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from itertools import product
import numpy as np
import pytest
from scipy.sparse import issparse
from sklearn import config_context, datasets
from sklearn.model_selection import ShuffleSplit
from sklearn.svm import SVC
from sklearn.utils._array_api import yield_namespace_device_dtype_combinations
from sklearn.utils._testing import (
_array_api_for_tests,
_convert_container,
assert_allclose,
assert_array_almost_equal,
assert_array_equal,
)
from sklearn.utils.estimator_checks import _NotAnArray
from sklearn.utils.fixes import (
COO_CONTAINERS,
CSC_CONTAINERS,
CSR_CONTAINERS,
DOK_CONTAINERS,
LIL_CONTAINERS,
)
from sklearn.utils.metaestimators import _safe_split
from sklearn.utils.multiclass import (
_ovr_decision_function,
check_classification_targets,
class_distribution,
is_multilabel,
type_of_target,
unique_labels,
)
multilabel_explicit_zero = np.array([[0, 1], [1, 0]])
multilabel_explicit_zero[:, 0] = 0
def _generate_sparse(
data,
sparse_containers=tuple(
COO_CONTAINERS
+ CSC_CONTAINERS
+ CSR_CONTAINERS
+ DOK_CONTAINERS
+ LIL_CONTAINERS
),
dtypes=(bool, int, np.int8, np.uint8, float, np.float32),
):
return [
sparse_container(data, dtype=dtype)
for sparse_container in sparse_containers
for dtype in dtypes
]
EXAMPLES = {
"multilabel-indicator": [
# valid when the data is formatted as sparse or dense, identified
# by CSR format when the testing takes place
*_generate_sparse(
np.random.RandomState(42).randint(2, size=(10, 10)),
sparse_containers=CSR_CONTAINERS,
dtypes=(int,),
),
[[0, 1], [1, 0]],
[[0, 1]],
*_generate_sparse(
multilabel_explicit_zero, sparse_containers=CSC_CONTAINERS, dtypes=(int,)
),
*_generate_sparse([[0, 1], [1, 0]]),
*_generate_sparse([[0, 0], [0, 0]]),
*_generate_sparse([[0, 1]]),
# Only valid when data is dense
[[-1, 1], [1, -1]],
np.array([[-1, 1], [1, -1]]),
np.array([[-3, 3], [3, -3]]),
_NotAnArray(np.array([[-3, 3], [3, -3]])),
],
"multiclass": [
[1, 0, 2, 2, 1, 4, 2, 4, 4, 4],
np.array([1, 0, 2]),
np.array([1, 0, 2], dtype=np.int8),
np.array([1, 0, 2], dtype=np.uint8),
np.array([1, 0, 2], dtype=float),
np.array([1, 0, 2], dtype=np.float32),
np.array([[1], [0], [2]]),
_NotAnArray(np.array([1, 0, 2])),
[0, 1, 2],
["a", "b", "c"],
np.array(["a", "b", "c"]),
np.array(["a", "b", "c"], dtype=object),
np.array(["a", "b", "c"], dtype=object),
],
"multiclass-multioutput": [
[[1, 0, 2, 2], [1, 4, 2, 4]],
[["a", "b"], ["c", "d"]],
np.array([[1, 0, 2, 2], [1, 4, 2, 4]]),
np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.int8),
np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.uint8),
np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=float),
np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.float32),
*_generate_sparse(
[[1, 0, 2, 2], [1, 4, 2, 4]],
sparse_containers=CSC_CONTAINERS + CSR_CONTAINERS,
dtypes=(int, np.int8, np.uint8, float, np.float32),
),
np.array([["a", "b"], ["c", "d"]]),
np.array([["a", "b"], ["c", "d"]]),
np.array([["a", "b"], ["c", "d"]], dtype=object),
np.array([[1, 0, 2]]),
_NotAnArray(np.array([[1, 0, 2]])),
],
"binary": [
[0, 1],
[1, 1],
[],
[0],
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1]),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=bool),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.int8),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.uint8),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=float),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.float32),
np.array([[0], [1]]),
_NotAnArray(np.array([[0], [1]])),
[1, -1],
[3, 5],
["a"],
["a", "b"],
["abc", "def"],
np.array(["abc", "def"]),
["a", "b"],
np.array(["abc", "def"], dtype=object),
],
"continuous": [
[1e-5],
[0, 0.5],
np.array([[0], [0.5]]),
np.array([[0], [0.5]], dtype=np.float32),
],
"continuous-multioutput": [
np.array([[0, 0.5], [0.5, 0]]),
