New translations untilHPathKernel.py (Chinese Simplified)

lang/zh/gklearn/kernels/untilHPathKernel.py

@@ -0,0 +1,726 @@
+"""
+@author: linlin
+
+@references: 
+
+	[1] Liva Ralaivola, Sanjay J Swamidass, Hiroto Saigo, and Pierre 
+	Baldi. Graph kernels for chemical informatics. Neural networks, 
+	18(8):1093–1110, 2005.
+"""
+
+import sys
+import time
+from collections import Counter
+from itertools import chain
+from functools import partial
+from multiprocessing import Pool
+from tqdm import tqdm
+
+import networkx as nx
+import numpy as np
+
+from gklearn.utils.graphdataset import get_dataset_attributes
+from gklearn.utils.parallel import parallel_gm
+from gklearn.utils.trie import Trie
+
+
+def untilhpathkernel(*args,
+					 node_label='atom',
+					 edge_label='bond_type',
+					 depth=10,
+					 k_func='MinMax',
+					 compute_method='trie',
+					 parallel='imap_unordered',
+					 n_jobs=None,
+					 chunksize=None,
+					 verbose=True):
+	"""Calculate path graph kernels up to depth/hight h between graphs.
+	
+	Parameters
+	----------
+	Gn : List of NetworkX graph
+		List of graphs between which the kernels are calculated.
+	
+	G1, G2 : NetworkX graphs
+		Two 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.
+
+	depth : integer
+		Depth of search. Longest length of paths.
+
+	k_func : function
+		A kernel function applied using different notions of fingerprint 
+		similarity, defining the type of feature map and normalization method 
+		applied for the graph kernel. The Following choices are available:
+
+		'MinMax': use the MiniMax kernel and counting feature map.
+
+		'tanimoto': use the Tanimoto kernel and binary feature map.
+
+		None: no sub-kernel is used, the kernel is computed directly.
+
+	compute_method : string
+		Computation method to store paths and compute the graph kernel. The 
+		Following choices are available:
+
+		'trie': store paths as tries.
+
+		'naive': store paths to lists.
+
+	n_jobs : int
+		Number of jobs for parallelization.
+
+	Return
+	------
+	Kmatrix : Numpy matrix
+		Kernel matrix, each element of which is the path kernel up to h between
+		2 praphs.
+	"""
+	# pre-process
+	depth = int(depth)
+	Gn = args[0] if len(args) == 1 else [args[0], args[1]]
+	Gn = [g.copy() for g in Gn]
+	Kmatrix = np.zeros((len(Gn), len(Gn)))
+	ds_attrs = get_dataset_attributes(
+		Gn,
+		attr_names=['node_labeled', 'node_attr_dim', 'edge_labeled', 
+					'edge_attr_dim', 'is_directed'],
+		node_label=node_label, edge_label=edge_label)
+	if k_func != None:
+		if not ds_attrs['node_labeled']:
+			for G in Gn:
+				nx.set_node_attributes(G, '0', 'atom')
+		if not ds_attrs['edge_labeled']:
+			for G in Gn:
+				nx.set_edge_attributes(G, '0', 'bond_type')
+
+	start_time = time.time()		
+
+	if parallel == 'imap_unordered':
+		# ---- use pool.imap_unordered to parallel and track progress. ----
+		# get all paths of all graphs before calculating kernels to save time,
+		# but this may cost a lot of memory for large datasets.
