334 lines
11 KiB
Python
334 lines
11 KiB
Python
# Sebastian Raschka 2014-2020
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# mlxtend Machine Learning Library Extensions
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#
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# Author: Sebastian Raschka <sebastianraschka.com>
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#
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# License: BSD 3 clause
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import numpy as np
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from scipy import stats
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from sklearn.model_selection import train_test_split
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from sklearn.model_selection import KFold
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from sklearn.metrics import get_scorer
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def paired_ttest_resampled(estimator1, estimator2, X, y,
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num_rounds=30, test_size=0.3,
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scoring=None,
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random_seed=None):
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"""
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Implements the resampled paired t test procedure
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to compare the performance of two models
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(also called k-hold-out paired t test).
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Parameters
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----------
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estimator1 : scikit-learn classifier or regressor
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estimator2 : scikit-learn classifier or regressor
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X : {array-like, sparse matrix}, shape = [n_samples, n_features]
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Training vectors, where n_samples is the number of samples and
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n_features is the number of features.
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y : array-like, shape = [n_samples]
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Target values.
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num_rounds : int (default: 30)
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Number of resampling iterations
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(i.e., train/test splits)
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test_size : float or int (default: 0.3)
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If float, should be between 0.0 and 1.0 and
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represent the proportion of the dataset to use
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as a test set.
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If int, represents the absolute number of test exsamples.
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scoring : str, callable, or None (default: None)
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If None (default), uses 'accuracy' for sklearn classifiers
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and 'r2' for sklearn regressors.
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If str, uses a sklearn scoring metric string identifier, for example
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{accuracy, f1, precision, recall, roc_auc} for classifiers,
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{'mean_absolute_error', 'mean_squared_error'/'neg_mean_squared_error',
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'median_absolute_error', 'r2'} for regressors.
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If a callable object or function is provided, it has to be conform with
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sklearn's signature ``scorer(estimator, X, y)``; see
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http://scikit-learn.org/stable/modules/generated/sklearn.metrics.make_scorer.html
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for more information.
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random_seed : int or None (default: None)
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Random seed for creating the test/train splits.
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Returns
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----------
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t : float
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The t-statistic
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pvalue : float
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Two-tailed p-value.
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If the chosen significance level is larger
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than the p-value, we reject the null hypothesis
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and accept that there are significant differences
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in the two compared models.
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Examples
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-----------
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For usage examples, please see
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http://rasbt.github.io/mlxtend/user_guide/evaluate/paired_ttest_resampled/
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"""
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if (not isinstance(test_size, int) and not isinstance(test_size, float)):
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raise ValueError('train_size must be of '
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'type int or float. Got %s.' % type(test_size))
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rng = np.random.RandomState(random_seed)
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if scoring is None:
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if estimator1._estimator_type == 'classifier':
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scoring = 'accuracy'
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elif estimator1._estimator_type == 'regressor':
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scoring = 'r2'
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else:
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raise AttributeError('Estimator must '
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'be a Classifier or Regressor.')
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if isinstance(scoring, str):
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scorer = get_scorer(scoring)
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else:
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scorer = scoring
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score_diff = []
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for i in range(num_rounds):
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randint = rng.randint(low=0, high=32767)
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X_train, X_test, y_train, y_test = \
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train_test_split(X, y, test_size=test_size,
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random_state=randint)
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estimator1.fit(X_train, y_train)
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estimator2.fit(X_train, y_train)
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est1_score = scorer(estimator1, X_test, y_test)
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est2_score = scorer(estimator2, X_test, y_test)
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score_diff.append(est1_score - est2_score)
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avg_diff = np.mean(score_diff)
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numerator = avg_diff * np.sqrt(num_rounds)
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denominator = np.sqrt(sum([(diff - avg_diff)**2 for diff in score_diff])
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/ (num_rounds - 1))
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t_stat = numerator / denominator
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pvalue = stats.t.sf(np.abs(t_stat), num_rounds - 1)*2.
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return float(t_stat), float(pvalue)
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def paired_ttest_kfold_cv(estimator1, estimator2, X, y,
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cv=10,
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scoring=None,
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shuffle=False,
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random_seed=None):
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"""
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Implements the k-fold paired t test procedure
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to compare the performance of two models.
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Parameters
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----------
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estimator1 : scikit-learn classifier or regressor
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estimator2 : scikit-learn classifier or regressor
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X : {array-like, sparse matrix}, shape = [n_samples, n_features]
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Training vectors, where n_samples is the number of samples and
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n_features is the number of features.
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y : array-like, shape = [n_samples]
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Target values.
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cv : int (default: 10)
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Number of splits and iteration for the
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cross-validation procedure
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scoring : str, callable, or None (default: None)
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If None (default), uses 'accuracy' for sklearn classifiers
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and 'r2' for sklearn regressors.
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If str, uses a sklearn scoring metric string identifier, for example
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{accuracy, f1, precision, recall, roc_auc} for classifiers,
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{'mean_absolute_error', 'mean_squared_error'/'neg_mean_squared_error',
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'median_absolute_error', 'r2'} for regressors.
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If a callable object or function is provided, it has to be conform with
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sklearn's signature ``scorer(estimator, X, y)``; see
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http://scikit-learn.org/stable/modules/generated/sklearn.metrics.make_scorer.html
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for more information.
