scikit-network 0.30.0__cp39-cp39-win_amd64.whl → 0.32.1__cp39-cp39-win_amd64.whl

sknetwork/clustering/leiden_core.pyx

@@ -0,0 +1,124 @@
+# distutils: language=c++
+# cython: language_level=3
+from libcpp.set cimport set
+from libc.stdlib cimport rand
+
+cimport cython
+
+ctypedef fused int_or_long:
+    int
+    long
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+def optimize_refine_core(int_or_long[:] labels, int_or_long[:] labels_refined, int_or_long[:] indices,
+    int_or_long[:] indptr, float[:] data, float[:] out_weights, float[:] in_weights, float[:] out_cluster_weights,
+    float[:] in_cluster_weights, float[:] cluster_weights, float[:] self_loops, float resolution):  # pragma: no cover
+    """Refine clusters while maximizing modularity.
+
+    Parameters
+    ----------
+    labels :
+        Labels (initial partition).
+    labels_refined :
+        Refined labels.
+    indices :
+        CSR format index array of the normalized adjacency matrix.
+    indptr :
+        CSR format index pointer array of the normalized adjacency matrix.
+    data :
+        CSR format data array of the normalized adjacency matrix.
+    out_weights :
+        Out-weights of nodes (sum to 1).
+    in_weights :
+        In-weights of nodes (sum to 1).
+    out_cluster_weights :
+        Out-weights of clusters (sum to 1).
+    in_cluster_weights :
+        In-weights of clusters (sum to 1).
+    cluster_weights :
+        Weights of clusters (initialized to 0).
+    self_loops :
+        Weights of self loops.
+    resolution :
+        Resolution parameter (positive).
+
+    Returns
+    -------
+    labels_refined :
+        Refined labels.
+    """
+    cdef int_or_long n
+    cdef int_or_long label
+    cdef int_or_long label_refined
+    cdef int_or_long label_target
+    cdef int_or_long label_best
+    cdef int_or_long i
+    cdef int_or_long j
+    cdef int_or_long start
+    cdef int_or_long end
+
+    cdef float increase = 1
+    cdef float delta
+    cdef float delta_local
+    cdef float delta_best
+    cdef float in_weight
+    cdef float out_weight
+
+    cdef set[int_or_long] label_set
+    cdef set[int_or_long] label_target_set
+
+    n = labels.shape[0]
+    while increase:
+        increase = 0
+
+        for i in range(n):
+            label_set = ()
+            label = labels[i]
+            label_refined = labels_refined[i]
+            start = indptr[i]
+            end = indptr[i+1]
+
+            # neighboring clusters
+            for j in range(start, end):
+                if labels[indices[j]] == label:
+                    label_target = labels_refined[indices[j]]
+                    label_set.insert(label_target)
+                    cluster_weights[label_target] += data[j]
+            label_set.erase(label_refined)
+
+            if not label_set.empty():
+                out_weight = out_weights[i]
+                in_weight = in_weights[i]
+
+                # node leaving the current cluster
+                delta = 2 * (cluster_weights[label_refined] - self_loops[i])
+                delta -= resolution * out_weight * (in_cluster_weights[label_refined] - in_weight)
+                delta -= resolution * in_weight * (out_cluster_weights[label_refined] - out_weight)
+
+                label_target_set = ()
+                for label_target in label_set:
+                    delta_local = 2 * cluster_weights[label_target]
+                    delta_local -= resolution * out_weight * in_cluster_weights[label_target]
+                    delta_local -= resolution * in_weight * out_cluster_weights[label_target]
+                    delta_local -= delta
+                    if delta_local > 0:
+                        label_target_set.insert(label_target)
+                    cluster_weights[label_target] = 0
+
+                if not label_target_set.empty():
+                    increase = 1
+                    k = rand() % label_target_set.size()
+                    for label_target in label_target_set:
+                        k -= 1
+                        if k == 0:
+                            break
+                    labels_refined[i] = label_target
+                    # update weights
+                    out_cluster_weights[label_refined] -= out_weight
+                    in_cluster_weights[label_refined] -= in_weight
+                    out_cluster_weights[label_target] += out_weight
+                    in_cluster_weights[label_target] += in_weight
+            cluster_weights[label_refined] = 0
+
+    return labels_refined