+		pool = Pool(n_jobs)
+		itr = zip(Gn, range(0, len(Gn)))
+		if chunksize is None:
+			if len(Gn) < 100 * n_jobs:
+				chunksize = int(len(Gn) / n_jobs) + 1
+			else:
+				chunksize = 100
+		all_paths = [[] for _ in range(len(Gn))]
+		if compute_method == 'trie' and k_func != None:
+			getps_partial = partial(wrapper_find_all_path_as_trie, depth, 
+									ds_attrs, node_label, edge_label)
+		elif compute_method != 'trie' and k_func != None:  
+			getps_partial = partial(wrapper_find_all_paths_until_length, depth, 
+									ds_attrs, node_label, edge_label, True)  
+		else: 
+			getps_partial = partial(wrapper_find_all_paths_until_length, depth, 
+									ds_attrs, node_label, edge_label, False)
+		if verbose:
+			iterator = tqdm(pool.imap_unordered(getps_partial, itr, chunksize),
+							desc='getting paths', file=sys.stdout)
+		else:
+			iterator = pool.imap_unordered(getps_partial, itr, chunksize)
+		for i, ps in iterator:
+			all_paths[i] = ps
+		pool.close()
+		pool.join()
+	
+#	for g in Gn:
+#		if compute_method == 'trie' and k_func != None:
+#			find_all_path_as_trie(g, depth, ds_attrs, node_label, edge_label)
+#		elif compute_method != 'trie' and k_func != None:  
+#			find_all_paths_until_length(g, depth, ds_attrs, node_label, edge_label)
+#		else: 
+#			find_all_paths_until_length(g, depth, ds_attrs, node_label, edge_label, False)
+		
+##	size = sys.getsizeof(all_paths)
+##	for item in all_paths:
+##		size += sys.getsizeof(item)
+##		for pppps in item:
+##			size += sys.getsizeof(pppps)
+##	print(size)
+#			
+##	ttt = time.time()
+##	# ---- ---- use pool.map to parallel ----
+##	for i, ps in tqdm(
+##			pool.map(getps_partial, range(0, len(Gn))),
+##			desc='getting paths', file=sys.stdout):
+##		all_paths[i] = ps
+##	print(time.time() - ttt)
+	 
+		if compute_method == 'trie' and k_func != None:
+			def init_worker(trie_toshare):
+				global G_trie
+				G_trie = trie_toshare
+			do_partial = partial(wrapper_uhpath_do_trie, k_func)
+			parallel_gm(do_partial, Kmatrix, Gn, init_worker=init_worker, 
+						glbv=(all_paths,), n_jobs=n_jobs, chunksize=chunksize, verbose=verbose) 
+		elif compute_method != 'trie' and k_func != None:
+			def init_worker(plist_toshare):
+				global G_plist
+				G_plist = plist_toshare
+			do_partial = partial(wrapper_uhpath_do_naive, k_func)   
+			parallel_gm(do_partial, Kmatrix, Gn, init_worker=init_worker, 
+						glbv=(all_paths,), n_jobs=n_jobs, chunksize=chunksize, verbose=verbose) 
+		else:
+			def init_worker(plist_toshare):
+				global G_plist
+				G_plist = plist_toshare
+			do_partial = partial(wrapper_uhpath_do_kernelless, ds_attrs, edge_kernels)   
+			parallel_gm(do_partial, Kmatrix, Gn, init_worker=init_worker, 
+						glbv=(all_paths,), n_jobs=n_jobs, chunksize=chunksize, verbose=verbose) 
+	
+	elif parallel == None:
+#		from pympler import asizeof
+		# ---- direct running, normally use single CPU core. ----
+#		print(asizeof.asized(all_paths, detail=1).format())
+	
+		if compute_method == 'trie':
+			all_paths = [
+				find_all_path_as_trie(Gn[i],
+					 depth,
+					 ds_attrs,
+					 node_label=node_label,
+					 edge_label=edge_label) for i in tqdm(
+						range(0, len(Gn)), desc='getting paths', file=sys.stdout)
+			]
