742 lines
26 KiB
Python
742 lines
26 KiB
Python
# Authors: Manoj Kumar <manojkumarsivaraj334@gmail.com>
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# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
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# Joel Nothman <joel.nothman@gmail.com>
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# License: BSD 3 clause
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import warnings
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from math import sqrt
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from numbers import Integral, Real
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import numpy as np
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from scipy import sparse
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from .._config import config_context
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from ..base import (
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BaseEstimator,
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ClassNamePrefixFeaturesOutMixin,
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ClusterMixin,
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TransformerMixin,
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_fit_context,
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)
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from ..exceptions import ConvergenceWarning
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from ..metrics import pairwise_distances_argmin
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from ..metrics.pairwise import euclidean_distances
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from ..utils._param_validation import Interval
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from ..utils.extmath import row_norms
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from ..utils.validation import check_is_fitted
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from . import AgglomerativeClustering
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def _iterate_sparse_X(X):
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"""This little hack returns a densified row when iterating over a sparse
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matrix, instead of constructing a sparse matrix for every row that is
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expensive.
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"""
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n_samples = X.shape[0]
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X_indices = X.indices
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X_data = X.data
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X_indptr = X.indptr
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for i in range(n_samples):
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row = np.zeros(X.shape[1])
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startptr, endptr = X_indptr[i], X_indptr[i + 1]
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nonzero_indices = X_indices[startptr:endptr]
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row[nonzero_indices] = X_data[startptr:endptr]
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yield row
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def _split_node(node, threshold, branching_factor):
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"""The node has to be split if there is no place for a new subcluster
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in the node.
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1. Two empty nodes and two empty subclusters are initialized.
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2. The pair of distant subclusters are found.
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3. The properties of the empty subclusters and nodes are updated
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according to the nearest distance between the subclusters to the
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pair of distant subclusters.
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4. The two nodes are set as children to the two subclusters.
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"""
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new_subcluster1 = _CFSubcluster()
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new_subcluster2 = _CFSubcluster()
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new_node1 = _CFNode(
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threshold=threshold,
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branching_factor=branching_factor,
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is_leaf=node.is_leaf,
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n_features=node.n_features,
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dtype=node.init_centroids_.dtype,
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)
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new_node2 = _CFNode(
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threshold=threshold,
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branching_factor=branching_factor,
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is_leaf=node.is_leaf,
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n_features=node.n_features,
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dtype=node.init_centroids_.dtype,
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)
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new_subcluster1.child_ = new_node1
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new_subcluster2.child_ = new_node2
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if node.is_leaf:
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if node.prev_leaf_ is not None:
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node.prev_leaf_.next_leaf_ = new_node1
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new_node1.prev_leaf_ = node.prev_leaf_
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new_node1.next_leaf_ = new_node2
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new_node2.prev_leaf_ = new_node1
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new_node2.next_leaf_ = node.next_leaf_
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if node.next_leaf_ is not None:
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node.next_leaf_.prev_leaf_ = new_node2
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dist = euclidean_distances(
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node.centroids_, Y_norm_squared=node.squared_norm_, squared=True
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)
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n_clusters = dist.shape[0]
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farthest_idx = np.unravel_index(dist.argmax(), (n_clusters, n_clusters))
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node1_dist, node2_dist = dist[(farthest_idx,)]
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node1_closer = node1_dist < node2_dist
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# make sure node1 is closest to itself even if all distances are equal.
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# This can only happen when all node.centroids_ are duplicates leading to all
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# distances between centroids being zero.
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node1_closer[farthest_idx[0]] = True
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for idx, subcluster in enumerate(node.subclusters_):
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if node1_closer[idx]:
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new_node1.append_subcluster(subcluster)
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new_subcluster1.update(subcluster)
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else:
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new_node2.append_subcluster(subcluster)
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new_subcluster2.update(subcluster)
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return new_subcluster1, new_subcluster2
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class _CFNode:
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"""Each node in a CFTree is called a CFNode.
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The CFNode can have a maximum of branching_factor
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number of CFSubclusters.
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Parameters
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----------
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threshold : float
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Threshold needed for a new subcluster to enter a CFSubcluster.
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branching_factor : int
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Maximum number of CF subclusters in each node.
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is_leaf : bool
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We need to know if the CFNode is a leaf or not, in order to
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retrieve the final subclusters.