sknetwork/clustering/louvain.py

@@ -12,15 +12,15 @@ import numpy as np
 from scipy import sparse
 
 from sknetwork.clustering.base import BaseClustering
-from sknetwork.clustering.louvain_core import fit_core
+from sknetwork.clustering.louvain_core import optimize_core
 from sknetwork.clustering.postprocess import reindex_labels
 from sknetwork.utils.check import check_random_state, get_probs
 from sknetwork.utils.format import check_format, get_adjacency, directed2undirected
 from sknetwork.utils.membership import get_membership
-from sknetwork.utils.verbose import VerboseMixin
+from sknetwork.log import Log
 
 
-class Louvain(BaseClustering, VerboseMixin):
+class Louvain(BaseClustering, Log):
     """Louvain algorithm for clustering graphs by maximization of modularity.
 
     For bipartite graphs, the algorithm maximizes Barber's modularity by default.
@@ -30,11 +30,11 @@ class Louvain(BaseClustering, VerboseMixin):
     resolution :
         Resolution parameter.
     modularity : str
-        Which objective function to maximize. Can be ``'Dugue'``, ``'Newman'`` or ``'Potts'`` (default = ``'dugue'``).
+        Type of modularity to maximize. Can be ``'Dugue'``, ``'Newman'`` or ``'Potts'`` (default = ``'dugue'``).
     tol_optimization :
-        Minimum increase in the objective function to enter a new optimization pass.
+        Minimum increase in modularity to enter a new optimization pass in the local search.
     tol_aggregation :
-        Minimum increase in the objective function to enter a new aggregation pass.
+        Minimum increase in modularity to enter a new aggregation pass.
     n_aggregations :
         Maximum number of aggregations.
         A negative value is interpreted as no limit.
@@ -42,8 +42,8 @@ class Louvain(BaseClustering, VerboseMixin):
         Enables node shuffling before optimization.
     sort_clusters :
         If ``True``, sort labels in decreasing order of cluster size.
-    return_membership :
-        If ``True``, return the membership matrix of nodes to each cluster (soft clustering).
+    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 :
@@ -53,18 +53,14 @@ class Louvain(BaseClustering, VerboseMixin):
 
     Attributes
     ----------
-    labels_ : np.ndarray
-        Labels of the nodes.
-    labels_row_ : np.ndarray
-        Labels of the rows (for bipartite graphs).
-    labels_col_ : np.ndarray
-        Labels of the columns (for bipartite graphs).
-    membership_ : sparse.csr_matrix
-        Membership matrix of the nodes, shape (n_nodes, n_clusters).
-    membership_row_ : sparse.csr_matrix
-        Membership matrix of the rows (for bipartite graphs).
-    membership_col_ : sparse.csr_matrix
-        Membership matrix of the columns (for bipartite graphs).
+    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.
 
@@ -95,84 +91,88 @@ class Louvain(BaseClustering, VerboseMixin):
       <https://arxiv.org/pdf/0707.1616>`_
       Physical Review E, 76(6).
     """
+
     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_membership: bool = True, return_aggregate: bool = True,
+                 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(Louvain, self).__init__(sort_clusters=sort_clusters, return_membership=return_membership,
+        super(Louvain, self).__init__(sort_clusters=sort_clusters, return_probs=return_probs,
                                       return_aggregate=return_aggregate)
-        VerboseMixin.__init__(self, verbose)
+        Log.__init__(self, verbose)
 
         self.labels_ = None
         self.resolution = resolution
         self.modularity = modularity.lower()
-        self.tol = tol_optimization
+        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, adjacency_norm, probs_ou, probs_in):
-        """One local optimization pass of the Louvain algorithm
+    def _optimize(self, labels, adjacency, out_weights, in_weights):
+        """One optimization pass of the Louvain algorithm.
 
