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graphsageAPI as a class & add save emb method

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This commit is contained in:
Chengbin Hou 2018-11-21 21:39:55 +00:00
parent ce0ce07d4c
commit fa2fd1f21f
5 changed files with 167 additions and 160 deletions
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1
.gitignore vendored
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@ -18,6 +18,7 @@ db.ini
deploy_key_rsa
log
bash
emb
#zeyu--------------------------------

23
src/libnrl/graphsage/__init__.py
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@ -1,34 +1,33 @@
from __future__ import print_function
from __future__ import division
import numpy as np
import tensorflow as tf
#default parameters
''' global parameters for graphsage models
tune these parameters here if needed
if needed use: from libnrl.graphsage.__init__ import *
'''
#seed = 2018
#np.random.seed(seed)
#tf.set_random_seed(seed)
log_device_placement = False
# follow the orignal code by the paper author https://github.com/williamleif/GraphSAGE
# we follow the opt parameters given by papers GCN and graphSAGE
# note: citeseer+pubmed all follow the same parameters as cora, see their papers)
# tensorflow + Adam optimizer + Random weight init + row norm of attr
epochs = 100
dim_1 = 64 #dim = dim1+dim2 = 128
dim_1 = 64 #dim = dim1+dim2 = 128 for sage-mean and sage-gcn
dim_2 = 64
samples_1 = 25
samples_2 = 10
learning_rate = 0.001
dropout = 0.5
weight_decay = 0.0001
learning_rate = 0.0001
batch_size = 128 #if run out of memory, try to reduce them, but we use the default e.g. 64, default=512
normalize = True #row norm of node attributes/features
samples_1 = 25
samples_2 = 10
#other parameters that paper did not mentioned, but we also follow the defaults https://github.com/williamleif/GraphSAGE
model_size = 'small'
max_degree = 100
neg_sample_size = 20
random_context= True
validate_batch_size = 64 #if run out of memory, try to reduce them, but we use the default e.g. 64, default=256
validate_iter = 5000

204
src/libnrl/graphsage/graphsageAPI.py
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@ -1,112 +1,120 @@
# -*- coding: utf-8 -*-
'''
# author: Chengbin Hou @ SUSTech 2018 \n
# to tune parameters, refer to graphsage->__init__.py \n
# we provide utils to transform the orignal data into graphSAGE format \n
# the APIs are designed for unsupervised, \n
# for supervised way, plz refer and complete 'to do...' \n
# currently only support 'mean' and 'gcn' model \n
'''
#-----------------------------------------------------------------------------
# author: Chengbin Hou @ SUSTech 2018
# Email: Chengbin.Hou10@foxmail.com
# we provide utils to transform the orignal data into graphSAGE format
# you may easily use these APIs as what we demostrated in main.py of OpenANE
# the APIs are designed for unsupervised, for supervised way, plz complete 'label' to do codes...
#-----------------------------------------------------------------------------
'''
from networkx.readwrite import json_graph
import json
import random
import networkx as nx
import numpy as np
from libnrl.graphsage import unsupervised_train
from libnrl.graphsage.__init__ import * #import default parameters
def add_train_val_test_to_G(graph, test_perc=0.0, val_perc=0.1): #due to unsupervised, we do not need test data
G = graph.G #take out nx G
random.seed(2018)
num_nodes = nx.number_of_nodes(G)
test_ind = random.sample(range(0, num_nodes), int(num_nodes*test_perc))
val_ind = random.sample(range(0, num_nodes), int(num_nodes*val_perc))
for ind in range(0, num_nodes):
id = graph.look_back_list[ind]
if ind in test_ind:
G.nodes[id]['test'] = True
G.nodes[id]['val'] = False
elif ind in val_ind:
G.nodes[id]['test'] = False
G.nodes[id]['val'] = True
class graphSAGE(object):
def __init__(self, graph, sage_model='mean', is_supervised=False):
self.graph = graph
self.normalize = True #row normalization of node attributes
self.num_walks = 50
self.walk_len = 5
self.add_train_val_test_to_G(test_perc=0.0, val_perc=0.1) #if unsupervised, no test data
train_data = self.tranform_data_for_graphsage() #obtain graphSAGE required training data
self.vectors = None
if not is_supervised:
from libnrl.graphsage import unsupervised_train
self.vectors = unsupervised_train.train(train_data=train_data, test_data=None, model=sage_model)
else:
G.nodes[id]['test'] = False
G.nodes[id]['val'] = False
## Make sure the graph has edge train_removed annotations
## (some datasets might already have this..)
print("Loaded data.. now preprocessing..")
for edge in G.edges():
if (G.node[edge[0]]['val'] or G.node[edge[1]]['val'] or
G.node[edge[0]]['test'] or G.node[edge[1]]['test']):
G[edge[0]][edge[1]]['train_removed'] = True
else:
G[edge[0]][edge[1]]['train_removed'] = False
return G
#to do...
