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import pytest
import torch
from torch_geometric.data import Data, HeteroData
from torch_geometric.loader import LinkNeighborLoader
from torch_geometric.testing import (
MyFeatureStore,
MyGraphStore,
get_random_edge_index,
onlyNeighborSampler,
withCUDA,
withPackage,
)
def unique_edge_pairs(edge_index):
return set(map(tuple, edge_index.t().tolist()))
@withCUDA
@onlyNeighborSampler
@pytest.mark.parametrize('subgraph_type', ['directional', 'bidirectional'])
@pytest.mark.parametrize('neg_sampling_ratio', [None, 1.0])
@pytest.mark.parametrize('filter_per_worker', [None, True, False])
def test_homo_link_neighbor_loader_basic(device, subgraph_type,
neg_sampling_ratio,
filter_per_worker):
pos_edge_index = get_random_edge_index(50, 50, 500, device=device)
neg_edge_index = get_random_edge_index(50, 50, 500, device=device)
neg_edge_index += 50
input_edges = torch.cat([pos_edge_index, neg_edge_index], dim=-1)
edge_label = torch.cat([
torch.ones(500, device=device),
torch.zeros(500, device=device),
], dim=0)
data = Data()
data.edge_index = pos_edge_index
data.x = torch.arange(100, device=device)
data.edge_attr = torch.arange(500, device=device)
loader = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
batch_size=20,
edge_label_index=input_edges,
edge_label=edge_label if neg_sampling_ratio is None else None,
subgraph_type=subgraph_type,
neg_sampling_ratio=neg_sampling_ratio,
shuffle=True,
filter_per_worker=filter_per_worker,
)
assert str(loader) == 'LinkNeighborLoader()'
assert len(loader) == 1000 / 20
batch = loader([0])
assert isinstance(batch, Data)
assert int(input_edges[0, 0]) in batch.n_id.tolist()
assert int(input_edges[1, 0]) in batch.n_id.tolist()
for batch in loader:
assert isinstance(batch, Data)
assert batch.n_id.size() == (batch.num_nodes, )
assert batch.e_id.size() == (batch.num_edges, )
assert batch.x.device == device
assert batch.x.size(0) <= 100
assert batch.x.min() >= 0 and batch.x.max() < 100
assert batch.input_id.numel() == 20
assert batch.edge_index.device == device
assert batch.edge_index.min() >= 0
assert batch.edge_index.max() < batch.num_nodes
assert batch.edge_attr.device == device
assert batch.edge_attr.min() >= 0
assert batch.edge_attr.max() < 500
if neg_sampling_ratio is None:
assert batch.edge_label_index.size(1) == 20
# Assert positive samples are present in the original graph:
edge_index = unique_edge_pairs(batch.edge_index)
edge_label_index = batch.edge_label_index[:, batch.edge_label == 1]
edge_label_index = unique_edge_pairs(edge_label_index)
assert len(edge_index | edge_label_index) == len(edge_index)
# Assert negative samples are not present in the original graph:
edge_index = unique_edge_pairs(batch.edge_index)
edge_label_index = batch.edge_label_index[:, batch.edge_label == 0]
edge_label_index = unique_edge_pairs(edge_label_index)
assert len(edge_index & edge_label_index) == 0
else:
assert batch.edge_label_index.size(1) == 40
assert torch.all(batch.edge_label[:20] == 1)
assert torch.all(batch.edge_label[20:] == 0)
