def get_dataset(name, root, use_sparse_tensor):
path = osp.join(osp.dirname(osp.realpath(__file__)), root, name)
transform = T.ToSparseTensor() if use_sparse_tensor else None
if name == 'ogbn-mag':
if transform is None:
transform = T.ToUndirected(merge=True)
else:
transform = T.Compose([T.ToUndirected(merge=True), transform])
dataset = OGB_MAG(root=path,
preprocess='metapath2vec',
transform=transform)
elif name == 'ogbn-products':
dataset = PygNodePropPredDataset('ogbn-products',
root=path,
transform=transform)
elif name == 'Reddit':
dataset = Reddit(root=path, transform=transform)
return dataset[0], dataset.num_classes
def create_hetero_mock_data(n_count, feature_dict):
_x_dict = {
'author':
torch.FloatTensor(
np.random.uniform(0, 1, (n_count, feature_dict['author']))),
'paper':
torch.FloatTensor(
np.random.uniform(0, 1, (n_count, feature_dict['paper'])))
}
_edge_index_dict = {
('author', 'writes', 'paper'):
torch.LongTensor(get_edge_array(n_count))
}
data = HeteroData()
data['author'].x = _x_dict['author']
data['paper'].x = _x_dict['paper']
data[('author', 'writes',
'paper')].edge_index = _edge_index_dict[('author', 'writes',
'paper')]
data = T.ToUndirected()(data)
return data.x_dict, data.edge_index_dict, data.metadata()
import os.path as osp
from ogb.nodeproppred import PygNodePropPredDataset, Evaluator
import torch_geometric.transforms as T
from torch_geometric.nn import LabelPropagation
root = osp.join(osp.dirname(osp.realpath(__file__)), '..', 'data', 'OGB')
dataset = PygNodePropPredDataset('ogbn-arxiv',
root,
transform=T.Compose([
T.ToUndirected(),
T.ToSparseTensor(),
]))
split_idx = dataset.get_idx_split()
evaluator = Evaluator(name='ogbn-arxiv')
data = dataset[0]
model = LabelPropagation(num_layers=3, alpha=0.9)
out = model(data.y, data.adj_t, mask=split_idx['train'])
y_pred = out.argmax(dim=-1, keepdim=True)
val_acc = evaluator.eval({
'y_true': data.y[split_idx['valid']],
'y_pred': y_pred[split_idx['valid']],
})['acc']
test_acc = evaluator.eval({
'y_true': data.y[split_idx['test']],
'y_pred': y_pred[split_idx['test']],
})['acc']
def __init__(self, root: str):
super().__init__()
self.root = root
self.transform = T.ToUndirected(merge=False)
action='store_true',
help='Whether to use weighted MSE loss.')
args = parser.parse_args()
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
path = osp.join(osp.dirname(osp.realpath(__file__)), '../../data/MovieLens')
dataset = MovieLens(path, model_name='all-MiniLM-L6-v2')
data = dataset[0].to(device)
# Add user node features for message passing:
data['user'].x = torch.eye(data['user'].num_nodes, device=device)
del data['user'].num_nodes
# Add a reverse ('movie', 'rev_rates', 'user') relation for message passing:
data = T.ToUndirected()(data)
del data['movie', 'rev_rates', 'user'].edge_label # Remove "reverse" label.
# Perform a link-level split into training, validation, and test edges:
train_data, val_data, test_data = T.RandomLinkSplit(
num_val=0.1,
num_test=0.1,
neg_sampling_ratio=0.0,
edge_types=[('user', 'rates', 'movie')],
rev_edge_types=[('movie', 'rev_rates', 'user')],
)(data)
