def time_for_unsupervised_sampling(G, id_map, walks, num_classes):
tf.reset_default_graph()
placeholders = {
'labels':
tf.placeholder(tf.float32, shape=(None, num_classes), name='labels'),
'batch1':
tf.placeholder(tf.int32, shape=(None, ), name='batch1'),
'batch2':
tf.placeholder(tf.int32, shape=(None, ), name='batch2'),
'dropout':
tf.placeholder_with_default(0., shape=(), name='dropout'),
'batch_size':
tf.placeholder(tf.int32, name='batch_size'),
}
minibatch = EdgeMinibatchIterator(G,
id_map,
placeholders,
walks,
batch_size=512,
max_degree=100)
label = tf.cast(minibatch.placeholders["batch2"], dtype=tf.int64)
labels = tf.reshape(label, [placeholders['batch_size'], 1])
neg_samples, _, _ = (tf.nn.fixed_unigram_candidate_sampler(
true_classes=labels,
num_true=1,
num_sampled=20,
unique=False,
range_max=len(minibatch.deg),
distortion=0.75,
unigrams=minibatch.deg.tolist()))
pruned_adj_matrix = tf.constant(minibatch.adj, dtype=tf.int32)
sampler = UniformNeighborSampler(pruned_adj_matrix)
def get_two_hop_sampled(input_t):
sample1 = sampler((input_t, 25))
reshaped_sample1 = tf.reshape(sample1, [
tf.shape(sample1)[0] * 25,
])
sample2 = sampler((reshaped_sample1, 10))
return sample2
source = get_two_hop_sampled(minibatch.placeholders["batch1"])
target = get_two_hop_sampled(minibatch.placeholders["batch2"])
neg_samples = get_two_hop_sampled(neg_samples)
minibatch.shuffle()
sess = tf.Session()
start_time = time.time()
i = 0
max_steps = 1000
while not minibatch.end():
feed_dict = minibatch.next_minibatch_feed_dict()
sess.run([source, target, neg_samples], feed_dict)
i = i + 1
if (i > 1000):
break
print("Total number of steps run {}".format(i))
end_time = time.time()
print("Sampling time with negative {}".format(end_time - start_time))
sess.close()
add_to_dict("UNSSAMPLE", (end_time - start_time))
def train(train_data, test_data=None):
G = train_data[0]
features = train_data[1]
id_map = train_data[2]
if not features is None:
# pad with dummy zero vector
features = np.vstack([features, np.zeros((features.shape[1], ))])
context_pairs = train_data[3] if FLAGS.random_context else None
placeholders = construct_placeholders()
minibatch = EdgeMinibatchIterator(G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=context_pairs)
adj_info_ph = tf.placeholder(tf.int32, shape=minibatch.adj.shape)
adj_info = tf.Variable(adj_info_ph, trainable=False, name="adj_info")
if FLAGS.model == 'graphsage_mean':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'gcn':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, 2 * FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, 2 * FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="gcn",
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
concat=False,
logging=True)
elif FLAGS.model == 'graphsage_seq':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
identity_dim=FLAGS.identity_dim,
aggregator_type="seq",
model_size=FLAGS.model_size,
logging=True)
elif FLAGS.model == 'graphsage_maxpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="maxpool",
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'graphsage_meanpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="meanpool",
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'n2v':
model = Node2VecModel(
placeholders,
features.shape[0],
minibatch.deg,
#2x because graphsage uses concat
nodevec_dim=2 * FLAGS.dim_1,
lr=FLAGS.learning_rate)
else:
raise Exception('Error: model name unrecognized.')
config = tf.ConfigProto(log_device_placement=FLAGS.log_device_placement)
config.gpu_options.allow_growth = True
#config.gpu_options.per_process_gpu_memory_fraction = GPU_MEM_FRACTION
config.allow_soft_placement = True
# default to saving all variables : added by wy
saver = tf.train.Saver()
# Initialize session
sess = tf.Session(config=config)
merged = tf.summary.merge_all()
summary_writer = tf.summary.FileWriter(log_dir(), sess.graph)
# Init variables
sess.run(tf.global_variables_initializer(),
feed_dict={adj_info_ph: minibatch.adj})
# Train model
if FLAGS.isTrain:
print("== Training Model ==")
train_shadow_mrr = None
shadow_mrr = None
total_steps = 0
avg_time = 0.0
epoch_val_costs = []
train_adj_info = tf.assign(adj_info, minibatch.adj)
val_adj_info = tf.assign(adj_info, minibatch.test_adj)
for epoch in range(FLAGS.epochs):
minibatch.shuffle()
iter = 0
print('Epoch: %04d' % (epoch + 1))
epoch_val_costs.append(0)
while not minibatch.end():
# Construct feed dictionary
feed_dict = minibatch.next_minibatch_feed_dict()
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
t = time.time()
# Training step
outs = sess.run([
merged, model.opt_op, model.loss, model.ranks,
model.aff_all, model.mrr, model.outputs1
],
feed_dict=feed_dict)
train_cost = outs[2]
train_mrr = outs[5]
if train_shadow_mrr is None:
train_shadow_mrr = train_mrr #
else:
train_shadow_mrr -= (1 - 0.99) * (train_shadow_mrr -
train_mrr)
if iter % FLAGS.validate_iter == 0:
# Validation
sess.run(val_adj_info.op)
val_cost, ranks, val_mrr, duration = evaluate(
sess, model, minibatch, size=FLAGS.validate_batch_size)
sess.run(train_adj_info.op)
epoch_val_costs[-1] += val_cost
if shadow_mrr is None:
shadow_mrr = val_mrr
else:
shadow_mrr -= (1 - 0.99) * (shadow_mrr - val_mrr)
if total_steps % FLAGS.print_every == 0:
summary_writer.add_summary(outs[0], total_steps)
# Print results
avg_time = (avg_time * total_steps + time.time() -
t) / (total_steps + 1)
if total_steps % FLAGS.print_every == 0:
print(
"Iter:",
'%04d' % iter,
"train_loss=",
"{:.5f}".format(train_cost),
"train_mrr=",
"{:.5f}".format(train_mrr),
"train_mrr_ema=",
"{:.5f}".format(
train_shadow_mrr), # exponential moving average
"val_loss=",
"{:.5f}".format(val_cost),
"val_mrr=",
"{:.5f}".format(val_mrr),
"val_mrr_ema=",
"{:.5f}".format(
shadow_mrr), # exponential moving average
"time=",
"{:.5f}".format(avg_time))
iter += 1
total_steps += 1
if total_steps > FLAGS.max_total_steps:
break
if total_steps > FLAGS.max_total_steps:
break
print("Optimization Finished!")
# save model
saver.save(sess, log_dir() + 'model.ckpt')
print("save model succeed!")
else:
print("==Testing Model==")
ckpt = tf.train.get_checkpoint_state(log_dir())
print(log_dir())
print(ckpt)
print(ckpt.model_ckeckpoint_path)
raw_input()
if ckpt and ckpt.model_checkpoint_path:
saver.restore(sess, ckpt.model_ckeckpoint_path)
else:
pass
raw_input()
if FLAGS.save_embeddings:
sess.run(val_adj_info.op)
save_val_embeddings(sess, model, minibatch, FLAGS.validate_batch_size,
log_dir())
if FLAGS.model == "n2v":
# stopping the gradient for the already trained nodes
train_ids = tf.constant(
[[id_map[n]] for n in G.nodes_iter()
if not G.node[n]['val'] and not G.node[n]['test']],
dtype=tf.int32)
test_ids = tf.constant([[id_map[n]] for n in G.nodes_iter()
if G.node[n]['val'] or G.node[n]['test']],
dtype=tf.int32)
update_nodes = tf.nn.embedding_lookup(model.context_embeds,
tf.squeeze(test_ids))
no_update_nodes = tf.nn.embedding_lookup(model.context_embeds,
tf.squeeze(train_ids))
update_nodes = tf.scatter_nd(test_ids, update_nodes,
tf.shape(model.context_embeds))
no_update_nodes = tf.stop_gradient(
tf.scatter_nd(train_ids, no_update_nodes,
tf.shape(model.context_embeds)))
model.context_embeds = update_nodes + no_update_nodes
sess.run(model.context_embeds)
# run random walks
from graphsage.utils import run_random_walks
nodes = [
n for n in G.nodes_iter()
if G.node[n]["val"] or G.node[n]["test"]
]
start_time = time.time()
pairs = run_random_walks(G, nodes, num_walks=50)
walk_time = time.time() - start_time
test_minibatch = EdgeMinibatchIterator(
G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=pairs,
n2v_retrain=True,
fixed_n2v=True)
start_time = time.time()
print("Doing test training for n2v.")
