545 lines
18 KiB
Python
545 lines
18 KiB
Python
# Author: Arnaud Joly, Joel Nothman, Hamzeh Alsalhi
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#
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# License: BSD 3 clause
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"""
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Multi-class / multi-label utility function
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==========================================
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"""
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from collections.abc import Sequence
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from itertools import chain
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import warnings
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from scipy.sparse import issparse
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from scipy.sparse import dok_matrix
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from scipy.sparse import lil_matrix
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import numpy as np
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from .validation import check_array, _assert_all_finite
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from ..utils._array_api import get_namespace
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def _unique_multiclass(y):
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xp, is_array_api = get_namespace(y)
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if hasattr(y, "__array__") or is_array_api:
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return xp.unique_values(xp.asarray(y))
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else:
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return set(y)
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def _unique_indicator(y):
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return np.arange(
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check_array(y, input_name="y", accept_sparse=["csr", "csc", "coo"]).shape[1]
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)
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_FN_UNIQUE_LABELS = {
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"binary": _unique_multiclass,
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"multiclass": _unique_multiclass,
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"multilabel-indicator": _unique_indicator,
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}
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def unique_labels(*ys):
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"""Extract an ordered array of unique labels.
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We don't allow:
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- mix of multilabel and multiclass (single label) targets
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- mix of label indicator matrix and anything else,
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because there are no explicit labels)
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- mix of label indicator matrices of different sizes
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- mix of string and integer labels
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At the moment, we also don't allow "multiclass-multioutput" input type.
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Parameters
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----------
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*ys : array-likes
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Label values.
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Returns
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-------
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out : ndarray of shape (n_unique_labels,)
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An ordered array of unique labels.
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Examples
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--------
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>>> from sklearn.utils.multiclass import unique_labels
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>>> unique_labels([3, 5, 5, 5, 7, 7])
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array([3, 5, 7])
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>>> unique_labels([1, 2, 3, 4], [2, 2, 3, 4])
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array([1, 2, 3, 4])
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>>> unique_labels([1, 2, 10], [5, 11])
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array([ 1, 2, 5, 10, 11])
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"""
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xp, is_array_api = get_namespace(*ys)
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if not ys:
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raise ValueError("No argument has been passed.")
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# Check that we don't mix label format
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ys_types = set(type_of_target(x) for x in ys)
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if ys_types == {"binary", "multiclass"}:
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ys_types = {"multiclass"}
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if len(ys_types) > 1:
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raise ValueError("Mix type of y not allowed, got types %s" % ys_types)
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label_type = ys_types.pop()
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# Check consistency for the indicator format
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if (
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label_type == "multilabel-indicator"
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and len(
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set(
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check_array(y, accept_sparse=["csr", "csc", "coo"]).shape[1] for y in ys
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)
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)
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> 1
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):
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raise ValueError(
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"Multi-label binary indicator input with different numbers of labels"
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)
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# Get the unique set of labels
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_unique_labels = _FN_UNIQUE_LABELS.get(label_type, None)
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if not _unique_labels:
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raise ValueError("Unknown label type: %s" % repr(ys))
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if is_array_api:
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# array_api does not allow for mixed dtypes
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unique_ys = xp.concat([_unique_labels(y) for y in ys])
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return xp.unique_values(unique_ys)
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ys_labels = set(chain.from_iterable((i for i in _unique_labels(y)) for y in ys))
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# Check that we don't mix string type with number type
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if len(set(isinstance(label, str) for label in ys_labels)) > 1:
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raise ValueError("Mix of label input types (string and number)")
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return xp.asarray(sorted(ys_labels))
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def _is_integral_float(y):
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return y.dtype.kind == "f" and np.all(y.astype(int) == y)
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def is_multilabel(y):
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"""Check if ``y`` is in a multilabel format.
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Parameters
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----------
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y : ndarray of shape (n_samples,)
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Target values.
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Returns
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-------
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out : bool
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Return ``True``, if ``y`` is in a multilabel format, else ```False``.
