6.3 Training GNN for Link Prediction with Neighborhood Samplingο
Define a data loader with neighbor and negative samplingο
You can still use the same data loader as the one in node/edge classification. The only difference is that you need to add an additional stage negative sampling before neighbor sampling stage. The following data loader will pick 5 negative destination nodes uniformly for each source node of an edge.
datapipe = datapipe.sample_uniform_negative(graph, 5)
The whole data loader pipeline is as follows:
datapipe = gb.ItemSampler(itemset, batch_size=1024, shuffle=True)
datapipe = datapipe.sample_uniform_negative(graph, 5)
datapipe = datapipe.sample_neighbor(g, [10, 10]) # 2 layers.
datapipe = datapipe.transform(gb.exclude_seed_edges)
datapipe = datapipe.fetch_feature(feature, node_feature_keys=["feat"])
datapipe = datapipe.copy_to(device)
dataloader = gb.DataLoader(datapipe)
For the details about the builtin uniform negative sampler please see
UniformNegativeSampler.
You can also give your own negative sampler function, as long as it inherits
from NegativeSampler and overrides the
_sample_with_etype() method which takes in
the node pairs in minibatch, and returns the negative node pairs back.
The following gives an example of custom negative sampler that samples negative destination nodes according to a probability distribution proportional to a power of degrees.
@functional_datapipe("customized_sample_negative")
class CustomizedNegativeSampler(dgl.graphbolt.NegativeSampler):
def __init__(self, datapipe, k, node_degrees):
super().__init__(datapipe, k)
# caches the probability distribution
self.weights = node_degrees ** 0.75
self.k = k
def _sample_with_etype(node_pairs, etype=None):
src, _ = node_pairs
src = src.repeat_interleave(self.k)
dst = self.weights.multinomial(len(src), replacement=True)
return src, dst
datapipe = datapipe.customized_sample_negative(5, node_degrees)
Define a GraphSAGE model for minibatch trainingο
class SAGE(nn.Module):
def __init__(self, in_size, hidden_size):
super().__init__()
self.layers = nn.ModuleList()
self.layers.append(dglnn.SAGEConv(in_size, hidden_size, "mean"))
self.layers.append(dglnn.SAGEConv(hidden_size, hidden_size, "mean"))
self.layers.append(dglnn.SAGEConv(hidden_size, hidden_size, "mean"))
self.hidden_size = hidden_size
self.predictor = nn.Sequential(
nn.Linear(hidden_size, hidden_size),
nn.ReLU(),
nn.Linear(hidden_size, hidden_size),
nn.ReLU(),
nn.Linear(hidden_size, 1),
)
def forward(self, blocks, x):
hidden_x = x
for layer_idx, (layer, block) in enumerate(zip(self.layers, blocks)):
hidden_x = layer(block, hidden_x)
is_last_layer = layer_idx == len(self.layers) - 1
if not is_last_layer:
hidden_x = F.relu(hidden_x)
return hidden_x
When a negative sampler is provided, the data loader will generate positive and negative node pairs for each minibatch besides the Message Flow Graphs (MFGs). Use node_pairs_with_labels to get compact node pairs with corresponding labels.
Training loopο
The training loop simply involves iterating over the data loader and feeding in the graphs as well as the input features to the model defined above.
optimizer = torch.optim.Adam(model.parameters(), lr=0.01)
for epoch in tqdm.trange(args.epochs):
model.train()
total_loss = 0
start_epoch_time = time.time()
for step, data in enumerate(dataloader):
# Unpack MiniBatch.
compacted_pairs, labels = data.node_pairs_with_labels
node_feature = data.node_features["feat"]
# Convert sampled subgraphs to DGL blocks.
blocks = data.blocks
# Get the embeddings of the input nodes.
y = model(blocks, node_feature)
logits = model.predictor(
y[compacted_pairs[0]] * y[compacted_pairs[1]]
).squeeze()
# Compute loss.
loss = F.binary_cross_entropy_with_logits(logits, labels)
optimizer.zero_grad()
loss.backward()
optimizer.step()
total_loss += loss.item()
end_epoch_time = time.time()
DGL provides the unsupervised learning GraphSAGE that shows an example of link prediction on homogeneous graphs.