# Ensure local `edge_label_index` correctly maps to input edges.
global_edge_label_index = batch.n_id[batch.edge_label_index]
global_edge_label_index = (
global_edge_label_index[:, batch.edge_label >= 1])
global_edge_label_index = unique_edge_pairs(global_edge_label_index)
assert (len(global_edge_label_index & unique_edge_pairs(input_edges))
== len(global_edge_label_index))
@onlyNeighborSampler
@pytest.mark.parametrize('subgraph_type', ['directional', 'bidirectional'])
@pytest.mark.parametrize('neg_sampling_ratio', [None, 1.0])
def test_hetero_link_neighbor_loader_basic(subgraph_type, neg_sampling_ratio):
data = HeteroData()
data['paper'].x = torch.arange(100)
data['author'].x = torch.arange(100, 300)
data['paper', 'paper'].edge_index = get_random_edge_index(100, 100, 500)
data['paper', 'paper'].edge_attr = torch.arange(500)
data['paper', 'author'].edge_index = get_random_edge_index(100, 200, 1000)
data['paper', 'author'].edge_attr = torch.arange(500, 1500)
data['author', 'paper'].edge_index = get_random_edge_index(200, 100, 1000)
data['author', 'paper'].edge_attr = torch.arange(1500, 2500)
loader = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
edge_label_index=('paper', 'author'),
batch_size=20,
subgraph_type=subgraph_type,
neg_sampling_ratio=neg_sampling_ratio,
shuffle=True,
)
assert str(loader) == 'LinkNeighborLoader()'
assert len(loader) == 1000 / 20
for batch in loader:
assert isinstance(batch, HeteroData)
if neg_sampling_ratio is None:
# Assert only positive samples are present in the original graph:
edge_index = unique_edge_pairs(batch['paper', 'author'].edge_index)
edge_label_index = batch['paper', 'author'].edge_label_index
edge_label_index = unique_edge_pairs(edge_label_index)
assert len(edge_index | edge_label_index) == len(edge_index)
else:
assert batch['paper', 'author'].edge_label_index.size(1) == 40
assert torch.all(batch['paper', 'author'].edge_label[:20] == 1)
assert torch.all(batch['paper', 'author'].edge_label[20:] == 0)
@onlyNeighborSampler
@pytest.mark.parametrize('subgraph_type', ['directional', 'bidirectional'])
def test_hetero_link_neighbor_loader_loop(subgraph_type):
data = HeteroData()
data['paper'].x = torch.arange(100)
data['author'].x = torch.arange(100, 300)
data['paper', 'paper'].edge_index = get_random_edge_index(100, 100, 500)
data['paper', 'author'].edge_index = get_random_edge_index(100, 200, 1000)
data['author', 'paper'].edge_index = get_random_edge_index(200, 100, 1000)
loader = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
edge_label_index=('paper', 'paper'),
batch_size=20,
subgraph_type=subgraph_type,
)
for batch in loader:
assert batch['paper'].x.size(0) <= 100
assert batch['paper'].x.min() >= 0 and batch['paper'].x.max() < 100
# Assert positive samples are present in the original graph:
edge_index = unique_edge_pairs(batch['paper', 'paper'].edge_index)
edge_label_index = batch['paper', 'paper'].edge_label_index
edge_label_index = unique_edge_pairs(edge_label_index)
assert len(edge_index | edge_label_index) == len(edge_index)
@onlyNeighborSampler
def test_link_neighbor_loader_edge_label():
edge_index = get_random_edge_index(100, 100, 500)
data = Data(edge_index=edge_index, x=torch.arange(100))
loader = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
batch_size=10,
neg_sampling_ratio=1.0,
)
for batch in loader:
assert batch.edge_label.dtype == torch.float
assert torch.all(batch.edge_label[:10] == 1.0)
assert torch.all(batch.edge_label[10:] == 0.0)
loader = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
batch_size=10,
edge_label=torch.ones(500, dtype=torch.long),
neg_sampling_ratio=1.0,
)
for batch in loader:
assert batch.edge_label.dtype == torch.long
assert torch.all(batch.edge_label[:10] == 1)
assert torch.all(batch.edge_label[10:] == 0)
@withPackage('pyg_lib')
