New translations graphdataset.py (French)

lang/fr/gklearn/utils/graphdataset.py

@@ -0,0 +1,419 @@
+""" Obtain all kinds of attributes of a graph dataset.
+
+This file is for old version of graphkit-learn.
+"""
+
+
+def get_dataset_attributes(Gn,
+                           target=None,
+                           attr_names=[],
+                           node_label=None,
+                           edge_label=None):
+    """Returns the structure and property information of the graph dataset Gn.
+
+    Parameters
+    ----------
+    Gn : List of NetworkX graph
+        List of graphs whose information will be returned.
+
+    target : list
+        The list of classification targets corresponding to Gn. Only works for 
+        classification problems.
+
+    attr_names : list
+        List of strings which indicate which informations will be returned. The
+        possible choices includes:
+
+        'substructures': sub-structures Gn contains, including 'linear', 'non 
+	linear' and 'cyclic'.
+
+        'node_labeled': whether vertices have symbolic labels.
+
+        'edge_labeled': whether egdes have symbolic labels.
+
+        'is_directed': whether graphs in Gn are directed.
+
+        'dataset_size': number of graphs in Gn.
+
+        'ave_node_num': average number of vertices of graphs in Gn.
+
+        'min_node_num': minimum number of vertices of graphs in Gn.
+
+        'max_node_num': maximum number of vertices of graphs in Gn.
+
+        'ave_edge_num': average number of edges of graphs in Gn.
+
+        'min_edge_num': minimum number of edges of graphs in Gn.
+
+        'max_edge_num': maximum number of edges of graphs in Gn.
+
+        'ave_node_degree': average vertex degree of graphs in Gn.
+
+        'min_node_degree': minimum vertex degree of graphs in Gn.
+
+        'max_node_degree': maximum vertex degree of graphs in Gn.
+
+        'ave_fill_factor': average fill factor (number_of_edges / 
+	(number_of_nodes ** 2)) of graphs in Gn.
+
+        'min_fill_factor': minimum fill factor of graphs in Gn.
+
+        'max_fill_factor': maximum fill factor of graphs in Gn.
+
+        'node_label_num': number of symbolic vertex labels.
+
+        'edge_label_num': number of symbolic edge labels.
+
+        'node_attr_dim': number of dimensions of non-symbolic vertex labels. 
+	Extracted from the 'attributes' attribute of graph nodes.
+
+        'edge_attr_dim': number of dimensions of non-symbolic edge labels. 
+	Extracted from the 'attributes' attribute of graph edges.
+
+        'class_number': number of classes. Only available for classification problems.
+
+    node_label : string
+        Node attribute used as label. The default node label is atom. Mandatory
+        when 'node_labeled' or 'node_label_num' is required.
+
+    edge_label : string
+        Edge attribute used as label. The default edge label is bond_type. 
+        Mandatory when 'edge_labeled' or 'edge_label_num' is required.
+
+    Return
+    ------
+    attrs : dict
+        Value for each property.
+    """
+    import networkx as nx
+    import numpy as np
+
+    attrs = {}
+
+    def get_dataset_size(Gn):
+        return len(Gn)
+
+    def get_all_node_num(Gn):
+        return [nx.number_of_nodes(G) for G in Gn]
+
+    def get_ave_node_num(all_node_num):
+        return np.mean(all_node_num)
+
+    def get_min_node_num(all_node_num):
+        return np.amin(all_node_num)
+
+    def get_max_node_num(all_node_num):
+        return np.amax(all_node_num)
+
+    def get_all_edge_num(Gn):
+        return [nx.number_of_edges(G) for G in Gn]
+
+    def get_ave_edge_num(all_edge_num):
+        return np.mean(all_edge_num)
+
+    def get_min_edge_num(all_edge_num):
+        return np.amin(all_edge_num)
+
+    def get_max_edge_num(all_edge_num):
+        return np.amax(all_edge_num)
+
+    def is_node_labeled(Gn):
+        return False if node_label is None else True
+
+    def get_node_label_num(Gn):
+        nl = set()
+        for G in Gn:
+            nl = nl | set(nx.get_node_attributes(G, node_label).values())
+        return len(nl)
+
+    def is_edge_labeled(Gn):
+        return False if edge_label is None else True
+
+    def get_edge_label_num(Gn):
+        el = set()
+        for G in Gn:
+            el = el | set(nx.get_edge_attributes(G, edge_label).values())
+        return len(el)
+
+    def is_directed(Gn):
+        return nx.is_directed(Gn[0])
+
+    def get_ave_node_degree(Gn):
+        return np.mean([np.mean(list(dict(G.degree()).values())) for G in Gn])
+
+    def get_max_node_degree(Gn):
+        return np.amax([np.mean(list(dict(G.degree()).values())) for G in Gn])
+
+    def get_min_node_degree(Gn):
+        return np.amin([np.mean(list(dict(G.degree()).values())) for G in Gn])
+    
+    # get fill factor, the number of non-zero entries in the adjacency matrix.
