Add parallelization + prepare test

gmatch4py/base.pxd

@@ -7,9 +7,11 @@ cdef class Base:
 
     ## Methods
     cpdef np.ndarray compare(self,list graph_list, list selected)
+    cpdef np.ndarray compare_old(self,list listgs, list selected)
     cpdef np.ndarray distance(self, np.ndarray matrix)
     cpdef np.ndarray similarity(self, np.ndarray matrix)
     cpdef bint isAccepted(self,G,index,selected)
+    cpdef list get_selected_array(self,selected,size_corpus)
 
 cpdef intersection(G,H)
 cpdef union_(G,H)

gmatch4py/base.pyx

@@ -136,6 +136,17 @@ cdef class Base:
         else:
             self.type_alg=type_alg
         self.normalized=normalized
+
+    cpdef list get_selected_array(self,selected,size_corpus):
+        cdef list selected_test = [True]*size_corpus
+        if selected:
+            selected_test = [False]*size_corpus
+            for ix in range(len(selected)):
+                selected_test[ix]=True
+        return selected
+
+    cpdef np.ndarray compare_old(self,list listgs, list selected):
+        pass
     cpdef np.ndarray compare(self,list graph_list, list selected):
         """
         Return the similarity/distance matrix using the current algorithm.

gmatch4py/ged/abstract_graph_edit_dist.pxd

@@ -16,3 +16,4 @@ cdef class AbstractGraphEditDistance(Base):
     cdef double insert_cost(self, int i, int j, nodesH, H)
     cdef double delete_cost(self, int i, int j, nodesG, G)
     cpdef double substitute_cost(self, node1, node2, G, H)
+    

gmatch4py/ged/abstract_graph_edit_dist.pyx

@@ -4,14 +4,18 @@ from __future__ import print_function
 import sys
 import warnings
 import numpy as np
+cimport numpy as np
 try:
     from munkres import munkres
 except ImportError:
     warnings.warn("To obtain optimal results install the Cython 'munkres' module at  https://github.com/jfrelinger/cython-munkres-wrapper")
     from scipy.optimize import linear_sum_assignment as munkres
-cimport numpy as np
+
 from ..base cimport Base
 import networkx as nx
+from ..helpers.general import parsenx2graph
+from cython.parallel cimport prange,parallel
+
 
 cdef class AbstractGraphEditDistance(Base):
 
@@ -90,7 +94,7 @@ cdef class AbstractGraphEditDistance(Base):
     cpdef double substitute_cost(self, node1, node2, G, H):
         raise NotImplementedError
 
-    cpdef np.ndarray compare(self,list listgs, list selected):
+    cpdef np.ndarray compare_old(self,list listgs, list selected):
         cdef int n = len(listgs)
         cdef np.ndarray comparison_matrix = np.zeros((n, n)).astype(float)
         cdef int i,j
@@ -105,3 +109,23 @@ cdef class AbstractGraphEditDistance(Base):
                 #comparison_matrix[j, i] = comparison_matrix[i, j]
         np.fill_diagonal(comparison_matrix,0)
         return comparison_matrix
+
+    cpdef np.ndarray compare(self,list listgs, list selected):
+        cdef int n = len(listgs)
+        cdef double[:,:] comparison_matrix = np.zeros((n, n))
+        listgs=parsenx2graph(listgs)
+        cdef long[:] n_nodes = np.array([g.size() for g in listgs])
+
+        cdef bint[:] selected_test = self.get_selected_array(selected,n)
+        cdef int i,j
+        val=np.inf
+        with nogil, parallel(num_threads=8):
+            for i in prange(n,schedule='static'):
+                for j in range(n):
+                        if n_nodes[i]>0 and n_nodes[j]>0 and selected_test[i] :
+                            with gil:
+                                comparison_matrix[i][j] = self.distance_ged(listgs[i],listgs[j])
+                        else:
+                            comparison_matrix[i][j] = 0
+                    #comparison_matrix[j, i] = comparison_matrix[i, j]
+        return np.array(comparison_matrix)

gmatch4py/ged/bipartite_graph_matching_2.pyx

@@ -2,7 +2,8 @@
 import numpy as np
 cimport numpy as np
 from ..base cimport Base
-
+from cython.parallel cimport prange,parallel
+from ..helpers.general import parsenx2graph
 cdef class BP_2(Base):
 