# We have an unbalanced dataset with many labels for rating 3 and 4, and very
# few for 0 and 1. Therefore we use a weighted MSE loss.
if args.use_weighted_loss:
weight = torch.bincount(train_data['user', 'movie'].edge_label)
import os.path as osp
import torch
import torch.nn.functional as F
from ogb.nodeproppred import PygNodePropPredDataset
import torch_geometric.transforms as T
from torch_geometric.nn import MaskLabel, TransformerConv
from torch_geometric.utils import index_to_mask
root = osp.join(osp.dirname(osp.realpath(__file__)), '..', 'data', 'OGB')
dataset = PygNodePropPredDataset('ogbn-arxiv', root, T.ToUndirected())
class UniMP(torch.nn.Module):
def __init__(self,
in_channels,
num_classes,
hidden_channels,
num_layers,
heads,
dropout=0.3):
super().__init__()
self.label_emb = MaskLabel(num_classes, in_channels)
self.convs = torch.nn.ModuleList()
self.norms = torch.nn.ModuleList()
for i in range(1, num_layers + 1):
if i < num_layers:
out_channels = hidden_channels // heads
from torch.nn import ReLU
from tqdm import tqdm
import torch_geometric.transforms as T
from torch_geometric.datasets import OGB_MAG
from torch_geometric.loader import HGTLoader, NeighborLoader
from torch_geometric.nn import Linear, SAGEConv, Sequential, to_hetero
parser = argparse.ArgumentParser()
parser.add_argument('--use_hgt_loader', action='store_true')
args = parser.parse_args()
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
path = osp.join(osp.dirname(osp.realpath(__file__)), '../../data/OGB')
transform = T.ToUndirected(merge=True)
dataset = OGB_MAG(path, preprocess='metapath2vec', transform=transform)
# Already send node features/labels to GPU for faster access during sampling:
data = dataset[0].to(device, 'x', 'y')
train_input_nodes = ('paper', data['paper'].train_mask)
val_input_nodes = ('paper', data['paper'].val_mask)
kwargs = {'batch_size': 1024, 'num_workers': 6, 'persistent_workers': True}
if not args.use_hgt_loader:
train_loader = NeighborLoader(data,
num_neighbors=[10] * 2,
shuffle=True,
input_nodes=train_input_nodes,
**kwargs)
def run(args: argparse.ArgumentParser) -> None:
for dataset_name in args.datasets:
print(f"Dataset: {dataset_name}")
root = osp.join(args.root, dataset_name)
if dataset_name == 'mag':
transform = T.ToUndirected(merge=True)
dataset = OGB_MAG(root=root, transform=transform)
train_idx = ('paper', dataset[0]['paper'].train_mask)
eval_idx = ('paper', None)
neighbor_sizes = args.hetero_neighbor_sizes
else:
dataset = PygNodePropPredDataset(f'ogbn-{dataset_name}', root)
split_idx = dataset.get_idx_split()
train_idx = split_idx['train']
eval_idx = None
neighbor_sizes = args.homo_neighbor_sizes
data = dataset[0].to(args.device)
for num_neighbors in neighbor_sizes:
print(f'Training sampling with {num_neighbors} neighbors')
for batch_size in args.batch_sizes:
train_loader = NeighborLoader(
data,
num_neighbors=num_neighbors,
input_nodes=train_idx,
batch_size=batch_size,
shuffle=True,
num_workers=args.num_workers,
)
runtimes = []
num_iterations = 0
for run in range(args.runs):
start = default_timer()
for batch in tqdm.tqdm(train_loader):
num_iterations += 1
stop = default_timer()
runtimes.append(round(stop - start, 3))
average_time = round(sum(runtimes) / args.runs, 3)
print(f'batch size={batch_size}, iterations={num_iterations}, '
f'runtimes={runtimes}, average runtime={average_time}')
print('Evaluation sampling with all neighbors')
for batch_size in args.eval_batch_sizes:
subgraph_loader = NeighborLoader(
data,
num_neighbors=[-1],
input_nodes=eval_idx,
batch_size=batch_size,
shuffle=False,
num_workers=args.num_workers,
)
runtimes = []
num_iterations = 0
for run in range(args.runs):
start = default_timer()
for batch in tqdm.tqdm(subgraph_loader):
num_iterations += 1
stop = default_timer()
runtimes.append(round(stop - start, 3))
average_time = round(sum(runtimes) / args.runs, 3)
print(f'batch size={batch_size}, iterations={num_iterations}, '
f'runtimes={runtimes}, average runtime={average_time}')
else:
x = torch.tensor(tmp_event[['charge_log10','time','dom_x','dom_y','dom_z']].values,dtype=torch.float) #Features
pos = torch.tensor(tmp_event[['dom_x','dom_y','dom_z']].values,dtype=torch.float) #Position
query = "SELECT energy_log10, time, position_x, position_y, position_z, direction_x, direction_y, direction_z, azimuth, zenith FROM truth WHERE event_no = {}".format(event_no)
y = pd.read_sql(query,con)
y = torch.tensor(y.values,dtype=torch.float) #Target
dat = Data(x=x,edge_index=None,edge_attr=None,y=y,pos=pos)
# T.KNNGraph(loop=True)(dat) #defining edges by k-NN with k=6 !!! Make sure .pos is not scaled!!! ie. x,y,z -!-> ax,by,cz
T.KNNGraph(k=6, loop=False, force_undirected = False)(dat)
dat.adj_t = None
T.ToUndirected()(dat)
T.AddSelfLoops()(dat)
(row, col) = dat.edge_index
dat.edge_index = torch.stack([col,row],dim=0)
data_list.append(dat)
if (i+1) % subdivides == 0:
data, slices = InMemoryDataset.collate(data_list)
torch.save((data,slices), destination + '/{}k_{}{}.pt'.format(subdivides//1000,save_filename,subset))
subset += 1
data_list = [] #Does this free up the memory?
if i % 500 == 0:
print("{}: Completed {}/{}".format(datetime.now(),i,N))