         Parameters
         ----------
-        adjacency_norm :
-            the norm of the adjacency
-        probs_ou :
-            the array of degrees of the adjacency
-        probs_in :
-            the array of degrees of the transpose of the adjacency
+        labels :
+            Labels of nodes.
+        adjacency :
+            Adjacency matrix.
+        out_weights :
+            Out-weights of nodes.
+        in_weights :
+            In-weights of nodes
 
         Returns
         -------
         labels :
-            the communities of each node after optimization
-        pass_increase :
-            the increase in modularity gained after optimization
+            Labels of nodes after optimization.
+        increase :
+            Gain in modularity after optimization.
         """
-        node_probs_in = probs_in.astype(np.float32)
-        node_probs_ou = probs_ou.astype(np.float32)
-
-        adjacency = 0.5 * directed2undirected(adjacency_norm)
-
+        labels = labels.astype(np.int32)
+        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)
+        out_cluster_weights = out_weights.copy()
+        in_cluster_weights = in_weights.copy()
+        cluster_weights = np.zeros_like(out_cluster_weights).astype(np.float32)
         self_loops = adjacency.diagonal().astype(np.float32)
-
-        indptr: np.ndarray = adjacency.indptr
-        indices: np.ndarray = adjacency.indices
-        data: np.ndarray = adjacency.data.astype(np.float32)
-
-        return fit_core(self.resolution, self.tol, node_probs_ou, node_probs_in, self_loops, data, indices, indptr)
+        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)
 
     @staticmethod
-    def _aggregate(adjacency_norm, probs_out, probs_in, membership: Union[sparse.csr_matrix, np.ndarray]):
+    def _aggregate(labels, adjacency, out_weights, in_weights):
         """Aggregate nodes belonging to the same cluster.
 
         Parameters
         ----------
-        adjacency_norm :
-            the norm of the adjacency
-        probs_out :
-            the array of degrees of the adjacency
-        probs_in :
-            the array of degrees of the transpose of the adjacency
-        membership :
-            membership matrix (rows).
+        labels :
+            Labels of nodes.
+        adjacency :
+            Adjacency matrix.
+        out_weights :
+            Out-weights of nodes.
+        in_weights :
+            In-weights of nodes.
 
         Returns
         -------
-        Aggregate graph.
+        Aggregate graph (adjacency matrix, out-weights, in-weights).
         """
-        adjacency_norm = (membership.T.dot(adjacency_norm.dot(membership))).tocsr()
-        probs_in = np.array(membership.T.dot(probs_in).T)
-        probs_out = np.array(membership.T.dot(probs_out).T)
-        return adjacency_norm, probs_out, probs_in
+        membership = get_membership(labels)
+        adjacency_ = membership.T.tocsr().dot(adjacency.dot(membership))
+        out_weights_ = membership.T.dot(out_weights)
+        in_weights_ = membership.T.dot(in_weights)
+        return adjacency_, out_weights_, in_weights_
 
-    def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], force_bipartite: bool = False) -> 'Louvain':
-        """Fit algorithm to data.
+    def _pre_processing(self, input_matrix, force_bipartite):
+        """Pre-processing for Louvain.
 
-        Parameters
+         Parameters
         ----------
         input_matrix :
             Adjacency matrix or biadjacency matrix of the graph.
@@ -181,63 +181,64 @@ class Louvain(BaseClustering, VerboseMixin):
 
         Returns
         -------
-        self: :class:`Louvain`
+        adjacency :
+            Adjacency matrix.
+        out_weights, in_weights :
+            Node weights.
+        membership :
+            Membership matrix (labels).
+        index :
+            Index of nodes.
         """
         self._init_vars()
+
+        # adjacency matrix
         input_matrix = check_format(input_matrix)
-        if self.modularity == 'dugue':
-            adjacency, self.bipartite = get_adjacency(input_matrix, force_directed=True,
-                                                      force_bipartite=force_bipartite)
-        else:
-            adjacency, self.bipartite = get_adjacency(input_matrix, force_bipartite=force_bipartite)
+        force_directed = self.modularity == 'dugue'
+        adjacency, self.bipartite = get_adjacency(input_matrix, force_directed=force_directed,
+                                                  force_bipartite=force_bipartite)
 