 
@@ -32,7 +33,7 @@ cdef class BP_2(Base):
         self.edge_del = edge_del
         self.edge_ins = edge_ins
 
-    cpdef np.ndarray compare(self,list listgs, list selected):
+    cpdef np.ndarray compare_old(self,list listgs, list selected):
         cdef int n = len(listgs)
         cdef np.ndarray comparison_matrix = np.zeros((n, n)).astype(float)
         cdef int i,j
@@ -48,6 +49,27 @@ cdef class BP_2(Base):
 
         return comparison_matrix
 
+    cpdef np.ndarray compare(self,list listgs, list selected):
+        cdef int n = len(listgs)
+        cdef list new_gs=parsenx2graph(listgs)
+        cdef double[:,:] comparison_matrix = np.zeros((n, n))
+        cdef bint[:] selected_test = self.get_selected_array(selected,n)
+        cdef int i,j
+        cdef long[:] n_nodes = np.array([g.size() for g in new_gs])
+        cdef long[:] n_edges = np.array([g.density() for g in new_gs])
+
+        with nogil, parallel(num_threads=4):
+            for i in prange(n,schedule='static'):
+                for j in range(i,n):
+                    if  n_nodes[i] > 0 and n_nodes[j] > 0  and selected_test[i] == True:
+                        with gil:
+                            comparison_matrix[i, j] = self.bp2(new_gs[i], new_gs[j])
+                    else:
+                        comparison_matrix[i, j] = 0
+                    comparison_matrix[j, i] = comparison_matrix[i, j]
+
+        return comparison_matrix
+
 
     cdef double bp2(self, g1, g2):
         """
@@ -100,8 +122,8 @@ cdef class BP_2(Base):
             list containing costs from the optimal edit path
         """
         cdef list psi_=[]
-        cdef list nodes1 = list(g1.nodes)
-        cdef list nodes2 = list(g2.nodes)
+        cdef list nodes1 = list(g1.nodes())
+        cdef list nodes2 = list(g2.nodes())
         for u in nodes1:
             v=None
             for w in nodes2:
@@ -125,9 +147,9 @@ cdef class BP_2(Base):
         :param g2: Second Graph
         :return:
         """
-        cdef np.ndarray min_sum = np.zeros(len(g1))
-        nodes1 = list(g1.nodes)
-        nodes2 = list(g2.nodes)
+        cdef np.ndarray min_sum = np.zeros(g1.size())
+        nodes1 = list(g1.nodes())
+        nodes2 = list(g2.nodes())
         nodes2.extend([None])
         cdef np.ndarray min_i
         for i in range(len(nodes1)):
@@ -178,8 +200,8 @@ cdef class BP_2(Base):
         """
 
         #if isinstance(g1, nx.MultiDiGraph):
-        cdef list edges1 = list(g1.edges(n1)) if n1 else []
-        cdef list edges2 =  list(g2.edges(n2)) if n2 else []
+        cdef list edges1 = g1.get_edges_no(n1) if n1 else []
+        cdef list edges2 = g2.get_edges_no(n2) if n2 else []
 
         cdef np.ndarray min_sum = np.zeros(len(edges1))
         edges2.extend([None])

gmatch4py/ged/graph_edit_dist.pxd

@@ -4,6 +4,7 @@ from .abstract_graph_edit_dist cimport AbstractGraphEditDistance
 
 
 cdef class GraphEditDistance(AbstractGraphEditDistance):
+    cpdef object relabel_cost(self, node1, node2, G, H)
     cpdef double substitute_cost(self, node1, node2, G, H)
     cdef double delete_cost(self, int i, int j, nodesG, G)
     cdef double insert_cost(self, int i, int j, nodesH, H)
\ No newline at end of file