np.array([[0, 0.5], [0.5, 0]], dtype=np.float32),
np.array([[0, 0.5]]),
*_generate_sparse(
[[0, 0.5], [0.5, 0]],
sparse_containers=CSC_CONTAINERS + CSR_CONTAINERS,
dtypes=(float, np.float32),
),
*_generate_sparse(
[[0, 0.5]],
sparse_containers=CSC_CONTAINERS + CSR_CONTAINERS,
dtypes=(float, np.float32),
),
],
"unknown": [
[[]],
np.array([[]], dtype=object),
[()],
# sequence of sequences that weren't supported even before deprecation
np.array([np.array([]), np.array([1, 2, 3])], dtype=object),
[np.array([]), np.array([1, 2, 3])],
[{1, 2, 3}, {1, 2}],
[frozenset([1, 2, 3]), frozenset([1, 2])],
# and also confusable as sequences of sequences
[{0: "a", 1: "b"}, {0: "a"}],
# ndim 0
np.array(0),
# empty second dimension
np.array([[], []]),
# 3d
np.array([[[0, 1], [2, 3]], [[4, 5], [6, 7]]]),
],
}
ARRAY_API_EXAMPLES = {
"multilabel-indicator": [
np.random.RandomState(42).randint(2, size=(10, 10)),
[[0, 1], [1, 0]],
[[0, 1]],
multilabel_explicit_zero,
[[0, 0], [0, 0]],
[[-1, 1], [1, -1]],
np.array([[-1, 1], [1, -1]]),
np.array([[-3, 3], [3, -3]]),
_NotAnArray(np.array([[-3, 3], [3, -3]])),
],
"multiclass": [
[1, 0, 2, 2, 1, 4, 2, 4, 4, 4],
np.array([1, 0, 2]),
np.array([1, 0, 2], dtype=np.int8),
np.array([1, 0, 2], dtype=np.uint8),
np.array([1, 0, 2], dtype=float),
np.array([1, 0, 2], dtype=np.float32),
np.array([[1], [0], [2]]),
_NotAnArray(np.array([1, 0, 2])),
[0, 1, 2],
],
"multiclass-multioutput": [
[[1, 0, 2, 2], [1, 4, 2, 4]],
np.array([[1, 0, 2, 2], [1, 4, 2, 4]]),
np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.int8),
np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.uint8),
np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=float),
np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.float32),
np.array([[1, 0, 2]]),
_NotAnArray(np.array([[1, 0, 2]])),
],
"binary": [
[0, 1],
[1, 1],
[],
[0],
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1]),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=bool),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.int8),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.uint8),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=float),
np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.float32),
np.array([[0], [1]]),
_NotAnArray(np.array([[0], [1]])),
[1, -1],
[3, 5],
],
"continuous": [
[1e-5],
[0, 0.5],
np.array([[0], [0.5]]),
np.array([[0], [0.5]], dtype=np.float32),
],
"continuous-multioutput": [
np.array([[0, 0.5], [0.5, 0]]),
np.array([[0, 0.5], [0.5, 0]], dtype=np.float32),
np.array([[0, 0.5]]),
],
"unknown": [
[[]],
[()],
np.array(0),
np.array([[[0, 1], [2, 3]], [[4, 5], [6, 7]]]),
],
}
NON_ARRAY_LIKE_EXAMPLES = [
{1, 2, 3},
{0: "a", 1: "b"},
{0: [5], 1: [5]},
"abc",
frozenset([1, 2, 3]),
None,
]
MULTILABEL_SEQUENCES = [
[[1], [2], [0, 1]],
[(), (2), (0, 1)],
np.array([[], [1, 2]], dtype="object"),
_NotAnArray(np.array([[], [1, 2]], dtype="object")),
]
def test_unique_labels():
# Empty iterable
with pytest.raises(ValueError):
unique_labels()
# Multiclass problem
assert_array_equal(unique_labels(range(10)), np.arange(10))
assert_array_equal(unique_labels(np.arange(10)), np.arange(10))
assert_array_equal(unique_labels([4, 0, 2]), np.array([0, 2, 4]))
# Multilabel indicator
assert_array_equal(
unique_labels(np.array([[0, 0, 1], [1, 0, 1], [0, 0, 0]])), np.arange(3)
)
assert_array_equal(unique_labels(np.array([[0, 0, 1], [0, 0, 0]])), np.arange(3))
# Several arrays passed
assert_array_equal(unique_labels([4, 0, 2], range(5)), np.arange(5))
assert_array_equal(unique_labels((0, 1, 2), (0,), (2, 1)), np.arange(3))
# Border line case with binary indicator matrix
with pytest.raises(ValueError):
unique_labels([4, 0, 2], np.ones((5, 5)))
with pytest.raises(ValueError):
unique_labels(np.ones((5, 4)), np.ones((5, 5)))
assert_array_equal(unique_labels(np.ones((4, 5)), np.ones((5, 5))), np.arange(5))
