def setup_logger(args):
log_file = args.log_file
tensorboard_log_dir = 'tensorboard_' + args.name
shutil.rmtree(tensorboard_log_dir)
if args.log_file is None:
if args.name == '':
log_file = 'train.log'
else:
log_file = args.name + '.log'
print('Logging to: ' + log_file)
logging.basicConfig(filename=log_file, level=logging.INFO)
tensorboard_logger.configure(tensorboard_log_dir)
def __init__(self, args, net, G_data):
self.args = args
self.net = net
self.feat_dim = G_data.feat_dim
# self.fold_idx = G_data.fold_idx
self.fold_idx = 0
self.init(args, G_data.train_gs, G_data.valid_gs, G_data.test_gs)
if torch.cuda.is_available():
self.net.cuda()
tensorboard_log_dir = 'tensorboard/%s_%s_%s' % (
"graph-u-net", args.data, args.label_type)
os.makedirs(tensorboard_log_dir, exist_ok=True)
shutil.rmtree(tensorboard_log_dir)
tensorboard_logger.configure(tensorboard_log_dir)
logger.info('tensorboard logging to %s', tensorboard_log_dir)
type=int,
default=5,
help="Neighborhood size (only useful for pscn)")
args = parser.parse_args()
args.cuda = not args.no_cuda and torch.cuda.is_available()
np.random.seed(args.seed)
torch.manual_seed(args.seed)
if args.cuda:
torch.cuda.manual_seed(args.seed)
tensorboard_log_dir = 'tensorboard/%s_%s' % (args.model, args.tensorboard_log)
os.makedirs(tensorboard_log_dir, exist_ok=True)
shutil.rmtree(tensorboard_log_dir)
tensorboard_logger.configure(tensorboard_log_dir)
logger.info('tensorboard logging to %s', tensorboard_log_dir)
# adj N*n*n
# feature N*n*f
# labels N*n*c
# Load data
# vertex: vertex id in global network N*n
if args.model == "pscn":
influence_dataset = PatchySanDataSet(args.file_dir,
args.dim,
args.seed,
args.shuffle,
args.model,
sequence_size=args.sequence_size,
def train_evaluate_model(data_path, model_name, model_type, hidden_units,
instance_normalization, class_weight_balanced,
use_vertex_feature):
print("EXPERIMENT START------", model_name, model_type, hidden_units)
logger = logging.getLogger(__name__)
logging.basicConfig(level=logging.INFO,
format='%(asctime)s %(message)s') # include timestamp
# Training settings
parser = argparse.ArgumentParser()
parser.add_argument('--tensorboard-log',
type=str,
default='',
help="name of this run")
parser.add_argument('--model',
type=str,
default=model_name,
help="models used")
parser.add_argument('--model_type',
type=str,
default=model_type,
help="model type used")
parser.add_argument('--no-cuda',
action='store_true',
default=False,
help='Disables CUDA training.')
parser.add_argument('--seed', type=int, default=42, help='Random seed.')
parser.add_argument('--epochs',
type=int,
default=500,
help='Number of epochs to train.')
parser.add_argument('--lr',
type=float,
default=0.1,
help='Initial learning rate.')
parser.add_argument('--weight-decay',
type=float,
default=5e-4,
help='Weight decay (L2 loss on parameters).')
parser.add_argument('--dropout',
type=float,
default=0.2,
help='Dropout rate (1 - keep probability).')
parser.add_argument(
'--hidden-units',
type=str,
default=hidden_units,
help="Hidden units in each hidden layer, splitted with comma")
parser.add_argument('--heads',
type=str,
default="1,1,1",
help="Heads in each layer, splitted with comma")
parser.add_argument('--batch', type=int, default=1024, help="Batch size")
parser.add_argument('--dim',
type=int,
default=64,
help="Embedding dimension")
parser.add_argument('--check-point',
type=int,
default=10,
help="Eheck point")
parser.add_argument('--instance-normalization',
action='store_true',
default=instance_normalization,
help="Enable instance normalization")
parser.add_argument('--shuffle',
action='store_true',
default=True,
help="Shuffle dataset")
parser.add_argument('--file-dir',
type=str,
required=False,
default=data_path,
help="Input file directory")
parser.add_argument('--train-ratio',
type=float,
default=75,
help="Training ratio (0, 100)")
parser.add_argument('--valid-ratio',
type=float,
default=12.5,
help="Validation ratio (0, 100)")
parser.add_argument('--class-weight-balanced',
action='store_true',
default=class_weight_balanced,
help="Adjust weights inversely proportional"
" to class frequencies in the input data")
parser.add_argument('--use-vertex-feature',
action='store_true',
default=use_vertex_feature,
help="Whether to use vertices' structural features")
parser.add_argument('--sequence-size',
type=int,
default=16,
help="Sequence size (only useful for pscn)")
parser.add_argument('--neighbor-size',
type=int,
default=5,
help="Neighborhood size (only useful for pscn)")