test_steps = 0
for epoch in range(FLAGS.n2v_test_epochs):
test_minibatch.shuffle()
while not test_minibatch.end():
feed_dict = test_minibatch.next_minibatch_feed_dict()
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
outs = sess.run([
model.opt_op, model.loss, model.ranks, model.aff_all,
model.mrr, model.outputs1
],
feed_dict=feed_dict)
if test_steps % FLAGS.print_every == 0:
print("Iter:", '%04d' % test_steps, "train_loss=",
"{:.5f}".format(outs[1]), "train_mrr=",
"{:.5f}".format(outs[-2]))
test_steps += 1
train_time = time.time() - start_time
save_val_embeddings(sess,
model,
minibatch,
FLAGS.validate_batch_size,
log_dir(),
mod="-test")
print("Total time: ", train_time + walk_time)
print("Walk time: ", walk_time)
print("Train time: ", train_time)
def train(train_data, test_data=None):
G = train_data[0]
features = train_data[1]
id_map = train_data[2]
if not features is None:
# pad with dummy zero vector
features = np.vstack([features, np.zeros((features.shape[1], ))])
context_pairs = train_data[3] if FLAGS.random_context else None
placeholders = construct_placeholders()
minibatch = EdgeMinibatchIterator(G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=context_pairs)
adj_info_ph = tf.compat.v1.placeholder(tf.int32, shape=minibatch.adj.shape)
adj_info = tf.Variable(adj_info_ph, trainable=False, name="adj_info")
if FLAGS.model == 'graphsage_mean':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'gcn':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, 2 * FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, 2 * FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="gcn",
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
concat=False,
logging=True)
elif FLAGS.model == 'graphsage_seq':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
identity_dim=FLAGS.identity_dim,
aggregator_type="seq",
model_size=FLAGS.model_size,
logging=True)
elif FLAGS.model == 'graphsage_maxpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="maxpool",
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'graphsage_meanpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="meanpool",
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'n2v':
model = Node2VecModel(
placeholders,
features.shape[0],
minibatch.deg,
#2x because graphsage uses concat
nodevec_dim=2 * FLAGS.dim_1,
lr=FLAGS.learning_rate)
else:
raise Exception('Error: model name unrecognized.')
config = tf.compat.v1.ConfigProto(
log_device_placement=FLAGS.log_device_placement)
config.gpu_options.allow_growth = True
#config.gpu_options.per_process_gpu_memory_fraction = GPU_MEM_FRACTION
config.allow_soft_placement = True
# Initialize WandB experiment
wandb.init(project='GraphSAGE_trial',
entity='cvl-liu-01',
save_code=True,
tags=['unsupervised'])
wandb.config.update(flags.FLAGS)
# Initialize session
sess = tf.compat.v1.Session(config=config)
merged = tf.compat.v1.summary.merge_all()
summary_writer = tf.compat.v1.summary.FileWriter(log_dir(), sess.graph)
# Init variables
sess.run(tf.compat.v1.global_variables_initializer(),
feed_dict={adj_info_ph: minibatch.adj})
# Init saver
saver = tf.compat.v1.train.Saver(max_to_keep=8,
keep_checkpoint_every_n_hours=1)
# Train model
train_shadow_mrr = None
val_shadow_mrr = None
total_steps = 0
avg_time = 0.0
epoch_val_costs = []
train_adj_info = tf.compat.v1.assign(adj_info, minibatch.adj)
val_adj_info = tf.compat.v1.assign(adj_info, minibatch.test_adj)
for epoch in range(FLAGS.epochs):
minibatch.shuffle()
iter = 0
print('Epoch: %04d' % (epoch + 1))
epoch_val_costs.append(0)
while not minibatch.end():
# Construct feed dictionary
feed_dict = minibatch.next_minibatch_feed_dict()
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
t = time.time()
# Training step
outs = sess.run([
merged, model.opt_op, model.loss, model.ranks, model.aff_all,
model.mrr, model.outputs1
],
feed_dict=feed_dict)
train_cost = outs[2]
train_mrr = outs[5]
if train_shadow_mrr is None:
train_shadow_mrr = train_mrr #
else:
train_shadow_mrr -= (1 - 0.99) * (train_shadow_mrr - train_mrr)
# Validation
if iter % FLAGS.validate_iter == 0:
sess.run(val_adj_info.op)
val_cost, ranks, val_mrr, duration = evaluate(
sess, model, minibatch, size=FLAGS.validate_batch_size)
sess.run(train_adj_info.op)
epoch_val_costs[-1] += val_cost
if val_shadow_mrr is None:
val_shadow_mrr = val_mrr
else:
val_shadow_mrr -= (1 - 0.99) * (val_shadow_mrr - val_mrr)
if total_steps % FLAGS.print_every == 0:
summary_writer.add_summary(outs[0], total_steps)
# Print results
avg_time = (avg_time * total_steps + time.time() -
t) / (total_steps + 1)
if total_steps % FLAGS.print_every == 0:
print(
"[%03d/%03d]" % (epoch + 1, FLAGS.epochs),
"Iter:",
'[%05d/%05d]' % (iter, minibatch.num_training_batches()),
"train_loss =",
"{:.5f}".format(train_cost),
"train_mrr =",
"{:.5f}".format(train_mrr),
"train_mrr_ema =",
"{:.5f}".format(
train_shadow_mrr), # exponential moving average
"val_loss =",
"{:.5f}".format(val_cost),
"val_mrr =",
"{:.5f}".format(val_mrr),
"val_mrr_ema =",
"{:.5f}".format(
val_shadow_mrr), # exponential moving average
"time =",
"{:.5f}".format(avg_time))
# W&B Logging
if FLAGS.wandb_log and iter % FLAGS.wandb_log_iter == 0:
wandb.log({'train_loss': train_cost, 'epoch': epoch})
wandb.log({'train_mrr': train_mrr, 'epoch': epoch})
wandb.log({'train_mrr_ema': train_shadow_mrr, 'epoch': epoch})
wandb.log({'val_loss': val_cost, 'epoch': epoch})
wandb.log({'val_mrr': val_mrr, 'epoch': epoch})
wandb.log({'val_mrr_ema': val_shadow_mrr, 'epoch': epoch})
wandb.log({'time': avg_time, 'epoch': epoch})
iter += 1
total_steps += 1
if total_steps > FLAGS.max_total_steps:
print('Max total steps reached!')
break
# Save embeddings
if FLAGS.save_embeddings and epoch % FLAGS.save_embeddings_epoch == 0:
save_val_embeddings(sess, model, minibatch,
FLAGS.validate_batch_size, log_dir())
# Also report classifier metric on the embedding
all_tr_res, all_ts_res = osm_classif_eval.evaluate(
FLAGS.train_prefix, log_dir(), n_iter=FLAGS.classif_n_iter)
if FLAGS.wandb_log:
wandb.log(all_tr_res)
wandb.log(all_ts_res)
# Save Model checkpoints
if FLAGS.save_checkpoints and epoch % FLAGS.save_checkpoints_epoch == 0:
# saver.save(sess, log_dir() + 'model', global_step=1000)
print('Save model checkpoint:', wandb.run.dir, iter, total_steps,
epoch)
saver.save(
sess,
os.path.join(wandb.run.dir,
"model-" + str(epoch + 1) + ".ckpt"))
if total_steps > FLAGS.max_total_steps:
print('Max total steps reached!')
break
print("Optimization Finished!")
if FLAGS.save_embeddings:
sess.run(val_adj_info.op)
save_val_embeddings(sess, model, minibatch, FLAGS.validate_batch_size,
log_dir())
if FLAGS.model == "n2v":
# stopping the gradient for the already trained nodes
train_ids = tf.constant(
[[id_map[n]] for n in G.nodes_iter()
if not G.node[n]['val'] and not G.node[n]['test']],
dtype=tf.int32)
test_ids = tf.constant([[id_map[n]] for n in G.nodes_iter()
if G.node[n]['val'] or G.node[n]['test']],
dtype=tf.int32)
update_nodes = tf.nn.embedding_lookup(model.context_embeds,
tf.squeeze(test_ids))
no_update_nodes = tf.nn.embedding_lookup(model.context_embeds,
tf.squeeze(train_ids))
update_nodes = tf.scatter_nd(test_ids, update_nodes,
tf.shape(model.context_embeds))
no_update_nodes = tf.stop_gradient(
tf.scatter_nd(train_ids, no_update_nodes,
tf.shape(model.context_embeds)))
model.context_embeds = update_nodes + no_update_nodes
sess.run(model.context_embeds)
# run random walks
from graphsage.utils import run_random_walks
nodes = [
n for n in G.nodes_iter()
if G.node[n]["val"] or G.node[n]["test"]
]
start_time = time.time()
pairs = run_random_walks(G, nodes, num_walks=50)
walk_time = time.time() - start_time
test_minibatch = EdgeMinibatchIterator(
G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=pairs,
n2v_retrain=True,
fixed_n2v=True)
start_time = time.time()
print("Doing test training for n2v.")
