class MethodGraphBertGraphClustering(BertPreTrainedModel):
learning_record_dict = {}
use_raw_feature = True
cluster_number = 0
lr = 0.001
weight_decay = 5e-4
max_epoch = 500
load_pretrained_path = ''
save_pretrained_path = ''
def __init__(self, config):
super(MethodGraphBertGraphClustering, self).__init__(config)
self.config = config
self.bert = MethodGraphBert(config)
self.init_weights()
def forward(self, raw_features, wl_role_ids, init_pos_ids, hop_dis_ids):
outputs = self.bert(raw_features, wl_role_ids, init_pos_ids,
hop_dis_ids)
sequence_output = 0
for i in range(self.config.k + 1):
sequence_output += outputs[0][:, i, :]
sequence_output /= float(self.config.k + 1)
kmeans = KMeans(n_clusters=self.cluster_number,
max_iter=self.max_epoch)
if self.use_raw_feature:
clustering_result = kmeans.fit_predict(self.data['X'])
else:
clustering_result = kmeans.fit_predict(sequence_output.tolist())
return {'pred_y': clustering_result, 'true_y': self.data['y']}
def train_model(self, max_epoch):
t_begin = time.time()
clustering = self.forward(self.data['raw_embeddings'],
self.data['wl_embedding'],
self.data['int_embeddings'],
self.data['hop_embeddings'])
self.learning_record_dict = clustering
def run(self):
if self.load_pretrained_path != '':
self.use_raw_feature = False
print('loading pretrained model from ' +
self.load_pretrained_path + '...')
self.bert = MethodGraphBert.from_pretrained(
self.load_pretrained_path)
self.train_model(self.max_epoch)
if self.save_pretrained_path != '':
print('saving pretrained model to ' + self.save_pretrained_path +
'...')
self.bert.save_pretrained(self.save_pretrained_path)
return self.learning_record_dict
def __init__(self, config):
super(MethodGraphBertNodeConstruct, self).__init__(config)
self.place = torch.device('cuda:0')
self.config = config
self.bert = MethodGraphBert(config).to(device=self.place)
self.cls_y = torch.nn.Linear(config.hidden_size, config.x_size).to(device=self.place)
self.init_weights()
def __init__(self, config):
super(MethodGraphBertNodeClassification, self).__init__(config)
self.config = config
self.bert = MethodGraphBert(config)
self.res_h = torch.nn.Linear(config.x_size, config.hidden_size)
self.res_y = torch.nn.Linear(config.x_size, config.y_size)
self.cls_y = torch.nn.Linear(config.hidden_size, config.y_size)
self.init_weights()
def __init__(self, config, pretrained_path):
super(MethodGraphBertGraphRecovery, self).__init__(config)
self.place = torch.device('cuda:0')
self.config = config
self.bert = MethodGraphBert(config).to(self.place)
if pretrained_path is not None:
print("Load pretraiend model from {}".format(pretrained_path))
self.bert.from_pretrained(pretrained_path).to(self.place)
self.init_weights()
def __init__(self, config, pretrained_path, dataset_name):
super(MethodGraphBertNodeClassification, self).__init__(config)
self.place = torch.device('cuda:0')
self.config = config
self.bert = MethodGraphBert(config).to(device=self.place)
# load from pretrained model if necessary
if pretrained_path is not None:
self.bert = self.bert.from_pretrained(pretrained_path).to(device=self.place)
self.res_h = torch.nn.Linear(config.x_size, config.hidden_size).to(device=self.place)
self.res_y = torch.nn.Linear(config.x_size, config.y_size).to(device=self.place)
self.cls_y = torch.nn.Linear(config.hidden_size, config.y_size).to(device=self.place)
self.init_weights()
self.evaluator = Evaluator(dataset_name)
def __init__(self, config, pretrained_path):
super(MethodGraphBertNodeClassification, self).__init__(config)
self.device = torch.device('cuda:0')
self.config = config
self.bert = MethodGraphBert(config).to(self.device)
if pretrained_path is not None:
print("Load pretrained model from {}".format(pretrained_path))
self.bert.from_pretrained(pretrained_path).to(self.device)
self.res_h = torch.nn.Linear(config.x_size,
config.hidden_size).to(self.device)
self.res_y = torch.nn.Linear(config.x_size,
config.y_size).to(self.device)
self.cls_y = torch.nn.Linear(config.hidden_size,
config.y_size).to(self.device)
self.init_weights()
def run(self):
if self.load_pretrained_path != '':
print('loading pretrained model from ' + self.load_pretrained_path + '...')