def test_unique_labels_non_specific():
# Test unique_labels with a variety of collected examples
# Smoke test for all supported format
for format in ["binary", "multiclass", "multilabel-indicator"]:
for y in EXAMPLES[format]:
unique_labels(y)
# We don't support those format at the moment
for example in NON_ARRAY_LIKE_EXAMPLES:
with pytest.raises(ValueError):
unique_labels(example)
for y_type in [
"unknown",
"continuous",
"continuous-multioutput",
"multiclass-multioutput",
]:
for example in EXAMPLES[y_type]:
with pytest.raises(ValueError):
unique_labels(example)
def test_unique_labels_mixed_types():
# Mix with binary or multiclass and multilabel
mix_clf_format = product(
EXAMPLES["multilabel-indicator"], EXAMPLES["multiclass"] + EXAMPLES["binary"]
)
for y_multilabel, y_multiclass in mix_clf_format:
with pytest.raises(ValueError):
unique_labels(y_multiclass, y_multilabel)
with pytest.raises(ValueError):
unique_labels(y_multilabel, y_multiclass)
with pytest.raises(ValueError):
unique_labels([[1, 2]], [["a", "d"]])
with pytest.raises(ValueError):
unique_labels(["1", 2])
with pytest.raises(ValueError):
unique_labels([["1", 2], [1, 3]])
with pytest.raises(ValueError):
unique_labels([["1", "2"], [2, 3]])
def test_is_multilabel():
for group, group_examples in EXAMPLES.items():
dense_exp = group == "multilabel-indicator"
for example in group_examples:
# Only mark explicitly defined sparse examples as valid sparse
# multilabel-indicators
sparse_exp = dense_exp and issparse(example)
if issparse(example) or (
hasattr(example, "__array__")
and np.asarray(example).ndim == 2
and np.asarray(example).dtype.kind in "biuf"
and np.asarray(example).shape[1] > 0
):
examples_sparse = [
sparse_container(example)
for sparse_container in (
COO_CONTAINERS
+ CSC_CONTAINERS
+ CSR_CONTAINERS
+ DOK_CONTAINERS
+ LIL_CONTAINERS
)
]
for exmpl_sparse in examples_sparse:
assert sparse_exp == is_multilabel(
exmpl_sparse
), f"is_multilabel({exmpl_sparse!r}) should be {sparse_exp}"
# Densify sparse examples before testing
if issparse(example):
example = example.toarray()
assert dense_exp == is_multilabel(
example
), f"is_multilabel({example!r}) should be {dense_exp}"
@pytest.mark.parametrize(
"array_namespace, device, dtype_name",
yield_namespace_device_dtype_combinations(),
)
def test_is_multilabel_array_api_compliance(array_namespace, device, dtype_name):
xp = _array_api_for_tests(array_namespace, device)
for group, group_examples in ARRAY_API_EXAMPLES.items():
dense_exp = group == "multilabel-indicator"
for example in group_examples:
if np.asarray(example).dtype.kind == "f":
example = np.asarray(example, dtype=dtype_name)
else:
example = np.asarray(example)
example = xp.asarray(example, device=device)
with config_context(array_api_dispatch=True):
assert dense_exp == is_multilabel(
example
), f"is_multilabel({example!r}) should be {dense_exp}"
def test_check_classification_targets():
for y_type in EXAMPLES.keys():
if y_type in ["unknown", "continuous", "continuous-multioutput"]:
for example in EXAMPLES[y_type]:
msg = "Unknown label type: "
with pytest.raises(ValueError, match=msg):
check_classification_targets(example)
else:
for example in EXAMPLES[y_type]:
check_classification_targets(example)
def test_type_of_target():
for group, group_examples in EXAMPLES.items():
for example in group_examples:
assert (
type_of_target(example) == group
), "type_of_target(%r) should be %r, got %r" % (
example,
group,
type_of_target(example),
)
for example in NON_ARRAY_LIKE_EXAMPLES:
msg_regex = r"Expected array-like \(array or non-string sequence\).*"
with pytest.raises(ValueError, match=msg_regex):
type_of_target(example)
for example in MULTILABEL_SEQUENCES:
msg = (
"You appear to be using a legacy multi-label data "
"representation. Sequence of sequences are no longer supported;"
" use a binary array or sparse matrix instead."
