def visualize_glayout_without_training(layout="tsne", **kwargs):
_args = get_args(**kwargs)
pprint_args(_args)
train_d, val_d, test_d = get_dataset_or_loader(
_args.dataset_class,
_args.dataset_name,
_args.data_root,
batch_size=_args.batch_size,
seed=_args.seed,
)
data = train_d[0]
plot_graph_layout(data.x.numpy(),
data.y.numpy(),
data.edge_index.numpy(),
args=_args,
edge_to_attention=None,
key="raw",
layout=layout)
def visualize_attention_metric_for_multiple_models(
name_prefix_and_kwargs: List[Tuple[str, Dict]],
unit_width_per_name=3,
extension="png"):
res = None
total_args, num_layers, custom_key_list, name_prefix_list = None, None, [], []
kld1_list, kld2_list, jsd_list, ent_list = [], [], [], [] # [L * M, N]
for name_prefix, kwargs in name_prefix_and_kwargs:
args = get_args(**kwargs)
custom_key_list.append(args.custom_key)
num_layers = args.num_layers
train_d, val_d, test_d = get_dataset_or_loader(
args.dataset_class,
args.dataset_name,
args.data_root,
batch_size=args.batch_size,
seed=args.seed,
)
if val_d is None and test_d is None:
data_list = [train_d[0]]
else:
data_list = []
for _data in chain(train_d, val_d, test_d):
if _data.x.size(0) != len(_data.agreement_dist):
_data.agreement_dist = [
_ad for _ad in _data.agreement_dist[0]
]
_data.uniform_att_dist = [
_uad for _uad in _data.uniform_att_dist[0]
]
data_list.append(_data)
gpu_id = [
int(
np.random.choice([
g for g in range(args.num_gpus_total)
if g not in args.gpu_deny_list
], 1))
][0]
if args.verbose >= 1:
pprint_args(args)
cprint("Use GPU the ID of which is {}".format(gpu_id), "yellow")
device = "cpu" if gpu_id is None \
else torch.device('cuda:{}'.format(gpu_id) if torch.cuda.is_available() else 'cpu')
model, ret = run(args, gpu_id=gpu_id, return_model=True)
kld1_layer, kld2_layer, jsd_layer, ent_layer, *res = \
get_attention_metric_for_single_model_and_multiple_data(model, data_list, device)
kld1_list += kld1_layer
kld2_list += kld2_layer
jsd_list += jsd_layer
ent_list += ent_layer
name_prefix_list.append(name_prefix)
total_args = args
torch.cuda.empty_cache()
total_args.custom_key = "-".join(sorted(custom_key_list))
plot_kld_jsd_ent(kld1_list,
kld2_list,
jsd_list,
ent_list,
*res,
num_layers=num_layers,
model_args=total_args,
epoch=-1,
name_prefix_list=name_prefix_list,
unit_width_per_name=unit_width_per_name,
extension=extension,
flierprops={
"marker": "x",
"markersize": 12
})
def get_degree_and_homophily(dataset_class,
dataset_name,
data_root,
use_multiprocessing=False,
use_loader=False,
**kwargs) -> np.ndarray:
"""
:param dataset_class: str
:param dataset_name: str
:param data_root: str
:param use_multiprocessing:
:param use_loader:
:return: np.ndarray the shape of which is [N, 2] (degree, homophily) for Ns
"""
print(f"{dataset_class} / {dataset_name} / {data_root}")