gmatch4py/ged/graph_edit_dist.pyx

@@ -7,6 +7,7 @@ import numpy as np
 cimport numpy as np
 from .abstract_graph_edit_dist cimport AbstractGraphEditDistance
 from ..base cimport intersection,union_
+from ..graph cimport Graph
 
 
 cdef class GraphEditDistance(AbstractGraphEditDistance):
@@ -14,52 +15,43 @@ cdef class GraphEditDistance(AbstractGraphEditDistance):
     def __init__(self,node_del,node_ins,edge_del,edge_ins,weighted=False):
         AbstractGraphEditDistance.__init__(self,node_del,node_ins,edge_del,edge_ins)
         self.weighted=weighted
+        
     cpdef double substitute_cost(self, node1, node2, G, H):
         return self.relabel_cost(node1, node2, G, H)
 
-    def add_edges(self,node1,node2,G):
-        R=nx.create_empty_copy(G)
-        try:
-            R.add_edges_from(G.edges(node1,node2))
-        except Exception as e:
-            # To counter bug with a None for attribute... weird ??
-            arr_=G.edges(node1,node2)
-            new_list=[]
-            for item in arr_:
-                new_list.append((item[0],item[1]))
-            R.add_edges_from(new_list)
-        return R
-
-    def relabel_cost(self, node1, node2, G, H):
+    cpdef object relabel_cost(self, node1, node2, G, H):
         ## Si deux noeuds égaux
         if node1 == node2 and G.degree(node1) == H.degree(node2):
             return 0.0
         elif node1 == node2 and G.degree(node1) != H.degree(node2):
-            R = self.add_edges(node1,node2,G)
-            R2 = self.add_edges(node1,node2,H)
-            inter_=intersection(R,R2).number_of_edges()
-            add_diff=abs(R2.number_of_edges()-inter_)
-            del_diff=abs(R.number_of_edges()-inter_)
+            #R = Graph(self.add_edges(node1,node2,G),G.get_node_key(),G.get_egde_key())
+            #R2 = Graph(self.add_edges(node1,node2,H),H.get_node_key(),H.get_egde_key())
+            #inter_= R.size_edge_intersect(R2)
+            R=set(G.get_edges_no(node1))
+            R2=set(H.get_edges_no(node2))
+            inter_=R.intersection(R2)
+            add_diff=abs(len(R2)-len(inter_))#abs(R2.density()-inter_)
+            del_diff=abs(len(R)-len(inter_))#abs(R.density()-inter_)
             return (add_diff*self.edge_ins)+(del_diff*self.edge_del)
 
 
         #si deux noeuds connectés
-        if (node1,node2) in G.edges() or (node2,node1) in G.edges():
+        if  G.has_edge(node1,node2) or G.has_edge(node2,node1):
             return self.node_ins+self.node_del
-        if not node2 in G:
-            nodesH=list(H.nodes())
-            index=nodesH.index(node2)
+        if not node2 in G.nodes():
+            nodesH=H.nodes()
+            index=list(nodesH).index(node2)
             return self.node_del+self.node_ins+self.insert_cost(index,index,nodesH,H)
         return sys.maxsize
 
     cdef double delete_cost(self, int i, int j, nodesG, G):
         if i == j:
-            return self.node_del+(G.degree(nodesG[i],weight=("weight" if self.weighted else None))*self.edge_del) # Deleting a node implicate to delete in and out edges
+            return self.node_del+(G.degree(nodesG[i],weight=True)*self.edge_del) # Deleting a node implicate to delete in and out edges
         return sys.maxsize
 
     cdef double insert_cost(self, int i, int j, nodesH, H):
         if i == j:
-            deg=H.degree(nodesH[j],weight=("weight" if self.weighted else None))
+            deg=H.degree(nodesH[j],weight=True)
             if isinstance(deg,dict):deg=0
             return self.node_ins+(deg*self.edge_ins)
         else:

gmatch4py/ged/graph_edit_dist_2.pyx

-# -*- coding: UTF-8 -*-
-
-import sys
-
-import networkx as nx
-import numpy as np
-cimport numpy as np
-from .abstract_graph_edit_dist cimport AbstractGraphEditDistance
-from ..base cimport intersection,union_
-from ..graph cimport Graph
-
-
-cdef class GraphEditDistance(AbstractGraphEditDistance):
-
-    def __init__(self,node_del,node_ins,edge_del,edge_ins,weighted=False):
-        AbstractGraphEditDistance.__init__(self,node_del,node_ins,edge_del,edge_ins)
-        self.weighted=weighted
-        
-    cpdef double substitute_cost(self, node1, node2, G, H):
-        return self.relabel_cost(node1, node2, G, H)
-
-    def add_edges(self,node1,node2,G):
-        R=nx.create_empty_copy(G.get_nx())
-        try:
-            R.add_edges_from(G.edges(node1,node2))
-        except Exception as e:
-            # To counter bug with a None for attribute... weird ??
-            arr_=G.edges(node1,node2)
-            new_list=[]
-            for item in arr_:
-                new_list.append((item[0],item[1]))
-            R.add_edges_from(new_list)
-        return R
-
-    cpdef relabel_cost(self, node1, node2, G, H):
-        ## Si deux noeuds égaux
-        if node1 == node2 and G.degree(node1) == H.degree(node2):
-            return 0.0
-        elif node1 == node2 and G.degree(node1) != H.degree(node2):
-            R = Graph(self.add_edges(node1,node2,G),G.get_node_key(),G.get_egde_key())
-            R2 = Graph(self.add_edges(node1,node2,H),H.get_node_key(),H.get_egde_key())
-            inter_= R.size_edge_intersect(R2)
-            add_diff=abs(R2.density()-inter_)
-            del_diff=abs(R.density()-inter_)
-            return (add_diff*self.edge_ins)+(del_diff*self.edge_del)
-
-
-        #si deux noeuds connectés
-        if  G.has_edge(*(node1,node2)) or G.has_edge(*(node2,node1)):
-            return self.node_ins+self.node_del
-        if not node2 in G:
-            nodesH=H.nodes()
-            index=list(nodesH).index(node2)
-            return self.node_del+self.node_ins+self.insert_cost(index,index,nodesH,H)
-        return sys.maxsize
-
-    cdef double delete_cost(self, int i, int j, nodesG, G):
-        if i == j:
-            return self.node_del+(G.degree(nodesG[i],weight=True)*self.edge_del) # Deleting a node implicate to delete in and out edges
-        return sys.maxsize
-
-    cdef double insert_cost(self, int i, int j, nodesH, H):
-        if i == j:
-            deg=H.degree(nodesH[j],weight=True)
-            if isinstance(deg,dict):deg=0
-            return self.node_ins+(deg*self.edge_ins)
-        else:
-            return sys.maxsize
\ No newline at end of file

gmatch4py/ged/greedy_edit_distance.pyx

@@ -4,6 +4,7 @@ import sys
 from .graph_edit_dist cimport GraphEditDistance
 import numpy as np
 cimport numpy as np
+from cython.parallel cimport prange,parallel
 
 cdef class GreedyEditDistance(GraphEditDistance):
     """
@@ -20,15 +21,6 @@ cdef class GreedyEditDistance(GraphEditDistance):
 
     cdef list edit_costs(self, G, H):
         cdef np.ndarray cost_matrix=self.create_cost_matrix(G,H)
-        """
-        cdef np.ndarray cost_matrix_2=cost_matrix.copy()
-        cdef list psi=[]
-        for i in range(len(cost_matrix)):
-            phi_i=np.argmin((cost_matrix[i]))
-            cost_matrix=np.delete(cost_matrix,phi_i,1)
-            psi.append([i,phi_i+i]) #+i to compensate the previous column deletion
-        return [cost_matrix_2[psi[i][0]][psi[i][1]] for i in range(len(psi))]
-        """
         cdef np.ndarray cost_matrix_2=cost_matrix.copy().astype(np.double)
         cdef list psi=[]
         for i in range(len(cost_matrix)):

gmatch4py/ged/hausdorff_edit_distance.pyx

@@ -3,6 +3,8 @@
 import numpy as np
 cimport numpy as np
 from ..base cimport Base
+from cython.parallel cimport prange,parallel
+from ..helpers.general import parsenx2graph
 
 cdef class HED(Base):
     """
@@ -27,7 +29,7 @@ cdef class HED(Base):
         self.edge_ins = edge_ins
 