test_steps = 0
for epoch in range(FLAGS.n2v_test_epochs):
test_minibatch.shuffle()
while not test_minibatch.end():
feed_dict = test_minibatch.next_minibatch_feed_dict()
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
outs = sess.run([
model.opt_op, model.loss, model.ranks, model.aff_all,
model.mrr, model.outputs1
],
feed_dict=feed_dict)
if test_steps % FLAGS.print_every == 0:
print("Iter:", '%04d' % test_steps, "train_loss=",
"{:.5f}".format(outs[1]), "train_mrr=",
"{:.5f}".format(outs[-2]))
test_steps += 1
train_time = time.time() - start_time
save_val_embeddings(sess,
model,
minibatch,
FLAGS.validate_batch_size,
log_dir(),
mod="-test")
print("Total time: ", train_time + walk_time)
print("Walk time: ", walk_time)
print("Train time: ", train_time)
def train(train_data, action, test_data=None, regress_fun=run_regression):
config = tf.ConfigProto(log_device_placement=FLAGS.log_device_placement)
config.gpu_options.allow_growth = True
# config.gpu_options.per_process_gpu_memory_fraction = GPU_MEM_FRACTION
config.allow_soft_placement = True
# Initialize session
# 定义作用域，不然会与Controller发生冲突
with tf.Session(config=config, graph=tf.Graph()) as sess:
with sess.as_default():
with sess.graph.as_default():
# Set random seed
seed = 123
np.random.seed(seed)
tf.set_random_seed(seed)
G = train_data[0]
features = train_data[1]
id_map = train_data[2]
if not features is None:
# pad with dummy zero vector
features = np.vstack(
[features, np.zeros((features.shape[1], ))])
context_pairs = train_data[3] if FLAGS.random_context else None
placeholders = construct_placeholders()
minibatch = EdgeMinibatchIterator(
G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=context_pairs)
adj_info_ph = tf.placeholder(tf.int32,
shape=minibatch.adj.shape)
adj_info = tf.Variable(adj_info_ph,
trainable=False,
name="adj_info")
sampler = UniformNeighborSampler(adj_info) # 邻居采样，方式为随机重排邻居
state_nums = 2 # Controller定义的状态数量
layers_num = len(action) // state_nums # 计算层数
layer_infos = []
# 用于指导最终GNN的生成
layer_infos.append(
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1))
layer_infos.append(
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_1))
# 用于NAS的无监督GraphSage
model = NASUnsupervisedGraphsage(
placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
action=action,
state_nums=state_nums,
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
merged = tf.summary.merge_all()
summary_writer = tf.summary.FileWriter(log_dir(action),
sess.graph)
# Init variables
sess.run(tf.global_variables_initializer(),
feed_dict={adj_info_ph: minibatch.adj})
# Train model
train_shadow_mrr = None
shadow_mrr = None
total_steps = 0
avg_time = 0.0
epoch_val_costs = []
train_adj_info = tf.assign(adj_info, minibatch.adj)
val_adj_info = tf.assign(adj_info, minibatch.test_adj)
for epoch in range(FLAGS.epochs):
minibatch.shuffle()
iter = 0
print('Epoch: %04d' % (epoch + 1))
epoch_val_costs.append(0)
while not minibatch.end():
# Construct feed dictionary
feed_dict = minibatch.next_minibatch_feed_dict()
feed_dict.update(
{placeholders['dropout']: FLAGS.dropout})
t = time.time()
# Training step
outs = sess.run([
merged, model.opt_op, model.loss, model.ranks,
model.aff_all, model.mrr, model.outputs1
],
feed_dict=feed_dict)
train_cost = outs[2]
train_mrr = outs[5]
if train_shadow_mrr is None:
train_shadow_mrr = train_mrr #
else:
train_shadow_mrr -= (1 - 0.99) * (
train_shadow_mrr - train_mrr)
if iter % FLAGS.validate_iter == 0:
# Validation
sess.run(val_adj_info.op)
val_cost, ranks, val_mrr, duration = evaluate(
sess,
model,
minibatch,
size=FLAGS.validate_batch_size)
sess.run(train_adj_info.op)
epoch_val_costs[-1] += val_cost
if shadow_mrr is None:
shadow_mrr = val_mrr
else:
shadow_mrr -= (1 - 0.99) * (shadow_mrr - val_mrr)
if total_steps % FLAGS.print_every == 0:
summary_writer.add_summary(outs[0], total_steps)
# Print results
avg_time = (avg_time * total_steps + time.time() -
t) / (total_steps + 1)
if total_steps % FLAGS.print_every == 0:
print(
"Iter:",
'%04d' % iter,
"train_loss=",
"{:.5f}".format(train_cost),
"train_mrr=",
"{:.5f}".format(train_mrr),
"train_mrr_ema=",
"{:.5f}".format(
train_shadow_mrr
), # exponential moving average
"val_loss=",
"{:.5f}".format(val_cost),
"val_mrr=",
"{:.5f}".format(val_mrr),
"val_mrr_ema=",
"{:.5f}".format(
shadow_mrr), # exponential moving average
"time=",
"{:.5f}".format(avg_time))
iter += 1
total_steps += 1
if total_steps > FLAGS.max_total_steps:
break
if total_steps > FLAGS.max_total_steps:
break
print("Optimization Finished!")
sess.run(val_adj_info.op)
# val_losess,val_mrr, duration = incremental_evaluate(sess, model, minibatch,
# FLAGS.batch_size)
# print("Full validation stats:",
# "loss=", "{:.5f}".format(val_losess),
# "val_mrr=", "{:.5f}".format(val_mrr),
# "time=", "{:.5f}".format(duration))
if FLAGS.save_embeddings:
sess.run(val_adj_info.op)
embeds = save_val_embeddings(sess, model, minibatch,
FLAGS.validate_batch_size,
log_dir(action))
if FLAGS.model == "n2v":
# stopping the gradient for the already trained nodes
train_ids = tf.constant(
[[id_map[n]] for n in G.nodes_iter()
if not G.node[n]['val'] and not G.node[n]['test']
],
dtype=tf.int32)
test_ids = tf.constant(
[[id_map[n]] for n in G.nodes_iter()
if G.node[n]['val'] or G.node[n]['test']],
dtype=tf.int32)
update_nodes = tf.nn.embedding_lookup(
model.context_embeds, tf.squeeze(test_ids))
no_update_nodes = tf.nn.embedding_lookup(
model.context_embeds, tf.squeeze(train_ids))
update_nodes = tf.scatter_nd(
test_ids, update_nodes,
tf.shape(model.context_embeds))
no_update_nodes = tf.stop_gradient(
tf.scatter_nd(train_ids, no_update_nodes,
tf.shape(model.context_embeds)))
model.context_embeds = update_nodes + no_update_nodes
sess.run(model.context_embeds)
# run random walks
from graphsage.utils import run_random_walks
nodes = [
n for n in G.nodes_iter()
if G.node[n]["val"] or G.node[n]["test"]
]
start_time = time.time()
pairs = run_random_walks(G, nodes, num_walks=50)
walk_time = time.time() - start_time
test_minibatch = EdgeMinibatchIterator(
G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=pairs,
n2v_retrain=True,
fixed_n2v=True)
start_time = time.time()
print("Doing test training for n2v.")
test_steps = 0
for epoch in range(FLAGS.n2v_test_epochs):
test_minibatch.shuffle()
while not test_minibatch.end():
feed_dict = test_minibatch.next_minibatch_feed_dict(
)
feed_dict.update(
{placeholders['dropout']: FLAGS.dropout})
outs = sess.run([
model.opt_op, model.loss, model.ranks,
model.aff_all, model.mrr, model.outputs1
],
feed_dict=feed_dict)
if test_steps % FLAGS.print_every == 0:
print("Iter:", '%04d' % test_steps,
"train_loss=",
"{:.5f}".format(outs[1]),
"train_mrr=",
"{:.5f}".format(outs[-2]))
test_steps += 1
train_time = time.time() - start_time
save_val_embeddings(sess,
model,
minibatch,
FLAGS.validate_batch_size,
log_dir(action),
mod="-test")
print("Total time: ", train_time + walk_time)
print("Walk time: ", walk_time)
print("Train time: ", train_time)
setting = "val"
tf.reset_default_graph()
labels = train_data[4]
train_ids = [
n for n in G.nodes() if not G.node[n]['val'] and not G.node[n]['test']
]
test_ids = [n for n in G.nodes() if G.node[n][setting]]
train_labels = np.array([labels[i] for i in train_ids])
if train_labels.ndim == 1:
train_labels = np.expand_dims(train_labels, 1)
test_labels = np.array([labels[i] for i in test_ids])
id_map = {}
with open(log_dir(action) + "/val.txt") as fp:
for i, line in enumerate(fp):
id_map[line.strip()] = i
train_embeds = embeds[[id_map[str(id)] for id in train_ids]]
test_embeds = embeds[[id_map[str(id)] for id in test_ids]]
print("Running regression..")
