from functools import partial import pytest import numpy as np from sklearn.metrics.cluster import adjusted_mutual_info_score from sklearn.metrics.cluster import adjusted_rand_score from sklearn.metrics.cluster import rand_score from sklearn.metrics.cluster import completeness_score from sklearn.metrics.cluster import fowlkes_mallows_score from sklearn.metrics.cluster import homogeneity_score from sklearn.metrics.cluster import mutual_info_score from sklearn.metrics.cluster import normalized_mutual_info_score from sklearn.metrics.cluster import v_measure_score from sklearn.metrics.cluster import silhouette_score from sklearn.metrics.cluster import calinski_harabasz_score from sklearn.metrics.cluster import davies_bouldin_score from sklearn.utils._testing import assert_allclose # Dictionaries of metrics # ------------------------ # The goal of having those dictionaries is to have an easy way to call a # particular metric and associate a name to each function: # - SUPERVISED_METRICS: all supervised cluster metrics - (when given a # ground truth value) # - UNSUPERVISED_METRICS: all unsupervised cluster metrics # # Those dictionaries will be used to test systematically some invariance # properties, e.g. invariance toward several input layout. # SUPERVISED_METRICS = { "adjusted_mutual_info_score": adjusted_mutual_info_score, "adjusted_rand_score": adjusted_rand_score, "rand_score": rand_score, "completeness_score": completeness_score, "homogeneity_score": homogeneity_score, "mutual_info_score": mutual_info_score, "normalized_mutual_info_score": normalized_mutual_info_score, "v_measure_score": v_measure_score, "fowlkes_mallows_score": fowlkes_mallows_score } UNSUPERVISED_METRICS = { "silhouette_score": silhouette_score, "silhouette_manhattan": partial(silhouette_score, metric='manhattan'), "calinski_harabasz_score": calinski_harabasz_score, "davies_bouldin_score": davies_bouldin_score } # Lists of metrics with common properties # --------------------------------------- # Lists of metrics with common properties are used to test systematically some # functionalities and invariance, e.g. SYMMETRIC_METRICS lists all metrics # that are symmetric with respect to their input argument y_true and y_pred. # # -------------------------------------------------------------------- # Symmetric with respect to their input arguments y_true and y_pred. # Symmetric metrics only apply to supervised clusters. SYMMETRIC_METRICS = [ "adjusted_rand_score", "rand_score", "v_measure_score", "mutual_info_score", "adjusted_mutual_info_score", "normalized_mutual_info_score", "fowlkes_mallows_score" ] NON_SYMMETRIC_METRICS = ["homogeneity_score", "completeness_score"] # Metrics whose upper bound is 1 NORMALIZED_METRICS = [ "adjusted_rand_score", "rand_score", "homogeneity_score", "completeness_score", "v_measure_score", "adjusted_mutual_info_score", "fowlkes_mallows_score", "normalized_mutual_info_score" ] rng = np.random.RandomState(0) y1 = rng.randint(3, size=30) y2 = rng.randint(3, size=30) def test_symmetric_non_symmetric_union(): assert (sorted(SYMMETRIC_METRICS + NON_SYMMETRIC_METRICS) == sorted(SUPERVISED_METRICS)) # 0.22 AMI and NMI changes @pytest.mark.filterwarnings('ignore::FutureWarning') @pytest.mark.parametrize( 'metric_name, y1, y2', [(name, y1, y2) for name in SYMMETRIC_METRICS] ) def test_symmetry(metric_name, y1, y2): metric = SUPERVISED_METRICS[metric_name] assert metric(y1, y2) == pytest.approx(metric(y2, y1)) @pytest.mark.parametrize( 'metric_name, y1, y2', [(name, y1, y2) for name in NON_SYMMETRIC_METRICS] ) def test_non_symmetry(metric_name, y1, y2): metric = SUPERVISED_METRICS[metric_name] assert metric(y1, y2) != pytest.approx(metric(y2, y1)) # 