+#			sizeof_allpaths = asizeof.asizeof(all_paths)
+#			print(sizeof_allpaths)
+			pbar = tqdm(
+				total=((len(Gn) + 1) * len(Gn) / 2),
+				desc='calculating kernels',
+				file=sys.stdout)
+			for i in range(0, len(Gn)):
+				for j in range(i, len(Gn)):
+					Kmatrix[i][j] = _untilhpathkernel_do_trie(all_paths[i], 
+						   all_paths[j], k_func)
+					Kmatrix[j][i] = Kmatrix[i][j]
+					pbar.update(1)
+		else:
+			all_paths = [
+				find_all_paths_until_length(
+					Gn[i],
+					depth,
+					ds_attrs,
+					node_label=node_label,
+					edge_label=edge_label) for i in tqdm(
+						range(0, len(Gn)), desc='getting paths', file=sys.stdout)
+			]
+#			sizeof_allpaths = asizeof.asizeof(all_paths)
+#			print(sizeof_allpaths)
+			pbar = tqdm(
+				total=((len(Gn) + 1) * len(Gn) / 2),
+				desc='calculating kernels',
+				file=sys.stdout)
+			for i in range(0, len(Gn)):
+				for j in range(i, len(Gn)):
+					Kmatrix[i][j] = _untilhpathkernel_do_naive(all_paths[i], all_paths[j],
+														 k_func)
+					Kmatrix[j][i] = Kmatrix[i][j]
+					pbar.update(1)
+
+	run_time = time.time() - start_time
+	if verbose:
+		print("\n --- kernel matrix of path kernel up to %d of size %d built in %s seconds ---"
+			  % (depth, len(Gn), run_time))
+
+#	print(Kmatrix[0][0:10])
+	return Kmatrix, run_time
+
+
+def _untilhpathkernel_do_trie(trie1, trie2, k_func):
+	"""Calculate path graph kernels up to depth d between 2 graphs using trie.
+
+	Parameters
+	----------
+	trie1, trie2 : list
+		Tries that contains all paths in 2 graphs.
+	k_func : function
+		A kernel function applied using different notions of fingerprint 
+		similarity.
+
+	Return
+	------
+	kernel : float
+		Path kernel up to h between 2 graphs.
+	"""
+	if k_func == 'tanimoto':	  
+		# traverse all paths in graph1 and search them in graph2. Deep-first 
+		# search is applied.
+		def traverseTrie1t(root, trie2, setlist, pcurrent=[]):
+			for key, node in root['children'].items():
+				pcurrent.append(key)
+				if node['isEndOfWord']:					
+					setlist[1] += 1
+					count2 = trie2.searchWord(pcurrent)
+					if count2 != 0:
+						setlist[0] += 1
+				if node['children'] != {}:
+					traverseTrie1t(node, trie2, setlist, pcurrent)
+				else:
+					del pcurrent[-1]
+			if pcurrent != []:
+				del pcurrent[-1]
+				
+				
+		# traverse all paths in graph2 and find out those that are not in 
+		# graph1. Deep-first search is applied. 
+		def traverseTrie2t(root, trie1, setlist, pcurrent=[]):
+			for key, node in root['children'].items():
+				pcurrent.append(key)
+				if node['isEndOfWord']:
+		#					print(node['count'])
+					count1 = trie1.searchWord(pcurrent)
+					if count1 == 0:	
+						setlist[1] += 1
+				if node['children'] != {}:
+					traverseTrie2t(node, trie1, setlist, pcurrent)
+				else:
+					del pcurrent[-1]
+			if pcurrent != []:
+				del pcurrent[-1]
+		
+		setlist = [0, 0] # intersection and union of path sets of g1, g2.
+#		print(trie1.root)
+#		print(trie2.root)
+		traverseTrie1t(trie1.root, trie2, setlist)
+#		print(setlist)
+		traverseTrie2t(trie2.root, trie1, setlist)
+#		print(setlist)
+		kernel = setlist[0] / setlist[1]
+		
+	else: # MinMax kernel		  
+		# traverse all paths in graph1 and search them in graph2. Deep-first 
+		# search is applied.