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n_features : int
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The number of features.
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Attributes
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----------
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subclusters_ : list
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List of subclusters for a particular CFNode.
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prev_leaf_ : _CFNode
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Useful only if is_leaf is True.
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next_leaf_ : _CFNode
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next_leaf. Useful only if is_leaf is True.
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the final subclusters.
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init_centroids_ : ndarray of shape (branching_factor + 1, n_features)
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Manipulate ``init_centroids_`` throughout rather than centroids_ since
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the centroids are just a view of the ``init_centroids_`` .
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init_sq_norm_ : ndarray of shape (branching_factor + 1,)
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manipulate init_sq_norm_ throughout. similar to ``init_centroids_``.
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centroids_ : ndarray of shape (branching_factor + 1, n_features)
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View of ``init_centroids_``.
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squared_norm_ : ndarray of shape (branching_factor + 1,)
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View of ``init_sq_norm_``.
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"""
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def __init__(self, *, threshold, branching_factor, is_leaf, n_features, dtype):
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self.threshold = threshold
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self.branching_factor = branching_factor
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self.is_leaf = is_leaf
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self.n_features = n_features
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# The list of subclusters, centroids and squared norms
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# to manipulate throughout.
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self.subclusters_ = []
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self.init_centroids_ = np.zeros((branching_factor + 1, n_features), dtype=dtype)
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self.init_sq_norm_ = np.zeros((branching_factor + 1), dtype)
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self.squared_norm_ = []
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self.prev_leaf_ = None
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self.next_leaf_ = None
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def append_subcluster(self, subcluster):
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n_samples = len(self.subclusters_)
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self.subclusters_.append(subcluster)
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self.init_centroids_[n_samples] = subcluster.centroid_
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self.init_sq_norm_[n_samples] = subcluster.sq_norm_
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# Keep centroids and squared norm as views. In this way
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# if we change init_centroids and init_sq_norm_, it is
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# sufficient,
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self.centroids_ = self.init_centroids_[: n_samples + 1, :]
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self.squared_norm_ = self.init_sq_norm_[: n_samples + 1]
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def update_split_subclusters(self, subcluster, new_subcluster1, new_subcluster2):
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"""Remove a subcluster from a node and update it with the
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split subclusters.
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"""
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ind = self.subclusters_.index(subcluster)
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self.subclusters_[ind] = new_subcluster1
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self.init_centroids_[ind] = new_subcluster1.centroid_
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self.init_sq_norm_[ind] = new_subcluster1.sq_norm_
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self.append_subcluster(new_subcluster2)
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def insert_cf_subcluster(self, subcluster):
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"""Insert a new subcluster into the node."""
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if not self.subclusters_:
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self.append_subcluster(subcluster)
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return False
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threshold = self.threshold
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branching_factor = self.branching_factor
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# We need to find the closest subcluster among all the
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# subclusters so that we can insert our new subcluster.
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dist_matrix = np.dot(self.centroids_, subcluster.centroid_)
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dist_matrix *= -2.0
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dist_matrix += self.squared_norm_
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closest_index = np.argmin(dist_matrix)
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closest_subcluster = self.subclusters_[closest_index]
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# If the subcluster has a child, we need a recursive strategy.
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if closest_subcluster.child_ is not None:
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split_child = closest_subcluster.child_.insert_cf_subcluster(subcluster)
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if not split_child:
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# If it is determined that the child need not be split, we
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# can just update the closest_subcluster
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closest_subcluster.update(subcluster)
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self.init_centroids_[closest_index] = self.subclusters_[
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closest_index
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].centroid_
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self.init_sq_norm_[closest_index] = self.subclusters_[
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closest_index
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].sq_norm_
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return False
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# things not too good. we need to redistribute the subclusters in
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# our child node, and add a new subcluster in the parent
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# subcluster to accommodate the new child.
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else:
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new_subcluster1, new_subcluster2 = _split_node(
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closest_subcluster.child_,
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threshold,
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branching_factor,
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)
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self.update_split_subclusters(
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closest_subcluster, new_subcluster1, new_subcluster2
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)
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if len(self.subclusters_) > self.branching_factor:
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return True
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return False
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# good to go!
