partial_dependence.rst

Partial dependence plots

.. currentmodule:: sklearn.inspection

Partial dependence plots (PDP) show the dependence between the target response [1] and a set of 'target' features, marginalizing over the values of all other features (the 'complement' features). Intuitively, we can interpret the partial dependence as the expected target response as a function of the 'target' features.

Due to the limits of human perception the size of the target feature set must be small (usually, one or two) thus the target features are usually chosen among the most important features.

The figure below shows four one-way and one two-way partial dependence plots for the California housing dataset, with a :class:`GradientBoostingRegressor <sklearn.ensemble.GradientBoostingRegressor>`:

One-way PDPs tell us about the interaction between the target response and the target feature (e.g. linear, non-linear). The upper left plot in the above figure shows the effect of the median income in a district on the median house price; we can clearly see a linear relationship among them. Note that PDPs assume that the target features are independent from the complement features, and this assumption is often violated in practice.

PDPs with two target features show the interactions among the two features. For example, the two-variable PDP in the above figure shows the dependence of median house price on joint values of house age and average occupants per household. We can clearly see an interaction between the two features: for an average occupancy greater than two, the house price is nearly independent of the house age, whereas for values less than 2 there is a strong dependence on age.

The :mod:`sklearn.inspection` module provides a convenience function :func:`plot_partial_dependence` to create one-way and two-way partial dependence plots. In the below example we show how to create a grid of partial dependence plots: two one-way PDPs for the features 0 and 1 and a two-way PDP between the two features:

>>> from sklearn.datasets import make_hastie_10_2
>>> from sklearn.ensemble import GradientBoostingClassifier
>>> from sklearn.inspection import plot_partial_dependence

>>> X, y = make_hastie_10_2(random_state=0)
>>> clf = GradientBoostingClassifier(n_estimators=100, learning_rate=1.0,
...     max_depth=1, random_state=0).fit(X, y)
>>> features = [0, 1, (0, 1)]
>>> plot_partial_dependence(clf, X, features) #doctest: +SKIP

You can access the newly created figure and Axes objects using plt.gcf() and plt.gca().

For multi-class classification, you need to set the class label for which the PDPs should be created via the target argument:

>>> from sklearn.datasets import load_iris
>>> iris = load_iris()
>>> mc_clf = GradientBoostingClassifier(n_estimators=10,
...     max_depth=1).fit(iris.data, iris.target)
>>> features = [3, 2, (3, 2)]
>>> plot_partial_dependence(mc_clf, X, features, target=0) #doctest: +SKIP

The same parameter target is used to specify the target in multi-output regression settings.

If you need the raw values of the partial dependence function rather than the plots, you can use the :func:`sklearn.inspection.partial_dependence` function:

>>> from sklearn.inspection import partial_dependence

>>> pdp, axes = partial_dependence(clf, X, [0])
>>> pdp
array([[ 2.466...,  2.466..., ...
>>> axes
[array([-1.624..., -1.592..., ...

The values at which the partial dependence should be evaluated are directly generated from X. For 2-way partial dependence, a 2D-grid of values is generated. The values field returned by :func:`sklearn.inspection.partial_dependence` gives the actual values used in the grid for each target feature. They also correspond to the axis of the plots.

Mathematical Definition

Let X_S be the set of target features (i.e. the features parameter) and let X_C be its complement.

The partial dependence of the response f at a point x_S is defined as:

pd_{X_S}(x_S) &\overset{def}{=} \mathbb{E}_{X_C}\left[ f(x_S, X_C) \right]\\
              &= \int f(x_S, x_C) p(x_C) dx_C,

where f(x_S, x_C) is the response function (:term:`predict`, :term:`predict_proba` or :term:`decision_function`) for a given sample whose values are defined by x_S for the features in X_S, and by x_C for the features in X_C. Note that x_S and x_C may be tuples.

Computing this integral for various values of x_S produces a plot as above.

Computation methods

There are two main methods to approximate the integral above, namely the 'brute' and 'recursion' methods. The method parameter controls which method to use.

The 'brute' method is a generic method that works with any estimator. It approximates the above integral by computing an average over the data X:

pd_{X_S}(x_S) \approx \frac{1}{n_\text{samples}} \sum_{i=1}^n f(x_S, x_C^{(i)}),

where x_C^{(i)} is the value of the i-th sample for the features in X_C. For each value of x_S, this method requires a full pass over the dataset X which is computationally intensive.

The 'recursion' method is faster than the 'brute' method, but it is only supported by some tree-based estimators. It is computed as follows. For a given point x_S, a weighted tree traversal is performed: if a split node involves a 'target' feature, the corresponding left or right branch is followed; otherwise both branches are followed, each branch being weighted by the fraction of training samples that entered that branch. Finally, the partial dependence is given by a weighted average of all the visited leaves values.

With the 'brute' method, the parameter X is used both for generating the grid of values x_S and the complement feature values x_C. However with the 'recursion' method, X is only used for the grid values: implicitly, the x_C values are those of the training data.

By default, the 'recursion' method is used on tree-based estimators that support it, and 'brute' is used for the rest.

Note

While both methods should be close in general, they might differ in some specific settings. The 'brute' method assumes the existence of the data points (x_S, x_C^{(i)}). When the features are correlated, such artificial samples may have a very low probability mass. The 'brute' and 'recursion' methods will likely disagree regarding the value of the partial dependence, because they will treat these unlikely samples differently. Remember, however, that the primary assumption for interpreting PDPs is that the features should be independent.

Footnotes

[1]	For classification, the target response may be the probability of a class (the positive class for binary classification), or the decision function.

Examples:

• :ref:`sphx_glr_auto_examples_inspection_plot_partial_dependence.py`

References

T. Hastie, R. Tibshirani and J. Friedman, The Elements of Statistical Learning, Second Edition, Section 10.13.2, Springer, 2009.

C. Molnar, Interpretable Machine Learning, Section 5.1, 2019.