import sys import pathlib sys.path.insert(0, "../") import networkx as nx import numpy as np import time from pygraph.kernels.spkernel import spkernel from pygraph.kernels.pathKernel import pathkernel # test of WL subtree kernel on many graphs import sys import pathlib from collections import Counter sys.path.insert(0, "../") import networkx as nx import numpy as np import time from pygraph.kernels.spkernel import spkernel from pygraph.kernels.pathKernel import pathkernel def weisfeilerlehmankernel(*args, node_label = 'atom', edge_label = 'bond_type', height = 0, base_kernel = 'subtree'): """Calculate Weisfeiler-Lehman kernels between graphs. Parameters ---------- Gn : List of NetworkX graph List of graphs between which the kernels are calculated. / G1, G2 : NetworkX graphs 2 graphs between which the kernel is calculated. node_label : string node attribute used as label. The default node label is atom. edge_label : string edge attribute used as label. The default edge label is bond_type. height : int subtree height base_kernel : string base kernel used in each iteration of WL kernel. The default base kernel is subtree kernel. Return ------ Kmatrix/Kernel : Numpy matrix/int Kernel matrix, each element of which is the Weisfeiler-Lehman kernel between 2 praphs. / Weisfeiler-Lehman Kernel between 2 graphs. Notes ----- This function now supports WL subtree kernel and WL shortest path kernel. References ---------- [1] Shervashidze N, Schweitzer P, Leeuwen EJ, Mehlhorn K, Borgwardt KM. Weisfeiler-lehman graph kernels. Journal of Machine Learning Research. 2011;12(Sep):2539-61. """ if len(args) == 1: # for a list of graphs start_time = time.time() # for WL subtree kernel if base_kernel == 'subtree': Kmatrix = _wl_subtreekernel_do(args[0], node_label, edge_label, height = height, base_kernel = 'subtree') # for WL edge kernel elif base_kernel == 'edge': print('edge') # for WL shortest path kernel elif base_kernel == 'sp': Gn = args[0] Kmatrix = np.zeros((len(Gn), len(Gn))) for i in range(0, len(Gn)): for j in range(i, len(Gn)): Kmatrix[i][j] = _weisfeilerlehmankernel_do(Gn[i], Gn[j], height = height) Kmatrix[j][i] = Kmatrix[i][j] run_time = time.time() - start_time print("\n --- Weisfeiler-Lehman %s kernel matrix of size %d built in %s seconds ---" % (base_kernel, len(args[0]), run_time)) return Kmatrix, run_time else: # for only 2 graphs start_time = time.time() # for WL subtree kernel if base_kernel == 'subtree': args = [args[0], args[1]] kernel = _wl_subtreekernel_do(args, node_label, edge_label, height = height, base_kernel = 'subtree') # for WL edge kernel elif base_kernel == 'edge': print('edge') # for WL shortest path kernel elif base_kernel == 'sp': kernel = _pathkernel_do(args[0], args[1]) run_time = time.time() - start_time print("\n --- Weisfeiler-Lehman %s kernel built in %s seconds ---" % (base_kernel, run_time)) return kernel, run_time def _wl_subtreekernel_do(*args, node_label = 'atom', edge_label = 'bond_type', height = 0, base_kernel = 'subtree'): """Calculate Weisfeiler-Lehman subtree kernels between graphs. Parameters ---------- Gn : List of NetworkX graph List of graphs between which the kernels are calculated. node_label : string node attribute used as label. The default node label is atom. edge_label : string edge attribute used as label. The default edge label is bond_type. height : int subtree height base_kernel : string base kernel used in each iteration of WL kernel. The default base kernel is subtree kernel. Return ------ Kmatrix/Kernel : Numpy matrix/int Kernel matrix, each element of which is the Weisfeiler-Lehman kernel between 2 praphs. """ Gn = args[0] Kmatrix = np.zeros((len(Gn), len(Gn))) all_num_of_labels_occured = 0 # number of the set of letters that occur before as node labels at least once in all graphs # initial for height = 0 all_labels_ori = set() # all unique orignal labels in all graphs in this iteration all_num_of_each_label = [] # number of occurence of each label in each graph in this iteration all_set_compressed = {} # a dictionary mapping original labels to new ones in all graphs in this iteration num_of_labels_occured = all_num_of_labels_occured # number of the set of letters that occur before as node labels at least once in all graphs # for each graph for G in Gn: # get the set of original labels labels_ori = list(nx.get_node_attributes(G, node_label).values()) all_labels_ori.update(labels_ori) num_of_each_label = dict(Counter(labels_ori)) # number of occurence of each label in graph all_num_of_each_label.append(num_of_each_label) num_of_labels = len(num_of_each_label) # number of all unique labels all_labels_ori.update(labels_ori) all_num_of_labels_occured += len(all_labels_ori) # calculate subtree kernel with the 0th iteration and add it to the final kernel for i in range(0, len(Gn)): for j in range(i, len(Gn)): labels = set(list(all_num_of_each_label[i].keys()) + list(all_num_of_each_label[j].keys())) vector1 = np.matrix([ (all_num_of_each_label[i][label] if (label in all_num_of_each_label[i].keys()) else 0) for label in labels ]) vector2 = np.matrix([ (all_num_of_each_label[j][label] if (label in all_num_of_each_label[j].keys()) else 0) for label in labels ]) Kmatrix[i][j] += np.dot(vector1, vector2.transpose()) Kmatrix[j][i] = Kmatrix[i][j] # iterate each height for h in range(1, height + 1): all_set_compressed = {} # a dictionary mapping original labels to new ones in all graphs in this iteration num_of_labels_occured = all_num_of_labels_occured # number of the set of letters that occur before as node labels at least once in all graphs all_labels_ori = set() all_num_of_each_label = [] # for each graph for idx, G in enumerate(Gn): set_multisets = [] for node in G.nodes(data = True): # Multiset-label determination. multiset = [ G.node[neighbors][node_label] for neighbors in G[node[0]] ] # sorting each multiset multiset.sort() multiset = node[1][node_label] + ''.join(multiset) # concatenate to a string and add the prefix set_multisets.append(multiset) # label compression set_unique = list(set(set_multisets)) # set of unique multiset labels # a dictionary mapping original labels to new ones. set_compressed = {} # if a label occured before, assign its former compressed label, else assign the number of labels occured + 1 as the compressed label for value in set_unique: if value in all_set_compressed.keys(): set_compressed.update({ value : all_set_compressed[value] }) else: set_compressed.update({ value : str(num_of_labels_occured + 1) }) num_of_labels_occured += 1 all_set_compressed.update(set_compressed) # relabel nodes for node in G.nodes(data = True): node[1][node_label] = set_compressed[set_multisets[node[0]]] # get the set of compressed labels labels_comp = list(nx.get_node_attributes(G, node_label).values()) all_labels_ori.update(labels_comp) num_of_each_label = dict(Counter(labels_comp)) all_num_of_each_label.append(num_of_each_label) all_num_of_labels_occured += len(all_labels_ori) # calculate subtree kernel with h iterations and add it to the final kernel for i in range(0, len(Gn)): for j in range(i, len(Gn)): labels = set(list(all_num_of_each_label[i].keys()) + list(all_num_of_each_label[j].keys())) vector1 = np.matrix([ (all_num_of_each_label[i][label] if (label in all_num_of_each_label[i].keys()) else 0) for label in labels ]) vector2 = np.matrix([ (all_num_of_each_label[j][label] if (label in all_num_of_each_label[j].keys()) else 0) for label in labels ]) Kmatrix[i][j] += np.dot(vector1, vector2.transpose()) Kmatrix[j][i] = Kmatrix[i][j] return Kmatrix def _weisfeilerlehmankernel_do(G1, G2, height = 0): """Calculate Weisfeiler-Lehman kernels between 2 graphs. This kernel use shortest path kernel to calculate kernel between two graphs in each iteration. Parameters ---------- G1, G2 : NetworkX graphs 2 graphs between which the kernel is calculated. Return ------ Kernel : int Weisfeiler-Lehman Kernel between 2 graphs. """ # init. kernel = 0 # init kernel num_nodes1 = G1.number_of_nodes() num_nodes2 = G2.number_of_nodes() # the first iteration. # labelset1 = { G1.nodes(data = True)[i]['label'] for i in range(num_nodes1) } # labelset2 = { G2.nodes(data = True)[i]['label'] for i in range(num_nodes2) } kernel += spkernel(G1, G2) # change your base kernel here (and one more below) for h in range(0, height + 1): # if labelset1 != labelset2: # break # Weisfeiler-Lehman test of graph isomorphism. relabel(G1) relabel(G2) # calculate kernel kernel += spkernel(G1, G2) # change your base kernel here (and one more before) # get label sets of both graphs # labelset1 = { G1.nodes(data = True)[i]['label'] for i in range(num_nodes1) } # labelset2 = { G2.nodes(data = True)[i]['label'] for i in range(num_nodes2) } return kernel def relabel(G): ''' Relabel nodes in graph G in one iteration of the 1-dim. WL test of graph isomorphism. Parameters ---------- G : NetworkX graph The graphs whose nodes are relabeled. ''' # get the set of original labels labels_ori = list(nx.get_node_attributes(G, 'label').values()) num_of_each_label = dict(Counter(labels_ori)) num_of_labels = len(num_of_each_label) set_multisets = [] for node in G.nodes(data = True): # Multiset-label determination. multiset = [ G.node[neighbors]['label'] for neighbors in G[node[0]] ] # sorting each multiset multiset.sort() multiset = node[1]['label'] + ''.join(multiset) # concatenate to a string and add the prefix set_multisets.append(multiset) # label compression # set_multisets.sort() # this is unnecessary set_unique = list(set(set_multisets)) # set of unique multiset labels set_compressed = { value : str(set_unique.index(value) + num_of_labels + 1) for value in set_unique } # assign new labels # relabel nodes # nx.relabel_nodes(G, set_compressed, copy = False) for node in G.nodes(data = True): node[1]['label'] = set_compressed[set_multisets[node[0]]] # get the set of compressed labels labels_comp = list(nx.get_node_attributes(G, 'label').values()) num_of_each_label.update(dict(Counter(labels_comp)))