scikit-network 0.30.0__cp310-cp310-win_amd64.whl → 0.32.1__cp310-cp310-win_amd64.whl

sknetwork/topology/cliques.pyx

@@ -0,0 +1,149 @@
+# distutils: language = c++
+# cython: language_level=3
+"""
+Created in June 2020
+@author: Julien Simonnet <julien.simonnet@etu.upmc.fr>
+@author: Yohann Robert <yohann.robert@etu.upmc.fr>
+"""
+from libcpp.vector cimport vector
+import numpy as np
+cimport numpy as np
+from scipy import sparse
+
+cimport cython
+
+from sknetwork.path.dag import get_dag
+from sknetwork.topology.core import get_core_decomposition
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+cdef class ListingBox:
+    cdef int[:] ns
+    cdef np.ndarray degrees
+    cdef np.ndarray subs
+    cdef short[:] lab
+
+    def __cinit__(self, vector[int] indptr, int k):
+        cdef int n = indptr.size() - 1
+        cdef int i
+        cdef int max_deg = 0
+
+        cdef np.ndarray[int, ndim=1] ns = np.empty((k+1,), dtype=np.int32)
+        ns[k] = n
+        self.ns = ns
+
+        cdef np.ndarray[short, ndim=1] lab = np.full((n,), k, dtype=np.int16)
+        self.lab = lab
+
+        cdef np.ndarray[int, ndim=1] deg = np.zeros(n, dtype=np.int32)
+        cdef np.ndarray[int, ndim=1] sub = np.zeros(n, dtype=np.int32)
+
+        for i in range(n):
+            deg[i] = indptr[i+1] - indptr[i]
+            max_deg = max(deg[i], max_deg)
+            sub[i] = i
+
+        self.degrees = np.empty((k+1,), dtype=object)
+        self.subs = np.empty((k+1,), dtype=object)
+
+        self.degrees[k] = deg
+        self.subs[k] = sub
+
+        for i in range(2, k):
+            deg = np.zeros(n, dtype=np.int32)
+            sub = np.zeros(max_deg, dtype=np.int32)
+            self.degrees[i] = deg
+            self.subs[i] = sub
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+cdef long count_cliques_from_dag(vector[int] indptr, vector[int] indices, int clique_size, ListingBox box):
+    cdef int n = indptr.size() - 1
+    cdef long n_cliques = 0
+    cdef int i, j, k, k_max
+    cdef int u, v, w
+
+    if clique_size == 2:
+        degree_ = box.degrees[2]
+        sub_ = box.subs[2]
+        for i in range(box.ns[2]):
+            j = sub_[i]
+            n_cliques += degree_[j]
+        return n_cliques
+
+    sub_ = box.subs[clique_size]
+    sub_prev = box.subs[clique_size - 1]
+    degree_ = box.degrees[clique_size]
+    deg_prev = box.degrees[clique_size - 1]
+    for i in range(box.ns[clique_size]):
+        u = sub_[i]
+        box.ns[clique_size - 1] = 0
+        for j in range(indptr[u], indptr[u] + degree_[u]):
+            v = indices[j]
+            if box.lab[v] == clique_size:
+                box.lab[v] = clique_size - 1
+                sub_prev[box.ns[clique_size - 1]] = v
+                box.ns[clique_size - 1] += 1
+                deg_prev[v] = 0
+        for j in range(box.ns[clique_size - 1]):
+            v = sub_prev[j]
+            k = indptr[v]
+            k_max = indptr[v] + degree_[v]
+            while k < k_max:
+                w = indices[k]
+                if box.lab[w] == clique_size - 1:
+                    deg_prev[v] += 1
+                else:
+                    k_max -= 1
+                    indices[k] = indices[k_max]
+                    k -= 1
+                    indices[k_max] = w
+                k += 1
+        n_cliques += count_cliques_from_dag(indptr, indices, clique_size - 1, box)
+        for j in range(box.ns[clique_size - 1]):
+            v = sub_prev[j]
+            box.lab[v] = clique_size
+    return n_cliques
+
+
+def count_cliques(adjacency: sparse.csr_matrix, clique_size: int = 3) -> int:
+    """Count the number of cliques of some size.
+
+    Parameters
+    ----------
+    adjacency :
+        Adjacency matrix of the graph.
+    clique_size : int
+        Clique size (default = 3, corresponding to triangles.
+
+    Returns
+    -------
+    n_cliques : int
+        Number of cliques.
+
+    Example
+    -------
+    >>> from sknetwork.data import karate_club
+    >>> adjacency = karate_club()
+    >>> count_cliques(adjacency, 3)
+    45
+
+    References
+    ----------
+    Danisch, M., Balalau, O., & Sozio, M. (2018, April).
+    `Listing k-cliques in sparse real-world graphs.
+    <https://dl.acm.org/doi/pdf/10.1145/3178876.3186125>`_
+    In Proceedings of the 2018 World Wide Web Conference (pp. 589-598).
+    """
+    if clique_size < 2:
+        raise ValueError("The clique size must be at least 2.")
+
+    values = get_core_decomposition(adjacency)
+    dag = get_dag(adjacency, order=np.argsort(values))
+    indptr = dag.indptr
+    indices = dag.indices
+    box = ListingBox.__new__(ListingBox, indptr, clique_size)
+    n_cliques = count_cliques_from_dag(indptr, indices, clique_size, box)
+    return n_cliques