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shuffle : bool (default: True)
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Whether to shuffle the dataset for generating
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the k-fold splits.
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random_seed : int or None (default: None)
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Random seed for shuffling the dataset
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for generating the k-fold splits.
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Ignored if shuffle=False.
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Returns
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----------
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t : float
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The t-statistic
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pvalue : float
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Two-tailed p-value.
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If the chosen significance level is larger
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than the p-value, we reject the null hypothesis
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and accept that there are significant differences
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in the two compared models.
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Examples
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-----------
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For usage examples, please see
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http://rasbt.github.io/mlxtend/user_guide/evaluate/paired_ttest_kfold_cv/
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"""
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kf = KFold(n_splits=cv, random_state=random_seed, shuffle=shuffle)
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if scoring is None:
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if estimator1._estimator_type == 'classifier':
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scoring = 'accuracy'
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elif estimator1._estimator_type == 'regressor':
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scoring = 'r2'
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else:
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raise AttributeError('Estimator must '
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'be a Classifier or Regressor.')
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if isinstance(scoring, str):
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scorer = get_scorer(scoring)
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else:
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scorer = scoring
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score_diff = []
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for train_index, test_index in kf.split(X):
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X_train, X_test = X[train_index], X[test_index]
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y_train, y_test = y[train_index], y[test_index]
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estimator1.fit(X_train, y_train)
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estimator2.fit(X_train, y_train)
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est1_score = scorer(estimator1, X_test, y_test)
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est2_score = scorer(estimator2, X_test, y_test)
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score_diff.append(est1_score - est2_score)
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avg_diff = np.mean(score_diff)
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numerator = avg_diff * np.sqrt(cv)
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denominator = np.sqrt(sum([(diff - avg_diff)**2 for diff in score_diff])
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/ (cv - 1))
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t_stat = numerator / denominator
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pvalue = stats.t.sf(np.abs(t_stat), cv - 1)*2.
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return float(t_stat), float(pvalue)
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def paired_ttest_5x2cv(estimator1, estimator2, X, y,
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scoring=None,
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random_seed=None):
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"""
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Implements the 5x2cv paired t test proposed
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by Dieterrich (1998)
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to compare the performance of two models.
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Parameters
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----------
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estimator1 : scikit-learn classifier or regressor
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estimator2 : scikit-learn classifier or regressor
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X : {array-like, sparse matrix}, shape = [n_samples, n_features]
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Training vectors, where n_samples is the number of samples and
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n_features is the number of features.
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y : array-like, shape = [n_samples]
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Target values.
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scoring : str, callable, or None (default: None)
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If None (default), uses 'accuracy' for sklearn classifiers
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and 'r2' for sklearn regressors.
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If str, uses a sklearn scoring metric string identifier, for example
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{accuracy, f1, precision, recall, roc_auc} for classifiers,
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{'mean_absolute_error', 'mean_squared_error'/'neg_mean_squared_error',
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'median_absolute_error', 'r2'} for regressors.
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If a callable object or function is provided, it has to be conform with
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sklearn's signature ``scorer(estimator, X, y)``; see
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http://scikit-learn.org/stable/modules/generated/sklearn.metrics.make_scorer.html
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for more information.
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random_seed : int or None (default: None)
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Random seed for creating the test/train splits.
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Returns
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----------
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t : float
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The t-statistic
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pvalue : float
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Two-tailed p-value.
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If the chosen significance level is larger
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than the p-value, we reject the null hypothesis
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and accept that there are significant differences
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in the two compared models.
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Examples
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-----------
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For usage examples, please see
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http://rasbt.github.io/mlxtend/user_guide/evaluate/paired_ttest_5x2cv/
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"""
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rng = np.random.RandomState(random_seed)
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if scoring is None:
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if estimator1._estimator_type == 'classifier':
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scoring = 'accuracy'
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elif estimator1._estimator_type == 'regressor':
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scoring = 'r2'
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else:
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raise AttributeError('Estimator must '
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'be a Classifier or Regressor.')
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if isinstance(scoring, str):
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scorer = get_scorer(scoring)
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else:
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scorer = scoring
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variance_sum = 0.
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first_diff = None
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def score_diff(X_1, X_2, y_1, y_2):
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estimator1.fit(X_1, y_1)
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estimator2.fit(X_1, y_1)
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est1_score = scorer(estimator1, X_2, y_2)
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est2_score = scorer(estimator2, X_2, y_2)
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score_diff = est1_score - est2_score
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return score_diff
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for i in range(5):
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randint = rng.randint(low=0, high=32767)
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X_1, X_2, y_1, y_2 = \
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train_test_split(X, y, test_size=0.5,
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random_state=randint)
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score_diff_1 = score_diff(X_1, X_2, y_1, y_2)
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score_diff_2 = score_diff(X_2, X_1, y_2, y_1)
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score_mean = (score_diff_1 + score_diff_2) / 2.
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score_var = ((score_diff_1 - score_mean)**2 +
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(score_diff_2 - score_mean)**2)
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variance_sum += score_var
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if first_diff is None:
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first_diff = score_diff_1
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numerator = first_diff
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denominator = np.sqrt(1/5. * variance_sum)
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t_stat = numerator / denominator
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pvalue = stats.t.sf(np.abs(t_stat), 5)*2.
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return float(t_stat), float(pvalue)
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