_data_attr = get_dataset_or_loader(dataset_class,
dataset_name,
data_root,
seed=42,
**kwargs)
val_d, test_d, train_loader, eval_loader = None, None, None, None
if not use_loader:
train_d, val_d, test_d = _data_attr
else:
train_d, train_loader, eval_loader = _data_attr
if dataset_name in ["PPI", "WebKB4Univ", "CLUSTER"]:
cum_sum = 0
y_list, edge_index_list = [], []
for _data in chain(train_d, val_d, test_d):
y_list.append(_data.y)
edge_index_list.append(_data.edge_index + cum_sum)
cum_sum += _data.y.size(0)
y = torch.cat(y_list, dim=0)
edge_index = torch.cat(edge_index_list, dim=1)
elif use_loader and dataset_name in ["Reddit"]:
cum_sum = 0
y_list, edge_index_list = [], []
data = train_d[0]
for _data in chain(
train_loader(data.train_mask),
eval_loader(data.val_mask),
eval_loader(data.test_mask),
):
y_list.append(data.y[_data.n_id])
edge_index_list.append(_data.edge_index + cum_sum)
cum_sum += _data.n_id.size(0)
y = torch.cat(y_list, dim=0)
edge_index = torch.cat(edge_index_list, dim=1)
cprint(f"Edges: {edge_index.size()}, Y: {y.size()}", "yellow")
else:
data = train_d[0]
y_list, edge_index_list = None, None
y, edge_index = data.y, data.edge_index
deg = degree(edge_index[0], num_nodes=y.size(0))
if y_list is None:
homophily = get_homophily(edge_index,
y,
use_multiprocessing=use_multiprocessing)
else:
homophily = get_homophily_from_list(edge_index_list, y_list,
use_multiprocessing)
degree_and_homophily = []
for _deg, _hom in zip(deg, homophily):
_deg, _hom = int(_deg), float(_hom)
if _deg != 0:
degree_and_homophily.append([_deg, _hom])
return np.asarray(degree_and_homophily)
def get_graph_property(graph_property_list,
dataset_class,
dataset_name,
data_root,
verbose=True,
**kwargs):
_data_attr = get_dataset_or_loader(dataset_class,
dataset_name,
data_root,
seed=42,
**kwargs)
train_d, val_d, test_d = _data_attr
if dataset_name in ["PPI", "WebKB4Univ", "CLUSTER"]:
cum_sum = 0
y_list, edge_index_list = [], []
for _data in chain(train_d, val_d, test_d):
y_list.append(_data.y)
edge_index_list.append(_data.edge_index + cum_sum)
cum_sum += _data.y.size(0)
y = torch.cat(y_list, dim=0)
edge_index = torch.cat(edge_index_list, dim=1)
else:
data = train_d[0]
y, edge_index = data.y, data.edge_index
y_list, edge_index_list = [y], [edge_index]
# to_undirected
one_nxg = to_networkx(Data(edge_index=edge_index),
to_undirected=is_undirected(edge_index))
nxg_list = [
to_networkx(Data(edge_index=ei),
to_undirected=is_undirected(edge_index))
for ei in edge_index_list
]
ni_nxg_list = [deepcopy(nxg) for nxg in nxg_list]
for ni_nxg in ni_nxg_list:
ni_nxg.remove_nodes_from(list(nx.isolates(ni_nxg)))
gp_dict = {}
if graph_property_list is None or "diameter" in graph_property_list:
diameter_list = []
for ni_nxg in ni_nxg_list:
ni_nxg = ni_nxg.to_undirected() # important for computing cc.