+        # shuffling
         n = adjacency.shape[0]
-
         index = np.arange(n)
         if self.shuffle_nodes:
             index = self.random_state.permutation(index)
             adjacency = adjacency[index][:, index]
 
+        # node weights
         if self.modularity == 'potts':
-            probs_out = get_probs('uniform', adjacency)
-            probs_in = probs_out.copy()
+            out_weights = get_probs('uniform', adjacency)
+            in_weights = out_weights.copy()
         elif self.modularity == 'newman':
-            probs_out = get_probs('degree', adjacency)
-            probs_in = probs_out.copy()
+            out_weights = get_probs('degree', adjacency)
+            in_weights = out_weights.copy()
         elif self.modularity == 'dugue':
-            probs_out = get_probs('degree', adjacency)
-            probs_in = get_probs('degree', adjacency.T)
+            out_weights = get_probs('degree', adjacency)
+            in_weights = get_probs('degree', adjacency.T)
         else:
             raise ValueError('Unknown modularity function.')
 
-        adjacency_cluster = adjacency / adjacency.data.sum()
+        # normalized, symmetric adjacency matrix (sums to 1)
+        adjacency = directed2undirected(adjacency)
+        adjacency = adjacency / adjacency.data.sum()
 
+        # cluster membership
         membership = sparse.identity(n, format='csr')
-        increase = True
-        count_aggregations = 0
-        self.log.print("Starting with", n, "nodes.")
-        while increase:
-            count_aggregations += 1
-
-            labels_cluster, pass_increase = self._optimize(adjacency_cluster, probs_out, probs_in)
-            _, labels_cluster = np.unique(labels_cluster, return_inverse=True)
-
-            if pass_increase <= self.tol_aggregation:
-                increase = False
-            else:
-                membership_cluster = get_membership(labels_cluster)
-                membership = membership.dot(membership_cluster)
-                adjacency_cluster, probs_out, probs_in = self._aggregate(adjacency_cluster, probs_out, probs_in,
-                                                                         membership_cluster)
-
-                n = adjacency_cluster.shape[0]
-                if n == 1:
-                    break
-            self.log.print("Aggregation", count_aggregations, "completed with", n, "clusters and ",
-                           pass_increase, "increment.")
-            if count_aggregations == self.n_aggregations:
-                break
 
+        return adjacency, out_weights, in_weights, membership, index
+
+    def _post_processing(self, input_matrix, membership, index):
+        """Post-processing for Louvain.
+
+         Parameters
+        ----------
+        input_matrix :
+            Adjacency matrix or biadjacency matrix of the graph.
+        membership :
+            Membership matrix (labels).
+        index :
+            Index of nodes.
+        """
         if self.sort_clusters:
             labels = reindex_labels(membership.indices)
         else:
@@ -246,10 +247,40 @@ class Louvain(BaseClustering, VerboseMixin):
             reverse = np.empty(index.size, index.dtype)
             reverse[index] = np.arange(index.size)
             labels = labels[reverse]
-
         self.labels_ = labels
         if self.bipartite:
             self._split_vars(input_matrix.shape)
         self._secondary_outputs(input_matrix)
 
+    def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], force_bipartite: bool = False) -> 'Louvain':
+        """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:`Louvain`
+        """
+        adjacency, out_weights, in_weights, membership, index = self._pre_processing(input_matrix, force_bipartite)
+        n = adjacency.shape[0]
+        count = 0
+        stop = False
+        while not stop:
+            count += 1
+            labels = np.arange(n)
+            labels, increase = self._optimize(labels, adjacency, out_weights, in_weights)
+            _, labels = np.unique(labels, return_inverse=True)
+            adjacency, out_weights, in_weights = self._aggregate(labels, adjacency, out_weights, in_weights)
+            membership = membership.dot(get_membership(labels))
+            n = adjacency.shape[0]
+            stop = n == 1
+            stop |= increase <= self.tol_aggregation
+            stop |= count == self.n_aggregations
+            self.print_log("Aggregation:", count, " Clusters:", n, " Increase:", increase)
+        self._post_processing(input_matrix, membership, index)
         return self