)
with pytest.raises(ValueError, match=msg):
type_of_target(example)
def test_type_of_target_pandas_sparse():
pd = pytest.importorskip("pandas")
y = pd.arrays.SparseArray([1, np.nan, np.nan, 1, np.nan])
msg = "y cannot be class 'SparseSeries' or 'SparseArray'"
with pytest.raises(ValueError, match=msg):
type_of_target(y)
def test_type_of_target_pandas_nullable():
"""Check that type_of_target works with pandas nullable dtypes."""
pd = pytest.importorskip("pandas")
for dtype in ["Int32", "Float32"]:
y_true = pd.Series([1, 0, 2, 3, 4], dtype=dtype)
assert type_of_target(y_true) == "multiclass"
y_true = pd.Series([1, 0, 1, 0], dtype=dtype)
assert type_of_target(y_true) == "binary"
y_true = pd.DataFrame([[1.4, 3.1], [3.1, 1.4]], dtype="Float32")
assert type_of_target(y_true) == "continuous-multioutput"
y_true = pd.DataFrame([[0, 1], [1, 1]], dtype="Int32")
assert type_of_target(y_true) == "multilabel-indicator"
y_true = pd.DataFrame([[1, 2], [3, 1]], dtype="Int32")
assert type_of_target(y_true) == "multiclass-multioutput"
@pytest.mark.parametrize("dtype", ["Int64", "Float64", "boolean"])
def test_unique_labels_pandas_nullable(dtype):
"""Checks that unique_labels work with pandas nullable dtypes.
Non-regression test for gh-25634.
"""
pd = pytest.importorskip("pandas")
y_true = pd.Series([1, 0, 0, 1, 0, 1, 1, 0, 1], dtype=dtype)
y_predicted = pd.Series([0, 0, 1, 1, 0, 1, 1, 1, 1], dtype="int64")
labels = unique_labels(y_true, y_predicted)
assert_array_equal(labels, [0, 1])
@pytest.mark.parametrize("csc_container", CSC_CONTAINERS)
def test_class_distribution(csc_container):
y = np.array(
[
[1, 0, 0, 1],
[2, 2, 0, 1],
[1, 3, 0, 1],
[4, 2, 0, 1],
[2, 0, 0, 1],
[1, 3, 0, 1],
]
)
# Define the sparse matrix with a mix of implicit and explicit zeros
data = np.array([1, 2, 1, 4, 2, 1, 0, 2, 3, 2, 3, 1, 1, 1, 1, 1, 1])
indices = np.array([0, 1, 2, 3, 4, 5, 0, 1, 2, 3, 5, 0, 1, 2, 3, 4, 5])
indptr = np.array([0, 6, 11, 11, 17])
y_sp = csc_container((data, indices, indptr), shape=(6, 4))
classes, n_classes, class_prior = class_distribution(y)
classes_sp, n_classes_sp, class_prior_sp = class_distribution(y_sp)
classes_expected = [[1, 2, 4], [0, 2, 3], [0], [1]]
n_classes_expected = [3, 3, 1, 1]
class_prior_expected = [[3 / 6, 2 / 6, 1 / 6], [1 / 3, 1 / 3, 1 / 3], [1.0], [1.0]]
for k in range(y.shape[1]):
assert_array_almost_equal(classes[k], classes_expected[k])
assert_array_almost_equal(n_classes[k], n_classes_expected[k])
assert_array_almost_equal(class_prior[k], class_prior_expected[k])
assert_array_almost_equal(classes_sp[k], classes_expected[k])
assert_array_almost_equal(n_classes_sp[k], n_classes_expected[k])
assert_array_almost_equal(class_prior_sp[k], class_prior_expected[k])
# Test again with explicit sample weights
(classes, n_classes, class_prior) = class_distribution(
y, [1.0, 2.0, 1.0, 2.0, 1.0, 2.0]
)
(classes_sp, n_classes_sp, class_prior_sp) = class_distribution(
y, [1.0, 2.0, 1.0, 2.0, 1.0, 2.0]
)