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else:
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merged = closest_subcluster.merge_subcluster(subcluster, self.threshold)
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if merged:
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self.init_centroids_[closest_index] = closest_subcluster.centroid_
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self.init_sq_norm_[closest_index] = closest_subcluster.sq_norm_
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return False
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# not close to any other subclusters, and we still
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# have space, so add.
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elif len(self.subclusters_) < self.branching_factor:
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self.append_subcluster(subcluster)
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return False
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# We do not have enough space nor is it closer to an
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# other subcluster. We need to split.
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else:
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self.append_subcluster(subcluster)
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return True
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class _CFSubcluster:
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"""Each subcluster in a CFNode is called a CFSubcluster.
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A CFSubcluster can have a CFNode has its child.
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Parameters
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----------
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linear_sum : ndarray of shape (n_features,), default=None
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Sample. This is kept optional to allow initialization of empty
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subclusters.
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Attributes
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----------
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n_samples_ : int
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Number of samples that belong to each subcluster.
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linear_sum_ : ndarray
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Linear sum of all the samples in a subcluster. Prevents holding
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all sample data in memory.
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squared_sum_ : float
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Sum of the squared l2 norms of all samples belonging to a subcluster.
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centroid_ : ndarray of shape (branching_factor + 1, n_features)
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Centroid of the subcluster. Prevent recomputing of centroids when
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``CFNode.centroids_`` is called.
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child_ : _CFNode
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Child Node of the subcluster. Once a given _CFNode is set as the child
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of the _CFNode, it is set to ``self.child_``.
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sq_norm_ : ndarray of shape (branching_factor + 1,)
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Squared norm of the subcluster. Used to prevent recomputing when
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pairwise minimum distances are computed.
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"""
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def __init__(self, *, linear_sum=None):
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if linear_sum is None:
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self.n_samples_ = 0
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self.squared_sum_ = 0.0
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self.centroid_ = self.linear_sum_ = 0
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else:
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self.n_samples_ = 1
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self.centroid_ = self.linear_sum_ = linear_sum
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self.squared_sum_ = self.sq_norm_ = np.dot(
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self.linear_sum_, self.linear_sum_
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)
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self.child_ = None
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def update(self, subcluster):
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self.n_samples_ += subcluster.n_samples_
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self.linear_sum_ += subcluster.linear_sum_
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self.squared_sum_ += subcluster.squared_sum_
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self.centroid_ = self.linear_sum_ / self.n_samples_
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self.sq_norm_ = np.dot(self.centroid_, self.centroid_)
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def merge_subcluster(self, nominee_cluster, threshold):
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"""Check if a cluster is worthy enough to be merged. If
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yes then merge.
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"""
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new_ss = self.squared_sum_ + nominee_cluster.squared_sum_
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new_ls = self.linear_sum_ + nominee_cluster.linear_sum_
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new_n = self.n_samples_ + nominee_cluster.n_samples_
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new_centroid = (1 / new_n) * new_ls
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new_sq_norm = np.dot(new_centroid, new_centroid)
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# The squared radius of the cluster is defined:
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# r^2 = sum_i ||x_i - c||^2 / n
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# with x_i the n points assigned to the cluster and c its centroid:
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# c = sum_i x_i / n
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# This can be expanded to:
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# r^2 = sum_i ||x_i||^2 / n - 2 < sum_i x_i / n, c> + n ||c||^2 / n
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# and therefore simplifies to:
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# r^2 = sum_i ||x_i||^2 / n - ||c||^2
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sq_radius = new_ss / new_n - new_sq_norm
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if sq_radius <= threshold**2:
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(
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self.n_samples_,
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self.linear_sum_,
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self.squared_sum_,
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self.centroid_,
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self.sq_norm_,
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) = (new_n, new_ls, new_ss, new_centroid, new_sq_norm)
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return True
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return False
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@property
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def radius(self):
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"""Return radius of the subcluster"""
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# Because of numerical issues, this could become negative
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sq_radius = self.squared_sum_ / self.n_samples_ - self.sq_norm_
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return sqrt(max(0, sq_radius))
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class Birch(
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ClassNamePrefixFeaturesOutMixin, ClusterMixin, TransformerMixin, BaseEstimator
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):
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"""Implements the BIRCH clustering algorithm.
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It is a memory-efficient, online-learning algorithm provided as an
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alternative to :class:`MiniBatchKMeans`. It constructs a tree
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data structure with the cluster centroids being read off the leaf.