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Examples
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--------
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>>> import numpy as np
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>>> from sklearn.utils.multiclass import is_multilabel
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>>> is_multilabel([0, 1, 0, 1])
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False
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>>> is_multilabel([[1], [0, 2], []])
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False
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>>> is_multilabel(np.array([[1, 0], [0, 0]]))
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True
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>>> is_multilabel(np.array([[1], [0], [0]]))
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False
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>>> is_multilabel(np.array([[1, 0, 0]]))
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True
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"""
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xp, is_array_api = get_namespace(y)
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if hasattr(y, "__array__") or isinstance(y, Sequence) or is_array_api:
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# DeprecationWarning will be replaced by ValueError, see NEP 34
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# https://numpy.org/neps/nep-0034-infer-dtype-is-object.html
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check_y_kwargs = dict(
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accept_sparse=True,
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allow_nd=True,
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force_all_finite=False,
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ensure_2d=False,
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ensure_min_samples=0,
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ensure_min_features=0,
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)
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with warnings.catch_warnings():
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warnings.simplefilter("error", np.VisibleDeprecationWarning)
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try:
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y = check_array(y, dtype=None, **check_y_kwargs)
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except (np.VisibleDeprecationWarning, ValueError) as e:
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if str(e).startswith("Complex data not supported"):
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raise
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# dtype=object should be provided explicitly for ragged arrays,
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# see NEP 34
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y = check_array(y, dtype=object, **check_y_kwargs)
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if not (hasattr(y, "shape") and y.ndim == 2 and y.shape[1] > 1):
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return False
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if issparse(y):
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if isinstance(y, (dok_matrix, lil_matrix)):
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y = y.tocsr()
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labels = xp.unique_values(y.data)
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return (
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len(y.data) == 0
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or (labels.size == 1 or (labels.size == 2) and (0 in labels))
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and (y.dtype.kind in "biu" or _is_integral_float(labels)) # bool, int, uint
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)
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else:
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labels = xp.unique_values(y)
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return len(labels) < 3 and (
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y.dtype.kind in "biu" or _is_integral_float(labels) # bool, int, uint
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)
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def check_classification_targets(y):
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"""Ensure that target y is of a non-regression type.
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Only the following target types (as defined in type_of_target) are allowed:
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'binary', 'multiclass', 'multiclass-multioutput',
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'multilabel-indicator', 'multilabel-sequences'
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Parameters
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----------
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y : array-like
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Target values.
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"""
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y_type = type_of_target(y, input_name="y")
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if y_type not in [
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"binary",
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"multiclass",
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"multiclass-multioutput",
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"multilabel-indicator",
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"multilabel-sequences",
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]:
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raise ValueError("Unknown label type: %r" % y_type)
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def type_of_target(y, input_name=""):
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"""Determine the type of data indicated by the target.
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Note that this type is the most specific type that can be inferred.
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For example:
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* ``binary`` is more specific but compatible with ``multiclass``.
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* ``multiclass`` of integers is more specific but compatible with
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``continuous``.
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* ``multilabel-indicator`` is more specific but compatible with
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``multiclass-multioutput``.
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Parameters
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----------
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y : {array-like, sparse matrix}
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Target values. If a sparse matrix, `y` is expected to be a
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CSR/CSC matrix.
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input_name : str, default=""
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The data name used to construct the error message.
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.. versionadded:: 1.1.0
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Returns
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-------
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target_type : str
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One of:
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* 'continuous': `y` is an array-like of floats that are not all
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integers, and is 1d or a column vector.
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* 'continuous-multioutput': `y` is a 2d array of floats that are
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not all integers, and both dimensions are of size > 1.
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* 'binary': `y` contains <= 2 discrete values and is 1d or a column
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vector.
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* 'multiclass': `y` contains more than two discrete values, is not a
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sequence of sequences, and is 1d or a column vector.
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* 'multiclass-multioutput': `y` is a 2d array that contains more
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than two discrete values, is not a sequence of sequences, and both
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dimensions are of size > 1.
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* 'multilabel-indicator': `y` is a label indicator matrix, an array
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of two dimensions with at least two columns, and at most 2 unique
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values.
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* 'unknown': `y` is array-like but none of the above, such as a 3d
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array, sequence of sequences, or an array of non-sequence objects.
