def fit(self):
path = path_to_embedding(root=self.path_to_dumps,
method='hist_loss_' +
str(self.hist_loss_configuration),
name=self.graph_name,
dim=self.dim)
if self.use_cached:
if Path(path).exists():
E = read_embedding(path)
print("Loaded cached embedding from " + path)
return E
if self.hist_loss_configuration.linearity == 'linear':
E = self.run(should_stop=self.should_stop)
elif self.hist_loss_configuration.linearity == 'direct':
E = self.run_direct(should_stop=self.should_stop)
elif self.hist_loss_configuration.linearity == 'nonlinear2':
E = self.run_nonlinear2(should_stop=self.should_stop)
elif self.hist_loss_configuration.linearity == 'nonlinear2-reduce':
E = self.run_nonlinear2_reduce(should_stop=self.should_stop)
elif self.hist_loss_configuration.linearity == 'nonlinear3':
E = self.run_nonlinear3(should_stop=self.should_stop)
else:
raise Exception('Unknown linearity: ' +
self.hist_loss_configuration.linearity)
save_embedding(path, E=np.array(E), normalize=True)
def fit(self):
path = path_to_embedding(root=self.path_to_dumps,
method='hope',
name=self.graph_name,
dim=self.dim)
if self.use_cached:
if Path(path).exists():
E = read_embedding(path)
print("Loaded cached embedding from " + path)
return E
E = self.learn_embedding()
save_embedding(path, E=np.array(E))
def run_nonlinear3(self,
patience=100,
patience_delta=0.001,
learning_rate=0.1,
LOG_DIR='./tensorflow_events/',
should_stop=None,
save_intermediate=False):
tf.reset_default_graph()
bin_num = 64
N = self.graph.number_of_nodes()
batch_size = min(800, N)
print("Batch size:", str(batch_size))
_A_batched = tf.placeholder(tf.float32, [batch_size, N])
_batch_indxs = tf.placeholder(tf.int32, [batch_size])
_neg_sampling_indxs = tf.placeholder(tf.int32, [None])
_W_1 = tf.Variable(tf.random_uniform([N, N], -1.0, 1.0), name="W1")
_b_1 = tf.Variable(tf.zeros([N, N]), name="b1")
_W_2 = tf.Variable(tf.random_uniform([N, N], -1.0, 1.0), name="W2")
_b_2 = tf.Variable(tf.zeros([N, N]), name="b2")
_W_3 = tf.Variable(tf.random_uniform([N, self.dim], -1.0, 1.0),
name="W3")
_b_3 = tf.Variable(tf.zeros([N, self.dim]), name="b3")
_b_1_batched = tf.gather(_b_1, indices=_batch_indxs)
_b_2_batched = tf.gather(_b_2, indices=_batch_indxs)
_b_3_batched = tf.gather(_b_3, indices=_batch_indxs)
_E = tf.matmul(
tf.nn.sigmoid(
tf.matmul(
tf.nn.sigmoid(tf.matmul(_A_batched, _W_1) +
_b_1_batched), _W_2) + _b_2_batched),
_W_3) + _b_3_batched
_E_corr = self.preprocess_embedding(_E)
_A_batched_square = tf.gather(_A_batched, _batch_indxs, axis=1)
_neg_samples = self.calc_neg_samples(
_A_batched_square,
_E_corr,
method=self.hist_loss_configuration.calc_neg_method)
_pos_samples = self.calc_pos_samples(
_A_batched_square,
_E_corr,
method=self.hist_loss_configuration.calc_pos_method)
if N <= 1000:
_neg_samples = tf.gather(_neg_samples, _neg_sampling_indxs)
_pos_hist = self.calc_hist(
_pos_samples,
method=self.hist_loss_configuration.calc_hist_method,
bin_num=bin_num)
_neg_hist = self.calc_hist(
_neg_samples,
method=self.hist_loss_configuration.calc_hist_method,
bin_num=bin_num)
_loss = -self.calc_loss(
_neg_hist,
_pos_hist,
method=self.hist_loss_configuration.loss_method)
tf.summary.scalar("loss", _loss)
_optimizer = tf.train.GradientDescentOptimizer(
learning_rate=learning_rate).minimize(_loss)
_summary = tf.summary.merge_all()
G = self.graph
A = nx.adj_matrix(G).todense()
A = self.np_calc_simmatrix(
A, method=self.hist_loss_configuration.simmatrix_method)
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
writer = tf.summary.FileWriter(os.path.join(
LOG_DIR,
'{}_{}_{}_{}_{}').format(str(datetime.now().timestamp()),
self.dim,
self.hist_loss_configuration,
self.graph_name, batch_size),
graph=sess.graph)
prev_loss = 0
patience_counter = 0
for epoch in range(1000):
if epoch % 50 == 1:
print('epoch: ' + str(epoch) + ', loss: ' + str(loss))
if save_intermediate:
E = np.dot(
np.maximum(
np.dot(np.maximum(np.dot(A, W_1) + b_1, 0),
W_2) + b_2, 0), W_3) + b_3
save_embedding('E_' + str(epoch) + '.txt', np.array(E))
batch_indxs = np.random.choice(a=N,
size=batch_size).astype('int32')
A_batched = A[batch_indxs]
pos_count = np.count_nonzero(A_batched[:, batch_indxs])
neg_count = batch_size * N - pos_count
neg_sampling_indxs = np.random.choice(a=neg_count,
size=pos_count *
2).astype('int32')
run_options = tf.RunOptions(
trace_level=tf.RunOptions.FULL_TRACE)
run_metadata = tf.RunMetadata()
pos_hist, neg_hist, loss, _, summary, W_1, b_1, W_2, b_2, W_3, b_3 = sess.run(
[
_pos_hist,
_neg_hist,
_loss,
_optimizer,
_summary,
_W_1,
_b_1,
_W_2,
_b_2,
_W_3,
_b_3,
],
feed_dict={
_A_batched: A_batched,
_batch_indxs: batch_indxs,
_neg_sampling_indxs: neg_sampling_indxs,
},
options=run_options,
run_metadata=run_metadata)
writer.add_run_metadata(run_metadata, "step_{}".format(epoch))
writer.add_summary(summary, epoch)
if epoch > 0 and prev_loss - loss > patience_delta:
patience_counter = 0
else:
patience_counter += 1
if patience_counter > patience:
print("\tearly stopping at", epoch)
break
if should_stop:
if should_stop():
break
prev_loss = loss
E = np.dot(expit(np.dot(expit(np.dot(A, W_1) + b_1), W_2) + b_2),
W_3) + b_3
return E