 
-    cpdef np.ndarray compare(self,list listgs, list selected):
+    cpdef np.ndarray compare_old(self,list listgs, list selected):
         cdef int n = len(listgs)
         cdef np.ndarray comparison_matrix = np.zeros((n, n)).astype(float)
         cdef int i,j
@@ -42,6 +44,27 @@ cdef class HED(Base):
                 comparison_matrix[j, i] = comparison_matrix[i, j]
 
         return comparison_matrix
+    
+    cpdef np.ndarray compare(self,list listgs, list selected):
+        cdef int n = len(listgs)
+        cdef list new_gs=parsenx2graph(listgs)
+        cdef double[:,:] comparison_matrix = np.zeros((n, n))
+        cdef bint[:] selected_test = self.get_selected_array(selected,n)
+        cdef int i,j
+        cdef long[:] n_nodes = np.array([g.size() for g in new_gs])
+        cdef long[:] n_edges = np.array([g.density() for g in new_gs])
+
+        with nogil, parallel(num_threads=4):
+            for i in prange(n,schedule='static'):
+                for j in range(i,n):
+                    if  n_nodes[i] > 0 and n_nodes[j] > 0  and selected_test[i] == True:
+                        with gil:
+                            comparison_matrix[i, j] = self.hed(new_gs[i], new_gs[j])
+                    else:
+                        comparison_matrix[i, j] = 0
+                    comparison_matrix[j, i] = comparison_matrix[i, j]
+
+        return comparison_matrix
 
 
     cdef float hed(self, g1, g2):
@@ -61,8 +84,8 @@ cdef class HED(Base):
         :return:
         """
         cdef np.ndarray min_sum = np.zeros(len(g1))
-        nodes1 = list(g1.nodes)
-        nodes2 = list(g2.nodes)
+        nodes1 = list(g1.nodes())
+        nodes2 = list(g2.nodes())
         nodes2.extend([None])
         cdef np.ndarray min_i
         for i in range(len(nodes1)):
@@ -113,8 +136,8 @@ cdef class HED(Base):
         """
 
         #if isinstance(g1, nx.MultiDiGraph):
-        cdef list edges1 = list(g1.edges(n1)) if n1 else []
-        cdef list edges2 =  list(g2.edges(n2)) if n2 else []
+        cdef list edges1 = g1.get_edges_no(n1) if n1 else []
+        cdef list edges2 = g2.get_edges_no(n2) if n2 else []
 
         cdef np.ndarray min_sum = np.zeros(len(edges1))
         edges2.extend([None])

gmatch4py/graph.pxd

@@ -38,6 +38,7 @@ cdef class Graph:
     cdef dict degree_per_attr # degree information per attr val
     cdef dict degree_per_attr_weighted # degree information per attr val
     cdef list attr_nodes # list of attr(dict) values for each node
+    cdef dict edges_of_nodes # list of egdes connected to each node
 
     # EDGES ATTRIBUTES
     ##################
@@ -107,7 +108,8 @@ cdef class Graph:
     ## GETTER
     #########
 
-    cpdef list get_edges_(self,e1,e2)
+    cpdef list get_edges_ed(self,str e1, str e2)
+    cpdef list get_edges_no(self,str n)
     cpdef set get_edges_hash(self)
     cpdef set get_nodes_hash(self)
     

gmatch4py/graph.pyx

@@ -59,7 +59,9 @@ cdef class Graph:
             self.degree_per_attr_weighted={attr_v:{n:{"in":0,"out":0} for n in self.nodes_list} for attr_v in self.unique_edge_attr_vals}
             
