Source code for sknetwork.clustering.propagation_clustering

#!/usr/bin/env python3
# coding: utf-8
Created on May, 2020
@author: Thomas Bonald <>
from typing import Union

import numpy as np
from scipy import sparse

from sknetwork.classification.propagation import Propagation
from sknetwork.clustering.base import BaseClustering
from sknetwork.utils.format import check_format, get_adjacency

[docs]class PropagationClustering(BaseClustering, Propagation): """Clustering by label propagation. Parameters ---------- n_iter : int Maximum number of iterations (-1 for infinity). node_order : str * `'random'`: node labels are updated in random order. * `'increasing'`: node labels are updated by increasing order of weight. * `'decreasing'`: node labels are updated by decreasing order of weight. * Otherwise, node labels are updated by index order. weighted : bool If ``True``, the vote of each neighbor is proportional to the edge weight. Otherwise, all votes have weight 1. sort_clusters : bool If ``True``, sort labels in decreasing order of cluster size. return_probs : bool If ``True``, return the probability distribution over clusters (soft clustering). return_aggregate : bool If ``True``, return the aggregate adjacency matrix or biadjacency matrix between clusters. Attributes ---------- labels_ : np.ndarray, shape (n_labels,) Label of each node. probs_ : sparse.csr_matrix, shape (n_row, n_labels) Probability distribution over labels. labels_row_, labels_col_ : np.ndarray Labels of rows and columns, for bipartite graphs. probs_row_, probs_col_ : sparse.csr_matrix, shape (n_row, n_labels) Probability distributions over labels for rows and columns (for bipartite graphs). aggregate_ : sparse.csr_matrix Aggregate adjacency matrix or biadjacency matrix between clusters. Example ------- >>> from sknetwork.clustering import PropagationClustering >>> from import karate_club >>> propagation = PropagationClustering() >>> graph = karate_club(metadata=True) >>> adjacency = graph.adjacency >>> labels = propagation.fit_predict(adjacency) >>> len(set(labels)) 2 References ---------- Raghavan, U. N., Albert, R., & Kumara, S. (2007). `Near linear time algorithm to detect community structures in large-scale networks. <>`_ Physical review E, 76(3), 036106. """ def __init__(self, n_iter: int = 5, node_order: str = 'decreasing', weighted: bool = True, sort_clusters: bool = True, return_probs: bool = True, return_aggregate: bool = True): Propagation.__init__(self, n_iter, node_order, weighted) BaseClustering.__init__(self, sort_clusters, return_probs, return_aggregate) self.bipartite = None
[docs] def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray]) -> 'PropagationClustering': """Clustering by label propagation. Parameters ---------- input_matrix : sparse.csr_matrix, np.ndarray Adjacency matrix or biadjacency matrix of the graph. Returns ------- self: :class:`PropagationClustering` """ self._init_vars() # input input_matrix = check_format(input_matrix) adjacency, bipartite = get_adjacency(input_matrix) # propagation, adjacency) # output _, self.labels_ = np.unique(self.labels_, return_inverse=True) if bipartite: self._split_vars(input_matrix.shape) self.bipartite = True self._secondary_outputs(input_matrix) return self