For heterogeneous graphsο
The previous model could be easily extended to heterogeneous graphs. The only
difference is that you need to use HeteroGraphConv to wrap
SAGEConv according to edge types.
class SAGE(nn.Module):
def __init__(self, in_size, hidden_size):
super().__init__()
self.layers = nn.ModuleList()
self.layers.append(dglnn.HeteroGraphConv({
rel : dglnn.SAGEConv(in_size, hidden_size, "mean")
for rel in rel_names
}))
self.layers.append(dglnn.HeteroGraphConv({
rel : dglnn.SAGEConv(hidden_size, hidden_size, "mean")
for rel in rel_names
}))
self.layers.append(dglnn.HeteroGraphConv({
rel : dglnn.SAGEConv(hidden_size, hidden_size, "mean")
for rel in rel_names
}))
self.hidden_size = hidden_size
self.predictor = nn.Sequential(
nn.Linear(hidden_size, hidden_size),
nn.ReLU(),
nn.Linear(hidden_size, hidden_size),
nn.ReLU(),
nn.Linear(hidden_size, 1),
)
def forward(self, blocks, x):
hidden_x = x
for layer_idx, (layer, block) in enumerate(zip(self.layers, blocks)):
hidden_x = layer(block, hidden_x)
is_last_layer = layer_idx == len(self.layers) - 1
if not is_last_layer:
hidden_x = F.relu(hidden_x)
return hidden_x
Data loader definition is also very similar to that for homogeneous graph. The only difference is that you need to give edge types for feature fetching.
datapipe = gb.ItemSampler(itemset, batch_size=1024, shuffle=True)
datapipe = datapipe.sample_uniform_negative(graph, 5)
datapipe = datapipe.sample_neighbor(g, [10, 10]) # 2 layers.
datapipe = datapipe.transform(gb.exclude_seed_edges)
datapipe = datapipe.fetch_feature(
feature,
node_feature_keys={"user": ["feat"], "item": ["feat"]}
)
datapipe = datapipe.copy_to(device)
dataloader = gb.DataLoader(datapipe)
If you want to give your own negative sampling function, just inherit from the
NegativeSampler class and override the
_sample_with_etype() method.
@functional_datapipe("customized_sample_negative")
class CustomizedNegativeSampler(dgl.graphbolt.NegativeSampler):
def __init__(self, datapipe, k, node_degrees):
super().__init__(datapipe, k)
# caches the probability distribution
self.weights = {
etype: node_degrees[etype] ** 0.75 for etype in node_degrees
}
self.k = k
def _sample_with_etype(node_pairs, etype):
src, _ = node_pairs
src = src.repeat_interleave(self.k)
dst = self.weights[etype].multinomial(len(src), replacement=True)
return src, dst
datapipe = datapipe.customized_sample_negative(5, node_degrees)
For heterogeneous graphs, node pairs are grouped by edge types. The training loop is again almost the same as that on homogeneous graph, except for computing loss on specific edge type.
optimizer = torch.optim.Adam(model.parameters(), lr=0.01)
category = "user"
for epoch in tqdm.trange(args.epochs):
model.train()
total_loss = 0
start_epoch_time = time.time()
for step, data in enumerate(dataloader):
# Unpack MiniBatch.
compacted_pairs, labels = data.node_pairs_with_labels
node_features = {
ntype: data.node_features[(ntype, "feat")]
for ntype in data.blocks[0].srctypes
}
# Convert sampled subgraphs to DGL blocks.
blocks = data.blocks
# Get the embeddings of the input nodes.
y = model(blocks, node_feature)
logits = model.predictor(
y[category][compacted_pairs[category][0]]
* y[category][compacted_pairs[category][1]]
).squeeze()
# Compute loss.
loss = F.binary_cross_entropy_with_logits(logits, labels[category])
optimizer.zero_grad()
loss.backward()
optimizer.step()
total_loss += loss.item()
end_epoch_time = time.time()