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.. _sphx_glr_auto_examples_covariance_plot_robust_vs_empirical_covariance.py:
=======================================
Robust vs Empirical covariance estimate
=======================================
The usual covariance maximum likelihood estimate is very sensitive to the
presence of outliers in the data set. In such a case, it would be better to
use a robust estimator of covariance to guarantee that the estimation is
resistant to "erroneous" observations in the data set. [1]_, [2]_
Minimum Covariance Determinant Estimator
----------------------------------------
The Minimum Covariance Determinant estimator is a robust, high-breakdown point
(i.e. it can be used to estimate the covariance matrix of highly contaminated
datasets, up to
:math:`\frac{n_\text{samples} - n_\text{features}-1}{2}` outliers) estimator of
covariance. The idea is to find
:math:`\frac{n_\text{samples} + n_\text{features}+1}{2}`
observations whose empirical covariance has the smallest determinant, yielding
a "pure" subset of observations from which to compute standards estimates of
location and covariance. After a correction step aiming at compensating the
fact that the estimates were learned from only a portion of the initial data,
we end up with robust estimates of the data set location and covariance.
The Minimum Covariance Determinant estimator (MCD) has been introduced by
P.J.Rousseuw in [3]_.
Evaluation
----------
In this example, we compare the estimation errors that are made when using
various types of location and covariance estimates on contaminated Gaussian
distributed data sets:
- The mean and the empirical covariance of the full dataset, which break
down as soon as there are outliers in the data set
- The robust MCD, that has a low error provided
:math:`n_\text{samples} > 5n_\text{features}`
- The mean and the empirical covariance of the observations that are known
to be good ones. This can be considered as a "perfect" MCD estimation,
so one can trust our implementation by comparing to this case.
References
----------
.. [1] Johanna Hardin, David M Rocke. The distribution of robust distances.
Journal of Computational and Graphical Statistics. December 1, 2005,
14(4): 928-946.
.. [2] Zoubir A., Koivunen V., Chakhchoukh Y. and Muma M. (2012). Robust
estimation in signal processing: A tutorial-style treatment of
fundamental concepts. IEEE Signal Processing Magazine 29(4), 61-80.
.. [3] P. J. Rousseeuw. Least median of squares regression. Journal of American
Statistical Ass., 79:871, 1984.
.. GENERATED FROM PYTHON SOURCE LINES 55-186
.. image-sg:: /auto_examples/covariance/images/sphx_glr_plot_robust_vs_empirical_covariance_001.png
:alt: Influence of outliers on the location estimation, Influence of outliers on the covariance estimation
:srcset: /auto_examples/covariance/images/sphx_glr_plot_robust_vs_empirical_covariance_001.png
:class: sphx-glr-single-img
.. code-block:: Python
import matplotlib.font_manager
import matplotlib.pyplot as plt
import numpy as np
from sklearn.covariance import EmpiricalCovariance, MinCovDet
# example settings
n_samples = 80
n_features = 5
repeat = 10
range_n_outliers = np.concatenate(
(
np.linspace(0, n_samples / 8, 5),
np.linspace(n_samples / 8, n_samples / 2, 5)[1:-1],
)
).astype(int)
# definition of arrays to store results
err_loc_mcd = np.zeros((range_n_outliers.size, repeat))
err_cov_mcd = np.zeros((range_n_outliers.size, repeat))
err_loc_emp_full = np.zeros((range_n_outliers.size, repeat))
err_cov_emp_full = np.zeros((range_n_outliers.size, repeat))
err_loc_emp_pure = np.zeros((range_n_outliers.size, repeat))
err_cov_emp_pure = np.zeros((range_n_outliers.size, repeat))
# computation
for i, n_outliers in enumerate(range_n_outliers):
for j in range(repeat):
rng = np.random.RandomState(i * j)
# generate data
X = rng.randn(n_samples, n_features)
# add some outliers
outliers_index = rng.permutation(n_samples)[:n_outliers]
outliers_offset = 10.0 * (
np.random.randint(2, size=(n_outliers, n_features)) - 0.5
)
X[outliers_index] += outliers_offset
inliers_mask = np.ones(n_samples).astype(bool)
inliers_mask[outliers_index] = False
# fit a Minimum Covariance Determinant (MCD) robust estimator to data
mcd = MinCovDet().fit(X)
# compare raw robust estimates with the true location and covariance
err_loc_mcd[i, j] = np.sum(mcd.location_**2)
err_cov_mcd[i, j] = mcd.error_norm(np.eye(n_features))
# compare estimators learned from the full data set with true
# parameters
err_loc_emp_full[i, j] = np.sum(X.mean(0) ** 2)
err_cov_emp_full[i, j] = (
EmpiricalCovariance().fit(X).error_norm(np.eye(n_features))
)
# compare with an empirical covariance learned from a pure data set
# (i.e. "perfect" mcd)
pure_X = X[inliers_mask]
pure_location = pure_X.mean(0)
pure_emp_cov = EmpiricalCovariance().fit(pure_X)
err_loc_emp_pure[i, j] = np.sum(pure_location**2)
err_cov_emp_pure[i, j] = pure_emp_cov.error_norm(np.eye(n_features))
# Display results
font_prop = matplotlib.font_manager.FontProperties(size=11)
plt.subplot(2, 1, 1)
lw = 2
plt.errorbar(
range_n_outliers,
err_loc_mcd.mean(1),
yerr=err_loc_mcd.std(1) / np.sqrt(repeat),
label="Robust location",
lw=lw,
color="m",
)
plt.errorbar(
range_n_outliers,
err_loc_emp_full.mean(1),
yerr=err_loc_emp_full.std(1) / np.sqrt(repeat),
label="Full data set mean",
lw=lw,
color="green",
)
plt.errorbar(
range_n_outliers,
err_loc_emp_pure.mean(1),
yerr=err_loc_emp_pure.std(1) / np.sqrt(repeat),
label="Pure data set mean",
lw=lw,
color="black",
)
plt.title("Influence of outliers on the location estimation")
plt.ylabel(r"Error ($||\mu - \hat{\mu}||_2^2$)")
plt.legend(loc="upper left", prop=font_prop)
plt.subplot(2, 1, 2)
x_size = range_n_outliers.size
plt.errorbar(
range_n_outliers,
err_cov_mcd.mean(1),
yerr=err_cov_mcd.std(1),
label="Robust covariance (mcd)",
color="m",
)
plt.errorbar(
range_n_outliers[: (x_size // 5 + 1)],
err_cov_emp_full.mean(1)[: (x_size // 5 + 1)],
yerr=err_cov_emp_full.std(1)[: (x_size // 5 + 1)],
label="Full data set empirical covariance",
color="green",
)
plt.plot(
range_n_outliers[(x_size // 5) : (x_size // 2 - 1)],
err_cov_emp_full.mean(1)[(x_size // 5) : (x_size // 2 - 1)],
color="green",
ls="--",
)
plt.errorbar(
range_n_outliers,
err_cov_emp_pure.mean(1),
yerr=err_cov_emp_pure.std(1),
label="Pure data set empirical covariance",
color="black",
)
plt.title("Influence of outliers on the covariance estimation")
plt.xlabel("Amount of contamination (%)")
plt.ylabel("RMSE")
plt.legend(loc="upper center", prop=font_prop)
plt.show()
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