+		def traverseTrie1m(root, trie2, sumlist, pcurrent=[]):
+			for key, node in root['children'].items():
+				pcurrent.append(key)
+				if node['isEndOfWord']:
+		#					print(node['count'])
+					count1 = node['count']
+					count2 = trie2.searchWord(pcurrent)
+					sumlist[0] += min(count1, count2)
+					sumlist[1] += max(count1, count2)
+				if node['children'] != {}:
+					traverseTrie1m(node, trie2, sumlist, pcurrent)
+				else:
+					del pcurrent[-1]
+			if pcurrent != []:
+				del pcurrent[-1]
+		
+		# traverse all paths in graph2 and find out those that are not in 
+		# graph1. Deep-first search is applied.				
+		def traverseTrie2m(root, trie1, sumlist, pcurrent=[]):
+			for key, node in root['children'].items():
+				pcurrent.append(key)
+				if node['isEndOfWord']:				   
+		#					print(node['count'])
+					count1 = trie1.searchWord(pcurrent)
+					if count1 == 0:	
+						sumlist[1] += node['count']
+				if node['children'] != {}:
+					traverseTrie2m(node, trie1, sumlist, pcurrent)
+				else:
+					del pcurrent[-1]
+			if pcurrent != []:
+				del pcurrent[-1]
+		
+		sumlist = [0, 0] # sum of mins and sum of maxs
+#		print(trie1.root)
+#		print(trie2.root)
+		traverseTrie1m(trie1.root, trie2, sumlist)
+#		print(sumlist)
+		traverseTrie2m(trie2.root, trie1, sumlist)
+#		print(sumlist)
+		kernel = sumlist[0] / sumlist[1]
+
+	return kernel
+
+
+def wrapper_uhpath_do_trie(k_func, itr):
+	i = itr[0]
+	j = itr[1]
+	return i, j, _untilhpathkernel_do_trie(G_trie[i], G_trie[j], k_func)
+		
+
+def _untilhpathkernel_do_naive(paths1, paths2, k_func):
+	"""Calculate path graph kernels up to depth d between 2 graphs naively.
+
+	Parameters
+	----------
+	paths_list : list of list
+		List of list of paths in all graphs, where for unlabeled graphs, each 
+		path is represented by a list of nodes; while for labeled graphs, each 
+		path is represented by a string consists of labels of nodes and/or 
+		edges on that path.
+	k_func : function
+		A kernel function applied using different notions of fingerprint 
+		similarity.
+
+	Return
+	------
+	kernel : float
+		Path kernel up to h between 2 graphs.
+	"""
+	all_paths = list(set(paths1 + paths2))
+
+	if k_func == 'tanimoto':
+		length_union = len(set(paths1 + paths2))
+		kernel = (len(set(paths1)) + len(set(paths2)) -
+				  length_union) / length_union
+#		vector1 = [(1 if path in paths1 else 0) for path in all_paths]
+#		vector2 = [(1 if path in paths2 else 0) for path in all_paths]
+#		kernel_uv = np.dot(vector1, vector2)
+#		kernel = kernel_uv / (len(set(paths1)) + len(set(paths2)) - kernel_uv)
+
+	else:  # MinMax kernel
+		path_count1 = Counter(paths1)
+		path_count2 = Counter(paths2)
+		vector1 = [(path_count1[key] if (key in path_count1.keys()) else 0)
+				   for key in all_paths]
+		vector2 = [(path_count2[key] if (key in path_count2.keys()) else 0)
+				   for key in all_paths]
+		kernel = np.sum(np.minimum(vector1, vector2)) / \
+			np.sum(np.maximum(vector1, vector2))
+
+	return kernel
+
+
+def wrapper_uhpath_do_naive(k_func, itr):
+	i = itr[0]
+	j = itr[1]
+	return i, j, _untilhpathkernel_do_naive(G_plist[i], G_plist[j], k_func)
+
+
+def _untilhpathkernel_do_kernelless(paths1, paths2, k_func):
+	"""Calculate path graph kernels up to depth d between 2 graphs naively.
+
+	Parameters
+	----------
+	paths_list : list of list
+		List of list of paths in all graphs, where for unlabeled graphs, each 
+		path is represented by a list of nodes; while for labeled graphs, each 
+		path is represented by a string consists of labels of nodes and/or 
+		edges on that path.