regress_fun(train_embeds, train_labels, test_embeds, test_labels)
#用f1指数替换accuracy，此处未做滑动指数平均
return get_rewards(val_mrr), val_mrr
def train(train_data, test_data=None):
G = train_data[0]
features = train_data[1]
id_map = train_data[2]
homologs = train_data[5]
if not features is None:
# pad with dummy zero vector
features = np.vstack([features, np.zeros((features.shape[1],))])
context_pairs = train_data[3] if FLAGS.random_context else None
placeholders = construct_placeholders()
minibatch = EdgeMinibatchIterator(G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
homologs=homologs,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs = context_pairs)
adj_info_ph = tf.placeholder(tf.int32, shape=minibatch.adj.shape)
adj_info = tf.Variable(adj_info_ph, trainable=False, name="adj_info")
if FLAGS.model == 'graphsage_mean':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
model_size=FLAGS.model_size,
identity_dim = FLAGS.identity_dim,
homolog_loss=FLAGS.homolog_loss,
homolog_importance=FLAGS.homolog_importance,
logging=True)
elif FLAGS.model == 'gcn':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, 2*FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, 2*FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="gcn",
model_size=FLAGS.model_size,
identity_dim = FLAGS.identity_dim,
homolog_loss=FLAGS.homolog_loss,
homolog_importance=FLAGS.homolog_importance,
concat=False,
logging=True)
elif FLAGS.model == 'graphsage_seq':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
identity_dim = FLAGS.identity_dim,
aggregator_type="seq",
model_size=FLAGS.model_size,
homolog_loss=FLAGS.homolog_loss,
homolog_importance=FLAGS.homolog_importance,
logging=True)
elif FLAGS.model == 'graphsage_maxpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="maxpool",
model_size=FLAGS.model_size,
identity_dim = FLAGS.identity_dim,
homolog_loss=FLAGS.homolog_loss,
homolog_importance=FLAGS.homolog_importance,
logging=True)
elif FLAGS.model == 'graphsage_meanpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="meanpool",
model_size=FLAGS.model_size,
identity_dim = FLAGS.identity_dim,
homolog_loss=FLAGS.homolog_loss,
homolog_importance=FLAGS.homolog_importance,
logging=True)
elif FLAGS.model == 'n2v':
model = Node2VecModel(placeholders, features.shape[0],
minibatch.deg,
#2x because graphsage uses concat
nodevec_dim=2*FLAGS.dim_1,
lr=FLAGS.learning_rate)
else:
raise Exception('Error: model name unrecognized.')
config = tf.ConfigProto(log_device_placement=FLAGS.log_device_placement)
config.gpu_options.allow_growth = True
#config.gpu_options.per_process_gpu_memory_fraction = GPU_MEM_FRACTION
config.allow_soft_placement = True
# Initialize session
sess = tf.Session(config=config)
merged = tf.summary.merge_all()
summary_writer = tf.summary.FileWriter(log_dir(), sess.graph)
# Init variables
sess.run(tf.global_variables_initializer(), feed_dict={adj_info_ph: minibatch.adj})
# Train model
train_shadow_mrr = None
shadow_mrr = None
total_steps = 0
avg_time = 0.0
epoch_val_costs = []
train_adj_info = tf.assign(adj_info, minibatch.adj)
val_adj_info = tf.assign(adj_info, minibatch.test_adj)
for epoch in range(FLAGS.epochs):
minibatch.shuffle()
iter = 0
print('Epoch: %04d' % (epoch + 1))
epoch_val_costs.append(0)
while not minibatch.end():
# Construct feed dictionary
feed_dict = minibatch.next_minibatch_feed_dict()
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
t = time.time()
# Training step
outs = sess.run([merged, model.opt_op, model.loss, model.ranks, model.aff_all,
model.mrr, model.outputs1], feed_dict=feed_dict)
train_cost = outs[2]
train_mrr = outs[5]
train_embs = outs[-1]
# import pdb; pdb.set_trace()
if train_shadow_mrr is None:
train_shadow_mrr = train_mrr#
else:
train_shadow_mrr -= (1-0.99) * (train_shadow_mrr - train_mrr)
if iter % FLAGS.validate_iter == 0:
# Validation
sess.run(val_adj_info.op)
val_cost, ranks, val_mrr, duration = evaluate(sess, model, minibatch, size=FLAGS.validate_batch_size)
sess.run(train_adj_info.op)
epoch_val_costs[-1] += val_cost
if shadow_mrr is None:
shadow_mrr = val_mrr
else:
shadow_mrr -= (1-0.99) * (shadow_mrr - val_mrr)
if total_steps % FLAGS.print_every == 0:
summary_writer.add_summary(outs[0], total_steps)
# Print results
avg_time = (avg_time * total_steps + time.time() - t) / (total_steps + 1)
if total_steps % FLAGS.print_every == 0:
print("Iter:", '%010d' % iter,
"train_loss=", "{:.5f}".format(train_cost),
"train_mrr=", "{:.5f}".format(train_mrr),
"train_mrr_ema=", "{:.5f}".format(train_shadow_mrr), # exponential moving average
"val_loss=", "{:.5f}".format(val_cost),
"val_mrr=", "{:.5f}".format(val_mrr),
"val_mrr_ema=", "{:.5f}".format(shadow_mrr), # exponential moving average
"time=", "{:.5f}".format(avg_time))
iter += 1
total_steps += 1
if total_steps % 5000 == 0:
sess.run(val_adj_info.op)
save_val_embeddings(sess, model, minibatch, FLAGS.validate_batch_size, log_dir())
sess.run(train_adj_info.op)
if total_steps > FLAGS.max_total_steps:
break
if total_steps > FLAGS.max_total_steps:
break
print("Optimization Finished!")
if FLAGS.save_embeddings:
sess.run(val_adj_info.op)
save_val_embeddings(sess, model, minibatch, FLAGS.validate_batch_size, log_dir())
def train(train_data, test_data=None, sampler_name='Uniform'):
G = train_data[0]
features = train_data[1]
id_map = train_data[2]
if not features is None:
# pad with dummy zero vector
features = np.vstack([features, np.zeros((features.shape[1],))])
context_pairs = train_data[3] if FLAGS.random_context else None
placeholders = construct_placeholders()
minibatch = EdgeMinibatchIterator(G,
id_map,
placeholders, batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs = context_pairs)
adj_info_ph = tf.placeholder(tf.int32, shape=minibatch.adj.shape)
adj_info = tf.Variable(adj_info_ph, trainable=False, name="adj_info")
adj_shape = adj_info.get_shape().as_list()
if FLAGS.model == 'mean_concat':
# Create model
if sampler_name == 'Uniform':
sampler = UniformNeighborSampler(adj_info)
elif sampler_name == 'ML':
sampler = MLNeighborSampler(adj_info, features)
elif sampler_name == 'FastML':
sampler = FastMLNeighborSampler(adj_info, features)
#sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
concat=True,
layer_infos=layer_infos,
model_size=FLAGS.model_size,
identity_dim = FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'mean_add':
# Create model
if sampler_name == 'Uniform':
sampler = UniformNeighborSampler(adj_info)
elif sampler_name == 'ML':
sampler = MLNeighborSampler(adj_info, features)
elif sampler_name == 'FastML':
sampler = FastMLNeighborSampler(adj_info, features)
#sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
concat=False,
layer_infos=layer_infos,
model_size=FLAGS.model_size,
identity_dim = FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'gcn':
if sampler_name == 'Uniform':
sampler = UniformNeighborSampler(adj_info)
elif sampler_name == 'ML':
sampler = MLNeighborSampler(adj_info, features)
elif sampler_name == 'FastML':
sampler = FastMLNeighborSampler(adj_info, features)
# Create model
#sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, 2*FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, 2*FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="gcn",
model_size=FLAGS.model_size,
identity_dim = FLAGS.identity_dim,
concat=False,
logging=True)
elif FLAGS.model == 'graphsage_seq':
if sampler_name == 'Uniform':
sampler = UniformNeighborSampler(adj_info)
elif sampler_name == 'ML':
sampler = MLNeighborSampler(adj_info, features)
elif sampler_name == 'FastML':
sampler = FastMLNeighborSampler(adj_info, features)
#sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
identity_dim = FLAGS.identity_dim,
aggregator_type="seq",
model_size=FLAGS.model_size,
logging=True)
elif FLAGS.model == 'graphsage_maxpool':
if sampler_name == 'Uniform':
sampler = UniformNeighborSampler(adj_info)
elif sampler_name == 'ML':
sampler = MLNeighborSampler(adj_info, features)
elif sampler_name == 'FastML':
sampler = FastMLNeighborSampler(adj_info, features)
#sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="maxpool",
model_size=FLAGS.model_size,
identity_dim = FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'graphsage_meanpool':
if sampler_name == 'Uniform':
sampler = UniformNeighborSampler(adj_info)
elif sampler_name == 'ML':
sampler = MLNeighborSampler(adj_info, features)
elif sampler_name == 'FastML':
sampler = FastMLNeighborSampler(adj_info, features)
#sampler = UniformNeighborSampler(adj_info)
layer_infos = [SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="meanpool",
model_size=FLAGS.model_size,
identity_dim = FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'n2v':
model = Node2VecModel(placeholders, features.shape[0],
minibatch.deg,
#2x because graphsage uses concat
nodevec_dim=2*FLAGS.dim_1,
lr=FLAGS.learning_rate)
else:
raise Exception('Error: model name unrecognized.')