for cc in nx.connected_components(ni_nxg):
ni_nxg_cc = ni_nxg.subgraph(cc).copy()
diameter_list.append(
nx.algorithms.distance_measures.diameter(ni_nxg_cc))
gp_dict["diameter_mean"] = float(np.mean(diameter_list))
gp_dict["diameter_std"] = float(np.std(diameter_list))
gp_dict["diameter_max"] = float(np.max(diameter_list))
gp_dict["diameter_min"] = float(np.min(diameter_list))
gp_dict["diameter_n"] = len(diameter_list)
if graph_property_list is None or "average_clustering_coefficient" in graph_property_list:
gp_dict["average_clustering_coefficient"] = nx.average_clustering(
one_nxg)
if verbose:
print(f"{dataset_class} / {dataset_name} / {data_root}")
pprint(gp_dict)
if graph_property_list is None or "centrality" in graph_property_list:
dc = nx.degree_centrality(one_nxg)
gp_dict["degree_centrality_mean"] = float(np.mean(list(dc.values())))
gp_dict["degree_centrality_std"] = float(np.std(list(dc.values())))
cc = nx.closeness_centrality(one_nxg)
gp_dict["closeness_centrality_mean"] = float(np.mean(list(
cc.values())))
gp_dict["closeness_centrality_std"] = float(np.std(list(cc.values())))
if graph_property_list is None or "assortativity" in graph_property_list:
gp_dict[
"degree_assortativity_coefficient"] = nx.degree_assortativity_coefficient(
one_nxg)
if verbose:
print(f"{dataset_class} / {dataset_name} / {data_root}")
pprint(gp_dict)
return gp_dict
edge_index=edge_index,
edge_sampling_ratio=edge_sampling_ratio,
criterion=criterion,
)
return loss
if __name__ == '__main__':
from arguments import get_args
main_args = get_args(
model_name="GCN",
dataset_class="PPI",
dataset_name="PPI",
custom_key="NE",
)
train_d, val_d, test_d = get_dataset_or_loader(
main_args.dataset_class,
main_args.dataset_name,
main_args.data_root,
batch_size=main_args.batch_size,
seed=main_args.seed,
)
_m = LinkGNN(main_args, train_d)
for b in train_d:
ob = _m(b.x, b.edge_index)
print(b.x.size(), b.edge_index.size(), ob.size())
def run(args, gpu_id=None, return_model=False, return_time_series=False):
random.seed(args.seed)
torch.manual_seed(args.seed)
torch.cuda.manual_seed(args.seed)
np.random.seed(args.seed)
torch.backends.cudnn.deterministic = True
torch.backends.cudnn.benchmark = False
running_device = "cpu" if gpu_id is None \
else torch.device('cuda:{}'.format(gpu_id) if torch.cuda.is_available() else 'cpu')
best_val_perf = 0.
test_perf_at_best_val = 0.
best_test_perf = 0.
best_test_perf_at_best_val = 0.
link_test_perf_at_best_val = 0.
val_loss_deque = deque(maxlen=args.early_stop_queue_length)
val_perf_deque = deque(maxlen=args.early_stop_queue_length)
dataset_kwargs = {}
if args.dataset_class == "ENSPlanetoid":
dataset_kwargs["neg_sample_ratio"] = args.neg_sample_ratio
if args.dataset_name == "ogbn-arxiv":
dataset_kwargs["to_undirected"] = args.to_undirected
if args.dataset_name == "ogbn-products":
dataset_kwargs["size"] = args.data_sampling_size
dataset_kwargs["num_hops"] = args.data_sampling_num_hops
dataset_kwargs["shuffle"] = True
_data_attr = get_dataset_or_loader(
args.dataset_class,
args.dataset_name,
args.data_root,
batch_size=args.batch_size,
seed=args.seed,
**dataset_kwargs,
)
if _data_attr[-1] is None:
train_d, val_d, test_d = _data_attr
loader = None
dataset_or_loader = train_d
eval_dataset_or_loader = None
else:
train_d, train_loader, eval_loader = _data_attr
val_d, test_d = None, None
dataset_or_loader = (train_d, train_loader)
eval_dataset_or_loader = (train_d, eval_loader)
net_cls = _get_model_cls(args.model_name)
net = net_cls(args, train_d)
net = net.to(running_device)
loaded = load_model(net, args, target_epoch=None)
if loaded is not None:
net, other_state_dict = loaded
best_val_perf = other_state_dict["perf"]
args.start_epoch = other_state_dict["epoch"]
loss_func = eval(str(args.loss)) or nn.CrossEntropyLoss(
) # nn.BCEWithLogitsLoss(), nn.CrossEntropyLoss()
adam_optim = optim.Adam(net.parameters(),
lr=args.lr,
weight_decay=args.l2_lambda)
evaluator = Evaluator(name=args.dataset_name)
ret = {}
val_perf_list, test_perf_list, val_loss_list = [], [], []
perf_task_for_val = getattr(args, "perf_task_for_val", "Node")
for current_iter, epoch in enumerate(
tqdm(range(args.start_epoch, args.start_epoch + args.epochs))):
train_loss = train_model(running_device,
net,
dataset_or_loader,
loss_func,
adam_optim,
epoch=epoch,
_args=args)
if args.verbose >= 2 and epoch % args.val_interval == 0:
print("\n\t- Train loss: {}".format(train_loss))
