y_train)
LinearRegression()
>>> print(regr.coef_) # doctest: +SKIP
[ 0.30349955 -237.63931533 510.53060544 327.73698041 -814.13170937
492.81458798 102.84845219 184.60648906 743.51961675 76.09517222]
>>> # The mean square error
>>> np.mean((regr.predict(diabetes_X_test) - diabetes_y_test)**2)
2004.5...
>>> # Explained variance score: 1 is perfect prediction
>>> # and 0 means that there is no linear relationship
>>> # between X and y.
>>> regr.score(diabetes_X_test, diabetes_y_test)
0.585...
.. _shrinkage:
Shrinkage
----------
If there are few data points per dimension, noise in the observations
induces high variance:
::
>>> X = np.c_[ .5, 1].T
>>> y = [.5, 1]
>>> test = np.c_[ 0, 2].T
>>> regr = linear_model.LinearRegression()
>>> import matplotlib.pyplot as plt
>>> plt.figure()
<...>
>>> np.random.seed(0)
>>> for _ in range(6):
... this_X = .1 * np.random.normal(size=(2, 1)) + X
... regr.fit(this_X, y)
... plt.plot(test, regr.predict(test))
... plt.scatter(this_X, y, s=3)
LinearRegression...
.. image:: /auto_examples/linear_model/images/sphx_glr_plot_ols_ridge_variance_001.png
:target: ../../auto_examples/linear_model/plot_ols_ridge_variance.html
:align: center
A solution in high-dimensional statistical learning is to *shrink* the
regression coefficients to zero: any two randomly chosen set of
observations are likely to be uncorrelated. This is called :class:`Ridge`
regression:
::
>>> regr = linear_model.Ridge(alpha=.1)
>>> plt.figure()
<...>
>>> np.random.seed(0)
>>> for _ in range(6):
... this_X = .1 * np.random.normal(size=(2, 1)) + X
... regr.fit(this_X, y)
... plt.plot(test, regr.predict(test))
... plt.scatter(this_X, y, s=3)
Ridge...
.. image:: /auto_examples/linear_model/images/sphx_glr_plot_ols_ridge_variance_002.png
:target: ../../auto_examples/linear_model/plot_ols_ridge_variance.html
:align: center
This is an example of **bias/variance tradeoff**: the larger the ridge
``alpha`` parameter, the higher the bias and the lower the variance.
We can choose ``alpha`` to minimize left out error, this time using the
diabetes dataset rather than our synthetic data::
>>> alphas = np.logspace(-4, -1, 6)
>>> print([regr.set_params(alpha=alpha)
... .fit(diabetes_X_train, diabetes_y_train)
... .score(diabetes_X_test, diabetes_y_test)
... for alpha in alphas])
[0.585..., 0.585..., 0.5854..., 0.5855..., 0.583..., 0.570...]
.. note::
Capturing in the fitted parameters noise that prevents the model to
generalize to new data is called
`overfitting <https://en.wikipedia.org/wiki/Overfitting>`_. The bias introduced
by the ridge regression is called a
`regularization <https://en.wikipedia.org/wiki/Regularization_%28machine_learning%29>`_.
.. _sparsity:
Sparsity
----------
.. |diabetes_ols_1| image:: /auto_examples/linear_model/images/sphx_glr_plot_ols_3d_001.png
:target: ../../auto_examples/linear_model/plot_ols_3d.html
:scale: 65
.. |diabetes_ols_3| image:: /auto_examples/linear_model/images/sphx_glr_plot_ols_3d_003.png
:target: ../../auto_examples/linear_model/plot_ols_3d.html
:scale: 65
.. |diabetes_ols_2| image:: /auto_examples/linear_model/images/sphx_glr_plot_ols_3d_002.png
:target: ../../auto_examples/linear_model/plot_ols_3d.html
:scale: 65
.. rst-class:: centered
**Fitting only features 1 and 2**
.. centered:: |diabetes_ols_1| |diabetes_ols_3| |diabetes_ols_2|
.. note::
A representation of the full diabetes dataset would involve 11
dimensions (10 feature dimensions and one of the target variable). It
is hard to develop an intuition on such representation, but it may be
useful to keep in mind that it would be a fairly *empty* space.
