def main(argv=None):
print("Loading training data..")
if FLAGS.label_flip > 0:
train_data = load_data(
FLAGS.train_prefix,
feats_suf=FLAGS.feats_suffix,
corrupt_label=lambda l, g: random_flip(l, g, FLAGS.label_flip))
elif FLAGS.high_freq:
train_data = load_data_highfreq()
else:
train_data = load_data(FLAGS.train_prefix,
feats_suf=FLAGS.feats_suffix)
print("Done loading training data..")
train(train_data)
def main(argv=None):
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix,
FLAGS.weighted_adjacency_matrix_file,
load_walks=True)
print("Done loading training data..")
train(train_data)
def main(argv=None):
print("Loading training data..")
train_data = load_data(
FLAGS.train_prefix,
load_walks=True) # G, feats, id_map, walks, class_map
print("Done loading training data..")
train(train_data)
def main(self):
print("Loading training data..")
# 下载toy-ppi数据集，该数据集的json文件里有test，val等属性，相当于分好训练集、测试集、验证集了，
# 然后通过load_data()处理，就可以使用了
train_data = load_data(FLAGS.train_prefix)
print("Done loading training data.. ")
train(train_data)
def main(argv=None):
#print("Loading training data..")
train_data = load_data(FLAGS.train_prefix,
n_nodes=FLAGS.num_nodes,
load_walks=True,
graph_file=FLAGS.name)
#print("Done loading training data..")
train(train_data)
def main(argv=None):
start_time = time.time()
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix, load_walks=True)
print("Done loading training data..")
train(train_data)
end_time = time.time()
print('it take {} s'.format(end_time - start_time))
def main(argv=None):
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix,
load_walks=True,
unsupervised=True)
print("Training phase..")
start_time = time.time()
train(train_data)
print("--- %s seconds ---" % (time.time() - start_time))
def main(argv=None):
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix, load_walks=True)
print("Done loading training data..")
#print(learning_rate)
train(train_data)
#print(learning_rate)
print("cazzo dopo")
def main(argv=None, action=[2, 'leaky_relu', 3, 'leaky_relu']):
global train_data
print("action:", action)
# 共享训练数据
# if train_data == None:
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix, load_walks=True)
print("Done loading training data..")
return train(train_data, action)
def main(argv=None):
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix, FLAGS.walk_len, FLAGS.n_walks, load_walks=True)
print("Time for loading data: ", time.time() - T0)
# G, feats (None if no feature file), id_map, walks, class_map
print("Done loading training data..")
logging.info('start training')
train(train_data)
def main(argv=None, action=[4, 'sigmoid', 1, 'tanh']):
global train_data
print(action)
# 共享训练数据
if train_data == None:
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix)
print("Done loading training data..")
for _ in range(1):
train(train_data, action)
def main(argv=None, action=[4, 'relu', 4, 'linear']):
global train_data
# loadArgsForCora()
loadArgsForCiteseer()
print(action)
# 共享训练数据
if train_data == None:
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix)
print("Done loading training data..")
return train(train_data, action)
def main(argv=None):
## train graphsage model
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix)
print("Done loading training data..")
print("Start 1st phase: training graphsage model w/ uniform sampling...")
if FLAGS.allhop_rewards:
dim_2_org = FLAGS.dim_2
dim_3_org = FLAGS.dim_3
samples_2_org = FLAGS.samples_2
samples_3_org = FLAGS.samples_3
dims = [FLAGS.dim_1, FLAGS.dim_2, FLAGS.dim_3]
samples = [FLAGS.samples_1, FLAGS.samples_2, FLAGS.samples_3]
numhop = np.count_nonzero(samples)
for i in reversed(range(0, numhop)):
FLAGS.dim_2 = dims[1]
FLAGS.dim_3 = dims[2]
FLAGS.samples_2 = samples[1]
FLAGS.samples_3 = samples[2]
print('Obtainining %d/%d hop reward' % (i + 1, numhop))
train(train_data, sampler_name='Uniform')
dims[i] = 0
samples[i] = 0
FLAGS.dim_2 = dim_2_org
FLAGS.dim_3 = dim_3_org
FLAGS.samples_2 = samples_2_org
FLAGS.samples_3 = samples_3_org
else:
train(train_data, sampler_name='Uniform')
print("Done 1st phase: training graphsage model w/ uinform sampling..")
## train sampler
print("training RL-based regressor...")
train_sampler(train_data)
print("Done training RL-based regressor...")
## train
print(
"Start 2nd phase: training graphsage model w/ data-deriven sampler...")
if FLAGS.fast_ver:
train(train_data, sampler_name='FastML')
else:
train(train_data, sampler_name='ML')
print(
"Done 2nd phase: training graphsage model w/ data-deriven sampler...")
def main(argv=None):
print("Loading training data..")
# [z]: train_data
# type: tuple of size 2
# train_data[0]: networkx.Graph object
# train_data[1]: array of R^{|V|xD}
# train_data[2]: dict of size |V|, {id: id}. Vertex renaming, referred to as id2idx
# train_data[3]: empty
# train_data[4]: array of |V|xD', where D' is number of output classes
# ppi graph:
# |V|: 14755
# |E|: 228431
train_data = load_data(FLAGS.train_prefix)
print("Done loading training data..")
train(train_data)
def main(argv=None):
# python -m graphsage.unsupervised_train --train_prefix dbis/dbis --model graphsage_mean --max_total_steps 5000 --epochs 100 --validate_iter 10 --neg_sample_size 5 --batch_size 128 --gpu 0
#FLAGS.train_prefix = '/Volumes/DATA/AUS/2018/code/git/GraphSAGE/dbis/dbis'
#FLAGS.model = 'graphsage_mean'
#FLAGS.max_total_steps = 500
#FLAGS.epochs = 10
#FLAGS.validate_iter = 10
#FLAGS.neg_sample_size = 5
#FLAGS.batch_size = 128
#FLAGS.identity_dim = 50
#FLAGS.gpu = 0
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix, load_walks=True)
print("Done loading training data..")
train(train_data)
def main(self):
#print(device_lib.list_local_devices())
#gpu_device_name = tf.test.gpu_device_name()
#print(gpu_device_name)
#if tf.test.is_gpu_available():
#print("gpu on loading")
#else:
#print("no avilable gpu")
print("Loading training data..")