+    def get_ave_fill_factor(Gn):
+        return np.mean([nx.number_of_edges(G) / (nx.number_of_nodes(G) 
+                                           * nx.number_of_nodes(G)) for G in Gn])
+
+    def get_max_fill_factor(Gn):
+        return np.amax([nx.number_of_edges(G) / (nx.number_of_nodes(G) 
+                                           * nx.number_of_nodes(G)) for G in Gn])
+
+    def get_min_fill_factor(Gn):
+        return np.amin([nx.number_of_edges(G) / (nx.number_of_nodes(G) 
+                                           * nx.number_of_nodes(G)) for G in Gn])
+
+    def get_substructures(Gn):
+        subs = set()
+        for G in Gn:
+            degrees = list(dict(G.degree()).values())
+            if any(i == 2 for i in degrees):
+                subs.add('linear')
+            if np.amax(degrees) >= 3:
+                subs.add('non linear')
+            if 'linear' in subs and 'non linear' in subs:
+                break
+
+        if is_directed(Gn):
+            for G in Gn:
+                if len(list(nx.find_cycle(G))) > 0:
+                    subs.add('cyclic')
+                    break
+        # else:
+        #     # @todo: this method does not work for big graph with large amount of edges like D&D, try a better way.
+        #     upper = np.amin([nx.number_of_edges(G) for G in Gn]) * 2 + 10
+        #     for G in Gn:
+        #         if (nx.number_of_edges(G) < upper):
+        #             cyc = list(nx.simple_cycles(G.to_directed()))
+        #             if any(len(i) > 2 for i in cyc):
+        #                 subs.add('cyclic')
+        #                 break
+        #     if 'cyclic' not in subs:
+        #         for G in Gn:
+        #             cyc = list(nx.simple_cycles(G.to_directed()))
+        #             if any(len(i) > 2 for i in cyc):
+        #                 subs.add('cyclic')
+        #                 break
+
+        return subs
+
+    def get_class_num(target):
+        return len(set(target))
+
+    def get_node_attr_dim(Gn):
+        for G in Gn:
+            for n in G.nodes(data=True):
+                if 'attributes' in n[1]:
+                    return len(n[1]['attributes'])
+        return 0
+
+    def get_edge_attr_dim(Gn):
+        for G in Gn:
+            if nx.number_of_edges(G) > 0:
+                for e in G.edges(data=True):
+                    if 'attributes' in e[2]:
+                        return len(e[2]['attributes'])
+        return 0
+
+    if attr_names == []:
+        attr_names = [
+            'substructures',
+            'node_labeled',
+            'edge_labeled',
+            'is_directed',
+            'dataset_size',
+            'ave_node_num',
+            'min_node_num',
+            'max_node_num',
+            'ave_edge_num',
+            'min_edge_num',
+            'max_edge_num',
+            'ave_node_degree',
+            'min_node_degree',
+            'max_node_degree',
+            'ave_fill_factor',
+            'min_fill_factor',
+            'max_fill_factor',
+            'node_label_num',
+            'edge_label_num',
+            'node_attr_dim',
+            'edge_attr_dim',
+            'class_number',
+        ]
+
+    # dataset size
+    if 'dataset_size' in attr_names:
+
+        attrs.update({'dataset_size': get_dataset_size(Gn)})
+
+    # graph node number
+    if any(i in attr_names
+           for i in ['ave_node_num', 'min_node_num', 'max_node_num']):
+
+        all_node_num = get_all_node_num(Gn)
+
+    if 'ave_node_num' in attr_names:
+
+        attrs.update({'ave_node_num': get_ave_node_num(all_node_num)})
+
+    if 'min_node_num' in attr_names:
+
+        attrs.update({'min_node_num': get_min_node_num(all_node_num)})
+
+    if 'max_node_num' in attr_names:
+
+        attrs.update({'max_node_num': get_max_node_num(all_node_num)})
+
+    # graph edge number
+    if any(i in attr_names for i in
+           ['ave_edge_num', 'min_edge_num', 'max_edge_num']):
+
+        all_edge_num = get_all_edge_num(Gn)
+
+    if 'ave_edge_num' in attr_names:
+
+        attrs.update({'ave_edge_num': get_ave_edge_num(all_edge_num)})
+
+    if 'max_edge_num' in attr_names:
+
+        attrs.update({'max_edge_num': get_max_edge_num(all_edge_num)})
+
+    if 'min_edge_num' in attr_names:
+
+        attrs.update({'min_edge_num': get_min_edge_num(all_edge_num)})
+
+    # label number
+    if any(i in attr_names for i in ['node_labeled', 'node_label_num']):
+        is_nl = is_node_labeled(Gn)
+        node_label_num = get_node_label_num(Gn)
+
+    if 'node_labeled' in attr_names:
+        # graphs are considered node unlabeled if all nodes have the same label.