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These can be either the final cluster centroids or can be provided as input
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to another clustering algorithm such as :class:`AgglomerativeClustering`.
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Read more in the :ref:`User Guide <birch>`.
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.. versionadded:: 0.16
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Parameters
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----------
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threshold : float, default=0.5
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The radius of the subcluster obtained by merging a new sample and the
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closest subcluster should be lesser than the threshold. Otherwise a new
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subcluster is started. Setting this value to be very low promotes
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splitting and vice-versa.
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branching_factor : int, default=50
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Maximum number of CF subclusters in each node. If a new samples enters
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such that the number of subclusters exceed the branching_factor then
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that node is split into two nodes with the subclusters redistributed
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in each. The parent subcluster of that node is removed and two new
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subclusters are added as parents of the 2 split nodes.
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n_clusters : int, instance of sklearn.cluster model or None, default=3
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Number of clusters after the final clustering step, which treats the
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subclusters from the leaves as new samples.
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- `None` : the final clustering step is not performed and the
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subclusters are returned as they are.
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- :mod:`sklearn.cluster` Estimator : If a model is provided, the model
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is fit treating the subclusters as new samples and the initial data
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is mapped to the label of the closest subcluster.
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- `int` : the model fit is :class:`AgglomerativeClustering` with
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`n_clusters` set to be equal to the int.
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compute_labels : bool, default=True
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Whether or not to compute labels for each fit.
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copy : bool, default=True
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Whether or not to make a copy of the given data. If set to False,
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the initial data will be overwritten.
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Attributes
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----------
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root_ : _CFNode
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Root of the CFTree.
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dummy_leaf_ : _CFNode
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Start pointer to all the leaves.
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subcluster_centers_ : ndarray
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Centroids of all subclusters read directly from the leaves.
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subcluster_labels_ : ndarray
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Labels assigned to the centroids of the subclusters after
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they are clustered globally.
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labels_ : ndarray of shape (n_samples,)
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Array of labels assigned to the input data.
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if partial_fit is used instead of fit, they are assigned to the
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last batch of data.
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n_features_in_ : int
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Number of features seen during :term:`fit`.
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.. versionadded:: 0.24
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feature_names_in_ : ndarray of shape (`n_features_in_`,)
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Names of features seen during :term:`fit`. Defined only when `X`
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has feature names that are all strings.
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.. versionadded:: 1.0
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See Also
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--------
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MiniBatchKMeans : Alternative implementation that does incremental updates
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of the centers' positions using mini-batches.
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Notes
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-----
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The tree data structure consists of nodes with each node consisting of
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a number of subclusters. The maximum number of subclusters in a node
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is determined by the branching factor. Each subcluster maintains a
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linear sum, squared sum and the number of samples in that subcluster.
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In addition, each subcluster can also have a node as its child, if the
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subcluster is not a member of a leaf node.
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For a new point entering the root, it is merged with the subcluster closest
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to it and the linear sum, squared sum and the number of samples of that
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subcluster are updated. This is done recursively till the properties of
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the leaf node are updated.
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References
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----------
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* Tian Zhang, Raghu Ramakrishnan, Maron Livny
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BIRCH: An efficient data clustering method for large databases.
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https://www.cs.sfu.ca/CourseCentral/459/han/papers/zhang96.pdf
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* Roberto Perdisci
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JBirch - Java implementation of BIRCH clustering algorithm
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https://code.google.com/archive/p/jbirch
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Examples
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--------
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>>> from sklearn.cluster import Birch
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>>> X = [[0, 1], [0.3, 1], [-0.3, 1], [0, -1], [0.3, -1], [-0.3, -1]]
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>>> brc = Birch(n_clusters=None)
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>>> brc.fit(X)
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Birch(n_clusters=None)
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>>> brc.predict(X)
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array([0, 0, 0, 1, 1, 1])
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"""
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_parameter_constraints: dict = {
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"threshold": [Interval(Real, 0.0, None, closed="neither")],
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"branching_factor": [Interval(Integral, 1, None, closed="neither")],
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"n_clusters": [None, ClusterMixin, Interval(Integral, 1, None, closed="left")],
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"compute_labels": ["boolean"],
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"copy": ["boolean"],
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}
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|
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def __init__(
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self,
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*,
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threshold=0.5,
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branching_factor=50,
|
|
n_clusters=3,
|
|
compute_labels=True,
|
|
copy=True,
|
|
):
|
|
self.threshold = threshold
|
|
self.branching_factor = branching_factor
|
|
self.n_clusters = n_clusters
|
|
self.compute_labels = compute_labels
|
|
self.copy = copy
|
|
|
|
@_fit_context(prefer_skip_nested_validation=True)
|
|
def fit(self, X, y=None):
|
|
"""
|
|
Build a CF Tree for the input data.