@pytest.mark.parametrize('batch_size', [1])
def test_temporal_homo_link_neighbor_loader(batch_size):
data = Data(
x=torch.randn(10, 5),
edge_index=torch.randint(0, 10, (2, 123)),
time=torch.arange(10),
)
# Ensure that nodes exist at the time of the `edge_label_time`:
edge_label_time = torch.max(
data.time[data.edge_index[0]],
data.time[data.edge_index[1]],
)
loader = LinkNeighborLoader(
data,
num_neighbors=[-1],
time_attr='time',
edge_label=torch.ones(data.num_edges),
edge_label_time=edge_label_time,
batch_size=batch_size,
shuffle=True,
)
for batch in loader:
assert batch.edge_label_index.size() == (2, batch_size)
assert batch.edge_label_time.size() == (batch_size, )
assert batch.edge_label.size() == (batch_size, )
assert torch.all(batch.time <= batch.edge_label_time)
@withPackage('pyg_lib')
def test_temporal_hetero_link_neighbor_loader():
data = HeteroData()
data['paper'].x = torch.arange(100)
data['paper'].time = torch.arange(data['paper'].num_nodes) - 200
data['author'].x = torch.arange(100, 300)
data['author'].time = torch.arange(data['author'].num_nodes)
data['paper', 'paper'].edge_index = get_random_edge_index(100, 100, 500)
data['paper', 'author'].edge_index = get_random_edge_index(100, 200, 1000)
data['author', 'paper'].edge_index = get_random_edge_index(200, 100, 1000)
with pytest.raises(ValueError, match=r"'edge_label_time' is not set"):
loader = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
edge_label_index=('paper', 'paper'),
batch_size=32,
time_attr='time',
)
# With edge_time:
edge_time = torch.arange(data['paper', 'paper'].edge_index.size(1))
loader = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
edge_label_index=('paper', 'paper'),
edge_label_time=edge_time,
batch_size=32,
time_attr='time',
neg_sampling_ratio=0.5,
drop_last=True,
)
for batch in loader:
# Check if each seed edge has a different batch:
assert int(batch['paper'].batch.max()) + 1 == 32
author_max = batch['author'].time.max()
edge_max = batch['paper', 'paper'].edge_label_time.max()
assert edge_max >= author_max
author_min = batch['author'].time.min()
edge_min = batch['paper', 'paper'].edge_label_time.min()
assert edge_min >= author_min
@onlyNeighborSampler
def test_custom_hetero_link_neighbor_loader():
data = HeteroData()
feature_store = MyFeatureStore()
graph_store = MyGraphStore()
# Set up node features:
x = torch.arange(100)
data['paper'].x = x
feature_store.put_tensor(x, group_name='paper', attr_name='x', index=None)
x = torch.arange(100, 300)
data['author'].x = x
feature_store.put_tensor(x, group_name='author', attr_name='x', index=None)
# Set up edge indices (GraphStore does not support `edge_attr` at the
# moment):
edge_index = get_random_edge_index(100, 100, 500)
data['paper', 'to', 'paper'].edge_index = edge_index
graph_store.put_edge_index(edge_index=(edge_index[0], edge_index[1]),
edge_type=('paper', 'to', 'paper'),
layout='coo', size=(100, 100))
edge_index = get_random_edge_index(100, 200, 1000)
data['paper', 'to', 'author'].edge_index = edge_index
graph_store.put_edge_index(edge_index=(edge_index[0], edge_index[1]),
edge_type=('paper', 'to', 'author'),
layout='coo', size=(100, 200))
edge_index = get_random_edge_index(200, 100, 1000)
data['author', 'to', 'paper'].edge_index = edge_index
graph_store.put_edge_index(edge_index=(edge_index[0], edge_index[1]),
edge_type=('author', 'to', 'paper'),
layout='coo', size=(200, 100))
loader1 = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
edge_label_index=('paper', 'to', 'author'),
batch_size=20,
)
loader2 = LinkNeighborLoader(
(feature_store, graph_store),
num_neighbors=[-1] * 2,
edge_label_index=('paper', 'to', 'author'),
batch_size=20,
)
assert str(loader1) == str(loader2)
for (batch1, batch2) in zip(loader1, loader2):
# Mapped indices of neighbors may be differently sorted:
assert torch.allclose(batch1['paper'].x.sort()[0],