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Examples
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--------
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>>> from sklearn.utils.multiclass import type_of_target
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>>> import numpy as np
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>>> type_of_target([0.1, 0.6])
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'continuous'
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>>> type_of_target([1, -1, -1, 1])
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'binary'
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>>> type_of_target(['a', 'b', 'a'])
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'binary'
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>>> type_of_target([1.0, 2.0])
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'binary'
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>>> type_of_target([1, 0, 2])
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'multiclass'
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>>> type_of_target([1.0, 0.0, 3.0])
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'multiclass'
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>>> type_of_target(['a', 'b', 'c'])
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'multiclass'
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>>> type_of_target(np.array([[1, 2], [3, 1]]))
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'multiclass-multioutput'
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>>> type_of_target([[1, 2]])
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'multilabel-indicator'
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>>> type_of_target(np.array([[1.5, 2.0], [3.0, 1.6]]))
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'continuous-multioutput'
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>>> type_of_target(np.array([[0, 1], [1, 1]]))
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'multilabel-indicator'
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"""
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xp, is_array_api = get_namespace(y)
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valid = (
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(isinstance(y, Sequence) or issparse(y) or hasattr(y, "__array__"))
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and not isinstance(y, str)
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or is_array_api
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)
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if not valid:
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raise ValueError(
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"Expected array-like (array or non-string sequence), got %r" % y
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)
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sparse_pandas = y.__class__.__name__ in ["SparseSeries", "SparseArray"]
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if sparse_pandas:
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raise ValueError("y cannot be class 'SparseSeries' or 'SparseArray'")
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if is_multilabel(y):
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return "multilabel-indicator"
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# DeprecationWarning will be replaced by ValueError, see NEP 34
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# https://numpy.org/neps/nep-0034-infer-dtype-is-object.html
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# We therefore catch both deprecation (NumPy < 1.24) warning and
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# value error (NumPy >= 1.24).
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check_y_kwargs = dict(
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accept_sparse=True,
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allow_nd=True,
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force_all_finite=False,
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ensure_2d=False,
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ensure_min_samples=0,
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ensure_min_features=0,
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)
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with warnings.catch_warnings():
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warnings.simplefilter("error", np.VisibleDeprecationWarning)
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if not issparse(y):
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try:
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y = check_array(y, dtype=None, **check_y_kwargs)
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except (np.VisibleDeprecationWarning, ValueError) as e:
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if str(e).startswith("Complex data not supported"):
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raise
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# dtype=object should be provided explicitly for ragged arrays,
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# see NEP 34
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y = check_array(y, dtype=object, **check_y_kwargs)
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# The old sequence of sequences format
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try:
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if (
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not hasattr(y[0], "__array__")
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and isinstance(y[0], Sequence)
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and not isinstance(y[0], str)
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):
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raise ValueError(
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"You appear to be using a legacy multi-label data"
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" representation. Sequence of sequences are no"
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" longer supported; use a binary array or sparse"
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" matrix instead - the MultiLabelBinarizer"
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" transformer can convert to this format."
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)
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except IndexError:
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pass
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# Invalid inputs
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if y.ndim not in (1, 2):
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# Number of dimension greater than 2: [[[1, 2]]]
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return "unknown"
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if not min(y.shape):
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# Empty ndarray: []/[[]]
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if y.ndim == 1:
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# 1-D empty array: []
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return "binary" # []
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# 2-D empty array: [[]]
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return "unknown"
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if not issparse(y) and y.dtype == object and not isinstance(y.flat[0], str):
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# [obj_1] and not ["label_1"]
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return "unknown"
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# Check if multioutput
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if y.ndim == 2 and y.shape[1] > 1:
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suffix = "-multioutput" # [[1, 2], [1, 2]]
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else:
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suffix = "" # [1, 2, 3] or [[1], [2], [3]]
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# Check float and contains non-integer float values
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if y.dtype.kind == "f":
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# [.1, .2, 3] or [[.1, .2, 3]] or [[1., .2]] and not [1., 2., 3.]
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data = y.data if issparse(y) else y
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if xp.any(data != data.astype(int)):
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_assert_all_finite(data, input_name=input_name)
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return "continuous" + suffix
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# Check multiclass
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first_row = y[0] if not issparse(y) else y.getrow(0).data
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if xp.unique_values(y).shape[0] > 2 or (y.ndim == 2 and len(first_row) > 1):
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# [1, 2, 3] or [[1., 2., 3]] or [[1, 2]]
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return "multiclass" + suffix
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else:
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return "binary" # [1, 2] or [["a"], ["b"]]
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def _check_partial_fit_first_call(clf, classes=None):
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"""Private helper function for factorizing common classes param logic.
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Estimators that implement the ``partial_fit`` API need to be provided with
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the list of possible classes at the first call to partial_fit.
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Subsequent calls to partial_fit should check that ``classes`` is still
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consistent with a previous value of ``clf.classes_`` when provided.
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This function returns True if it detects that this was the first call to
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``partial_fit`` on ``clf``. In that case the ``classes_`` attribute is also
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set on ``clf``.
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"""
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if getattr(clf, "classes_", None) is None and classes is None:
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raise ValueError("classes must be passed on the first call to partial_fit.")