class_prior_expected = [[4 / 9, 3 / 9, 2 / 9], [2 / 9, 4 / 9, 3 / 9], [1.0], [1.0]]
for k in range(y.shape[1]):
assert_array_almost_equal(classes[k], classes_expected[k])
assert_array_almost_equal(n_classes[k], n_classes_expected[k])
assert_array_almost_equal(class_prior[k], class_prior_expected[k])
assert_array_almost_equal(classes_sp[k], classes_expected[k])
assert_array_almost_equal(n_classes_sp[k], n_classes_expected[k])
assert_array_almost_equal(class_prior_sp[k], class_prior_expected[k])
def test_safe_split_with_precomputed_kernel():
clf = SVC()
clfp = SVC(kernel="precomputed")
iris = datasets.load_iris()
X, y = iris.data, iris.target
K = np.dot(X, X.T)
cv = ShuffleSplit(test_size=0.25, random_state=0)
train, test = list(cv.split(X))[0]
X_train, y_train = _safe_split(clf, X, y, train)
K_train, y_train2 = _safe_split(clfp, K, y, train)
assert_array_almost_equal(K_train, np.dot(X_train, X_train.T))
assert_array_almost_equal(y_train, y_train2)
X_test, y_test = _safe_split(clf, X, y, test, train)
K_test, y_test2 = _safe_split(clfp, K, y, test, train)
assert_array_almost_equal(K_test, np.dot(X_test, X_train.T))
assert_array_almost_equal(y_test, y_test2)
def test_ovr_decision_function():
# test properties for ovr decision function
predictions = np.array([[0, 1, 1], [0, 1, 0], [0, 1, 1], [0, 1, 1]])
confidences = np.array(
[[-1e16, 0, -1e16], [1.0, 2.0, -3.0], [-5.0, 2.0, 5.0], [-0.5, 0.2, 0.5]]
)
n_classes = 3
dec_values = _ovr_decision_function(predictions, confidences, n_classes)
# check that the decision values are within 0.5 range of the votes
votes = np.array([[1, 0, 2], [1, 1, 1], [1, 0, 2], [1, 0, 2]])
assert_allclose(votes, dec_values, atol=0.5)
# check that the prediction are what we expect
# highest vote or highest confidence if there is a tie.
# for the second sample we have a tie (should be won by 1)
expected_prediction = np.array([2, 1, 2, 2])
assert_array_equal(np.argmax(dec_values, axis=1), expected_prediction)
# third and fourth sample have the same vote but third sample
# has higher confidence, this should reflect on the decision values
assert dec_values[2, 2] > dec_values[3, 2]
# assert subset invariance.
dec_values_one = [
_ovr_decision_function(
np.array([predictions[i]]), np.array([confidences[i]]), n_classes
)[0]
for i in range(4)
]
assert_allclose(dec_values, dec_values_one, atol=1e-6)
# TODO(1.7): Change to ValueError when byte labels is deprecated.
@pytest.mark.parametrize("input_type", ["list", "array"])
def test_labels_in_bytes_format(input_type):
# check that we raise an error with bytes encoded labels
# non-regression test for:
# https://github.com/scikit-learn/scikit-learn/issues/16980
target = _convert_container([b"a", b"b"], input_type)
err_msg = (
"Support for labels represented as bytes is deprecated in v1.5 and will"
" error in v1.7. Convert the labels to a string or integer format."
)
with pytest.warns(FutureWarning, match=err_msg):
type_of_target(target)
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