We can see that, although feature 2 has a strong coefficient on the full
model, it conveys little information on ``y`` when considered with feature 1.
To improve the conditioning of the problem (i.e. mitigating the
:ref:`curse_of_dimensionality`), it would be interesting to select only the
informative features and set non-informative ones, like feature 2 to 0. Ridge
regression will decrease their contribution, but not set them to zero. Another
penalization approach, called :ref:`lasso` (least absolute shrinkage and
selection operator), can set some coefficients to zero. Such methods are
called **sparse methods** and sparsity can be seen as an
application of Occam's razor: *prefer simpler models*.
::
>>> regr = linear_model.Lasso()
>>> scores = [regr.set_params(alpha=alpha)
... .fit(diabetes_X_train, diabetes_y_train)
... .score(diabetes_X_test, diabetes_y_test)
... for alpha in alphas]
>>> best_alpha = alphas[scores.index(max(scores))]
>>> regr.alpha = best_alpha
>>> regr.fit(diabetes_X_train, diabetes_y_train)
Lasso(alpha=0.025118864315095794)
>>> print(regr.coef_)
[ 0. -212.4... 517.2... 313.7... -160.8...
-0. -187.1... 69.3... 508.6... 71.8... ]
.. topic:: **Different algorithms for the same problem**
Different algorithms can be used to solve the same mathematical
problem. For instance the ``Lasso`` object in scikit-learn
solves the lasso regression problem using a
`coordinate descent <https://en.wikipedia.org/wiki/Coordinate_descent>`_ method,
that is efficient on large datasets. However, scikit-learn also
provides the :class:`LassoLars` object using the *LARS* algorithm,
which is very efficient for problems in which the weight vector estimated
is very sparse (i.e. problems with very few observations).
.. _clf_tut:
Classification
---------------
For classification, as in the labeling
`iris <https://en.wikipedia.org/wiki/Iris_flower_data_set>`_ task, linear
regression is not the right approach as it will give too much weight to
data far from the decision frontier. A linear approach is to fit a sigmoid
function or **logistic** function:
.. image:: /auto_examples/linear_model/images/sphx_glr_plot_logistic_001.png
:target: ../../auto_examples/linear_model/plot_logistic.html
:scale: 70
:align: center
.. math::
y = \textrm{sigmoid}(X\beta - \textrm{offset}) + \epsilon =
\frac{1}{1 + \textrm{exp}(- X\beta + \textrm{offset})} + \epsilon
::
>>> log = linear_model.LogisticRegression(C=1e5)
>>> log.fit(iris_X_train, iris_y_train)
LogisticRegression(C=100000.0)
This is known as :class:`LogisticRegression`.
.. image:: /auto_examples/linear_model/images/sphx_glr_plot_iris_logistic_001.png
:target: ../../auto_examples/linear_model/plot_iris_logistic.html
:scale: 83
:align: center
.. topic:: Multiclass classification
If you have several classes to predict, an option often used is to fit
one-versus-all classifiers and then use a voting heuristic for the final
decision.
.. topic:: Shrinkage and sparsity with logistic regression
The ``C`` parameter controls the amount of regularization in the
:class:`LogisticRegression` object: a large value for ``C`` results in
less regularization.
``penalty="l2"`` gives :ref:`shrinkage` (i.e. non-sparse coefficients), while
``penalty="l1"`` gives :ref:`sparsity`.
.. topic:: **Exercise**
:class: green
Try classifying the digits dataset with nearest neighbors and a linear
model. Leave out the last 10% and test prediction performance on these
observations.
.. literalinclude:: ../../auto_examples/exercises/plot_digits_classification_exercise.py
:lines: 15-19
A solution can be downloaded :download:`here <../../auto_examples/exercises/plot_digits_classification_exercise.py>`.