self.bert = MethodGraphBert.from_pretrained(self.load_pretrained_path)
self.train_model(self.max_epoch)
if self.save_pretrained_path != '':
print('saving pretrained model to ' + self.save_pretrained_path + '...')
self.bert.save_pretrained(self.save_pretrained_path)
return self.learning_record_dict
class MethodGraphBertNodeClassification(BertPreTrainedModel):
learning_record_dict = {}
lr = 0.001
weight_decay = 5e-4
max_epoch = 500
spy_tag = True
load_pretrained_path = ''
save_pretrained_path = ''
def __init__(self, config, pretrained_path):
super(MethodGraphBertNodeClassification, self).__init__(config)
self.device = torch.device('cuda:0')
self.config = config
self.bert = MethodGraphBert(config).to(self.device)
if pretrained_path is not None:
print("Load pretrained model from {}".format(pretrained_path))
self.bert.from_pretrained(pretrained_path).to(self.device)
self.res_h = torch.nn.Linear(config.x_size,
config.hidden_size).to(self.device)
self.res_y = torch.nn.Linear(config.x_size,
config.y_size).to(self.device)
self.cls_y = torch.nn.Linear(config.hidden_size,
config.y_size).to(self.device)
self.init_weights()
def forward(self,
raw_features,
wl_role_ids,
init_pos_ids,
hop_dis_ids,
idx=None):
residual_h, residual_y = self.residual_term()
if idx is not None:
if residual_h is None:
outputs = self.bert(raw_features[idx],
wl_role_ids[idx],
init_pos_ids[idx],
hop_dis_ids[idx],
residual_h=None)
else:
outputs = self.bert(raw_features[idx],
wl_role_ids[idx],
init_pos_ids[idx],
hop_dis_ids[idx],
residual_h=residual_h[idx])
residual_y = residual_y[idx]
else:
if residual_h is None:
outputs = self.bert(raw_features,
wl_role_ids,
init_pos_ids,
hop_dis_ids,
residual_h=None)
else:
outputs = self.bert(raw_features,
wl_role_ids,
init_pos_ids,
hop_dis_ids,
residual_h=residual_h)
sequence_output = 0
for i in range(self.config.k + 1):
sequence_output += outputs[0][:, i, :]
sequence_output /= float(self.config.k + 1)
labels = self.cls_y(sequence_output)
if residual_y is not None:
labels += residual_y
return F.log_softmax(labels, dim=1)
def residual_term(self):
if self.config.residual_type == 'none':
return None, None
elif self.config.residual_type == 'raw':
return self.res_h(self.data['X']), self.res_y(self.data['X'])
elif self.config.residual_type == 'graph_raw':
return torch.spmm(self.data['A'],
self.res_h(self.data['X'])), torch.spmm(
self.data['A'], self.res_y(self.data['X']))
def train_model(self, max_epoch):
t_begin = time.time()
optimizer = optim.Adam(self.parameters(),
lr=self.lr,
weight_decay=self.weight_decay)
accuracy = EvaluateAcc('', '')
for name in [
'raw_embeddings', 'wl_embedding', 'int_embeddings',
'hop_embeddings', 'idx_train', 'y', 'X', 'A'
]:
self.data[name] = self.data[name].to(self.device)
max_score = 0.0
for epoch in range(max_epoch):
t_epoch_begin = time.time()
self.train()
optimizer.zero_grad()
output = self.forward(self.data['raw_embeddings'],
self.data['wl_embedding'],
self.data['int_embeddings'],
self.data['hop_embeddings'],
self.data['idx_train'])
loss_train = F.cross_entropy(
output, self.data['y'][self.data['idx_train']])
accuracy.data = {
'true_y': self.data['y'][self.data['idx_train']],
'pred_y': output.max(1)[1]
}
acc_train = accuracy.evaluate()