         # Retrieving Degree Information
+        self.edges_of_nodes={}
         for n in self.nodes_list:
+            self.edges_of_nodes[n]=[self.hash_edge_attr(e1,e2,attr_dict[self.edge_attr_key]) if self.is_edge_attr else self.hash_edge(e1,e2) for e1,e2,attr_dict in G.edges(n,data=True)]
             degree_all.append(G.degree(n))
             degree_all_weighted.append(G.degree(n,weight="weight"))
             if self.is_directed:
@@ -161,12 +163,12 @@ cdef class Graph:
 
     cpdef bint has_edge(self,str n_id1,str n_id2):
         if self.is_directed:
-            if n_id1 in self.edges_hash_map and n_id2 in self.edges_hash_map[n_id1][n_id2]:
+            if n_id1 in self.edges_hash_map and n_id2 in self.edges_hash_map[n_id1]:
                 return True
         else:
-            if n_id1 in self.edges_hash_map and n_id2 in self.edges_hash_map[n_id1][n_id2]:
+            if n_id1 in self.edges_hash_map and n_id2 in self.edges_hash_map[n_id1]:
                 return True
-            if n_id2 in self.edges_hash_map and n_id1 in self.edges_hash_map[n_id2][n_id1]:
+            if n_id2 in self.edges_hash_map and n_id1 in self.edges_hash_map[n_id2]:
                 return True
         return False
 
@@ -199,12 +201,14 @@ cdef class Graph:
         else:
             return self.edges_list
     
-    cpdef list get_edges_(self,e1,e2):
+    cpdef list get_edges_ed(self,str e1,str e2):
         if self.is_edge_attr:
             hashes=self.edges_hash_map[e1][e2]
             return [(e1,e2,self.edges_attr_list[self.edges_hash_idx[hash_]])for hash_ in hashes]
         else:
             return [(e1,e2,None)]
+    cpdef list get_edges_no(self,str n):
+        return self.edges_of_nodes[n]
 
     cpdef dict get_edge_attr(self,edge_hash):
         return self.edges_attr_list[self.edges_hash_idx[edge_hash]]

gmatch4py/helpers/general.pyx

+from ..graph cimport Graph
+import networkx as nx
+
+def parsenx2graph(list_gs):
+    new_gs=[nx.relabel_nodes(g,{node:str(node) for node in list(g.nodes)},copy=True) for g in list_gs]
+    new_gs=[Graph(g) for g in new_gs]
+    return new_gs

gmatch4py/jaccard.pyx

@@ -5,14 +5,16 @@ cimport numpy as np
 
 from .base cimport Base
 from .base cimport intersection,union_
-
+from ..helpers.general import parsenx2graph
+from cython.parallel cimport prange,parallel
 
 cdef class Jaccard(Base):
 
     def __init__(self):
         Base.__init__(self,0,True)
 
-    cpdef np.ndarray compare(self,list listgs, list selected):
+
+    cpdef np.ndarray compare_old(self,list listgs, list selected):
         cdef int n = len(listgs)
         cdef np.ndarray comparison_matrix = np.zeros((n, n))
         cdef int i,j
@@ -37,5 +39,38 @@ cdef class Jaccard(Base):
 