Support vector machines (SVMs)
================================
Linear SVMs
-------------
:ref:`svm` belong to the discriminant model family: they try to find a combination of
samples to build a plane maximizing the margin between the two classes.
Regularization is set by the ``C`` parameter: a small value for ``C`` means the margin
is calculated using many or all of the observations around the separating line
(more regularization);
a large value for ``C`` means the margin is calculated on observations close to
the separating line (less regularization).
.. currentmodule :: sklearn.svm
.. figure:: /auto_examples/svm/images/sphx_glr_plot_svm_margin_001.png
:target: ../../auto_examples/svm/plot_svm_margin.html
**Unregularized SVM**
.. figure:: /auto_examples/svm/images/sphx_glr_plot_svm_margin_002.png
:target: ../../auto_examples/svm/plot_svm_margin.html
**Regularized SVM (default)**
.. topic:: Example:
- :ref:`sphx_glr_auto_examples_svm_plot_iris_svc.py`
SVMs can be used in regression --:class:`SVR` (Support Vector Regression)--, or in
classification --:class:`SVC` (Support Vector Classification).
::
>>> from sklearn import svm
>>> svc = svm.SVC(kernel='linear')
>>> svc.fit(iris_X_train, iris_y_train)
SVC(kernel='linear')
.. warning:: **Normalizing data**
For many estimators, including the SVMs, having datasets with unit
standard deviation for each feature is important to get good
prediction.
.. _using_kernels_tut:
Using kernels
-------------
Classes are not always linearly separable in feature space. The solution is to
build a decision function that is not linear but may be polynomial instead.
This is done using the *kernel trick* that can be seen as
creating a decision energy by positioning *kernels* on observations:
Linear kernel
^^^^^^^^^^^^^
::
>>> svc = svm.SVC(kernel='linear')
.. image:: /auto_examples/svm/images/sphx_glr_plot_svm_kernels_002.png
:target: ../../auto_examples/svm/plot_svm_kernels.html
Polynomial kernel
^^^^^^^^^^^^^^^^^
::
>>> svc = svm.SVC(kernel='poly',
... degree=3)
>>> # degree: polynomial degree
.. image:: /auto_examples/svm/images/sphx_glr_plot_svm_kernels_003.png
:target: ../../auto_examples/svm/plot_svm_kernels.html
RBF kernel (Radial Basis Function)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
::
>>> svc = svm.SVC(kernel='rbf')
>>> # gamma: inverse of size of
>>> # radial kernel
.. image:: /auto_examples/svm/images/sphx_glr_plot_svm_kernels_004.png
:target: ../../auto_examples/svm/plot_svm_kernels.html
Sigmoid kernel
^^^^^^^^^^^^^^
::
>>> svc = svm.SVC(kernel='sigmoid')
.. image:: /auto_examples/svm/images/sphx_glr_plot_svm_kernels_005.png
:target: ../../auto_examples/svm/plot_svm_kernels.html
.. topic:: **Interactive example**
See the :ref:`SVM GUI <sphx_glr_auto_examples_applications_svm_gui.py>` to download
``svm_gui.py``; add data points of both classes with right and left button,
fit the model and change parameters and data.
.. topic:: **Exercise**
:class: green
Try classifying classes 1 and 2 from the iris dataset with SVMs, with
the 2 first features. Leave out 10% of each class and test prediction
performance on these observations.
**Warning**: the classes are ordered, do not leave out the last 10%,
you would be testing on only one class.
**Hint**: You can use the ``decision_function`` method on a grid to get
intuitions.
.. literalinclude:: ../../auto_examples/exercises/plot_iris_exercise.py
:lines: 18-23
.. image:: /auto_examples/datasets/images/sphx_glr_plot_iris_dataset_001.png
:target: ../../auto_examples/datasets/plot_iris_dataset.html
:align: center
:scale: 70
A solution can be downloaded :download:`here <../../auto_examples/exercises/plot_iris_exercise.py>`