config = tf.ConfigProto(log_device_placement=FLAGS.log_device_placement)
config.gpu_options.allow_growth = True
#config.gpu_options.per_process_gpu_memory_fraction = GPU_MEM_FRACTION
config.allow_soft_placement = True
# Initialize session
sess = tf.Session(config=config)
merged = tf.summary.merge_all()
summary_writer = tf.summary.FileWriter(log_dir(sampler_name), sess.graph)
# Save model
saver = tf.train.Saver()
model_path = './model/unsup-' + FLAGS.train_prefix.split('/')[-1] + '-' + FLAGS.model_prefix + '-' + sampler_name
model_path += "/{model:s}_{model_size:s}_{lr:0.4f}/".format(
model=FLAGS.model,
model_size=FLAGS.model_size,
lr=FLAGS.learning_rate)
if not os.path.exists(model_path):
os.makedirs(model_path)
# Init variables
sess.run(tf.global_variables_initializer(), feed_dict={adj_info_ph: minibatch.adj})
# Restore params of ML sampler model
if sampler_name == 'ML' or sampler_name == 'FastML':
sampler_vars = tf.get_collection(tf.GraphKeys.GLOBAL_VARIABLES, scope="MLsampler")
#pdb.set_trace()
saver_sampler = tf.train.Saver(var_list=sampler_vars)
sampler_model_path = './model/MLsampler-unsup-' + FLAGS.train_prefix.split('/')[-1] + '-' + FLAGS.model_prefix
sampler_model_path += "/{model:s}_{model_size:s}_{lr:0.4f}/".format(
model=FLAGS.model,
model_size=FLAGS.model_size,
lr=FLAGS.learning_rate)
saver_sampler.restore(sess, sampler_model_path + 'model.ckpt')
# Train model
train_shadow_mrr = None
shadow_mrr = None
total_steps = 0
avg_time = 0.0
epoch_val_costs = []
train_adj_info = tf.assign(adj_info, minibatch.adj)
val_adj_info = tf.assign(adj_info, minibatch.test_adj)
val_cost_ = []
val_mrr_ = []
shadow_mrr_ = []
duration_ = []
ln_acc = sparse.csr_matrix((adj_shape[0], adj_shape[0]), dtype=np.float32)
lnc_acc = sparse.csr_matrix((adj_shape[0], adj_shape[0]), dtype=np.int32)
ln_acc = ln_acc.tolil()
lnc_acc = lnc_acc.tolil()
for epoch in range(FLAGS.epochs):
minibatch.shuffle()
iter = 0
print('Epoch: %04d' % (epoch + 1))
epoch_val_costs.append(0)
while not minibatch.end():
# Construct feed dictionary
feed_dict = minibatch.next_minibatch_feed_dict()
if feed_dict.values()[0] != FLAGS.batch_size:
break
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
t = time.time()
# Training step
outs = sess.run([merged, model.opt_op, model.loss, model.ranks, model.aff_all,
model.mrr, model.outputs1, model.loss_node, model.loss_node_count], feed_dict=feed_dict)
train_cost = outs[2]
train_mrr = outs[5]
if train_shadow_mrr is None:
train_shadow_mrr = train_mrr#
else:
train_shadow_mrr -= (1-0.99) * (train_shadow_mrr - train_mrr)
if iter % FLAGS.validate_iter == 0:
# Validation
sess.run(val_adj_info.op)
val_cost, ranks, val_mrr, duration = evaluate(sess, model, minibatch, size=FLAGS.validate_batch_size)
sess.run(train_adj_info.op)
epoch_val_costs[-1] += val_cost
if shadow_mrr is None:
shadow_mrr = val_mrr
else:
shadow_mrr -= (1-0.99) * (shadow_mrr - val_mrr)
val_cost_.append(val_cost)
val_mrr_.append(val_mrr)
shadow_mrr_.append(shadow_mrr)
duration_.append(duration)
if total_steps % FLAGS.print_every == 0:
summary_writer.add_summary(outs[0], total_steps)
# Print results
avg_time = (avg_time * total_steps + time.time() - t) / (total_steps + 1)
if total_steps % FLAGS.print_every == 0:
print("Iter:", '%04d' % iter,
"train_loss=", "{:.5f}".format(train_cost),
"train_mrr=", "{:.5f}".format(train_mrr),
"train_mrr_ema=", "{:.5f}".format(train_shadow_mrr), # exponential moving average
"val_loss=", "{:.5f}".format(val_cost),
"val_mrr=", "{:.5f}".format(val_mrr),
"val_mrr_ema=", "{:.5f}".format(shadow_mrr), # exponential moving average
"time=", "{:.5f}".format(avg_time))
ln = outs[7].values
ln_idx = outs[7].indices
ln_acc[ln_idx[:,0], ln_idx[:,1]] += ln
lnc = outs[8].values
lnc_idx = outs[8].indices
lnc_acc[lnc_idx[:,0], lnc_idx[:,1]] += lnc
iter += 1
total_steps += 1
if total_steps > FLAGS.max_total_steps:
break
if total_steps > FLAGS.max_total_steps:
break
print("Validation per epoch in training")
for ep in range(FLAGS.epochs):
print("Epoch: %04d"%ep, " val_cost={:.5f}".format(val_cost_[ep]), " val_mrr={:.5f}".format(val_mrr_[ep]), " val_mrr_ema={:.5f}".format(shadow_mrr_[ep]), " duration={:.5f}".format(duration_[ep]))
print("Optimization Finished!")
# Save model
save_path = saver.save(sess, model_path+'model.ckpt')
print ('model is saved at %s'%save_path)
# Save loss node and count
loss_node_path = './loss_node/unsup-' + FLAGS.train_prefix.split('/')[-1] + '-' + FLAGS.model_prefix + '-' + sampler_name
loss_node_path += "/{model:s}_{model_size:s}_{lr:0.4f}/".format(
model=FLAGS.model,
model_size=FLAGS.model_size,
lr=FLAGS.learning_rate)
if not os.path.exists(loss_node_path):
os.makedirs(loss_node_path)
loss_node = sparse.save_npz(loss_node_path + 'loss_node.npz', sparse.csr_matrix(ln_acc))
loss_node_count = sparse.save_npz(loss_node_path + 'loss_node_count.npz', sparse.csr_matrix(lnc_acc))
print ('loss and count per node is saved at %s'%loss_node_path)
if FLAGS.save_embeddings:
sess.run(val_adj_info.op)
save_val_embeddings(sess, model, minibatch, FLAGS.validate_batch_size, log_dir(sampler_name))
if FLAGS.model == "n2v":
# stopping the gradient for the already trained nodes
train_ids = tf.constant([[id_map[n]] for n in G.nodes_iter() if not G.node[n]['val'] and not G.node[n]['test']],
dtype=tf.int32)
test_ids = tf.constant([[id_map[n]] for n in G.nodes_iter() if G.node[n]['val'] or G.node[n]['test']],
dtype=tf.int32)
update_nodes = tf.nn.embedding_lookup(model.context_embeds, tf.squeeze(test_ids))
no_update_nodes = tf.nn.embedding_lookup(model.context_embeds,tf.squeeze(train_ids))
update_nodes = tf.scatter_nd(test_ids, update_nodes, tf.shape(model.context_embeds))
no_update_nodes = tf.stop_gradient(tf.scatter_nd(train_ids, no_update_nodes, tf.shape(model.context_embeds)))
model.context_embeds = update_nodes + no_update_nodes
sess.run(model.context_embeds)
# run random walks
from graphsage.utils import run_random_walks
nodes = [n for n in G.nodes_iter() if G.node[n]["val"] or G.node[n]["test"]]
start_time = time.time()
pairs = run_random_walks(G, nodes, num_walks=50)
walk_time = time.time() - start_time
test_minibatch = EdgeMinibatchIterator(G,
id_map,
placeholders, batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs = pairs,
n2v_retrain=True,
fixed_n2v=True)
start_time = time.time()
print("Doing test training for n2v.")