+        attrs.update({'node_labeled': is_nl if node_label_num > 1 else False})
+
+    if 'node_label_num' in attr_names:
+        attrs.update({'node_label_num': node_label_num})
+
+    if any(i in attr_names for i in ['edge_labeled', 'edge_label_num']):
+        is_el = is_edge_labeled(Gn)
+        edge_label_num = get_edge_label_num(Gn)
+
+    if 'edge_labeled' in attr_names:
+        # graphs are considered edge unlabeled if all edges have the same label.
+        attrs.update({'edge_labeled': is_el if edge_label_num > 1 else False})
+
+    if 'edge_label_num' in attr_names:
+        attrs.update({'edge_label_num': edge_label_num})
+
+    if 'is_directed' in attr_names:
+        attrs.update({'is_directed': is_directed(Gn)})
+
+    if 'ave_node_degree' in attr_names:
+        attrs.update({'ave_node_degree': get_ave_node_degree(Gn)})
+
+    if 'max_node_degree' in attr_names:
+        attrs.update({'max_node_degree': get_max_node_degree(Gn)})
+
+    if 'min_node_degree' in attr_names:
+        attrs.update({'min_node_degree': get_min_node_degree(Gn)})
+        
+    if 'ave_fill_factor' in attr_names:
+        attrs.update({'ave_fill_factor': get_ave_fill_factor(Gn)})
+
+    if 'max_fill_factor' in attr_names:
+        attrs.update({'max_fill_factor': get_max_fill_factor(Gn)})
+
+    if 'min_fill_factor' in attr_names:
+        attrs.update({'min_fill_factor': get_min_fill_factor(Gn)})
+
+    if 'substructures' in attr_names:
+        attrs.update({'substructures': get_substructures(Gn)})
+
+    if 'class_number' in attr_names:
+        attrs.update({'class_number': get_class_num(target)})
+
+    if 'node_attr_dim' in attr_names:
+        attrs['node_attr_dim'] = get_node_attr_dim(Gn)
+
+    if 'edge_attr_dim' in attr_names:
+        attrs['edge_attr_dim'] = get_edge_attr_dim(Gn)
+
+    from collections import OrderedDict
+    return OrderedDict(
+        sorted(attrs.items(), key=lambda i: attr_names.index(i[0])))
+
+
+def load_predefined_dataset(ds_name):
+	import os
+	from gklearn.utils.graphfiles import loadDataset
+	
+	current_path = os.path.dirname(os.path.realpath(__file__)) + '/'
+	if ds_name == 'Acyclic':
+		ds_file = current_path + '../../datasets/Acyclic/dataset_bps.ds'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'AIDS':
+		ds_file = current_path + '../../datasets/AIDS/AIDS_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'Alkane':
+		ds_file = current_path + '../../datasets/Alkane/dataset.ds'
+		fn_targets = current_path + '../../datasets/Alkane/dataset_boiling_point_names.txt'
+		graphs, targets = loadDataset(ds_file, filename_y=fn_targets)
+	elif ds_name == 'COIL-DEL':
+		ds_file = current_path + '../../datasets/COIL-DEL/COIL-DEL_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'COIL-RAG':
+		ds_file = current_path + '../../datasets/COIL-RAG/COIL-RAG_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'COLORS-3':
+		ds_file = current_path + '../../datasets/COLORS-3/COLORS-3_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'Cuneiform':
+		ds_file = current_path + '../../datasets/Cuneiform/Cuneiform_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'DD':
+		ds_file = current_path + '../../datasets/DD/DD_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'ENZYMES':
+		ds_file = current_path + '../../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'Fingerprint':
+		ds_file = current_path + '../../datasets/Fingerprint/Fingerprint_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'FRANKENSTEIN':
+		ds_file = current_path + '../../datasets/FRANKENSTEIN/FRANKENSTEIN_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'Letter-high': # node non-symb
+		ds_file = current_path + '../../datasets/Letter-high/Letter-high_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'Letter-low': # node non-symb
+		ds_file = current_path + '../../datasets/Letter-low/Letter-low_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'Letter-med': # node non-symb
+		ds_file = current_path + '../../datasets/Letter-med/Letter-med_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'MAO':
+		ds_file = current_path + '../../datasets/MAO/dataset.ds'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'Monoterpenoides':
+		ds_file = current_path + '../../datasets/Monoterpenoides/dataset_10+.ds'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'MUTAG':
+		ds_file = current_path + '../../datasets/MUTAG/MUTAG_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'NCI1':
+		ds_file = current_path + '../../datasets/NCI1/NCI1_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'NCI109':
+		ds_file = current_path + '../../datasets/NCI109/NCI109_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'PAH':
+		ds_file = current_path + '../../datasets/PAH/dataset.ds'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'SYNTHETIC':
+		pass
+	elif ds_name == 'SYNTHETICnew':
+		ds_file = current_path + '../../datasets/SYNTHETICnew/SYNTHETICnew_A.txt'
+		graphs, targets = loadDataset(ds_file)
+	elif ds_name == 'Synthie':
+		pass
+	else:
+		raise Exception('The dataset name "', ds_name, '" is not pre-defined.')
+		
+	return graphs, targets