loss_train.backward()
optimizer.step()
self.eval()
output = self.forward(self.data['raw_embeddings'],
self.data['wl_embedding'],
self.data['int_embeddings'],
self.data['hop_embeddings'],
self.data['idx_val'])
loss_val = F.cross_entropy(output,
self.data['y'][self.data['idx_val']])
accuracy.data = {
'true_y': self.data['y'][self.data['idx_val']],
'pred_y': output.max(1)[1]
}
acc_val = accuracy.evaluate()
#-------------------------
#---- keep records for drawing convergence plots ----
output = self.forward(self.data['raw_embeddings'],
self.data['wl_embedding'],
self.data['int_embeddings'],
self.data['hop_embeddings'],
self.data['idx_test'])
loss_test = F.cross_entropy(output,
self.data['y'][self.data['idx_test']])
accuracy.data = {
'true_y': self.data['y'][self.data['idx_test']],
'pred_y': output.max(1)[1]
}
acc_test = accuracy.evaluate()
self.learning_record_dict[epoch] = {
'loss_train': loss_train.item(),
'acc_train': acc_train.item(),
'loss_val': loss_val.item(),
'acc_val': acc_val.item(),
'loss_test': loss_test.item(),
'acc_test': acc_test.item(),
'time': time.time() - t_epoch_begin
}
# -------------------------
if epoch % 10 == 0:
print('Epoch: {:04d}'.format(epoch + 1),
'loss_train: {:.4f}'.format(loss_train.item()),
'acc_train: {:.4f}'.format(acc_train.item()),
'loss_val: {:.4f}'.format(loss_val.item()),
'acc_val: {:.4f}'.format(acc_val.item()),
'loss_test: {:.4f}'.format(loss_test.item()),
'acc_test: {:.4f}'.format(acc_test.item()),
'time: {:.4f}s'.format(time.time() - t_epoch_begin))
print("Optimization Finished!")
print("Total time elapsed: {:.4f}s".format(time.time() - t_begin) +
', best testing performance {: 4f}'.format(
np.max([
self.learning_record_dict[epoch]['acc_test']
for epoch in self.learning_record_dict
])) + ', minimun loss {: 4f}'.format(
np.min([
self.learning_record_dict[epoch]['loss_test']
for epoch in self.learning_record_dict
])))
return time.time() - t_begin, np.max([
self.learning_record_dict[epoch]['acc_test']
for epoch in self.learning_record_dict
])
def run(self):
self.train_model(self.max_epoch)
return self.learning_record_dict
def __init__(self, config):
super(MethodGraphBertGraphClustering, self).__init__(config)
self.config = config
self.bert = MethodGraphBert(config)
self.init_weights()
def __init__(self, config):
super(MethodGraphBertGraphRecovery, self).__init__(config)
self.config = config
self.bert = MethodGraphBert(config)
self.init_weights()
class MethodGraphBertGraphRecovery(BertPreTrainedModel):
learning_record_dict = {}
lr = 0.001
weight_decay = 5e-4
max_epoch = 500
load_pretrained_path = ''
save_pretrained_path = ''
def __init__(self, config):
super(MethodGraphBertGraphRecovery, self).__init__(config)
self.config = config
self.bert = MethodGraphBert(config)
self.init_weights()
def forward(self,
raw_features,
wl_role_ids,
init_pos_ids,
hop_dis_ids,
idx=None):
outputs = self.bert(raw_features, wl_role_ids, init_pos_ids,
hop_dis_ids)
sequence_output = 0
for i in range(self.config.k + 1):
sequence_output += outputs[0][:, i, :]
sequence_output /= float(self.config.k + 1)
x_hat = sequence_output
x_norm = torch.norm(x_hat, p=2, dim=1)
nume = torch.mm(x_hat, x_hat.t())
deno = torch.ger(x_norm, x_norm)
cosine_similarity = nume / deno