test_steps = 0
for epoch in range(FLAGS.n2v_test_epochs):
test_minibatch.shuffle()
while not test_minibatch.end():
feed_dict = test_minibatch.next_minibatch_feed_dict()
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
outs = sess.run([model.opt_op, model.loss, model.ranks, model.aff_all,
model.mrr, model.outputs1], feed_dict=feed_dict)
if test_steps % FLAGS.print_every == 0:
print("Iter:", '%04d' % test_steps,
"train_loss=", "{:.5f}".format(outs[1]),
"train_mrr=", "{:.5f}".format(outs[-2]))
test_steps += 1
train_time = time.time() - start_time
save_val_embeddings(sess, model, minibatch, FLAGS.validate_batch_size, log_dir(sampler_name), mod="-test")
print("Total time: ", train_time+walk_time)
print("Walk time: ", walk_time)
print("Train time: ", train_time)
def train(train_data,
log_dir,
Theta=None,
fixed_neigh_weights=None,
test_data=None,
neg_sample_weights=None):
G = train_data[0]
Gneg = Graph_complement(G)
features = train_data[1]
id_map = train_data[2]
Adj_mat = Edges_to_Adjacency_mat(G.edges(), len(G.nodes()))
# print('A in unsup: ', Adj_mat)
# negAdj_mat = Edges_to_Adjacency_mat(Gneg.edges(), len(Gneg.nodes()))
FLAGS.batch_size = batch_size_def(len(G.edges()))
FLAGS.negbatch_size = batch_size_def(len(Gneg.edges()))
FLAGS.samples_1 = min(25, len(G.nodes()))
FLAGS.samples_2 = min(10, len(G.nodes()))
FLAGS.negsamples_1 = min(25, len(Gneg.nodes()))
FLAGS.negsamples_2 = min(10, len(Gneg.nodes()))
FLAGS.neg_sample_size = FLAGS.batch_size
if (len(G.nodes()) <= small_big_threshold):
FLAGS.model_size = 'small'
else:
FLAGS.model_size = 'big'
if not features is None:
# pad with dummy zero vector
features = np.vstack([features, np.zeros((features.shape[1], ))])
context_pairs = train_data[3] if FLAGS.random_context else None
placeholders = construct_placeholders()
#print('placeholders: ', placeholders)
minibatch = EdgeMinibatchIterator(G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=context_pairs)
aggbatch_size = len(minibatch.agg_batch_Z1)
negaggbatch_size = len(minibatch.agg_batch_Z3)
negminibatch = EdgeMinibatchIterator(Gneg,
id_map,
placeholders,
batch_size=FLAGS.negbatch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=context_pairs)
#adj_info = tf.Variable(placeholders['adj_info_ph'], trainable=False, name="adj_info")
adj_info_ph = tf.placeholder(tf.int32,
shape=minibatch.adj.shape,
name="adj_info_ph")
adj_info = tf.Variable(adj_info_ph, trainable=False, name="adj_info")
if FLAGS.model == 'graphsage_mean':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1,
FLAGS.negsamples_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2,
FLAGS.negsamples_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
Adj_mat=Adj_mat,
non_edges=Gneg.edges(),
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True,
fixed_theta_1=Theta,
fixed_neigh_weights=fixed_neigh_weights,
neg_sample_weights=neg_sample_weights,
aggbatch_size=aggbatch_size,
negaggbatch_size=negaggbatch_size)
elif FLAGS.model == 'gcn':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, 2 * FLAGS.dim_1,
FLAGS.negsamples_1),
SAGEInfo("node", sampler, FLAGS.samples_2, 2 * FLAGS.dim_2,
FLAGS.negsamples_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="gcn",
Adj_mat=Adj_mat,
non_edges=Gneg.edges(),
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
concat=False,
logging=True,
fixed_theta_1=Theta,
fixed_neigh_weights=fixed_neigh_weights,
neg_sample_weights=neg_sample_weights,
aggbatch_size=aggbatch_size,
negaggbatch_size=negaggbatch_size)
elif FLAGS.model == 'graphsage_seq':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1,
FLAGS.negsamples_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2,
FLAGS.negsamples_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
identity_dim=FLAGS.identity_dim,
aggregator_type="seq",
Adj_mat=Adj_mat,
non_edges=Gneg.edges(),
model_size=FLAGS.model_size,
logging=True,
fixed_theta_1=Theta,
fixed_neigh_weights=fixed_neigh_weights,
neg_sample_weights=neg_sample_weights,
aggbatch_size=aggbatch_size,
negaggbatch_size=negaggbatch_size)
elif FLAGS.model == 'graphsage_maxpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1,
FLAGS.negsamples_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2,
FLAGS.negsamples_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="maxpool",
Adj_mat=Adj_mat,
non_edges=Gneg.edges(),
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True,
fixed_theta_1=Theta,
fixed_neigh_weights=fixed_neigh_weights,
neg_sample_weights=neg_sample_weights,
aggbatch_size=aggbatch_size,
negaggbatch_size=negaggbatch_size)
elif FLAGS.model == 'graphsage_meanpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1,
FLAGS.negsamples_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2,
FLAGS.negsamples_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="meanpool",
Adj_mat=Adj_mat,
non_edges=Gneg.edges(),
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True,
fixed_theta_1=Theta,
fixed_neigh_weights=fixed_neigh_weights,
neg_sample_weights=neg_sample_weights,
aggbatch_size=aggbatch_size,
negaggbatch_size=negaggbatch_size)
elif FLAGS.model == 'n2v':
model = Node2VecModel(
placeholders,
features.shape[0],
minibatch.deg,
#2x because graphsage uses concat
nodevec_dim=2 * FLAGS.dim_1,
lr=FLAGS.learning_rate)
else:
raise Exception('Error: model name unrecognized.')
