scikit-network 0.33.4__cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

sknetwork/clustering/leiden.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created in March 2024
+@author: Thomas Bonald <bonald@enst.fr>
+@author: Ahmed Zaiou <ahmed.zaiou@capgemini.com>
+"""
+from typing import Union, Optional
+
+import numpy as np
+from scipy import sparse
+
+from sknetwork.clustering import Louvain
+from sknetwork.clustering.louvain_core import optimize_core
+from sknetwork.clustering.leiden_core import optimize_refine_core
+from sknetwork.utils.membership import get_membership
+from sknetwork.utils.check import check_random_state
+from sknetwork.log import Log
+
+
+class Leiden(Louvain):
+    """Leiden algorithm for clustering graphs by maximization of modularity.
+    Compared to the Louvain algorithm, the partition is refined before each aggregation.
+
+    For bipartite graphs, the algorithm maximizes Barber's modularity by default.
+
+    Parameters
+    ----------
+    resolution :
+        Resolution parameter.
+    modularity : str
+        Type of modularity to maximize. Can be ``'Dugue'``, ``'Newman'`` or ``'Potts'`` (default = ``'dugue'``).
+    tol_optimization :
+        Minimum increase in modularity to enter a new optimization pass in the local search.
+    tol_aggregation :
+        Minimum increase in modularity to enter a new aggregation pass.
+    n_aggregations :
+        Maximum number of aggregations.
+        A negative value is interpreted as no limit.
+    shuffle_nodes :
+        Enables node shuffling before optimization.
+    sort_clusters :
+        If ``True``, sort labels in decreasing order of cluster size.
+    return_probs :
+        If ``True``, return the probability distribution over clusters (soft clustering).
+    return_aggregate :
+        If ``True``, return the adjacency matrix of the graph between clusters.
+    random_state :
+        Random number generator or random seed. If None, numpy.random is used.
+    verbose :
+        Verbose mode.
+
+    Attributes
+    ----------
+    labels\_ : np.ndarray, shape (n_nodes,)
+        Label of each node.
+    probs\_ : sparse.csr_matrix, shape (n_nodes, n_labels)
+        Probability distribution over labels.
+    aggregate\_ : sparse.csr_matrix
+        Aggregate adjacency matrix or biadjacency matrix between clusters.
+
+    Example
+    -------
+    >>> from sknetwork.clustering import Leiden
+    >>> from sknetwork.data import karate_club
+    >>> leiden = Leiden()
+    >>> adjacency = karate_club()
+    >>> labels = leiden.fit_predict(adjacency)
+    >>> len(set(labels))
+    4
+
+    References
+    ----------
+    * Traag, V. A., Waltman, L., & Van Eck, N. J. (2019).
+      `From Louvain to Leiden: guaranteeing well-connected communities`, Scientific reports.
+
+    """
+
+    def __init__(self, resolution: float = 1, modularity: str = 'dugue', tol_optimization: float = 1e-3,
+                 tol_aggregation: float = 1e-3, n_aggregations: int = -1, shuffle_nodes: bool = False,
+                 sort_clusters: bool = True, return_probs: bool = True, return_aggregate: bool = True,
+                 random_state: Optional[Union[np.random.RandomState, int]] = None, verbose: bool = False):
+        super(Leiden, self).__init__(sort_clusters=sort_clusters, return_probs=return_probs,
+                                     return_aggregate=return_aggregate)
+        Log.__init__(self, verbose)
+
+        self.labels_ = None
+        self.resolution = resolution
+        self.modularity = modularity.lower()
+        self.tol_optimization = tol_optimization
+        self.tol_aggregation = tol_aggregation
+        self.n_aggregations = n_aggregations
+        self.shuffle_nodes = shuffle_nodes
+        self.random_state = check_random_state(random_state)
+        self.bipartite = None
+
+    def _optimize(self, labels, adjacency, out_weights, in_weights):
+        """One optimization pass of the Leiden algorithm.
+
+        Parameters
+        ----------
+        labels :
+            Labels of nodes.
+        adjacency :
+            Adjacency matrix.
+        out_weights :
+            Out-weights of nodes.
+        in_weights :
+            In-weights of nodes
+
+        Returns
+        -------
+        labels :
+            Labels of nodes after optimization.
+        increase :
+            Gain in modularity after optimization.