+	k_func : function
+		A kernel function applied using different notions of fingerprint 
+		similarity.
+
+	Return
+	------
+	kernel : float
+		Path kernel up to h between 2 graphs.
+	"""
+	all_paths = list(set(paths1 + paths2))
+
+	if k_func == 'tanimoto':
+		length_union = len(set(paths1 + paths2))
+		kernel = (len(set(paths1)) + len(set(paths2)) -
+				  length_union) / length_union
+#		vector1 = [(1 if path in paths1 else 0) for path in all_paths]
+#		vector2 = [(1 if path in paths2 else 0) for path in all_paths]
+#		kernel_uv = np.dot(vector1, vector2)
+#		kernel = kernel_uv / (len(set(paths1)) + len(set(paths2)) - kernel_uv)
+
+	else:  # MinMax kernel
+		path_count1 = Counter(paths1)
+		path_count2 = Counter(paths2)
+		vector1 = [(path_count1[key] if (key in path_count1.keys()) else 0)
+				   for key in all_paths]
+		vector2 = [(path_count2[key] if (key in path_count2.keys()) else 0)
+				   for key in all_paths]
+		kernel = np.sum(np.minimum(vector1, vector2)) / \
+			np.sum(np.maximum(vector1, vector2))
+
+	return kernel
+
+
+def wrapper_uhpath_do_kernelless(k_func, itr):
+	i = itr[0]
+	j = itr[1]
+	return i, j, _untilhpathkernel_do_kernelless(G_plist[i], G_plist[j], k_func)
+
+
+# @todo: (can be removed maybe)  this method find paths repetively, it could be faster.
+def find_all_paths_until_length(G,
+								length,
+								ds_attrs,
+								node_label='atom',
+								edge_label='bond_type',
+								tolabelseqs=True):
+	"""Find all paths no longer than a certain maximum length in a graph. A 
+	recursive depth first search is applied.
+
+	Parameters
+	----------
+	G : NetworkX graphs
+		The graph in which paths are searched.
+	length : integer
+		The maximum length of paths.
+	ds_attrs: dict
+		Dataset attributes.
+	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.
+
+	Return
+	------
+	path : list
+		List of paths retrieved, where for unlabeled graphs, each path is 
+		represented by a list of nodes; while for labeled graphs, each path is 
+		represented by a list of strings consists of labels of nodes and/or 
+		edges on that path.
+	"""
+	# path_l = [tuple([n]) for n in G.nodes]  # paths of length l
+	# all_paths = path_l[:]
+	# for l in range(1, length + 1):
+	#	 path_l_new = []
+	#	 for path in path_l:
+	#		 for neighbor in G[path[-1]]:
+	#			 if len(path) < 2 or neighbor != path[-2]:
+	#				 tmp = path + (neighbor, )
+	#				 if tuple(tmp[::-1]) not in path_l_new:
+	#					 path_l_new.append(tuple(tmp))
+
+	#	 all_paths += path_l_new
+	#	 path_l = path_l_new[:]
+
+	path_l = [[n] for n in G.nodes]  # paths of length l
+	all_paths = [p.copy() for p in path_l]
+	for l in range(1, length + 1):
+		path_lplus1 = []
+		for path in path_l:
+			for neighbor in G[path[-1]]:
+				if neighbor not in path:
+					tmp = path + [neighbor]
+#					if tmp[::-1] not in path_lplus1:
+					path_lplus1.append(tmp)
+
+		all_paths += path_lplus1
+		path_l = [p.copy() for p in path_lplus1]
+
+	# for i in range(0, length + 1):
+	#	 new_paths = find_all_paths(G, i)
+	#	 if new_paths == []:
+	#		 break
+	#	 all_paths.extend(new_paths)
+
+	# consider labels
+#	print(paths2labelseqs(all_paths, G, ds_attrs, node_label, edge_label))
+#	print()
+	return (paths2labelseqs(all_paths, G, ds_attrs, node_label, edge_label) 