|
|
|
|
Parameters
|
|
----------
|
|
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
|
Input data.
|
|
|
|
y : Ignored
|
|
Not used, present here for API consistency by convention.
|
|
|
|
Returns
|
|
-------
|
|
self
|
|
Fitted estimator.
|
|
"""
|
|
return self._fit(X, partial=False)
|
|
|
|
def _fit(self, X, partial):
|
|
has_root = getattr(self, "root_", None)
|
|
first_call = not (partial and has_root)
|
|
|
|
X = self._validate_data(
|
|
X,
|
|
accept_sparse="csr",
|
|
copy=self.copy,
|
|
reset=first_call,
|
|
dtype=[np.float64, np.float32],
|
|
)
|
|
threshold = self.threshold
|
|
branching_factor = self.branching_factor
|
|
|
|
n_samples, n_features = X.shape
|
|
|
|
# If partial_fit is called for the first time or fit is called, we
|
|
# start a new tree.
|
|
if first_call:
|
|
# The first root is the leaf. Manipulate this object throughout.
|
|
self.root_ = _CFNode(
|
|
threshold=threshold,
|
|
branching_factor=branching_factor,
|
|
is_leaf=True,
|
|
n_features=n_features,
|
|
dtype=X.dtype,
|
|
)
|
|
|
|
# To enable getting back subclusters.
|
|
self.dummy_leaf_ = _CFNode(
|
|
threshold=threshold,
|
|
branching_factor=branching_factor,
|
|
is_leaf=True,
|
|
n_features=n_features,
|
|
dtype=X.dtype,
|
|
)
|
|
self.dummy_leaf_.next_leaf_ = self.root_
|
|
self.root_.prev_leaf_ = self.dummy_leaf_
|
|
|
|
# Cannot vectorize. Enough to convince to use cython.
|
|
if not sparse.issparse(X):
|
|
iter_func = iter
|
|
else:
|
|
iter_func = _iterate_sparse_X
|
|
|
|
for sample in iter_func(X):
|
|
subcluster = _CFSubcluster(linear_sum=sample)
|
|
split = self.root_.insert_cf_subcluster(subcluster)
|
|
|
|
if split:
|
|
new_subcluster1, new_subcluster2 = _split_node(
|
|
self.root_, threshold, branching_factor
|
|
)
|
|
del self.root_
|
|
self.root_ = _CFNode(
|
|
threshold=threshold,
|
|
branching_factor=branching_factor,
|
|
is_leaf=False,
|
|
n_features=n_features,
|
|
dtype=X.dtype,
|
|
)
|
|
self.root_.append_subcluster(new_subcluster1)
|
|
self.root_.append_subcluster(new_subcluster2)
|
|
|
|
centroids = np.concatenate([leaf.centroids_ for leaf in self._get_leaves()])
|
|
self.subcluster_centers_ = centroids
|
|
self._n_features_out = self.subcluster_centers_.shape[0]
|
|
|
|
self._global_clustering(X)
|
|
return self
|
|
|
|
def _get_leaves(self):
|
|
"""
|
|
Retrieve the leaves of the CF Node.
|
|
|
|
Returns
|
|
-------
|
|
leaves : list of shape (n_leaves,)
|
|
List of the leaf nodes.
|
|
"""
|
|
leaf_ptr = self.dummy_leaf_.next_leaf_
|
|
leaves = []
|
|
while leaf_ptr is not None:
|
|
leaves.append(leaf_ptr)
|
|
leaf_ptr = leaf_ptr.next_leaf_
|
|
return leaves
|
|
|
|
@_fit_context(prefer_skip_nested_validation=True)
|
|
def partial_fit(self, X=None, y=None):
|
|
"""
|
|
Online learning. Prevents rebuilding of CFTree from scratch.
