# -*- 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
"""Here is the baseclass to measure the quality of machine learning algorithms.
The concept of clustering quality measure is implemented with the
:class:`.MLClusteringMeasure` class and proposes different evaluation methods.
"""
from __future__ import division, unicode_literals
from copy import deepcopy
from typing import Dict, NoReturn, Optional, Sequence, Union
from numpy import arange
from numpy import delete as npdelete
from numpy import ndarray, unique
from numpy.random import choice
from gemseo.core.dataset import Dataset
from gemseo.mlearning.cluster.cluster import (
MLClusteringAlgo,
MLPredictiveClusteringAlgo,
)
from gemseo.mlearning.qual_measure.quality_measure import MLQualityMeasure
[docs]class MLClusteringMeasure(MLQualityMeasure):
"""An abstract clustering measure for clustering algorithms."""
def __init__(
self,
algo, # type: MLClusteringAlgo
): # type: (...) -> None
"""
Args:
algo: A machine learning algorithm for clustering.
"""
super(MLClusteringMeasure, self).__init__(algo)
[docs] def evaluate_learn(
self,
samples=None, # type: Optional[Sequence[int]]
multioutput=True, # type: bool
): # type: (...) -> Union[float,ndarray]
samples = self._assure_samples(samples)
if not self.algo.is_trained:
self.algo.learn(samples)
data = self._get_data()[samples]
labels = self.algo.labels
measure = self._compute_measure(data, labels, multioutput)
return measure
def _compute_measure(
self,
data, # type: ndarray
labels, # type: ndarray
multioutput=True, # type: bool
): # type: (...) -> Union[float,ndarray]
"""Compute the quality measure.
Args:
data: The reference data.
labels: The predicted labels.
multioutput: Whether to return the quality measure
for each output component; if not, average these measures.
Returns:
The value of the quality measure.
"""
raise NotImplementedError
def _get_data(self): # type: (...) -> Dict[str,ndarray]
"""Get data.
Returns:
The learning data indexed by the names of the variables.
"""
names = self.algo.var_names
data = self.algo.learning_set.get_data_by_names(names, False)
return data
[docs]class MLPredictiveClusteringMeasure(MLClusteringMeasure):
"""An abstract clustering measure for predictive clustering algorithms."""
def __init__(
self,
algo, # type: MLPredictiveClusteringAlgo
): # type: (...) -> None
"""
Args:
algo: A machine learning algorithm for predictive clustering.
"""
super(MLPredictiveClusteringMeasure, 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]
samples = self._assure_samples(samples)
if not self.algo.is_trained:
self.algo.learn(samples)
names = self.algo.var_names
data = test_data.get_data_by_names(names, False)
predictions = self.algo.predict(data)
measure = self._compute_measure(data, predictions, multioutput)
return measure
[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]
folds, samples = self._compute_folds(samples, n_folds, randomize)
data = self._get_data()
algo = deepcopy(self.algo)
qualities = []
for n_fold in range(n_folds):
test_indices = folds[n_fold]
train_indices = npdelete(samples, test_indices)
algo.learn(samples=train_indices)
test_data = data[test_indices]
predictions = algo.predict(test_data)
quality = self._compute_measure(test_data, predictions, multioutput)
qualities.append(quality)
quality = sum(qualities) / len(qualities)
return quality
[docs] def evaluate_bootstrap(
self,
n_replicates=100, # type: int
samples=None, # type: Optional[Sequence[int]]
multioutput=True, # type: bool
): # type: (...) -> Union[float,ndarray]
samples = self._assure_samples(samples)
n_samples = samples.size
indices = arange(n_samples)
data = self._get_data()
algo = deepcopy(self.algo)
qualities = []
for _ in range(n_replicates):
train_indices = unique(choice(n_samples, n_samples))
test_indices = npdelete(indices, train_indices)
algo.learn(samples=[samples[index] for index in train_indices])
test_data = data[[samples[index] for index in test_indices]]
predictions = algo.predict(test_data)
quality = self._compute_measure(test_data, predictions, multioutput)
qualities.append(quality)
quality = sum(qualities) / len(qualities)
return quality
def _compute_measure(
self,
data, # type: ndarray
labels, # type: ndarray
multioutput=True, # type: bool
): # type: (...) -> NoReturn
"""Compute the quality measure.
Args:
data: The reference data.
labels: The predicted labels.
multioutput: Whether to return the quality measure
for each output component. If not, average these measures.
Returns:
The value of the quality measure.
"""
raise NotImplementedError
def _get_data(self): # type: (...) -> Dict[str,ndarray]
"""Get data.
Returns:
The learning data indexed by the names of the variables.
"""
names = self.algo.var_names
data = self.algo.learning_set.get_data_by_names(names, False)
return data