         return comparison_matrix
 
+    cpdef np.ndarray compare(self,list listgs, list selected):
+        cdef int n = len(listgs)
+        cdef list new_gs=parsenx2graph(listgs)
+        cdef double[:,:] comparison_matrix = np.zeros((n, n))
+        cdef long[:] n_nodes = np.array([g.size() for g in new_gs])
+        cdef long[:] n_edges = np.array([g.density() for g in new_gs])
+        cdef int i,j
+
+        cdef bint[:] selected_test = self.get_selected_array(selected,n)
+
+        cdef double[:,:] intersect_len_nodes = np.zeros((n, n))
+        cdef double[:,:] intersect_len_edges = np.zeros((n, n))
+        cdef double[:,:] union_len_nodes = np.zeros((n, n))
+        cdef double[:,:] union_len_edges = np.zeros((n, n))
+        for i in range(n):
+            for j in range(i,n):
+                intersect_len_nodes[i][j]=new_gs[i].size_node_intersect(new_gs[j])
+                intersect_len_edges[i][j]=new_gs[i].size_edge_intersect(new_gs[j])#len(set(hash_edges[i]).intersection(hash_edges[j]))
+                union_len_nodes[i][j]=new_gs[i].size_node_union(new_gs[j])
+                union_len_edges[i][j]=new_gs[i].size_node_union(new_gs[j])
+        with nogil, parallel(num_threads=4):
+            for i in prange(n,schedule='static'):
+                for j in range(i,n):
+                    if  n_nodes[i] > 0 and n_nodes[j] > 0  and selected_test[i]:
+                        if union_len_edges[i][j] >0 and union_len_nodes[i][j] >0:
+                            comparison_matrix[i][j]= \
+                                (intersect_len_edges[i][j]/union_len_edges[i][j])*\
+                                (intersect_len_nodes[i][j]/union_len_nodes[i][j])
+                        
+                        else:
+                            comparison_matrix[i][j] = 0.
 
+                    comparison_matrix[j][i] = comparison_matrix[i][j]
 
+        return np.array(comparison_matrix)

gmatch4py/mcs.pyx

 # coding = utf-8
 import numpy as np
 cimport numpy as np
-
+from .graph cimport Graph
 from .base cimport Base
+from cython.parallel cimport prange,parallel
+from ..helpers.general import parsenx2graph
 
 cdef class MCS(Base):
     """
@@ -12,7 +14,7 @@ cdef class MCS(Base):
     def __init__(self):
         Base.__init__(self,0,True)
 
-    cpdef np.ndarray compare(self,list listgs, list selected):
+    cpdef np.ndarray compare_old(self,list listgs, list selected):
         cdef int n = len(listgs)
         cdef np.ndarray comparison_matrix = np.zeros((n, n))
         for i in range(n):
@@ -25,6 +27,28 @@ cdef class MCS(Base):
                     comparison_matrix[i, j] = 0.
                 comparison_matrix[j, i] = comparison_matrix[i, j]
         return comparison_matrix
+    
+    cpdef np.ndarray compare(self,list listgs, list selected):
+        cdef int n = len(listgs)
+        cdef double [:,:] comparison_matrix = np.zeros((n, n))
+        cdef bint[:] selected_test = self.get_selected_array(selected,n)
+        cdef list new_gs=parsenx2graph(listgs)
+        cdef long[:] n_nodes = np.array([g.size() for g in new_gs])
+        cdef double [:,:] intersect_len_nodes = np.zeros((n, n))
+        cdef int i,j
+        for i in range(n):
+            for j in range(i,n):
+                intersect_len_nodes[i][j]=new_gs[i].size_node_intersect(new_gs[j])
+
+        with nogil, parallel(num_threads=4):
+            for i in prange(n,schedule='static'):
+                for j in range(i, n):
+                    if  n_nodes[i] > 0 and n_nodes[j] > 0  and selected_test[i]:
+                        comparison_matrix[i][j] = intersect_len_nodes[i][j]/max(n_nodes[i],n_nodes[j])
+                    else:
+                        comparison_matrix[i][j] = 0.
+                    comparison_matrix[j][i] = comparison_matrix[i][j]
+        return np.array(comparison_matrix)
 
     def s_mcs(self,G, H):
         """

gmatch4py/vertex_edge_overlap.pyx

@@ -5,6 +5,7 @@ cimport numpy as np
 from .base cimport Base,intersection
 from .graph cimport Graph
 from cython.parallel cimport prange,parallel
+from ..helpers.general import parsenx2graph
 
 cdef class VertexEdgeOverlap(Base):
 
@@ -18,19 +19,35 @@ cdef class VertexEdgeOverlap(Base):
     def __init__(self):
             Base.__init__(self,0,True)
 
+    cpdef np.ndarray compare_old(self,list listgs, list selected):
+        n = len(listgs)