return cosine_similarity
def train_model(self, max_epoch):
t_begin = time.time()
optimizer = optim.Adam(self.parameters(),
lr=self.lr,
weight_decay=self.weight_decay)
for epoch in range(max_epoch):
t_epoch_begin = time.time()
# -------------------------
self.train()
optimizer.zero_grad()
output = self.forward(self.data['raw_embeddings'],
self.data['wl_embedding'],
self.data['int_embeddings'],
self.data['hop_embeddings'])
row_num, col_num = output.size()
loss_train = torch.sum(
(output - self.data['A'].to_dense())**2) / (row_num * col_num)
loss_train.backward()
optimizer.step()
self.learning_record_dict[epoch] = {
'loss_train': loss_train.item(),
'time': time.time() - t_epoch_begin
}
# -------------------------
if epoch % 50 == 0:
print('Epoch: {:04d}'.format(epoch + 1),
'loss_train: {:.4f}'.format(loss_train.item()),
'time: {:.4f}s'.format(time.time() - t_epoch_begin))
print("Optimization Finished!")
print("Total time elapsed: {:.4f}s".format(time.time() - t_begin))
return time.time() - t_begin
def run(self):
if self.load_pretrained_path != '':
print('loading pretrained model from ' +
self.load_pretrained_path + '...')
self.bert = MethodGraphBert.from_pretrained(
self.load_pretrained_path)
self.train_model(self.max_epoch)
if self.save_pretrained_path != '':
print('saving pretrained model to ' + self.save_pretrained_path +
'...')
self.bert.save_pretrained(self.save_pretrained_path)
return self.learning_record_dict
class MethodGraphBertNodeConstruct(BertPreTrainedModel):
learning_record_dict = {}
lr = 0.001
weight_decay = 5e-4
max_epoch = 500
load_pretrained_path = ''
save_pretrained_path = ''
def __init__(self, config):
super(MethodGraphBertNodeConstruct, self).__init__(config)
self.config = config
self.bert = MethodGraphBert(config)
self.cls_y = torch.nn.Linear(config.hidden_size, config.x_size)
self.init_weights()
def forward(self, raw_features, wl_role_ids, init_pos_ids, hop_dis_ids, idx=None):
outputs = self.bert(raw_features, wl_role_ids, init_pos_ids, hop_dis_ids)
sequence_output = 0
for i in range(self.config.k+1):
sequence_output += outputs[0][:,i,:]
sequence_output /= float(self.config.k+1)
x_hat = self.cls_y(sequence_output)
return x_hat
def train_model(self, max_epoch):
t_begin = time.time()
optimizer = optim.Adam(self.parameters(), lr=self.lr, weight_decay=self.weight_decay)
for epoch in range(max_epoch):
t_epoch_begin = time.time()
# -------------------------
self.train()
optimizer.zero_grad()
output = self.forward(self.data['raw_embeddings'], self.data['wl_embedding'], self.data['int_embeddings'], self.data['hop_embeddings'])
loss_train = F.mse_loss(output, self.data['X'])
loss_train.backward()
optimizer.step()
self.learning_record_dict[epoch] = {'loss_train': loss_train.item(), 'time': time.time() - t_epoch_begin}
# -------------------------
if epoch % 50 == 0:
print('Epoch: {:04d}'.format(epoch + 1),
'loss_train: {:.4f}'.format(loss_train.item()),
'time: {:.4f}s'.format(time.time() - t_epoch_begin))
print("Optimization Finished!")
print("Total time elapsed: {:.4f}s".format(time.time() - t_begin))
return time.time() - t_begin
def run(self):
if self.load_pretrained_path != '':
print('loading pretrained model from ' + self.load_pretrained_path + '...')