#from libnrl.graphsage import supervised_train
#self.vectors = supervised_train.train()
pass
def run_random_walks(G, num_walks=50, walk_len=5):
nodes = [n for n in G.nodes() if not G.node[n]["val"] and not G.node[n]["test"]]
G = G.subgraph(nodes)
pairs = []
for count, node in enumerate(nodes):
if G.degree(node) == 0:
continue
for i in range(num_walks):
curr_node = node
for j in range(walk_len):
if len(list(G.neighbors(curr_node))) == 0: #isolated nodes! often appeared in real-world
break
next_node = random.choice(list(G.neighbors(curr_node))) #changed due to compatibility
#next_node = random.choice(G.neighbors(curr_node))
# self co-occurrences are useless
if curr_node != node:
pairs.append((node,curr_node))
curr_node = next_node
if count % 1000 == 0:
print("Done walks for", count, "nodes")
return pairs
def tranform_data_for_graphsage(graph):
G = add_train_val_test_to_G(graph) #given OpenANE graph --> obtain graphSAGE graph
#G_json = json_graph.node_link_data(G) #train_data[0] in unsupervised_train.py
def add_train_val_test_to_G(self, test_perc=0.0, val_perc=0.1):
''' add if 'val' and/or 'test' to each node in G '''
G = self.graph.G
num_nodes = nx.number_of_nodes(G)
test_ind = random.sample(range(0, num_nodes), int(num_nodes*test_perc))
val_ind = random.sample(range(0, num_nodes), int(num_nodes*val_perc))
for ind in range(0, num_nodes):
id = self.graph.look_back_list[ind]
if ind in test_ind:
G.nodes[id]['test'] = True
G.nodes[id]['val'] = False
elif ind in val_ind:
G.nodes[id]['test'] = False
G.nodes[id]['val'] = True
else:
G.nodes[id]['test'] = False
G.nodes[id]['val'] = False
## Make sure the graph has edge train_removed annotations
## (some datasets might already have this..)
print("Loaded data.. now preprocessing..")
for edge in G.edges():
if (G.node[edge[0]]['val'] or G.node[edge[1]]['val'] or
G.node[edge[0]]['test'] or G.node[edge[1]]['test']):
G[edge[0]][edge[1]]['train_removed'] = True
else:
G[edge[0]][edge[1]]['train_removed'] = False
return G
id_map = graph.look_up_dict
#conversion = lambda n : int(n) # compatible with networkx >2.0
#id_map = {conversion(k):int(v) for k,v in id_map.items()} # due to graphSAGE requirement
def tranform_data_for_graphsage(self):
''' OpenANE graph -> graphSAGE required format '''
id_map = self.graph.look_up_dict
G = self.graph.G
feats = np.array([G.nodes[id]['attr'] for id in id_map.keys()])
normalize = self.normalize
if normalize and not feats is None:
print("------------- row norm of node attributes ------------------", normalize)
from sklearn.preprocessing import StandardScaler
train_inds = [id_map[n] for n in G.nodes() if not G.node[n]['val'] and not G.node[n]['test']]
train_feats = feats[train_inds]
scaler = StandardScaler()
scaler.fit(train_feats)
feats = scaler.transform(feats)
#feats1 = nx.get_node_attributes(G,'test')
#feats2 = nx.get_node_attributes(G,'val')
walks = []
walks = self.run_random_walks(num_walks=self.num_walks, walk_len=self.walk_len)
class_map = 0 #to do... use sklearn to make class into binary form, no need for unsupervised...