# Validation.
if epoch % args.val_interval == 0:
val_perf, val_loss, test_perf, test_loss = test_model(
running_device,
net,
eval_dataset_or_loader or dataset_or_loader,
loss_func,
evaluator=evaluator,
_args=args,
val_or_test="val",
verbose=args.verbose,
run_link_prediction=(perf_task_for_val == "Link"),
)
garbage_collection_cuda()
if args.save_plot:
val_perf_list.append(val_perf)
test_perf_list.append(test_perf)
val_loss_list.append(val_loss.item())
if test_perf > best_test_perf:
best_test_perf = test_perf
if val_perf >= best_val_perf:
print_color = "yellow"
best_val_perf = val_perf
test_perf_at_best_val = test_perf
if test_perf_at_best_val > best_test_perf_at_best_val:
best_test_perf_at_best_val = test_perf_at_best_val
if args.task_type == "Link_Prediction":
link_test_perf, _ = test_model(running_device,
net,
test_d or train_d,
loss_func,
_args=args,
val_or_test="test",
verbose=0,
run_link_prediction=True)
link_test_perf_at_best_val = link_test_perf
if args.save_model:
save_model(net, args, target_epoch=epoch, perf=val_perf)
else:
print_color = None
ret = {
"best_val_perf": best_val_perf,
"test_perf_at_best_val": test_perf_at_best_val,
"best_test_perf": best_test_perf,
"best_test_perf_at_best_val": best_test_perf_at_best_val,
}
if args.verbose >= 1:
cprint_multi_lines("\t- ", print_color, **ret)
# Check early stop condition
if args.use_early_stop and current_iter > args.early_stop_patience:
recent_val_loss_mean = float(np.mean(val_loss_deque))
val_loss_change = abs(recent_val_loss_mean -
val_loss) / recent_val_loss_mean
recent_val_perf_mean = float(np.mean(val_perf_deque))
val_perf_change = abs(recent_val_perf_mean -
val_perf) / recent_val_perf_mean
if (val_loss_change < args.early_stop_threshold_loss) or \
(val_perf_change < args.early_stop_threshold_perf):
if args.verbose >= 1:
cprint("Early Stopped at epoch {}".format(epoch),
"red")
cprint(
"\t- val_loss_change is {} (thres: {}) | {} -> {}".
format(
round(val_loss_change, 6),
round(args.early_stop_threshold_loss, 6),
recent_val_loss_mean,
val_loss,
), "red")
cprint(
"\t- val_perf_change is {} (thres: {}) | {} -> {}".
format(
round(val_perf_change, 6),
round(args.early_stop_threshold_perf, 6),
recent_val_perf_mean,
val_perf,
), "red")
break
val_loss_deque.append(val_loss)
val_perf_deque.append(val_perf)
if args.task_type == "Link_Prediction":
ret = {"link_test_perf_at_best_val": link_test_perf_at_best_val, **ret}
if args.save_plot:
save_loss_and_perf_plot([val_loss_list, val_perf_list, test_perf_list],
ret,
args,
columns=["val_loss", "val_perf", "test_perf"])
if return_model:
return net, ret
if return_time_series:
return {
"val_loss_list": val_loss_list,
"val_perf_list": val_perf_list,
"test_perf_list": test_perf_list,
**ret
}
return ret