# Source code for gemseo.mlearning.qual_measure.silhouette

```
# -*- coding: utf-8 -*-
# Copyright 2021 IRT Saint Exupéry, https://www.irt-saintexupery.com
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License version 3 as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
# Contributors:
# INITIAL AUTHORS - initial API and implementation and/or initial
# documentation
# :author: Syver Doving Agdestein
# OTHER AUTHORS - MACROSCOPIC CHANGES
r"""The silhouette coefficient to measure the quality of a clustering algorithm.
The :mod:`~gemseo.mlearning.qual_measure.silhouette` module implements the
concept of silhouette coefficient measure for machine learning algorithms.
This concept is implemented through the
:class:`.SilhouetteMeasure` class and
overloads the :meth:`!MLClusteringMeasure._compute_measure` method.
The silhouette coefficient is defined for each point as the difference
between the average distance from the point to each of the other points in its cluster
and the average distance from the point to each of the points
in the nearest cluster different from its own.
More formally,
the silhouette coefficient :math:`s_i` of a point :math:`x_i` is given by
.. math::
a_i = \\frac{1}{|C_{k_i}| - 1} \\sum_{j\\in C_{k_i}\setminus\{i\} } \\|x_i-x_j\\|\\\\
b_i = \\underset{\\ell=1,\\cdots,K\\atop{\\ell\\neq k_i}}{\\min}\\
\\frac{1}{|C_\\ell|} \\sum_{j\\in C_\\ell} \\|x_i-x_j\\|\\\\
s_i = \\frac{b_i-a_i}{\\max(b_i,a_i)}
where
:math:`k_i` is the index of the cluster to which :math:`x_i` belongs,
:math:`K` is the number of clusters,
:math:`C_k` is the set of indices of points
belonging to the cluster :math:`k` (:math:`k=1,\\cdots,K`),
and :math:`|C_k| = \\sum_{j\\in C_k} 1` is the number of points
in the cluster :math:`k`, :math:`k=1,\\cdots,K`.
"""
from __future__ import division, unicode_literals
from typing import Optional, Sequence, Union
from numpy import ndarray
from sklearn.metrics import silhouette_score
from gemseo.core.dataset import Dataset
from gemseo.mlearning.cluster.cluster import MLPredictiveClusteringAlgo
from gemseo.mlearning.qual_measure.cluster_measure import MLPredictiveClusteringMeasure
[docs]class SilhouetteMeasure(MLPredictiveClusteringMeasure):
"""The silhouette coefficient measure for machine learning."""
SMALLER_IS_BETTER = False
def __init__(
self,
algo, # type: MLPredictiveClusteringAlgo
): # type: (...) -> None
"""
Args:
algo: A machine learning algorithm for clustering.
"""
super(SilhouetteMeasure, self).__init__(algo)
[docs] def evaluate_test(
self,
test_data, # type:Dataset
samples=None, # type: Optional[Sequence[int]]
multioutput=True, # type: bool
): # type: (...) -> Union[float,ndarray]
raise NotImplementedError
[docs] def evaluate_kfolds(
self,
n_folds=5, # type: int
samples=None, # type: Optional[Sequence[int]]
multioutput=True, # type: bool
randomize=False, # type:bool
): # type: (...) -> Union[float,ndarray]
raise NotImplementedError
[docs] def evaluate_bootstrap(
self,
n_replicates=100, # type: int
samples=None, # type: Optional[Sequence[int]]
multioutput=True, # type: bool
): # type: (...) -> Union[float,ndarray]
raise NotImplementedError
def _compute_measure(
self,
data, # type: ndarray
labels, # type: ndarray
multioutput=True, # type: bool
): # type: (...) -> Union[float,ndarray]
if multioutput:
raise NotImplementedError(
"The SilhouetteMeasure does not support the multioutput case."
)
measure = silhouette_score(data, labels)
return measure
```