+        """
+        indices = adjacency.indices
+        indptr = adjacency.indptr
+        data = adjacency.data.astype(np.float32)
+        out_weights = out_weights.astype(np.float32)
+        in_weights = in_weights.astype(np.float32)
+        membership = get_membership(labels)
+        out_cluster_weights = membership.T.dot(out_weights)
+        in_cluster_weights = membership.T.dot(in_weights)
+        cluster_weights = np.zeros_like(out_cluster_weights).astype(np.float32)
+        labels = labels.astype(np.int32)
+        self_loops = adjacency.diagonal().astype(np.float32)
+        return optimize_core(labels, indices, indptr, data, out_weights, in_weights, out_cluster_weights,
+                             in_cluster_weights, cluster_weights, self_loops, self.resolution, self.tol_optimization)
+
+    def _optimize_refine(self, labels, labels_refined, adjacency, out_weights, in_weights):
+        """Get the refined partition optimizing modularity.
+
+        Parameters
+        ----------
+        labels :
+            Labels of nodes.
+        labels_refined :
+            Refined labels of nodes.
+        adjacency :
+            Adjacency matrix.
+        out_weights :
+            Out-weights of nodes.
+        in_weights :
+            In-weights of nodes
+
+        Returns
+        -------
+        labels_refined :
+            Refined labels of nodes.
+        """
+        indices = adjacency.indices
+        indptr = adjacency.indptr
+        data = adjacency.data.astype(np.float32)
+        out_weights = out_weights.astype(np.float32)
+        in_weights = in_weights.astype(np.float32)
+        membership = get_membership(labels_refined)
+        out_cluster_weights = membership.T.dot(out_weights)
+        in_cluster_weights = membership.T.dot(in_weights)
+        cluster_weights = np.zeros_like(out_cluster_weights).astype(np.float32)
+        self_loops = adjacency.diagonal().astype(np.float32)
+        labels = labels.astype(np.int32)
+        labels_refined = labels_refined.astype(np.int32)
+        return optimize_refine_core(labels, labels_refined, indices, indptr, data, out_weights, in_weights,
+                                    out_cluster_weights, in_cluster_weights, cluster_weights, self_loops,
+                                    self.resolution)
+
+    @staticmethod
+    def _aggregate_refine(labels, labels_refined, adjacency, out_weights, in_weights):
+        """Aggregate nodes according to refined labels.
+
+        Parameters
+        ----------
+        labels :
+            Labels of nodes.
+        labels_refined :
+            Refined labels of nodes.
+        adjacency :
+            Adjacency matrix.
+        out_weights :
+            Out-weights of nodes.
+        in_weights :
+            In-weights of nodes.
+
+        Returns
+        -------
+        Aggregate graph (labels, adjacency matrix, out-weights, in-weights).
+        """
+        membership = get_membership(labels)
+        membership_refined = get_membership(labels_refined)
+        adjacency_ = membership_refined.T.tocsr().dot(adjacency.dot(membership_refined))
+        out_weights_ = membership_refined.T.dot(out_weights)
+        in_weights_ = membership_refined.T.dot(in_weights)
+        labels_ = membership_refined.T.tocsr().dot(membership).indices
+        return labels_, adjacency_, out_weights_, in_weights_
+
+    def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], force_bipartite: bool = False) -> 'Leiden':
+        """Fit algorithm to data.
+
+        Parameters
+        ----------
+        input_matrix :
+            Adjacency matrix or biadjacency matrix of the graph.
+        force_bipartite :
+            If ``True``, force the input matrix to be considered as a biadjacency matrix even if square.
+
+        Returns
+        -------
+        self : :class:`Leiden`
+        """
+        adjacency, out_weights, in_weights, membership, index = self._pre_processing(input_matrix, force_bipartite)
+        n = adjacency.shape[0]
+        labels = np.arange(n)
+        count = 0
+        stop = False
+        while not stop:
+            count += 1
+            labels, increase = self._optimize(labels, adjacency, out_weights, in_weights)
+            _, labels = np.unique(labels, return_inverse=True)
+            labels_original = labels.copy()
+            labels_refined = np.arange(len(labels))
+            labels_refined = self._optimize_refine(labels, labels_refined, adjacency, out_weights, in_weights)
+            _, labels_refined = np.unique(labels_refined, return_inverse=True)
+            labels, adjacency, out_weights, in_weights = self._aggregate_refine(labels, labels_refined, adjacency,
+                                                                                out_weights, in_weights)
+            n = adjacency.shape[0]
+            stop = n == 1
+            stop |= increase <= self.tol_aggregation
+            stop |= count == self.n_aggregations
+            if stop:
+                membership = membership.dot(get_membership(labels_original))
+            else:
+                membership = membership.dot(get_membership(labels_refined))
+            self.print_log("Aggregation:", count, " Clusters:", n, " Increase:", increase)
+
+        self._post_processing(input_matrix, membership, index)
+        return self