8000 FIX Fix recall in multilabel classification when true labels are all … · scikit-learn/scikit-learn@ea0571f · GitHub
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varunagrawalthomasjpfanjeremiedbb
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FIX Fix recall in multilabel classification when true labels are all negative (#19085)
Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com> Co-authored-by: jeremiedbb <jeremiedbb@yahoo.fr>
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‎doc/whats_new/v1.1.rst

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@@ -711,6 +711,9 @@ Changelog
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- |Fix| Fixed a bug in :func:`metrics.normalized_mutual_info_score` which could return
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unbounded values. :pr:`22635` by :user:`Jérémie du Boisberranger <jeremiedbb>`.
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- |Fix| Fixes `precision_recall_curve` and `average_precision_score` when true labels
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are all negative. :pr:`19085` by :user:`Varun Agrawal <varunagrawal>`.
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:mod:`sklearn.model_selection`
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..............................
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‎sklearn/metrics/_ranking.py

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@@ -865,15 +865,25 @@ def precision_recall_curve(y_true, probas_pred, *, pos_label=None, sample_weight
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y_true, probas_pred, pos_label=pos_label, sample_weight=sample_weight
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)
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868-
precision = tps / (tps + fps)
869-
precision[np.isnan(precision)] = 0
870-
recall = tps / tps[-1]
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ps = tps + fps
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precision = np.divide(tps, ps, where=(ps != 0))
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# When no positive label in y_true, recall is set to 1 for all thresholds
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# tps[-1] == 0 <=> y_true == all negative labels
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if tps[-1] == 0:
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warnings.warn(
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"No positive class found in y_true, "
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"recall is set to one for all thresholds."
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)
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recall = np.ones_like(tps)
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else:
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recall = tps / tps[-1]
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# stop when full recall attained
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# and reverse the outputs so recall is decreasing
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last_ind = tps.searchsorted(tps[-1])
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sl = slice(last_ind, None, -1)
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return np.r_[precision[sl], 1], np.r_[recall[sl], 0], thresholds[sl]
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return np.hstack((precision[sl], 1)), np.hstack((recall[sl], 0)), thresholds[sl]
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def roc_curve(

‎sklearn/metrics/tests/test_ranking.py

Lines changed: 60 additions & 23 deletions
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@@ -915,10 +915,13 @@ def test_precision_recall_curve_toydata():
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y_true = [0, 0]
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y_score = [0.25, 0.75]
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with pytest.raises(Exception):
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precision_recall_curve(y_true, y_score)
920-
with pytest.raises(Exception):
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average_precision_score(y_true, y_score)
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with pytest.warns(UserWarning, match="No positive class found in y_true"):
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p, r, _ = precision_recall_curve(y_true, y_score)
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with pytest.warns(UserWarning, match="No positive class found in y_true"):
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auc_prc = average_precision_score(y_true, y_score)
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assert_allclose(p, [0, 1])
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assert_allclose(r, [1, 0])
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assert_allclose(auc_prc, 0)
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y_true = [1, 1]
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y_score = [0.25, 0.75]
@@ -930,29 +933,33 @@ def test_precision_recall_curve_toydata():
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# Multi-label classification task
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y_true = np.array([[0, 1], [0, 1]])
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y_score = np.array([[0, 1], [0, 1]])
933-
with pytest.raises(Exception):
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average_precision_score(y_true, y_score, average="macro")
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with pytest.raises(Exception):
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average_precision_score(y_true, y_score, average="weighted")
937-
assert_almost_equal(
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with pytest.warns(UserWarning, match="No positive class found in y_true"):
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assert_allclose(
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average_precision_score(y_true, y_score, average="macro"), 0.5
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)
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with pytest.warns(UserWarning, match="No positive class found in y_true"):
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assert_allclose(
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average_precision_score(y_true, y_score, average="weighted"), 1.0
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)
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assert_allclose(
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average_precision_score(y_true, y_score, average="samples"), 1.0
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)
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assert_almost_equal(
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average_precision_score(y_true, y_score, average="micro"), 1.0
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)
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assert_allclose(average_precision_score(y_true, y_score, average="micro"), 1.0)
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y_true = np.array([[0, 1], [0, 1]])
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y_score = np.array([[0, 1], [1, 0]])
946-
with pytest.raises(Exception):
947-
average_precision_score(y_true, y_score, average="macro")
948-
with pytest.raises(Exception):
949-
average_precision_score(y_true, y_score, average="weighted")
950-
assert_almost_equal(
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with pytest.warns(UserWarning, match="No positive class found in y_true"):
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assert_allclose(
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average_precision_score(y_true, y_score, average="macro"), 0.5
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)
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with pytest.warns(UserWarning, match="No positive class found in y_true"):
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assert_allclose(
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average_precision_score(y_true, y_score, average="weighted"), 1.0
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)
959+
assert_allclose(
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average_precision_score(y_true, y_score, average="samples"), 0.75
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)
953-
assert_almost_equal(
954-
average_precision_score(y_true, y_score, average="micro"), 0.5
955-
)
962+
assert_allclose(average_precision_score(y_true, y_score, average="micro"), 0.5)
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957964
y_true = np.array([[1, 0], [0, 1]])
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y_score = np.array([[0, 1], [1, 0]])
@@ -969,6 +976,35 @@ def test_precision_recall_curve_toydata():
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average_precision_score(y_true, y_score, average="micro"), 0.5
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)
971978

979+
y_true = np.array([[0, 0], [0, 0]])
980+
y_score = np.array([[0, 1], [0, 1]])
981+
with pytest.warns(UserWarning, match="No positive class found in y_true"):
982+
assert_allclose(
983+
average_precision_score(y_true, y_score, average="macro"), 0.0
984+
)
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assert_allclose(
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average_precision_score(y_true, y_score, average="weighted"), 0.0
987+
)
988+
with pytest.warns(UserWarning, match="No positive class found in y_true"):
989+
assert_allclose(
990+
average_precision_score(y_true, y_score, average="samples"), 0.0
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)
992+
with pytest.warns(UserWarning, match="No positive class found in y_true"):
993+
assert_allclose(
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average_precision_score(y_true, y_score, average="micro"), 0.0
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)
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y_true = np.array([[1, 1], [1, 1]])
998+
y_score = np.array([[0, 1], [0, 1]])
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assert_allclose(average_precision_score(y_true, y_score, average="macro"), 1.0)
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assert_allclose(
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average_precision_score(y_true, y_score, average="weighted"), 1.0
1002+
)
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assert_allclose(
1004+
average_precision_score(y_true, y_score, average="samples"), 1.0
1005+
)
1006+
assert_allclose(average_precision_score(y_true, y_score, average="micro"), 1.0)
1007+
9721008
y_true = np.array([[1, 0], [0, 1]])
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y_score = np.array([[0.5, 0.5], [0.5, 0.5]])
9741010
assert_almost_equal(
@@ -988,9 +1024,10 @@ def test_precision_recall_curve_toydata():
9881024
# if one class is never present weighted should not be NaN
9891025
y_true = np.array([[0, 0], [0, 1]])
9901026
y_score = np.array([[0, 0], [0, 1]])
991-
assert_almost_equal(
992-
average_precision_score(y_true, y_score, average="weighted"), 1
993-
)
1027+
with pytest.warns(UserWarning, match="No positive class found in y_true"):
1028+
assert_allclose(
1029+
average_precision_score(y_true, y_score, average="weighted"), 1
1030+
)
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9951032

9961033
def test_average_precision_constant_values():

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