config = tf.ConfigProto(log_device_placement=FLAGS.log_device_placement)
config.gpu_options.allow_growth = True
#config.gpu_options.per_process_gpu_memory_fraction = GPU_MEM_FRACTION
config.allow_soft_placement = True
# Initialize session
sess = tf.Session(config=config)
merged = tf.summary.merge_all()
#summary_writer = tf.summary.FileWriter(log_dir(), sess.graph)
# Init variables
#minibatch.adj = minibatch.adj.astype(np.int32)
#print('minibatch.adj.shape: %s, dtype: %s' % (minibatch.adj.shape, np.ndarray.dtype(minibatch.adj)))
sess.run(tf.global_variables_initializer(),
feed_dict={adj_info_ph: minibatch.adj})
# Train model
train_shadow_mrr = None
shadow_mrr = None
total_steps = 0
avg_time = 0.0
epoch_val_costs = []
train_adj_info = tf.assign(adj_info, minibatch.adj)
val_adj_info = tf.assign(adj_info, minibatch.test_adj)
print_flag = False
if (Theta is None):
print_flag = True
for epoch in range(FLAGS.epochs):
minibatch.shuffle()
negminibatch.shuffle()
iter = 0
# print('Epoch: %04d' % (epoch + 1))
epoch_val_costs.append(0)
if (FLAGS.model_size == 'big'):
whichbatch = minibatch
elif (len(G.edges()) > len(Gneg.edges())):
whichbatch = minibatch
opwhichbatch = negminibatch
else:
whichbatch = negminibatch
opwhichbatch = minibatch
while (not whichbatch.end()):
if (FLAGS.model_size == 'small' and opwhichbatch.end()):
opwhichbatch.shuffle()
# Construct feed dictionary
feed_dict = minibatch.next_minibatch_feed_dict()
negfeed_dict = negminibatch.next_minibatch_feed_dict()
if (True):
feed_dict.update({
placeholders['negbatch1']:
negfeed_dict[placeholders['batch1']]
})
feed_dict.update({
placeholders['negbatch2']:
negfeed_dict[placeholders['batch2']]
})
feed_dict.update({
placeholders['negbatch_size']:
negfeed_dict[placeholders['batch_size']]
})
else:
batch1 = feed_dict[placeholders['batch1']]
feed_dict.update({placeholders['negbatch1']: batch1})
feed_dict.update({
placeholders['negbatch2']:
negminibatch.feed_dict_negbatch(batch1)
})
feed_dict.update({
placeholders['negbatch_size']:
negfeed_dict[placeholders['batch_size']]
})
if (Theta is not None):
break
if (total_steps == 0):
print_summary(model, feed_dict, sess, Adj_mat, 'first',
print_flag)
t = time.time()
# Training step
outs = sess.run(
[
merged, model.opt_op, model.loss, model.ranks,
model.aff_all, model.mrr, model.outputs1, model.outputs2,
model.negoutputs1, model.negoutputs2
],
feed_dict=feed_dict
) #, model.current_similarity , model.learned_vars['theta_1'] # , model.aggregation
train_cost = outs[2]
train_mrr = outs[5]
# Z = outs[8]
# outs = np.concatenate((outs[6],outs[7]), axis=0)
# indices = np.concatenate((feed_dict[placeholders['batch1']],feed_dict[placeholders['batch2']]))
# Z = np.zeros((len(G.nodes()),FLAGS.dim_2*2))
# for node in G.nodes():
# Z[node,:] = outs[int(np.argwhere(indices==node)[0]),:]#[0:len(G.nodes())] # 8
# print('Z shape: ', Z.shape)
# if train_shadow_mrr is None:
# train_shadow_mrr = train_mrr #
# else:
# train_shadow_mrr -= (1-0.99) * (train_shadow_mrr - train_mrr)
#
# if iter % FLAGS.validate_iter == 0:
# # Validation
# sess.run(val_adj_info.op)
# val_cost, ranks, val_mrr, duration = evaluate(sess, model, minibatch, size=FLAGS.validate_batch_size, negminibatch_iter=negminibatch, placeholders=placeholders)
# sess.run(train_adj_info.op)
# epoch_val_costs[-1] += val_cost
#
# if shadow_mrr is None:
# shadow_mrr = val_mrr
# else:
# shadow_mrr -= (1-0.99) * (shadow_mrr - val_mrr)
# if total_steps % FLAGS.print_every == 0:
# summary_writer.add_summary(outs[0], total_steps)
# Print results
avg_time = (avg_time * total_steps + time.time() -
t) / (total_steps + 1)
if total_steps % FLAGS.print_every == 0:
print('loss: ', outs[2])
# print("Iter:", '%04d' % iter,
# "train_loss=", "{:.5f}".format(train_cost),
# "train_mrr=", "{:.5f}".format(train_mrr),
# "train_mrr_ema=", "{:.5f}".format(train_shadow_mrr), # exponential moving average
# "val_loss=", "{:.5f}".format(val_cost),
# "val_mrr=", "{:.5f}".format(val_mrr),
# "val_mrr_ema=", "{:.5f}".format(shadow_mrr), # exponential moving average
# "time=", "{:.5f}".format(avg_time))
# similarity_weights = outs[7]
# [new_adj_info, new_batch_edges] = sess.run([model.adj_info, \
# model.new_batch_edges], \
# feed_dict=feed_dict)
# minibatch.graph_update(new_adj_info, new_batch_edges)
iter += 1
total_steps += 1
if total_steps > FLAGS.max_total_steps:
break
if (Theta is not None):
break
if total_steps > FLAGS.max_total_steps:
break
# print("SGD Optimization Finished!")
# feed_dict = dict()
# feed_dict.update({placeholders['batch_size'] : len(G.nodes())})
# minibatch = EdgeMinibatchIterator(G,
# id_map,
# placeholders, batch_size = len(G.edges()),
# max_degree = FLAGS.max_degree,
# num_neg_samples = FLAGS.neg_sample_size,
# context_pairs = context_pairs)
# feed_dict = minibatch.next_minibatch_feed_dict()
# _, Z = sess.run([merged, model.aggregation], feed_dict=feed_dict) #, model.concat , aggregator_cls.vars
# Z_tilde = np.repeat(Z, [len(G.nodes())], axis=0)
# Z_tilde_tilde = np.tile(Z, (len(G.nodes()),1))
# final_theta_1 = Quadratic_SDP_solver (Z_tilde, Z_tilde_tilde, FLAGS.dim_1*2, FLAGS.dim_2*2)
# # Z_centralized = Z - np.mean(Z, axis=0)
# # final_adj_matrix = np.abs(np.matmul(Z_centralized, np.matmul(final_theta_1, np.transpose(Z_centralized))))
# final_adj_matrix = np.matmul(Z, np.matmul(final_theta_1, np.transpose(Z)))
# feed_dict = minibatch.next_minibatch_feed_dict()
# feed_dict.update({placeholders['dropout']: FLAGS.dropout})
# feed_dict.update({placeholders['all_nodes']: all_nodes})
# FLAGS.batch_size = len(G.edges())
# FLAGS.negbatch_size = len(Gneg.edges())
# FLAGS.samples_1 = len(G.nodes())
# FLAGS.samples_2 = len(G.nodes())
# FLAGS.negsamples_1 = len(Gneg.nodes())
# FLAGS.negsamples_2 = len(Gneg.nodes())
# feed_dict = minibatch.batch_feed_dict(G.edges())
# negfeed_dict = negminibatch.batch_feed_dict(Gneg.edges())
# feed_dict.update({placeholders['negbatch1']: negfeed_dict[placeholders['batch1']]})
# feed_dict.update({placeholders['negbatch2']: negfeed_dict[placeholders['batch2']]})
# feed_dict.update({placeholders['negbatch_size']: negfeed_dict[placeholders['batch_size']]})
# if(outs is not None):
# print('loss: ', outs[2])
final_adj_matrix, final_theta_1, Z, loss, U = print_summary(
model, feed_dict, sess, Adj_mat, 'last', print_flag)
#print('Z shape: ', Z.shape)
if FLAGS.save_embeddings:
sess.run(val_adj_info.op)
save_val_embeddings(sess, model, minibatch, FLAGS.validate_batch_size,
log_dir())
if FLAGS.model == "n2v":
# stopping the gradient for the already trained nodes
train_ids = tf.constant(
[[id_map[n]] for n in G.nodes_iter()
if not G.node[n]['val'] and not G.node[n]['test']],
dtype=tf.int32)
test_ids = tf.constant([[id_map[n]] for n in G.nodes_iter()
if G.node[n]['val'] or G.node[n]['test']],
dtype=tf.int32)
update_nodes = tf.nn.embedding_lookup(model.context_embeds,
tf.squeeze(test_ids))
no_update_nodes = tf.nn.embedding_lookup(model.context_embeds,
tf.squeeze(train_ids))
update_nodes = tf.scatter_nd(test_ids, update_nodes,
tf.shape(model.context_embeds))
no_update_nodes = tf.stop_gradient(
tf.scatter_nd(train_ids, no_update_nodes,
tf.shape(model.context_embeds)))
model.context_embeds = update_nodes + no_update_nodes
sess.run(model.context_embeds)
# run random walks
from graphsage.utils import run_random_walks
nodes = [
n for n in G.nodes_iter()
if G.node[n]["val"] or G.node[n]["test"]
]
start_time = time.time()
pairs = run_random_walks(G, nodes, num_walks=50)
walk_time = time.time() - start_time
test_minibatch = EdgeMinibatchIterator(
G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=pairs,
n2v_retrain=True,
fixed_n2v=True)
start_time = time.time()
print("Doing test training for n2v.")
test_steps = 0
for epoch in range(FLAGS.n2v_test_epochs):
test_minibatch.shuffle()
while not test_minibatch.end():
feed_dict = test_minibatch.next_minibatch_feed_dict()
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
outs = sess.run([
model.opt_op, model.loss, model.ranks, model.aff_all,
model.mrr, model.outputs1
],
feed_dict=feed_dict)
if test_steps % FLAGS.print_every == 0:
print("Iter:", '%04d' % test_steps, "train_loss=",
"{:.5f}".format(outs[1]), "train_mrr=",
"{:.5f}".format(outs[-2]))
test_steps += 1
train_time = time.time() - start_time
save_val_embeddings(sess,
model,
minibatch,
FLAGS.validate_batch_size,
log_dir(),
mod="-test")
print("Total time: ", train_time + walk_time)
print("Walk time: ", walk_time)
print("Train time: ", train_time)
#del adj_info_ph, adj_info,placeholders
return final_adj_matrix, G, final_theta_1, Z, loss, U #, learned_vars
def train(train_data, test_data=None):
G = train_data[0]
features = train_data[1]
id_map = train_data[2]
prob_matrix = train_data[5]
if not features is None:
# pad with dummy zero vector
features = np.vstack([features, np.zeros((features.shape[1], ))])
context_pairs = train_data[3] if FLAGS.random_context else None
placeholders = construct_placeholders()
minibatch = EdgeMinibatchIterator(G,
id_map,
placeholders,
prob_matrix,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=context_pairs)
adj_info_ph = tf.placeholder(tf.int32, shape=minibatch.adj.shape)
adj_info = tf.Variable(adj_info_ph, trainable=False, name="adj_info")
if FLAGS.model == 'graphsage_mean':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'gcn':
# Create model
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, 2 * FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, 2 * FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="gcn",
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
concat=False,
logging=True)
elif FLAGS.model == 'graphsage_seq':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
identity_dim=FLAGS.identity_dim,
aggregator_type="seq",
model_size=FLAGS.model_size,
logging=True)
elif FLAGS.model == 'graphsage_maxpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="maxpool",
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'graphsage_meanpool':
sampler = UniformNeighborSampler(adj_info)
layer_infos = [
SAGEInfo("node", sampler, FLAGS.samples_1, FLAGS.dim_1),
SAGEInfo("node", sampler, FLAGS.samples_2, FLAGS.dim_2)
]
model = SampleAndAggregate(placeholders,
features,
adj_info,
minibatch.deg,
layer_infos=layer_infos,
aggregator_type="meanpool",
model_size=FLAGS.model_size,
identity_dim=FLAGS.identity_dim,
logging=True)
elif FLAGS.model == 'n2v':
model = Node2VecModel(
placeholders,
features.shape[0],
minibatch.deg,
#2x because graphsage uses concat
nodevec_dim=2 * FLAGS.dim_1,
lr=FLAGS.learning_rate)
else:
raise Exception('Error: model name unrecognized.')