return G, feats, id_map, walks, class_map
feats = np.array([G.nodes[id]['attr'] for id in id_map.keys()])
normalize = True #have decleared in __init__.py
if normalize and not feats is None:
print("-------------row norm of node attributes/features------------------")
from sklearn.preprocessing import StandardScaler
train_inds = [id_map[n] for n in G.nodes() if not G.node[n]['val'] and not G.node[n]['test']]
train_feats = feats[train_inds]
scaler = StandardScaler()
scaler.fit(train_feats)
feats = scaler.transform(feats)
#feats1 = nx.get_node_attributes(G,'test')
#feats2 = nx.get_node_attributes(G,'val')
def run_random_walks(self, num_walks=50, walk_len=5):
''' generate random walks '''
G = self.graph.G
nodes = [n for n in G.nodes() if not G.node[n]["val"] and not G.node[n]["test"]]
G = G.subgraph(nodes)
pairs = []
for count, node in enumerate(nodes):
if G.degree(node) == 0:
continue
for i in range(num_walks):
curr_node = node
for j in range(walk_len):
if len(list(G.neighbors(curr_node))) == 0: #isolated nodes! often appeared in real-world
break
next_node = random.choice(list(G.neighbors(curr_node))) #changed due to compatibility
#next_node = random.choice(G.neighbors(curr_node))
# self co-occurrences are useless
if curr_node != node:
pairs.append((node,curr_node))
curr_node = next_node
if count % 1000 == 0:
print("Done walks for", count, "nodes")
return pairs
walks = []
walks = run_random_walks(G, num_walks=50, walk_len=5) #use the defualt parameter in graphSAGE
class_map = 0 #to do... use sklearn to make class into binary form, no need for unsupervised...
return G, feats, id_map, walks, class_map
def graphsage_unsupervised_train(graph, graphsage_model = 'graphsage_mean'):
train_data = tranform_data_for_graphsage(graph)
#from unsupervised_train.py
vectors = unsupervised_train.train(train_data, test_data=None, model = graphsage_model)
return vectors
'''
def save_embeddings(self, filename):
fout = open(filename, 'w')
node_num = len(self.vectors.keys())
fout.write("{} {}\n".format(node_num, self.size))
for node, vec in self.vectors.items():
fout.write("{} {}\n".format(node,
' '.join([str(x) for x in vec])))
fout.close()
'''
def save_embeddings(self, filename):
''' save embeddings to file '''
fout = open(filename, 'w')
node_num = len(self.vectors.keys())
emb_dim = len(next(iter(self.vectors.values())))
fout.write("{} {}\n".format(node_num, emb_dim))
for node, vec in self.vectors.items():
fout.write("{} {}\n".format(node,' '.join([str(x) for x in vec])))
fout.close()

15
src/libnrl/graphsage/unsupervised_train.py
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@ -85,11 +85,10 @@ def construct_placeholders():
}
return placeholders
def train(train_data, test_data=None, model='graphsage_mean'):
def train(train_data, test_data, model):
print('---------- the graphsage model we used: ', model)
print('---------- parameters we sued: epochs, dim_1+dim_2, samples_1, samples_2, dropout, weight_decay, learning_rate, batch_size, normalize',
epochs, dim_1+dim_2, samples_1, samples_2, dropout, weight_decay, learning_rate, batch_size, normalize)
print('---------- parameters we sued: epochs, dim_1+dim_2, samples_1, samples_2, dropout, weight_decay, learning_rate, batch_size',
epochs, dim_1+dim_2, samples_1, samples_2, dropout, weight_decay, learning_rate, batch_size)
G = train_data[0]
features = train_data[1] #note: features are in order of graph.look_up_list, since id_map = {k: v for v, k in enumerate(graph.look_back_list)}
id_map = train_data[2]
@ -110,7 +109,7 @@ def train(train_data, test_data=None, model='graphsage_mean'):
adj_info_ph = tf.placeholder(tf.int32, shape=minibatch.adj.shape)
adj_info = tf.Variable(adj_info_ph, trainable=False, name="adj_info")
if model == 'graphsage_mean':
if model == 'mean':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, samples_1, dim_1),
@ -141,7 +140,7 @@ def train(train_data, test_data=None, model='graphsage_mean'):
concat=False,
logging=True)
elif model == 'graphsage_seq': #LSTM as stated in paper? very slow anyway...
elif model == 'seq': #LSTM as stated in paper? very slow anyway...
sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, samples_1, dim_1),
SAGEInfo("node", sampler, samples_2, dim_2)]
@ -156,7 +155,7 @@ def train(train_data, test_data=None, model='graphsage_mean'):
model_size=model_size,
logging=True)
elif model == 'graphsage_maxpool':
elif model == 'maxpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, samples_1, dim_1),
SAGEInfo("node", sampler, samples_2, dim_2)]
@ -170,7 +169,7 @@ def train(train_data, test_data=None, model='graphsage_mean'):
model_size=model_size,
identity_dim = identity_dim,
logging=True)
elif model == 'graphsage_meanpool':
elif model == 'meanpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, samples_1, dim_1),
SAGEInfo("node", sampler, samples_2, dim_2)]

84
src/main.py
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@ -5,7 +5,7 @@ STEP2: prepare data -->
STEP3: learn node embeddings -->
STEP4: downstream evaluations
python src/main.py --method abrw --save-emb False
python src/main.py --method abrw
by Chengbin Hou 2018 <chengbin.hou10@foxmail.com>
'''
@ -65,8 +65,9 @@ def parse_args():
parser.add_argument('--emb-file', default='emb/unnamed_node_embs.txt',
help='node embeddings file; suggest: data_method_dim_embs.txt')
#-------------------------------------------------method settings-----------------------------------------------------------
parser.add_argument('--method', default='abrw', choices=['node2vec', 'deepwalk', 'line', 'gcn', 'grarep', 'tadw',
'abrw', 'asne', 'aane', 'attrpure', 'attrcomb', 'graphsage'],
parser.add_argument('--method', default='abrw', choices=['deepwalk', 'node2vec', 'line', 'grarep',
'abrw', 'attrpure', 'attrcomb', 'tadw', 'aane',
'sagemean','sagegcn', 'gcn', 'asne'],
help='choices of Network Embedding methods')
parser.add_argument('--ABRW-topk', default=30, type=int,
help='select the most attr similar top k nodes of a node; ranging [0, # of nodes]')
@ -134,8 +135,8 @@ def main(args):
elif args.graph_format == 'edgelist':
g.read_edgelist(path=args.graph_file, weighted=args.weighted, directed=args.directed)
#load node attribute info------
is_ane = (args.method == 'abrw' or args.method == 'tadw' or args.method == 'gcn' or args.method == 'graphsage' or
args.method == 'attrpure' or args.method == 'attrcomb' or args.method == 'asne' or args.method == 'aane')
is_ane = (args.method == 'abrw' or args.method == 'tadw' or args.method == 'gcn' or args.method == 'sagemean' or args.method == 'sagegcn' or
args.method == 'attrpure' or args.method == 'attrcomb' or args.method == 'asne' or args.method == 'aane')
if is_ane:
assert args.attribute_file != ''
g.read_node_attr(args.attribute_file)
@ -188,6 +189,12 @@ def main(args):
elif args.method == 'line': #if auto_save, use label to justifiy the best embeddings by looking at micro / macro-F1 score
model = line.LINE(graph=g, epoch = args.epochs, rep_size=args.dim, order=args.LINE_order, batch_size=args.batch_size, negative_ratio=args.LINE_negative_ratio,
label_file=args.label_file, clf_ratio=args.label_reserved, auto_save=True, best='micro')
elif args.method == 'sagemean': #other choices: graphsage_seq, graphsage_maxpool, graphsage_meanpool, n2v
model = graphsageAPI.graphSAGE(graph=g, sage_model='mean', is_supervised=False)
elif args.method == 'sagegcn': #parameters for graphsage models are in 'graphsage' -> '__init__.py'
model = graphsageAPI.graphSAGE(graph=g, sage_model='gcn', is_supervised=False)
elif args.method == 'asne':
if args.task == 'nc':
model = asne.ASNE(graph=g, dim=args.dim, alpha=args.ASNE_lamb, epoch=args.epochs, learning_rate=args.learning_rate, batch_size=args.batch_size,
@ -195,53 +202,46 @@ def main(args):
else:
model = asne.ASNE(graph=g, dim=args.dim, alpha=args.ASNE_lamb, epoch=args.epochs, learning_rate=args.learning_rate, batch_size=args.batch_size,
X_test=test_node_pairs, Y_test=test_edge_labels, task=args.task, nc_ratio=args.label_reserved, lp_ratio=args.link_reserved, label_file=args.label_file)
elif args.method == 'graphsage': #we follow the default parameters, see __inti__.py in graphsage file
model = graphsageAPI.graphsage_unsupervised_train(graph=g, graphsage_model = 'graphsage_mean')
elif args.method == 'gcn':
model = graphsageAPI.graphsage_unsupervised_train(graph=g, graphsage_model = 'gcn') #graphsage-gcn
else:
print('no method was found...')