|
|
|
|
Parameters
|
|
----------
|
|
X : {array-like, sparse matrix} of shape (n_samples, n_features), \
|
|
default=None
|
|
Input data. If X is not provided, only the global clustering
|
|
step is done.
|
|
|
|
y : Ignored
|
|
Not used, present here for API consistency by convention.
|
|
|
|
Returns
|
|
-------
|
|
self
|
|
Fitted estimator.
|
|
"""
|
|
if X is None:
|
|
# Perform just the final global clustering step.
|
|
self._global_clustering()
|
|
return self
|
|
else:
|
|
return self._fit(X, partial=True)
|
|
|
|
def _check_fit(self, X):
|
|
check_is_fitted(self)
|
|
|
|
if (
|
|
hasattr(self, "subcluster_centers_")
|
|
and X.shape[1] != self.subcluster_centers_.shape[1]
|
|
):
|
|
raise ValueError(
|
|
"Training data and predicted data do not have same number of features."
|
|
)
|
|
|
|
def predict(self, X):
|
|
"""
|
|
Predict data using the ``centroids_`` of subclusters.
|
|
|
|
Avoid computation of the row norms of X.
|
|
|
|
Parameters
|
|
----------
|
|
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
|
Input data.
|
|
|
|
Returns
|
|
-------
|
|
labels : ndarray of shape(n_samples,)
|
|
Labelled data.
|
|
"""
|
|
check_is_fitted(self)
|
|
X = self._validate_data(X, accept_sparse="csr", reset=False)
|
|
return self._predict(X)
|
|
|
|
def _predict(self, X):
|
|
"""Predict data using the ``centroids_`` of subclusters."""
|
|
kwargs = {"Y_norm_squared": self._subcluster_norms}
|
|
|
|
with config_context(assume_finite=True):
|
|
argmin = pairwise_distances_argmin(
|
|
X, self.subcluster_centers_, metric_kwargs=kwargs
|
|
)
|
|
return self.subcluster_labels_[argmin]
|
|
|
|
def transform(self, X):
|
|
"""
|
|
Transform X into subcluster centroids dimension.
|
|
|
|
Each dimension represents the distance from the sample point to each
|
|
cluster centroid.
|
|
|
|
Parameters
|
|
----------
|
|
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
|
Input data.
|
|
|
|
Returns
|
|
-------
|
|
X_trans : {array-like, sparse matrix} of shape (n_samples, n_clusters)
|
|
Transformed data.
|
|
"""
|
|
check_is_fitted(self)
|
|
X = self._validate_data(X, accept_sparse="csr", reset=False)
|
|
with config_context(assume_finite=True):
|
|
return euclidean_distances(X, self.subcluster_centers_)
|
|
|
|
def _global_clustering(self, X=None):
|
|
"""
|
|
Global clustering for the subclusters obtained after fitting
|
|
"""
|
|
clusterer = self.n_clusters
|
|
centroids = self.subcluster_centers_
|
|
compute_labels = (X is not None) and self.compute_labels
|
|
|
|
# Preprocessing for the global clustering.
|
|
not_enough_centroids = False
|
|
if isinstance(clusterer, Integral):
|
|
clusterer = AgglomerativeClustering(n_clusters=self.n_clusters)
|
|
# There is no need to perform the global clustering step.
|
|
if len(centroids) < self.n_clusters:
|
|
not_enough_centroids = True
|
|
|
|
# To use in predict to avoid recalculation.
|
|
self._subcluster_norms = row_norms(self.subcluster_centers_, squared=True)
|
|
|
|
if clusterer is None or not_enough_centroids:
|
|
self.subcluster_labels_ = np.arange(len(centroids))
|
|
if not_enough_centroids:
|
|
warnings.warn(
|
|
"Number of subclusters found (%d) by BIRCH is less "
|
|
"than (%d). Decrease the threshold."
|
|
% (len(centroids), self.n_clusters),
|
|
ConvergenceWarning,
|
|
)
|
|
else:
|
|
# The global clustering step that clusters the subclusters of
|
|
# the leaves. It assumes the centroids of the subclusters as
|
|
# samples and finds the final centroids.
|
|
self.subcluster_labels_ = clusterer.fit_predict(self.subcluster_centers_)
|
|
|
|
if compute_labels:
|
|
self.labels_ = self._predict(X)
|
|
|
|
def _more_tags(self):
|
|
return {"preserves_dtype": [np.float64, np.float32]}
|