0.22 AMI and NMI changes @pytest.mark.filterwarnings('ignore::FutureWarning') @pytest.mark.parametrize("metric_name", NORMALIZED_METRICS) def test_normalized_output(metric_name): upper_bound_1 = [0, 0, 0, 1, 1, 1] upper_bound_2 = [0, 0, 0, 1, 1, 1] metric = SUPERVISED_METRICS[metric_name] assert metric([0, 0, 0, 1, 1], [0, 0, 0, 1, 2]) > 0.0 assert metric([0, 0, 1, 1, 2], [0, 0, 1, 1, 1]) > 0.0 assert metric([0, 0, 0, 1, 2], [0, 1, 1, 1, 1]) < 1.0 assert metric([0, 0, 0, 1, 2], [0, 1, 1, 1, 1]) < 1.0 assert metric(upper_bound_1, upper_bound_2) == pytest.approx(1.0) lower_bound_1 = [0, 0, 0, 0, 0, 0] lower_bound_2 = [0, 1, 2, 3, 4, 5] score = np.array([metric(lower_bound_1, lower_bound_2), metric(lower_bound_2, lower_bound_1)]) assert not (score < 0).any() # 0.22 AMI and NMI changes @pytest.mark.filterwarnings('ignore::FutureWarning') @pytest.mark.parametrize( "metric_name", dict(SUPERVISED_METRICS, **UNSUPERVISED_METRICS) ) def test_permute_labels(metric_name): # All clustering metrics do not change score due to permutations of labels # that is when 0 and 1 exchanged. y_label = np.array([0, 0, 0, 1, 1, 0, 1]) y_pred = np.array([1, 0, 1, 0, 1, 1, 0]) if metric_name in SUPERVISED_METRICS: metric = SUPERVISED_METRICS[metric_name] score_1 = metric(y_pred, y_label) assert_allclose(score_1, metric(1 - y_pred, y_label)) assert_allclose(score_1, metric(1 - y_pred, 1 - y_label)) assert_allclose(score_1, metric(y_pred, 1 - y_label)) else: metric = UNSUPERVISED_METRICS[metric_name] X = np.random.randint(10, size=(7, 10)) score_1 = metric(X, y_pred) assert_allclose(score_1, metric(X, 1 - y_pred)) # 0.22 AMI and NMI changes @pytest.mark.filterwarnings('ignore::FutureWarning') @pytest.mark.parametrize( "metric_name", dict(SUPERVISED_METRICS, **UNSUPERVISED_METRICS) ) # For all clustering metrics Input parameters can be both # in the form of arrays lists, positive, negative or string def test_format_invariance(metric_name): y_true = [0, 0, 0, 0, 1, 1, 1, 1] y_pred = [0, 1, 2, 3, 4, 5, 6, 7] def generate_formats(y): y = np.array(y) yield y, 'array of ints' yield y.tolist(), 'list of ints' yield [str(x) + "-a" for x in y.tolist()], 'list of strs' yield (np.array([str(x) + "-a" for x in y.tolist()], dtype=object), 'array of strs') yield y - 1, 'including negative ints' yield y + 1, 'strictly positive ints' if metric_name in SUPERVISED_METRICS: metric = SUPERVISED_METRICS[metric_name] score_1 = metric(y_true, y_pred) y_true_gen = generate_formats(y_true) y_pred_gen = generate_formats(y_pred) for (y_true_fmt, fmt_name), (y_pred_fmt, _) in zip(y_true_gen, y_pred_gen): assert score_1 == metric(y_true_fmt, y_pred_fmt) else: metric = UNSUPERVISED_METRICS[metric_name] X = np.random.randint(10, size=(8, 10)) score_1 = metric(X, y_true) assert score_1 == metric(X.astype(float), y_true) y_true_gen = generate_formats(y_true) for (y_true_fmt, fmt_name) in y_true_gen: assert score_1 == metric(X, y_true_fmt) @pytest.mark.parametrize("metric", SUPERVISED_METRICS.values()) def test_single_sample(metric): # only the supervised metrics support single sample for i, j in [(0, 0), (0, 1), (1, 0), (1, 1)]: metric([i], [j]) @pytest.mark.parametrize( "metric_name, metric_func", dict(SUPERVISED_METRICS, **UNSUPERVISED_METRICS).items() ) def test_inf_nan_input(metric_name, metric_func): if metric_name in SUPERVISED_METRICS: invalids = [([0, 1], [np.inf, np.inf]), ([0, 1], [np.nan, np.nan]), ([0, 1], [np.nan, np.inf])] else: X = np.random.randint(10, size=(2, 10)) invalids = [(X, [np.inf, np.inf]), (X, [np.nan, np.nan]), (X, [np.nan, np.inf])] with pytest.raises(ValueError, match='contains NaN, infinity'): for args in invalids: metric_func(*args)