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elif classes is not None:
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if getattr(clf, "classes_", None) is not None:
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if not np.array_equal(clf.classes_, unique_labels(classes)):
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raise ValueError(
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"`classes=%r` is not the same as on last call "
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"to partial_fit, was: %r" % (classes, clf.classes_)
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)
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else:
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# This is the first call to partial_fit
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clf.classes_ = unique_labels(classes)
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return True
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# classes is None and clf.classes_ has already previously been set:
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# nothing to do
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return False
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def class_distribution(y, sample_weight=None):
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"""Compute class priors from multioutput-multiclass target data.
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Parameters
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----------
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y : {array-like, sparse matrix} of size (n_samples, n_outputs)
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The labels for each example.
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sample_weight : array-like of shape (n_samples,), default=None
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Sample weights.
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Returns
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-------
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classes : list of size n_outputs of ndarray of size (n_classes,)
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List of classes for each column.
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n_classes : list of int of size n_outputs
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Number of classes in each column.
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class_prior : list of size n_outputs of ndarray of size (n_classes,)
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Class distribution of each column.
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"""
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classes = []
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n_classes = []
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class_prior = []
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n_samples, n_outputs = y.shape
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if sample_weight is not None:
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sample_weight = np.asarray(sample_weight)
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if issparse(y):
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y = y.tocsc()
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y_nnz = np.diff(y.indptr)
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for k in range(n_outputs):
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col_nonzero = y.indices[y.indptr[k] : y.indptr[k + 1]]
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# separate sample weights for zero and non-zero elements
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if sample_weight is not None:
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nz_samp_weight = sample_weight[col_nonzero]
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zeros_samp_weight_sum = np.sum(sample_weight) - np.sum(nz_samp_weight)
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else:
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nz_samp_weight = None
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zeros_samp_weight_sum = y.shape[0] - y_nnz[k]
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classes_k, y_k = np.unique(
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y.data[y.indptr[k] : y.indptr[k + 1]], return_inverse=True
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)
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class_prior_k = np.bincount(y_k, weights=nz_samp_weight)
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# An explicit zero was found, combine its weight with the weight
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# of the implicit zeros
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if 0 in classes_k:
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class_prior_k[classes_k == 0] += zeros_samp_weight_sum
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# If an there is an implicit zero and it is not in classes and
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# class_prior, make an entry for it
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if 0 not in classes_k and y_nnz[k] < y.shape[0]:
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classes_k = np.insert(classes_k, 0, 0)
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class_prior_k = np.insert(class_prior_k, 0, zeros_samp_weight_sum)
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classes.append(classes_k)
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n_classes.append(classes_k.shape[0])
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class_prior.append(class_prior_k / class_prior_k.sum())
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else:
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for k in range(n_outputs):
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classes_k, y_k = np.unique(y[:, k], return_inverse=True)
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classes.append(classes_k)
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n_classes.append(classes_k.shape[0])
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class_prior_k = np.bincount(y_k, weights=sample_weight)
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class_prior.append(class_prior_k / class_prior_k.sum())
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return (classes, n_classes, class_prior)
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def _ovr_decision_function(predictions, confidences, n_classes):
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"""Compute a continuous, tie-breaking OvR decision function from OvO.
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It is important to include a continuous value, not only votes,
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to make computing AUC or calibration meaningful.
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Parameters
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----------
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predictions : array-like of shape (n_samples, n_classifiers)
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Predicted classes for each binary classifier.
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confidences : array-like of shape (n_samples, n_classifiers)
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Decision functions or predicted probabilities for positive class
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for each binary classifier.
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n_classes : int
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Number of classes. n_classifiers must be
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``n_classes * (n_classes - 1 ) / 2``.
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"""
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n_samples = predictions.shape[0]
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votes = np.zeros((n_samples, n_classes))
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sum_of_confidences = np.zeros((n_samples, n_classes))
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k = 0
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for i in range(n_classes):
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for j in range(i + 1, n_classes):
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sum_of_confidences[:, i] -= confidences[:, k]
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sum_of_confidences[:, j] += confidences[:, k]
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votes[predictions[:, k] == 0, i] += 1
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votes[predictions[:, k] == 1, j] += 1
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k += 1
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# Monotonically transform the sum_of_confidences to (-1/3, 1/3)
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# and add it with votes. The monotonic transformation is
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# f: x -> x / (3 * (|x| + 1)), it uses 1/3 instead of 1/2
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# to ensure that we won't reach the limits and change vote order.
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# The motivation is to use confidence levels as a way to break ties in
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# the votes without switching any decision made based on a difference
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# of 1 vote.
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transformed_confidences = sum_of_confidences / (
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3 * (np.abs(sum_of_confidences) + 1)
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)
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return votes + transformed_confidences
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