# 下载toy-ppi数据集，该数据集的json文件里有test，val等属性，相当于分好训练集、测试集、验证集了，
# 然后通过load_data()处理，就可以使用了
train_data = load_data(FLAGS.train_prefix)
print("Done loading training data.. ")
train(train_data)
def main(argv=None):
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix, load_walks=True)
print("Done loading training data..")
print("Start training uniform sampling + graphsage model..")
train(train_data, sampler_name='Uniform')
print("Done training uniform sampling + graphsage model..")
print("Start training ML sampler..")
train_sampler(train_data)
print("Done training ML sampler..")
print("Start training ML sampling + graphsage model..")
train(train_data, sampler_name='FastML')
print("Done training ML sampling + graphsage model..")
def main(pure_filename, out_file_name, aggregator_model, D1, num_epochs, theta_exist, flag_normalized, \
G_data=None, id_map=None, feats=None, Theta=None, fixed_neigh_weights=None, neg_sample_weights=1.0,\
brain_similarity_sizes=None, loss_function=None): #argv=None
tf.reset_default_graph()
FLAGS.model = aggregator_model
FLAGS.dim_1 = D1
FLAGS.dim_2 = D1
FLAGS.epochs = num_epochs
FLAGS.theta_exist = theta_exist
FLAGS.flag_normalized = flag_normalized
if (brain_similarity_sizes is not None):
FLAGS.brain_similarity_sizes = brain_similarity_sizes
if (loss_function is not None):
FLAGS.loss_function = loss_function
#print("Loading training data..")
train_data = load_data(
G_data=G_data, id_map=id_map, feats=feats, prefix=pure_filename
) #changed, FLAGS.train_prefix -> and load_walks=True -> False
#print("Done loading training data..")
if (fixed_neigh_weights is not None):
# print('fixed_neigh_weights shape ', fixed_neigh_weights[0].shape)
Theta = tf.constant(Theta, dtype=tf.float32)
fixed_neigh_weights = [
tf.constant(a, dtype=tf.float32, name='neigh_weights')
for a in fixed_neigh_weights
]
final_adj_matrix, G, final_theta_1, Z, loss, U = train(
train_data,
log_dir,
Theta=Theta,
fixed_neigh_weights=fixed_neigh_weights,
neg_sample_weights=neg_sample_weights
) #, learned_vars # solve(train_data, log_dir)
#final_adj_matrix = np.abs(final_adj_matrix)
#post_processing_clip(final_adj_matrix, G, out_file_name)
return final_adj_matrix, final_theta_1, Z, loss, U #, learned_vars
def main(argv=None):
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix, load_walks=True)
print("Done loading training data..")
models = [
"graphsage_mean", "gcn", "graphsage_seq", "graphsage_maxpool",
"graphsage_meanpool"
]
# models = ["graphsage_mean"]
G = train_data[0]
# features = train_data[1]
id_map = train_data[1]
'''
if not features is None:
# pad with dummy zero vector
features = np.vstack([features, np.zeros((features.shape[1],))])
'''
context_pairs = train_data[2] if FLAGS.random_context else None
minibatch = EdgeMinibatchIterator(G,
id_map,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
neg_sample_size=FLAGS.neg_sample_size,
fea_dim=FLAGS.feats_dim,
fea_filename=FLAGS.train_prefix +
"-feats.npy",
data_num=FLAGS.nodes_number,
context_pairs=context_pairs)
for model in models:
# train(train_data, minibatch, model, True)
# tf.reset_default_graph()
# print("train {} profile done".format(model))
train(train_data, minibatch, model, False)
tf.reset_default_graph()
print("train {} no profile done".format(model))
import sys,os
from os import path
sys.path.insert(0, os.getcwd())
from graphsage.utils import load_data
if __name__ == "__main__" :
import sys
PREFIX = sys.argv[1]
print("PREFIX {}".format(PREFIX))
G, feats, id_map, walks, class_map = load_data(PREFIX)
fp = open("edgelist",'w')
for nodeid in G.nodes():
id_1 = id_map[nodeid]
for neighbor in G.neighbors(nodeid):
id_2 = id_map[neighbor]
fp.write("{}\t{}\n".format(id_1,id_2))
fp.close()
def main(argv=None):
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix)
print("Done loading training data..")
predict(train_data)
def main(self):
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix)
print("Done loading training data.. ")
train(train_data)
def main(argv=None):
print("Loading training data..")
train_data = load_data(os.environ['TMPDIR'] + '/' + FLAGS.train_prefix,
target_scaling=FLAGS.target_scaling)
print("Done loading training data..")
train(train_data)
def main(argv=None):
print("Loading training data..")
train_data = load_data(FLAGS.train_prefix, load_walks=True)
print("Done loading training data..")
train(train_data)
def main(argv=None):
print("Loading training data..")
train_data = load_data(os.environ['TMPDIR'] + '/' + FLAGS.train_prefix,
load_walks=True)
print("Done loading training data..")
train(train_data)