config = tf.ConfigProto(log_device_placement=FLAGS.log_device_placement)
config.gpu_options.allow_growth = True
#config.gpu_options.per_process_gpu_memory_fraction = GPU_MEM_FRACTION
config.allow_soft_placement = True
# Initialize session
sess = tf.Session(config=config)
merged = tf.summary.merge_all()
summary_writer = tf.summary.FileWriter(log_dir(), sess.graph)
# Init variables
sess.run(tf.global_variables_initializer(),
feed_dict={adj_info_ph: minibatch.adj})
# Train model
train_shadow_mrr = None
shadow_mrr = None
total_steps = 0
avg_time = 0.0
epoch_val_costs = []
train_adj_info = tf.assign(adj_info, minibatch.adj)
val_adj_info = tf.assign(adj_info, minibatch.test_adj)
min_train_loss = 0.0
fp = open(log_dir() + 'epoch_train_loss.txt', 'w')
loss_list = []
epoch_list = []
for epoch in range(FLAGS.epochs):
minibatch.shuffle()
epoch_train_loss = 0.0
iter = 0
print('Epoch: %04d' % (epoch + 1))
epoch_val_costs.append(0)
while not minibatch.end():
# Construct feed dictionary
feed_dict = minibatch.next_minibatch_feed_dict(layer_infos)
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
t = time.time()
# Training step
outs = sess.run([
merged, model.opt_op, model.loss, model.ranks, model.aff_all,
model.mrr, model.outputs1
],
feed_dict=feed_dict)
train_cost = outs[2]
train_mrr = outs[5]
epoch_train_loss += train_cost
if train_shadow_mrr is None:
train_shadow_mrr = train_mrr #
else:
train_shadow_mrr -= (1 - 0.99) * (train_shadow_mrr - train_mrr)
if total_steps % FLAGS.print_every == 0:
summary_writer.add_summary(outs[0], total_steps)
# Print results
avg_time = (avg_time * total_steps + time.time() -
t) / (total_steps + 1)
if total_steps % FLAGS.print_every == 0:
print(
"Iter:",
'%04d' % iter,
"train_loss=",
"{:.5f}".format(train_cost),
"train_mrr=",
"{:.5f}".format(train_mrr),
"train_mrr_ema=",
"{:.5f}".format(
train_shadow_mrr), # exponential moving average
"time=",
"{:.5f}".format(avg_time))
iter += 1
total_steps += 1
if total_steps > FLAGS.max_total_steps:
break
if total_steps > FLAGS.max_total_steps:
break
epoch_train_loss = epoch_train_loss / iter
print('epoch: ' + str(epoch) + '\t' + 'train_loss: ' +
str(epoch_train_loss) + '\n')
fp.write('epoch: ' + str(epoch) + '\t' + 'train_loss: ' +
str(epoch_train_loss) + '\n')
loss_list.append(epoch_train_loss)
epoch_list.append(epoch)
if epoch == 0:
min_train_loss = epoch_train_loss
sess.run(val_adj_info.op)
node_embeddings, node_list = save_val_embeddings(
sess, model, minibatch, FLAGS.validate_batch_size, log_dir(),
layer_infos)
elif epoch_train_loss < min_train_loss:
min_train_loss = epoch_train_loss
sess.run(val_adj_info.op)
node_embeddings, node_list = save_val_embeddings(
sess, model, minibatch, FLAGS.validate_batch_size, log_dir(),
layer_infos)
print("Optimization Finished!")
fp.close()
np.save(log_dir() + "val.npy", node_embeddings)
with open(log_dir() + "val.txt", "w") as fp:
fp.write("\n".join(map(str, node_list)))
plt.plot(epoch_list, loss_list)
plt.savefig(log_dir() + 'loss_trend.png')
plt.clf()
## t-SNE plot
## creating t-SNE embedding feature
#tsne_feat=TSNE(n_components=2).fit_transform(node_embeddings)
tsne_feat = node_embeddings
## plotting t-SNE embedding
tsne_df = pd.DataFrame(columns=['tsne0', 'tsne1'])
tsne_df['tsne0'] = tsne_feat[:, 0]
tsne_df['tsne1'] = tsne_feat[:, 1]
plt.figure(figsize=(16, 10))
sns.scatterplot(x="tsne0",
y="tsne1",
hue=node_list,
palette=sns.color_palette("hls", len(node_list)),
data=tsne_df,
legend=False,
alpha=0.3)
for i, txt in enumerate(node_list):
plt.annotate(txt, (tsne_df['tsne0'][i], tsne_df['tsne1'][i]))
plt.savefig(log_dir() + 't-SNE_plot_node_embeddings.png')
plt.show()
if FLAGS.save_embeddings:
sess.run(val_adj_info.op)
save_val_embeddings(sess, model, minibatch, FLAGS.validate_batch_size,
log_dir())
if FLAGS.model == "n2v":
# stopping the gradient for the already trained nodes
train_ids = tf.constant(
[[id_map[n]] for n in G.nodes_iter()
if not G.node[n]['val'] and not G.node[n]['test']],
dtype=tf.int32)
test_ids = tf.constant([[id_map[n]] for n in G.nodes_iter()
if G.node[n]['val'] or G.node[n]['test']],
dtype=tf.int32)
update_nodes = tf.nn.embedding_lookup(model.context_embeds,
tf.squeeze(test_ids))
no_update_nodes = tf.nn.embedding_lookup(model.context_embeds,
tf.squeeze(train_ids))
update_nodes = tf.scatter_nd(test_ids, update_nodes,
tf.shape(model.context_embeds))
no_update_nodes = tf.stop_gradient(
tf.scatter_nd(train_ids, no_update_nodes,
tf.shape(model.context_embeds)))
model.context_embeds = update_nodes + no_update_nodes
sess.run(model.context_embeds)
# run random walks
from graphsage.utils import run_random_walks
nodes = [
n for n in G.nodes_iter()
if G.node[n]["val"] or G.node[n]["test"]
]
start_time = time.time()
pairs = run_random_walks(G, nodes, num_walks=50)
walk_time = time.time() - start_time
test_minibatch = EdgeMinibatchIterator(
G,
id_map,
placeholders,
batch_size=FLAGS.batch_size,
max_degree=FLAGS.max_degree,
num_neg_samples=FLAGS.neg_sample_size,
context_pairs=pairs,
n2v_retrain=True,
fixed_n2v=True)
start_time = time.time()
print("Doing test training for n2v.")
test_steps = 0
for epoch in range(FLAGS.n2v_test_epochs):
test_minibatch.shuffle()
while not test_minibatch.end():
feed_dict = test_minibatch.next_minibatch_feed_dict(
layer_infos)
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
outs = sess.run([
model.opt_op, model.loss, model.ranks, model.aff_all,
model.mrr, model.outputs1
],
feed_dict=feed_dict)
if test_steps % FLAGS.print_every == 0:
print("Iter:", '%04d' % test_steps, "train_loss=",
"{:.5f}".format(outs[1]), "train_mrr=",
"{:.5f}".format(outs[-2]))
test_steps += 1
train_time = time.time() - start_time
save_val_embeddings(sess,
model,
minibatch,
FLAGS.validate_batch_size,
log_dir(),
mod="-test")
print("Total time: ", train_time + walk_time)
print("Walk time: ", walk_time)
print("Train time: ", train_time)