args = parser.parse_args()
args.cuda = not args.no_cuda and torch.cuda.is_available()
np.random.seed(args.seed)
torch.manual_seed(args.seed)
if args.cuda:
torch.cuda.manual_seed(args.seed)
tensorboard_log_dir = 'tensorboard/%s_%s' % (args.model,
args.tensorboard_log)
os.makedirs(tensorboard_log_dir, exist_ok=True)
shutil.rmtree(tensorboard_log_dir)
tensorboard_logger.configure(tensorboard_log_dir)
logger.info('tensorboard logging to %s', tensorboard_log_dir)
# adj N*n*n
# feature N*n*f
# labels N*n*c
# Load data
# vertex: vertex id in global network N*n
if args.model == "pscn":
influence_dataset = PatchySanDataSet(args.file_dir,
args.dim,
args.seed,
args.shuffle,
args.model,
sequence_size=args.sequence_size,
stride=1,
neighbor_size=args.neighbor_size)
else:
influence_dataset = InfluenceDataSet(args.file_dir, args.dim,
args.seed, args.shuffle,
args.model)
N = len(influence_dataset)
n_classes = 2
class_weight = influence_dataset.get_class_weight() \
if args.class_weight_balanced else torch.ones(n_classes)
logger.info("class_weight=%.2f:%.2f", class_weight[0], class_weight[1])
feature_dim = influence_dataset.get_feature_dimension()
n_units = [feature_dim] + [
int(x) for x in args.hidden_units.strip().split(",")
] + [n_classes]
logger.info("feature dimension=%d", feature_dim)
logger.info("number of classes=%d", n_classes)
train_start, valid_start, test_start = \
0, int(N * args.train_ratio / 100), int(N * (args.train_ratio + args.valid_ratio) / 100)
train_loader = DataLoader(influence_dataset,
batch_size=args.batch,
sampler=ChunkSampler(valid_start - train_start,
0))
valid_loader = DataLoader(influence_dataset,
batch_size=args.batch,
sampler=ChunkSampler(test_start - valid_start,
valid_start))
test_loader = DataLoader(influence_dataset,
batch_size=args.batch,
sampler=ChunkSampler(N - test_start, test_start))
# Model and optimizer
if args.model == "gcn":
model = BatchGCN(
pretrained_emb=influence_dataset.get_embedding(),
vertex_feature=influence_dataset.get_vertex_features(),
use_vertex_feature=args.use_vertex_feature,
n_units=n_units,
dropout=args.dropout,
instance_normalization=args.instance_normalization)
elif args.model == "gnn_sum":
model = BatchGNNSUM(
pretrained_emb=influence_dataset.get_embedding(),
vertex_feature=influence_dataset.get_vertex_features(),
use_vertex_feature=args.use_vertex_feature,
n_units=n_units,
dropout=args.dropout,
instance_normalization=args.instance_normalization,
model_type=args.model_type)
elif args.model == "gnn_mean":
model = BatchGNNMEAN(
pretrained_emb=influence_dataset.get_embedding(),
vertex_feature=influence_dataset.get_vertex_features(),
use_vertex_feature=args.use_vertex_feature,
n_units=n_units,
dropout=args.dropout,
instance_normalization=args.instance_normalization,
model_type=args.model_type)
elif args.model == "gat":
n_heads = [int(x) for x in args.heads.strip().split(",")]
model = BatchGAT(
pretrained_emb=influence_dataset.get_embedding(),
vertex_feature=influence_dataset.get_vertex_features(),
use_vertex_feature=args.use_vertex_feature,
n_units=n_units,
n_heads=n_heads,
dropout=args.dropout,
instance_normalization=args.instance_normalization)
elif args.model == "pscn":
model = BatchPSCN(
pretrained_emb=influence_dataset.get_embedding(),
vertex_feature=influence_dataset.get_vertex_features(),
use_vertex_feature=args.use_vertex_feature,
n_units=n_units,
dropout=args.dropout,
instance_normalization=args.instance_normalization,
sequence_size=args.sequence_size,
neighbor_size=args.neighbor_size)
else:
raise NotImplementedError
if args.cuda:
model.cuda()
class_weight = class_weight.cuda()
params = [{
'params':
filter(lambda p: p.requires_grad, model.parameters())
if args.model == "pscn" else model.layer_stack.parameters()
}]
optimizer = optim.Adagrad(params,
lr=args.lr,
weight_decay=args.weight_decay)
t_total = time.time()
logger.info("training...")
for epoch in range(args.epochs):
train(model, args, class_weight, logger, optimizer, epoch,
train_loader, valid_loader, test_loader)
logger.info("optimization Finished!")
logger.info("total time elapsed: {:.4f}s".format(time.time() - t_total))
logger.info("retrieve best threshold...")
best_thr = evaluate(model,
args,
class_weight,
logger,
args.epochs,
valid_loader,
return_best_thr=True,
log_desc='valid_')
# Testing
logger.info("testing...")
evaluate(model,
args,
class_weight,
logger,
args.epochs,
test_loader,
thr=best_thr,
log_desc='test_')
print("EXPERIMENT END------", model_name, model_type, hidden_units)