self.bert = MethodGraphBert.from_pretrained(self.load_pretrained_path)
self.train_model(self.max_epoch)
if self.save_pretrained_path != '':
print('saving pretrained model to ' + self.save_pretrained_path + '...')
self.bert.save_pretrained(self.save_pretrained_path)
return self.learning_record_dict
class MethodGraphBertNodeConstruct(BertPreTrainedModel):
learning_record_dict = {}
lr = 0.001
weight_decay = 5e-4
max_epoch = 500
load_pretrained_path = ''
save_pretrained_path = ''
def __init__(self, config):
super(MethodGraphBertNodeConstruct, self).__init__(config)
self.place = torch.device('cuda:0')
self.config = config
self.bert = MethodGraphBert(config).to(device=self.place)
self.cls_y = torch.nn.Linear(config.hidden_size, config.x_size).to(device=self.place)
self.init_weights()
def forward(self, raw_features, wl_role_ids=None, init_pos_ids=None, hop_dis_ids=None, idx=None):
# raw features (N, L, D)
outputs = self.bert(raw_features, wl_role_ids, init_pos_ids, hop_dis_ids)
sequence_output = 0
for i in range(self.config.k+1):
sequence_output += outputs[0][:,i,:]
sequence_output /= float(self.config.k+1)
x_hat = self.cls_y(sequence_output) # (N, D)
x_hat = torch.unsqueeze(x_hat, dim=1) # (N, L, D)
scores = torch.sum(x_hat * raw_features, axis=-1) # (N, L)
return scores
def train_epoch(self):
self.train()
total_loss = 0.0
total_num = 0
for x, x_context, x_wl, y in self.dataloader:
length = x.shape[0]
x_feat = x.to(self.place)
x_context_feat = x_context.to(self.place)
x_wl = x_wl.to(self.place)
output = self.forward(x_context_feat, x_wl)
_, y_pred = torch.max(output, dim=-1)
y_true = torch.zeros_like(y_pred, dtype=torch.int64) # (N, L)
loss_train = F.cross_entropy(output, y_true, reduce='sum')
self.optimizer.zero_grad()
loss_train.backward()
self.optimizer.step()
with torch.no_grad():
total_num += length
total_loss += loss_train.item()
return total_loss / total_num
def train_model(self, max_epoch):
t_begin = time.time()
self.optimizer = optim.Adam(self.parameters(), lr=self.lr, weight_decay=self.weight_decay)
self.dataloader = DataLoader(self.data, batch_size=512, shuffle=True, num_workers=2)
for epoch in range(max_epoch):
t_epoch_begin = time.time()
# -------------------------
loss_train = self.train_epoch()
self.learning_record_dict[epoch] = {'loss_train': loss_train, 'time': time.time() - t_epoch_begin}
# -------------------------
if epoch % 1 == 0:
print('Epoch: {:04d}'.format(epoch + 1),
'loss_train: {:.4f}'.format(loss_train),
'time: {:.4f}s'.format(time.time() - t_epoch_begin))
print("Optimization Finished!")