+			if tolabelseqs else all_paths)
+		
+		
+def wrapper_find_all_paths_until_length(length, ds_attrs, node_label, 
+									 edge_label, tolabelseqs, itr_item):
+	g = itr_item[0]
+	i = itr_item[1]
+	return i, find_all_paths_until_length(g, length, ds_attrs,
+				node_label=node_label, edge_label=edge_label, 
+				tolabelseqs=tolabelseqs)
+
+
+def find_all_path_as_trie(G,
+						 length,
+						 ds_attrs,
+						 node_label='atom',
+						 edge_label='bond_type'):
+#	time1 = time.time()
+	
+#	all_path = find_all_paths_until_length(G, length, ds_attrs, 
+#										   node_label=node_label,
+#										   edge_label=edge_label)
+#	ptrie = Trie()
+#	for path in all_path:
+#		ptrie.insertWord(path)
+	
+#	ptrie = Trie()
+#	path_l = [[n] for n in G.nodes]  # paths of length l
+#	path_l_str = paths2labelseqs(path_l, G, ds_attrs, node_label, edge_label)
+#	for p in path_l_str:
+#		ptrie.insertWord(p)
+#	for l in range(1, length + 1):
+#		path_lplus1 = []
+#		for path in path_l:
+#			for neighbor in G[path[-1]]:
+#				if neighbor not in path:
+#					tmp = path + [neighbor]
+##					if tmp[::-1] not in path_lplus1:
+#					path_lplus1.append(tmp)
+#		path_l = path_lplus1[:]
+#		# consider labels
+#		path_l_str = paths2labelseqs(path_l, G, ds_attrs, node_label, edge_label)
+#		for p in path_l_str:
+#			ptrie.insertWord(p)
+#	
+#	print(time.time() - time1)
+#	print(ptrie.root)
+#	print()
+			
+			
+	# traverse all paths up to length h in a graph and construct a trie with 
+	# them. Deep-first search is applied. Notice the reverse of each path is 
+	# also stored to the trie.			   
+	def traverseGraph(root, ptrie, length, G, ds_attrs, node_label, edge_label,
+					  pcurrent=[]):
+		if len(pcurrent) < length + 1:
+			for neighbor in G[root]:
+				if neighbor not in pcurrent:
+					pcurrent.append(neighbor)
+					plstr = paths2labelseqs([pcurrent], G, ds_attrs, 
+											node_label, edge_label)
+					ptrie.insertWord(plstr[0])
+					traverseGraph(neighbor, ptrie, length, G, ds_attrs, 
+								   node_label, edge_label, pcurrent)
+		del pcurrent[-1]
+
+
+	ptrie = Trie()
+	path_l = [[n] for n in G.nodes]  # paths of length l
+	path_l_str = paths2labelseqs(path_l, G, ds_attrs, node_label, edge_label)
+	for p in path_l_str:
+		ptrie.insertWord(p)
+	for n in G.nodes:
+		traverseGraph(n, ptrie, length, G, ds_attrs, node_label, edge_label, 
+					   pcurrent=[n])
+		
+		
+#	def traverseGraph(root, all_paths, length, G, ds_attrs, node_label, edge_label,
+#					  pcurrent=[]):
+#		if len(pcurrent) < length + 1:
+#			for neighbor in G[root]:
+#				if neighbor not in pcurrent:
+#					pcurrent.append(neighbor)
+#					plstr = paths2labelseqs([pcurrent], G, ds_attrs, 
+#											node_label, edge_label)
+#					all_paths.append(pcurrent[:])
+#					traverseGraph(neighbor, all_paths, length, G, ds_attrs, 
+#								   node_label, edge_label, pcurrent)
+#		del pcurrent[-1]
+#
+#
+#	path_l = [[n] for n in G.nodes]  # paths of length l
+#	all_paths = path_l[:]
+#	path_l_str = paths2labelseqs(path_l, G, ds_attrs, node_label, edge_label)
+##	for p in path_l_str:
+##		ptrie.insertWord(p)
+#	for n in G.nodes:
+#		traverseGraph(n, all_paths, length, G, ds_attrs, node_label, edge_label, 
+#					   pcurrent=[n])
+	
+#	print(ptrie.root)
