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"""
Nearest Centroid Classification
"""
# Author: Robert Layton <robertlayton@gmail.com>
# Olivier Grisel <olivier.grisel@ensta.org>
#
# License: BSD 3 clause
import warnings
import numpy as np
from numbers import Real
from scipy import sparse as sp
from ..base import BaseEstimator, ClassifierMixin
from ..metrics.pairwise import pairwise_distances_argmin
from ..preprocessing import LabelEncoder
from ..utils.validation import check_is_fitted
from ..utils.sparsefuncs import csc_median_axis_0
from ..utils.multiclass import check_classification_targets
from ..utils._param_validation import Interval, StrOptions
from sklearn.metrics.pairwise import _VALID_METRICS
class NearestCentroid(ClassifierMixin, BaseEstimator):
"""Nearest centroid classifier.
Each class is represented by its centroid, with test samples classified to
the class with the nearest centroid.
Read more in the :ref:`User Guide <nearest_centroid_classifier>`.
Parameters
----------
metric : str or callable, default="euclidean"
Metric to use for distance computation. See the documentation of
`scipy.spatial.distance
<https://docs.scipy.org/doc/scipy/reference/spatial.distance.html>`_ and
the metrics listed in
:class:`~sklearn.metrics.pairwise.distance_metrics` for valid metric
values. Note that "wminkowski", "seuclidean" and "mahalanobis" are not
supported.
The centroids for the samples corresponding to each class is
the point from which the sum of the distances (according to the metric)
of all samples that belong to that particular class are minimized.
If the `"manhattan"` metric is provided, this centroid is the median
and for all other metrics, the centroid is now set to be the mean.
.. versionchanged:: 0.19
`metric='precomputed'` was deprecated and now raises an error
shrink_threshold : float, default=None
Threshold for shrinking centroids to remove features.
Attributes
----------
centroids_ : array-like of shape (n_classes, n_features)
Centroid of each class.
classes_ : array of shape (n_classes,)
The unique classes labels.
n_features_in_ : int
Number of features seen during :term:`fit`.
.. versionadded:: 0.24
feature_names_in_ : ndarray of shape (`n_features_in_`,)
Names of features seen during :term:`fit`. Defined only when `X`
has feature names that are all strings.
.. versionadded:: 1.0
See Also
--------
KNeighborsClassifier : Nearest neighbors classifier.
Notes
-----
When used for text classification with tf-idf vectors, this classifier is
also known as the Rocchio classifier.
References
----------
Tibshirani, R., Hastie, T., Narasimhan, B., & Chu, G. (2002). Diagnosis of
multiple cancer types by shrunken centroids of gene expression. Proceedings
of the National Academy of Sciences of the United States of America,
99(10), 6567-6572. The National Academy of Sciences.
Examples
--------
>>> from sklearn.neighbors import NearestCentroid
>>> import numpy as np
>>> X = np.array([[-1, -1], [-2, -1], [-3, -2], [1, 1], [2, 1], [3, 2]])
>>> y = np.array([1, 1, 1, 2, 2, 2])
>>> clf = NearestCentroid()
>>> clf.fit(X, y)
NearestCentroid()
>>> print(clf.predict([[-0.8, -1]]))
[1]
"""
_parameter_constraints: dict = {
"metric": [
StrOptions(
set(_VALID_METRICS) - {"mahalanobis", "seuclidean", "wminkowski"}
),
callable,
],
"shrink_threshold": [Interval(Real, 0, None, closed="neither"), None],
}
def __init__(self, metric="euclidean", *, shrink_threshold=None):
self.metric = metric
self.shrink_threshold = shrink_threshold
def fit(self, X, y):
"""
Fit the NearestCentroid model according to the given training data.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training vector, where `n_samples` is the number of samples and
`n_features` is the number of features.
Note that centroid shrinking cannot be used with sparse matrices.
y : array-like of shape (n_samples,)
Target values.
Returns
-------
self : object
Fitted estimator.
"""
self._validate_params()
# If X is sparse and the metric is "manhattan", store it in a csc
# format is easier to calculate the median.
if self.metric == "manhattan":
X, y = self._validate_data(X, y, accept_sparse=["csc"])
else:
X, y = self._validate_data(X, y, accept_sparse=["csr", "csc"])
is_X_sparse = sp.issparse(X)
if is_X_sparse and self.shrink_threshold:
raise ValueError("threshold shrinking not supported for sparse input")
check_classification_targets(y)
n_samples, n_features = X.shape
le = LabelEncoder()
y_ind = le.fit_transform(y)
self.classes_ = classes = le.classes_
n_classes = classes.size
if n_classes < 2:
raise ValueError(
"The number of classes has to be greater than one; got %d class"
% (n_classes)
)
# Mask mapping each class to its members.
self.centroids_ = np.empty((n_classes, n_features), dtype=np.float64)
# Number of clusters in each class.
nk = np.zeros(n_classes)
for cur_class in range(n_classes):
center_mask = y_ind == cur_class
nk[cur_class] = np.sum(center_mask)
if is_X_sparse:
center_mask = np.where(center_mask)[0]
# XXX: Update other averaging methods according to the metrics.
if self.metric == "manhattan":
# NumPy does not calculate median of sparse matrices.
if not is_X_sparse:
self.centroids_[cur_class] = np.median(X[center_mask], axis=0)
else:
self.centroids_[cur_class] = csc_median_axis_0(X[center_mask])
else:
if self.metric != "euclidean":
warnings.warn(
"Averaging for metrics other than "
"euclidean and manhattan not supported. "
"The average is set to be the mean."
)
self.centroids_[cur_class] = X[center_mask].mean(axis=0)
if self.shrink_threshold:
if np.all(np.ptp(X, axis=0) == 0):
raise ValueError("All features have zero variance. Division by zero.")
dataset_centroid_ = np.mean(X, axis=0)
# m parameter for determining deviation
m = np.sqrt((1.0 / nk) - (1.0 / n_samples))
# Calculate deviation using the standard deviation of centroids.
variance = (X - self.centroids_[y_ind]) ** 2
variance = variance.sum(axis=0)
s = np.sqrt(variance / (n_samples - n_classes))
s += np.median(s) # To deter outliers from affecting the results.
mm = m.reshape(len(m), 1) # Reshape to allow broadcasting.
ms = mm * s
deviation = (self.centroids_ - dataset_centroid_) / ms
# Soft thresholding: if the deviation crosses 0 during shrinking,
# it becomes zero.
signs = np.sign(deviation)
deviation = np.abs(deviation) - self.shrink_threshold
np.clip(deviation, 0, None, out=deviation)
deviation *= signs
# Now adjust the centroids using the deviation
msd = ms * deviation
self.centroids_ = dataset_centroid_[np.newaxis, :] + msd
return self
def predict(self, X):
"""Perform classification on an array of test vectors `X`.
The predicted class `C` for each sample in `X` is returned.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Test samples.
Returns
-------
C : ndarray of shape (n_samples,)
The predicted classes.
Notes
-----
If the metric constructor parameter is `"precomputed"`, `X` is assumed
to be the distance matrix between the data to be predicted and
`self.centroids_`.
"""
check_is_fitted(self)
X = self._validate_data(X, accept_sparse="csr", reset=False)
return self.classes_[
pairwise_distances_argmin(X, self.centroids_, metric=self.metric)
]
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