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semiGAE_mult.py
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semiGAE_mult.py
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from __future__ import division
from __future__ import print_function
import time
import tensorflow as tf
from sklearn.metrics import average_precision_score, roc_auc_score,precision_recall_fscore_support
from gcn.utils import *
from gcn.models import GCN,SemiGraphEncoder
from gcn.attentionModel import AttSemiGraphEncoder
# Set random seed
seed = 123
np.random.seed(seed)
tf.set_random_seed(seed)
# Settings
flags = tf.app.flags
FLAGS = flags.FLAGS
flags.DEFINE_string('dataset', 'ddi', 'Dataset string.')
flags.DEFINE_string('model', 'semiencoder', 'Model string.') # 'gcn', 'semiencoder', 'attSemiGAE'
flags.DEFINE_float('learning_rate', 0.01, 'Initial learning rate.')
flags.DEFINE_integer('epochs', 200, 'Number of epochs to train.')
flags.DEFINE_integer('hidden0', 100, 'Number of units in hidden layer 0.')
flags.DEFINE_integer('hidden1', 64, 'Number of units in hidden layer 1.')
flags.DEFINE_integer('hidden2', 32, 'Number of units in hidden layer 2.') #dimension of the node embeddings
flags.DEFINE_float('dropout', 0.5, 'Dropout rate (1 - keep probability).')
flags.DEFINE_float('weight_decay', 5e-3, 'Weight for L2 loss on embedding matrix.')
flags.DEFINE_integer('early_stopping', 50, 'Tolerance for early stopping (# of epochs).')
flags.DEFINE_integer('max_degree', 3, 'Maximum Chebyshev polynomial degree.')
def ddi_load_data_GCN(dataset_str):
"""Load data."""
names = ['allx', 'ally', 'graph',"adjmat", "trainMask", "valMask", "testMask"]
objects = []
for i in range(len(names)):
with open("DDIdata/ind.{}.{}".format(dataset_str, names[i]), 'rb') as f:
if sys.version_info > (3, 0):
objects.append(pkl.load(f, encoding='latin1'))
else:
objects.append(pkl.load(f))
x, y, graphs, adjmats, train_mask, val_mask, test_mask = tuple(objects)
tmpx = np.multiply(y, train_mask)
features = x
adjs = []
for adjmat in adjmats:
adjs.append(adjmat)
return adjs, features, x, y, train_mask, val_mask, test_mask
# Load data
adjs, features, x, y, train_mask, val_mask, test_mask = ddi_load_data_GCN(FLAGS.dataset)
# print(sum(y[np.where(test_mask>0)]))
# Some preprocessing
#features = preprocess_features(densefeatures)
#features = sparse_to_tuple(densefeatures)
if FLAGS.model == 'gcn':
support = []
for adj in adjs:
support.append(preprocess_adj_dense(adj))
num_supports = len(support)
model_func = GCN
elif FLAGS.model == 'semiencoder':
support = []
for adj in adjs:
support.append(preprocess_adj_dense(adj))
num_supports = len(support)
model_func = SemiGraphEncoder
elif FLAGS.model =="attSemiGAE":
support = []
for adj in adjs:
support.append(preprocess_adj_dense(adj))
num_supports = len(support)
model_func = AttSemiGraphEncoder
else:
raise ValueError('Invalid argument for model: ' + str(FLAGS.model))
# Define placeholders
placeholders = {
'support': [tf.placeholder(tf.float32) for _ in range(num_supports)],
'features': tf.placeholder(tf.float32, shape=(None, features.shape[1])),
'x_input': tf.placeholder(tf.float32, shape=(None, x.shape[1])),
'labels': tf.placeholder(tf.float32, shape=(None, y.shape[1])),
'labels_mask': tf.placeholder(tf.int32),
'dropout': tf.placeholder_with_default(0., shape=()),
'num_features_nonzero': tf.placeholder(tf.int32) # helper variable for sparse dropout
}
input_dim = features.shape[1]
# Create model
model = model_func(placeholders, input_dim=input_dim, logging=True)
# Initialize session
sess = tf.Session()
# Define model evaluation function
def evaluate(x, features, support, labels, mask, placeholders):
t_test = time.time()
feed_dict_val = construct_feed_dict(x, features, support, labels, mask, placeholders)
outs_val = sess.run([model.loss, model.accuracy, model.predict()], feed_dict=feed_dict_val)
return outs_val[0], outs_val[1], outs_val[2], (time.time() - t_test)
# Init variables
sess.run(tf.global_variables_initializer())
cost_val = []
summary_writer = tf.train.SummaryWriter('./tmp/ddilogs', sess.graph)
# Train model
for epoch in range(FLAGS.epochs):
t = time.time()
# Construct feed dictionary
feed_dict = construct_feed_dict(x, features, support, y, train_mask, placeholders)
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
# Training step
outs = sess.run([model.opt_op, model.loss, model.accuracy, model.activations,model.predict(),model.mix], feed_dict=feed_dict)
# print(outs[-1])
# test_preds = outs[4]
# test_preds = test_preds + test_preds.T
# testsubs = np.where(test_mask > 0)
# roc = roc_auc_score(y[testsubs], test_preds[testsubs])
# prauc = average_precision_score(y[testsubs], test_preds[testsubs])
# print("Test set results:", roc, prauc)
#summary_writer.add_summary(outs[0],epoch)
# for var in tf.trainable_variables():
# sess.run(var)
# Validation
cost, acc,_, duration = evaluate(x, features, support, y, val_mask, placeholders)
cost_val.append(cost)
# Print results
# print("Epoch:", '%04d' % (epoch + 1), "train_loss=", "{:.5f}".format(outs[1]),
# "train_acc=", "{:.5f}".format(outs[2]), "val_loss=", "{:.5f}".format(cost),
# "val_acc=", "{:.5f}".format(acc), "time=", "{:.5f}".format(time.time() - t))
if epoch > FLAGS.early_stopping and cost_val[-1] > np.mean(cost_val[-(FLAGS.early_stopping+1):-1]):
# print("Early stopping...")
break
#print("Optimization Finished!")
# Testing
test_cost, test_acc, test_preds, test_duration = evaluate(x, features, support, y, test_mask, placeholders)
test_preds = test_preds+test_preds.T
testsubs = np.where(test_mask>0)
roc = roc_auc_score(y[testsubs], test_preds[testsubs])
prauc = average_precision_score(y[testsubs], test_preds[testsubs])
# print("Test set results:", "cost=", "{:.5f}".format(test_cost),
# "accuracy=", "{:.5f}".format(test_acc), "time=", "{:.5f}".format(test_duration))
print("semiGAE_mult",roc, prauc)
# prec, recall, f, _ = precision_recall_fscore_support(y[testsubs]>=0.5, test_preds[testsubs]>=0.5, labels=[1,0])
# print(prec,recall,f)