+	return ptrie
+
+
+def wrapper_find_all_path_as_trie(length, ds_attrs, node_label, 
+									 edge_label, itr_item):
+	g = itr_item[0]
+	i = itr_item[1]
+	return i, find_all_path_as_trie(g, length, ds_attrs,
+				node_label=node_label, edge_label=edge_label)
+
+
+def paths2labelseqs(plist, G, ds_attrs, node_label, edge_label):
+	if ds_attrs['node_labeled']:
+		if ds_attrs['edge_labeled']:
+			path_strs = [
+				tuple(
+					list(
+						chain.from_iterable(
+							(G.nodes[node][node_label],
+							 G[node][path[idx + 1]][edge_label])
+							for idx, node in enumerate(path[:-1]))) +
+					[G.nodes[path[-1]][node_label]]) for path in plist
+			]
+			# path_strs = []
+			# for path in all_paths:
+			#	 strlist = list(
+			#		 chain.from_iterable((G.node[node][node_label],
+			#							  G[node][path[idx + 1]][edge_label])
+			#							 for idx, node in enumerate(path[:-1])))
+			#	 strlist.append(G.node[path[-1]][node_label])
+			#	 path_strs.append(tuple(strlist))
+		else:
+			path_strs = [
+				tuple([G.nodes[node][node_label] for node in path])
+				for path in plist
+			]
+		return path_strs
+	else:
+		if ds_attrs['edge_labeled']:
+			return [
+				tuple([] if len(path) == 1 else [
+					G[node][path[idx + 1]][edge_label]
+					for idx, node in enumerate(path[:-1])
+				]) for path in plist
+			]
+		else:
+			return [tuple(['0' for node in path]) for path in plist]
+#			return [tuple([len(path)]) for path in all_paths]   
+
+#
+#def paths2GSuffixTree(paths):
+#	return Tree(paths, builder=ukkonen.Builder)
+
+
+# def find_paths(G, source_node, length):
+#	 """Find all paths no longer than a certain length those start from a source node. A recursive depth first search is applied.
+
+#	 Parameters
+#	 ----------
+#	 G : NetworkX graphs
+#		 The graph in which paths are searched.
+#	 source_node : integer
+#		 The number of the node from where all paths start.
+#	 length : integer
+#		 The length of paths.
+
+#	 Return
+#	 ------
+#	 path : list of list
+#		 List of paths retrieved, where each path is represented by a list of nodes.
+#	 """
+#	 return [[source_node]] if length == 0 else \
+#		 [[source_node] + path for neighbor in G[source_node]
+#		  for path in find_paths(G, neighbor, length - 1) if source_node not in path]
+
+# def find_all_paths(G, length):
+#	 """Find all paths with a certain length in a graph. A recursive depth first search is applied.
+
+#	 Parameters
+#	 ----------
+#	 G : NetworkX graphs
+#		 The graph in which paths are searched.
+#	 length : integer
+#		 The length of paths.
+
+#	 Return
+#	 ------
+#	 path : list of list
+#		 List of paths retrieved, where each path is represented by a list of nodes.
+#	 """
+#	 all_paths = []
+#	 for node in G:
+#		 all_paths.extend(find_paths(G, node, length))
+
+#	 # The following process is not carried out according to the original article
+#	 # all_paths_r = [ path[::-1] for path in all_paths ]
+
+#	 # # For each path, two presentation are retrieved from its two extremities. Remove one of them.
+#	 # for idx, path in enumerate(all_paths[:-1]):
+#	 #	 for path2 in all_paths_r[idx+1::]:
+#	 #		 if path == path2:
+#	 #			 all_paths[idx] = []
+#	 #			 break
+
+#	 # return list(filter(lambda a: a != [], all_paths))
+#	 return all_paths