print('method not found...')
exit(0)
'''
elif args.method == 'gcn': #OR use graphsage-gcn as in graphsage method...
assert args.label_file != '' #must have node label
assert args.feature_file != '' #different from previous ANE methods
g.read_node_label(args.label_file) #gcn is an end-to-end supervised ANE methoed
model = gcnAPI.GCN(graph=g, dropout=args.dropout,
weight_decay=args.weight_decay, hidden1=args.hidden,
epochs=args.epochs, clf_ratio=args.label_reserved)
#gcn does not have model.save_embeddings() func
'''
t2 = time.time()
print(f'STEP3: end learning embeddings; time cost: {(t2-t1):.2f}s')
if args.save_emb:
model.save_embeddings(args.emb_file + time.strftime(' %Y%m%d-%H%M%S', time.localtime()))
print(f'Save node embeddings in file: {args.emb_file}')
t2 = time.time()
print(f'STEP3: end learning embeddings; time cost: {(t2-t1):.2f}s')
'''
#to do.... semi-supervised methods: gcn, graphsage, etc...
if args.method == 'gcn': #semi-supervised gcn
assert args.label_file != '' #must have node label
assert args.feature_file != '' #different from previous ANE methods
g.read_node_label(args.label_file) #gcn is an end-to-end supervised ANE methoed
model = gcnAPI.GCN(graph=g, dropout=args.dropout, weight_decay=args.weight_decay, hidden1=args.hidden, epochs=args.epochs, clf_ratio=args.label_reserved)
print('semi-supervsied method, no embs, exit the program...') #semi-supervised gcn do not produce embs
exit(0)
'''
#---------------------------------------STEP4: downstream task-----------------------------------------------
print('\nSTEP4: start evaluating ......: ')
t1 = time.time()
if args.method != 'semi_supervised_gcn': #except semi-supervised methods, we will get emb first, and then eval emb
vectors = 0
if args.method == 'graphsage' or args.method == 'gcn': #to do... run without this 'if'
vectors = model
else:
vectors = model.vectors #for other methods....
del model, g
#------lp task
if args.task == 'lp' or args.task == 'lp_and_nc':
#X_test_lp, Y_test_lp = read_edge_label(args.label_file) #if you want to load your own lp testing data
print(f'Link Prediction task; the percentage of positive links for testing: {(args.link_remove*100):.2f}%'
+ ' (by default, also generate equal negative links for testing)')
clf = lpClassifier(vectors=vectors) #similarity/distance metric as clf; basically, lp is a binary clf probelm
clf.evaluate(test_node_pairs, test_edge_labels)
#------nc task
if args.task == 'nc' or args.task == 'lp_and_nc':
X, Y = read_node_label(args.label_file)
print(f'Node Classification task; the percentage of labels for testing: {((1-args.label_reserved)*100):.2f}%')
clf = ncClassifier(vectors=vectors, clf=LogisticRegression()) #use Logistic Regression as clf; we may choose SVM or more advanced ones
clf.split_train_evaluate(X, Y, args.label_reserved)
vectors = model.vectors
del model, g
#------lp task
if args.task == 'lp' or args.task == 'lp_and_nc':
#X_test_lp, Y_test_lp = read_edge_label(args.label_file) #if you want to load your own lp testing data
print(f'Link Prediction task; the percentage of positive links for testing: {(args.link_remove*100):.2f}%'
+ ' (by default, also generate equal negative links for testing)')
clf = lpClassifier(vectors=vectors) #similarity/distance metric as clf; basically, lp is a binary clf probelm
clf.evaluate(test_node_pairs, test_edge_labels)
#------nc task
if args.task == 'nc' or args.task == 'lp_and_nc':
X, Y = read_node_label(args.label_file)
print(f'Node Classification task; the percentage of labels for testing: {((1-args.label_reserved)*100):.2f}%')
clf = ncClassifier(vectors=vectors, clf=LogisticRegression()) #use Logistic Regression as clf; we may choose SVM or more advanced ones
clf.split_train_evaluate(X, Y, args.label_reserved)
t2 = time.time()
print(f'STEP4: end evaluating; time cost: {(t2-t1):.2f}s')