print("Total time elapsed: {:.4f}s".format(time.time() - t_begin))
return time.time() - t_begin
def run(self):
self.train_model(self.max_epoch)
self.bert.save_pretrained(self.save_pretrained_path)
print("Save pretrained model in {}".format(self.save_pretrained_path))
return self.learning_record_dict
class MethodGraphBertNodeClassification(BertPreTrainedModel):
learning_record_dict = {}
lr = 0.001
weight_decay = 5e-4
max_epoch = 500
load_pretrained_path = ''
save_pretrained_path = ''
def __init__(self, config, pretrained_path, dataset_name):
super(MethodGraphBertNodeClassification, self).__init__(config)
self.place = torch.device('cuda:0')
self.config = config
self.bert = MethodGraphBert(config).to(device=self.place)
# load from pretrained model if necessary
if pretrained_path is not None:
self.bert = self.bert.from_pretrained(pretrained_path).to(device=self.place)
self.res_h = torch.nn.Linear(config.x_size, config.hidden_size).to(device=self.place)
self.res_y = torch.nn.Linear(config.x_size, config.y_size).to(device=self.place)
self.cls_y = torch.nn.Linear(config.hidden_size, config.y_size).to(device=self.place)
self.init_weights()
self.evaluator = Evaluator(dataset_name)
def forward(self, context_feat, wl_role_ids=None, node_feat=None, init_pos_ids=None, hop_dis_ids=None, idx=None):
residual_h, residual_y = self.residual_term(node_feat)
outputs = self.bert(context_feat, wl_role_ids, init_pos_ids, hop_dis_ids, residual_h=residual_h)
sequence_output = 0
for i in range(self.config.k+1):
sequence_output += outputs[0][:,i,:]
sequence_output /= float(self.config.k+1)
labels = self.cls_y(sequence_output)
if residual_y is not None:
labels += residual_y
return F.log_softmax(labels, dim=1)
def residual_term(self, node_feat):
if self.config.residual_type == 'none':
return None, None
elif self.config.residual_type == 'raw':
return self.res_h(node_feat), self.res_y(node_feat)
elif self.config.residual_type == 'graph_raw':
return torch.spmm(self.data['A'], self.res_h(self.data['X'])), torch.spmm(self.data['A'], self.res_y(self.data['X']))
def train_epoch(self):
self.train()
total_loss, total_right, total_num = 0.0, 0.0, 0.0
for x, x_context, x_wl, y in self.dataloader:
length = x.shape[0]
x_feat = x.to(self.place)
x_context_feat = x_context.to(self.place)
x_wl = x_wl.to(self.place)
y = y.to(self.place)
output = self.forward(x_context_feat, wl_role_ids=x_wl, node_feat=x_feat)
loss_train = F.cross_entropy(output, y, reduction='sum')
self.optimizer.zero_grad()
loss_train.backward()
self.optimizer.step()
with torch.no_grad():
total_num += length
total_loss += loss_train.item()
_, pred = torch.max(output, dim=1)
total_right += torch.sum(pred == y)
return total_loss / total_num, total_right / total_num
def eval_epoch(self):
self.eval()
total_loss, total_right, total_num = 0.0, 0.0, 0.0
with torch.no_grad():
for x, x_context, x_wl, y in self.dataloader:
length = x.shape[0]
x_feat = x.to(self.place)
x_context_feat = x_context.to(self.place)
x_wl = x_wl.to(self.place)
y = y.to(self.place)
output = self.forward(x_context_feat, wl_role_ids=x_wl, node_feat=x_feat)
loss_train = F.cross_entropy(output, y, reduction='sum')
total_num += length
total_loss += loss_train.item()
_, pred = torch.max(output, dim=1)
total_right += torch.sum(pred == y)
return total_loss / total_num, total_right / total_num
def train_model(self, max_epoch):
t_begin = time.time()
self.optimizer = optim.Adam(self.parameters(), lr=self.lr, weight_decay=self.weight_decay)
self.dataloader = DataLoader(self.data, batch_size=512, shuffle=True, num_workers=2)
# self.val_dataloader = DataLoader(self.data[self.data.split['valid']], batch_size=512, shuffle=False, num_workers=2)
for epoch in range(max_epoch):
t_epoch_begin = time.time()
loss_train, acc_train = self.train_epoch()
self.learning_record_dict[epoch] = {'loss_train': loss_train, "acc_train": acc_train, 'time': time.time() - t_epoch_begin}
if epoch % 1 == 0:
print('| Epoch: {:04d} |'.format(epoch + 1),
'loss_train: {:.4f}'.format(loss_train),
'acc_train: {:.3f} |'.format(acc_train*100),
'time: {:.4f}s |'.format(time.time() - t_epoch_begin))
print("Optimization Finished!")
print("Total time elapsed: {:.4f}s".format(time.time() - t_begin))
return time.time() - t_begin
def run(self):
self.train_model(self.max_epoch)
self.bert.save_pretrained(self.save_pretrained_path)
print("Save Node Classification model in {}".format(self.save_pretrained_path))
return self.learning_record_dict
