8000 [MRG + 1] Add fowlkess-mallows and other supervised cluster metrics t… · scikit-learn/scikit-learn@2f7f5a1 · GitHub
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[MRG + 1] Add fowlkess-mallows and other supervised cluster metrics to SCORERS dict so it can be used in hyper-param search (#8117)
* Add supervised cluster metrics to metrics.scorers * Add all the supervised cluster metrics to the tests * Add test for fowlkes_mallows_score in unsupervised grid search * COSMIT: Clarify comment on CLUSTER_SCORERS * Fix doctest
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‎doc/modules/model_evaluation.rst

+1-1
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@@ -94,7 +94,7 @@ Usage examples:
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>>> model = svm.SVC()
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>>> cross_val_score(model, X, y, scoring='wrong_choice')
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Traceback (most recent call last):
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ValueError: 'wrong_choice' is not a valid scoring value. Valid options are ['accuracy', 'adjusted_rand_score', 'average_precision', 'f1', 'f1_macro', 'f1_micro', 'f1_samples', 'f1_weighted', 'neg_log_loss', 'neg_mean_absolute_error', 'neg_mean_squared_error', 'neg_mean_squared_log_error', 'neg_median_absolute_error', 'precision', 'precision_macro', 'precision_micro', 'precision_samples', 'precision_weighted', 'r2', 'recall', 'recall_macro', 'recall_micro', 'recall_samples', 'recall_weighted', 'roc_auc']
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ValueError: 'wrong_choice' is not a valid scoring value. Valid options are ['accuracy', 'adjusted_mutual_info_score', 'adjusted_rand_score', 'average_precision', 'completeness_score', 'f1', 'f1_macro', 'f1_micro', 'f1_samples', 'f1_weighted', 'fowlkes_mallows_score', 'homogeneity_score', 'mutual_info_score', 'neg_log_loss', 'neg_mean_absolute_error', 'neg_mean_squared_error', 'neg_mean_squared_log_error', 'neg_median_absolute_error', 'normalized_mutual_info_score', 'precision', 'precision_macro', 'precision_micro', 'precision_samples', 'precision_weighted', 'r2', 'recall', 'recall_macro', 'recall_micro', 'recall_samples', 'recall_weighted', 'roc_auc', 'v_measure_score']
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.. note::
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‎sklearn/metrics/scorer.py

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@@ -27,7 +27,16 @@
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mean_squared_error, mean_squared_log_error, accuracy_score,
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f1_score, roc_auc_score, average_precision_score,
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precision_score, recall_score, log_loss)
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from .cluster import adjusted_rand_score
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from .cluster import homogeneity_score
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from .cluster import completeness_score
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from .cluster import v_measure_score
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from .cluster import mutual_info_score
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from .cluster import adjusted_mutual_info_score
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from .cluster import normalized_mutual_info_score
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from .cluster import fowlkes_mallows_score
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from ..utils.multiclass import type_of_target
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from ..externals import six
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from ..base import is_regressor
@@ -393,6 +402,14 @@ def make_scorer(score_func, greater_is_better=True, needs_proba=False,
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# Clustering scores
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adjusted_rand_scorer = make_scorer(adjusted_rand_score)
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homogeneity_scorer = make_scorer(homogeneity_score)
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completeness_scorer = make_scorer(completeness_score)
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v_measure_scorer = make_scorer(v_measure_score)
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mutual_info_scorer = make_scorer(mutual_info_score)
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adjusted_mutual_info_scorer = make_scorer(adjusted_mutual_info_score)
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normalized_mutual_info_scorer = make_scorer(normalized_mutual_info_score)
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fowlkes_mallows_scorer = make_scorer(fowlkes_mallows_score)
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SCORERS = dict(r2=r2_scorer,
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neg_median_absolute_error=neg_median_absolute_error_scorer,
@@ -406,7 +423,16 @@ def make_scorer(score_func, greater_is_better=True, needs_proba=False,
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average_precision=average_precision_scorer,
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log_loss=log_loss_scorer,
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neg_log_loss=neg_log_loss_scorer,
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adjusted_rand_score=adjusted_rand_scorer)
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# Cluster metrics that use supervised evaluation
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adjusted_rand_score=adjusted_rand_scorer,
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homogeneity_score=homogeneity_scorer,
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completeness_score=completeness_scorer,
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v_measure_score=v_measure_scorer,
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mutual_info_score=mutual_info_scorer,
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adjusted_mutual_info_score=adjusted_mutual_info_scorer,
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normalized_mutual_info_score=normalized_mutual_info_scorer,
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fowlkes_mallows_score=fowlkes_mallows_scorer)
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for name, metric in [('precision', precision_score),
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('recall', recall_score), ('f1', f1_score)]:

‎sklearn/metrics/tests/test_score_objects.py

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@@ -18,7 +18,7 @@
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from sklearn.base import BaseEstimator
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from sklearn.metrics import (f1_score, r2_score, roc_auc_score, fbeta_score,
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log_loss, precision_score, recall_score)
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from sklearn.metrics.cluster import adjusted_rand_score
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from sklearn.metrics import cluster as cluster_module
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from sklearn.metrics.scorer import (check_scoring, _PredictScorer,
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_passthrough_scorer)
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from sklearn.metrics import make_scorer, get_scorer, SCORERS
@@ -47,9 +47,17 @@
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'roc_auc', 'average_precision', 'precision',
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'precision_weighted', 'precision_macro', 'precision_micro',
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'recall', 'recall_weighted', 'recall_macro', 'recall_micro',
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'neg_log_loss', 'log_loss',
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'adjusted_rand_score' # not really, but works
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]
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'neg_log_loss', 'log_loss']
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# All supervised cluster scorers (They behave like classification metric)
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CLUSTER_SCORERS = ["adjusted_rand_score",
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"homogeneity_score",
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"completeness_score",
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"v_measure_score",
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"mutual_info_score",
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"adjusted_mutual_info_score",
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"normalized_mutual_info_score",
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"fowlkes_mallows_score"]
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MULTILABEL_ONLY_SCORERS = ['precision_samples', 'recall_samples', 'f1_samples']
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@@ -65,6 +73,7 @@ def _make_estimators(X_train, y_train, y_ml_train):
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return dict(
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[(name, sensible_regr) for name in REGRESSION_SCORERS] +
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[(name, sensible_clf) for name in CLF_SCORERS] +
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[(name, sensible_clf) for name in CLUSTER_SCORERS] +
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[(name, sensible_ml_clf) for name in MULTILABEL_ONLY_SCORERS]
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)
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@@ -330,16 +339,16 @@ def test_thresholded_scorers_multilabel_indicator_data():
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assert_almost_equal(score1, score2)
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def test_unsupervised_scorers():
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def test_supervised_cluster_scorers():
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# Test clustering scorers against gold standard labeling.
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# We don't have any real unsupervised Scorers yet.
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X, y = make_blobs(random_state=0, centers=2)
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X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
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km = KMeans(n_clusters=3)
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km.fit(X_train)
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score1 = get_scorer('adjusted_rand_score')(km, X_test, y_test)
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score2 = adjusted_rand_score(y_test, km.predict(X_test))
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assert_almost_equal(score1, score2)
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for name in CLUSTER_SCORERS:
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score1 = get_scorer(name)(km, X_test, y_test)
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score2 = getattr(cluster_module, name)(y_test, km.predict(X_test))
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assert_almost_equal(score1, score2)
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@ignore_warnings
@@ -445,4 +454,4 @@ def test_scoring_is_not_metric():
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assert_raises_regexp(ValueError, 'make_scorer', check_scoring,
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Ridge(), r2_score)
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assert_raises_regexp(ValueError, 'make_scorer', check_scoring,
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KMeans(), adjusted_rand_score)
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KMeans(), cluster_module.adjusted_rand_score)

‎sklearn/model_selection/tests/test_search.py

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@@ -542,6 +542,12 @@ def test_unsupervised_grid_search():
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# ARI can find the right number :)
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assert_equal(grid_search.best_params_["n_clusters"], 3)
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grid_search = GridSearchCV(km, param_grid=dict(n_clusters=[2, 3, 4]),
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scoring='fowlkes_mallows_score')
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grid_search.fit(X, y)
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# So can FMS ;)
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assert_equal(grid_search.best_params_["n_clusters"], 3)
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# Now without a score, and without y
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grid_search = GridSearchCV(km, param_grid=dict(n_clusters=[2, 3, 4]))
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grid_search.fit(X)

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