batch2['paper'].x.sort()[0])
assert torch.allclose(batch1['author'].x.sort()[0],
batch2['author'].x.sort()[0])
# Assert that edge indices have the same size:
assert (batch1['paper', 'to', 'paper'].edge_index.size() == batch1[
'paper', 'to', 'paper'].edge_index.size())
assert (batch1['paper', 'to', 'author'].edge_index.size() == batch1[
'paper', 'to', 'author'].edge_index.size())
assert (batch1['author', 'to', 'paper'].edge_index.size() == batch1[
'author', 'to', 'paper'].edge_index.size())
@onlyNeighborSampler
def test_homo_link_neighbor_loader_no_edges():
loader = LinkNeighborLoader(
Data(num_nodes=100),
num_neighbors=[],
batch_size=20,
edge_label_index=get_random_edge_index(100, 100, 100),
)
for batch in loader:
assert isinstance(batch, Data)
assert batch.input_id.numel() == 20
assert batch.edge_label_index.size(1) == 20
assert batch.num_nodes == batch.edge_label_index.unique().numel()
@onlyNeighborSampler
def test_hetero_link_neighbor_loader_no_edges():
loader = LinkNeighborLoader(
HeteroData(paper=dict(num_nodes=100)),
num_neighbors=[],
edge_label_index=(
('paper', 'paper'),
get_random_edge_index(100, 100, 100),
),
batch_size=20,
)
for batch in loader:
assert isinstance(batch, HeteroData)
assert batch['paper', 'paper'].input_id.numel() == 20
assert batch['paper', 'paper'].edge_label_index.size(1) == 20
assert batch['paper'].num_nodes == batch[
'paper', 'paper'].edge_label_index.unique().numel()
@withPackage('pyg_lib')
@pytest.mark.parametrize('disjoint', [False, True])
@pytest.mark.parametrize('temporal', [False, True])
@pytest.mark.parametrize('amount', [1, 2])
def test_homo_link_neighbor_loader_triplet(disjoint, temporal, amount):
if not disjoint and temporal:
return
data = Data()
data.x = torch.arange(100)
data.edge_index = get_random_edge_index(100, 100, 400)
data.edge_label_index = get_random_edge_index(100, 100, 500)
data.edge_attr = torch.arange(data.num_edges)
time_attr = edge_label_time = None
if temporal:
time_attr = 'time'
data.time = torch.arange(data.num_nodes)
edge_label_time = torch.max(data.time[data.edge_label_index[0]],
data.time[data.edge_label_index[1]])
edge_label_time = edge_label_time + 50
batch_size = 20
loader = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
batch_size=batch_size,
edge_label_index=data.edge_label_index,
edge_label_time=edge_label_time,
time_attr=time_attr,
disjoint=disjoint,
neg_sampling=dict(mode='triplet', amount=amount),
shuffle=True,
)
assert str(loader) == 'LinkNeighborLoader()'
assert len(loader) == 500 / batch_size
for batch in loader:
assert isinstance(batch, Data)
# Check that `src_index` and `dst_pos_index` point to valid edges:
assert torch.equal(batch.x[batch.src_index],
data.edge_label_index[0, batch.input_id])
assert torch.equal(batch.x[batch.dst_pos_index],
data.edge_label_index[1, batch.input_id])
# Check that `dst_neg_index` points to valid nodes in the batch:
if amount == 1:
assert batch.dst_neg_index.size() == (batch_size, )
else:
assert batch.dst_neg_index.size() == (batch_size, amount)
assert batch.dst_neg_index.min() >= 0
assert batch.dst_neg_index.max() < batch.num_nodes
if disjoint:
# In disjoint mode, seed nodes should always be placed first:
assert batch.src_index.min() == 0
assert batch.src_index.max() == batch_size - 1
assert batch.dst_pos_index.min() == batch_size
assert batch.dst_pos_index.max() == 2 * batch_size - 1
assert batch.dst_neg_index.min() == 2 * batch_size
max_seed_nodes = 2 * batch_size + batch_size * amount
assert batch.dst_neg_index.max() == max_seed_nodes - 1
assert batch.batch.min() == 0
assert batch.batch.max() == batch_size - 1
# Check that `batch` is always increasing:
for i in range(0, max_seed_nodes, batch_size):
batch_vector = batch.batch[i:i + batch_size]
assert torch.equal(batch_vector, torch.arange(batch_size))
if temporal:
for i in range(batch_size):
assert batch.time[batch.batch == i].max() <= batch.seed_time[i]
@withPackage('pyg_lib')
@pytest.mark.parametrize('disjoint', [False, True])
@pytest.mark.parametrize('temporal', [False, True])
@pytest.mark.parametrize('amount', [1, 2])
def test_hetero_link_neighbor_loader_triplet(disjoint, temporal, amount):
if not disjoint and temporal:
return
data = HeteroData()
data['paper'].x = torch.arange(100)
data['author'].x = torch.arange(100, 300)
data['paper', 'paper'].edge_index = get_random_edge_index(100, 100, 400)
edge_label_index = get_random_edge_index(100, 100, 500)
data['paper', 'paper'].edge_label_index = edge_label_index
data['paper', 'author'].edge_index = get_random_edge_index(100, 200, 1000)
data['author', 'paper'].edge_index = get_random_edge_index(200, 100, 1000)
time_attr = edge_label_time = None
if temporal:
time_attr = 'time'
data['paper'].time = torch.arange(data['paper'].num_nodes)
data['author'].time = torch.arange(data['author'].num_nodes)
edge_label_time = torch.max(
data['paper'].time[data['paper', 'paper'].edge_label_index[0]],
data['paper'].time[data['paper', 'paper'].edge_label_index[1]],
)
edge_label_time = edge_label_time + 50
weight = torch.rand(data['paper'].num_nodes) if not temporal else None
batch_size = 20
index = (('paper', 'paper'), data['paper', 'paper'].edge_label_index)
loader = LinkNeighborLoader(
data,
num_neighbors=[-1] * 2,
batch_size=batch_size,
edge_label_index=index,
edge_label_time=edge_label_time,
time_attr=time_attr,
disjoint=disjoint,
neg_sampling=dict(
mode='triplet',
amount=amount,
src_weight=weight,
dst_weight=weight,
),
shuffle=True,
)
assert str(loader) == 'LinkNeighborLoader()'
assert len(loader) == 500 / batch_size
for batch in loader:
assert isinstance(batch, HeteroData)
node_store = batch['paper']
edge_store = batch['paper', 'paper']
# Check that `src_index` and `dst_pos_index` point to valid edges:
assert torch.equal(
node_store.x[node_store.src_index],
data['paper', 'paper'].edge_label_index[0, edge_store.input_id])
assert torch.equal(
node_store.x[node_store.dst_pos_index],
data['paper', 'paper'].edge_label_index[1, edge_store.input_id])
# Check that `dst_neg_index` points to valid nodes in the batch:
if amount == 1:
assert node_store.dst_neg_index.size() == (batch_size, )
else:
assert node_store.dst_neg_index.size() == (batch_size, amount)
assert node_store.dst_neg_index.min() >= 0
assert node_store.dst_neg_index.max() < node_store.num_nodes
if disjoint:
# In disjoint mode, seed nodes should always be placed first:
assert node_store.src_index.min() == 0
assert node_store.src_index.max() == batch_size - 1
assert node_store.dst_pos_index.min() == batch_size
assert node_store.dst_pos_index.max() == 2 * batch_size - 1
assert node_store.dst_neg_index.min() == 2 * batch_size
max_seed_nodes = 2 * batch_size + batch_size * amount
assert node_store.dst_neg_index.max() == max_seed_nodes - 1
assert node_store.batch.min() == 0
assert node_store.batch.max() == batch_size - 1
# Check that `batch` is always increasing:
for i in range(0, max_seed_nodes, batch_size):
batch_vector = node_store.batch[i:i + batch_size]
assert torch.equal(batch_vector, torch.arange(batch_size))
if temporal:
for i in range(batch_size):
assert (node_store.time[node_store.batch == i].max()
<= node_store.seed_time[i])
@withPackage('pyg_lib')
def test_link_neighbor_loader_mapping():
edge_index = torch.tensor([
[0, 0, 0, 0, 0, 1, 1, 1, 2, 2, 3, 5],
[1, 2, 3, 4, 5, 8, 6, 7, 9, 10, 6, 11],
])
data = Data(edge_index=edge_index, num_nodes=12)
loader = LinkNeighborLoader(
data,
edge_label_index=data.edge_index,
num_neighbors=[1],
batch_size=2,
shuffle=True,
)
for batch in loader:
assert torch.equal(
batch.n_id[batch.edge_index],
data.edge_index[:, batch.e_id],
)
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