Customize Models & Tasks

Node Representation Model

In VGAE, the node representation model is a variational graph convolutional network (VGCN). This can be implemented via standard graph convolution layers, plus a variational regularization loss. We define our model as a subclass of nn.Module and :class:`core.Configurable <torchdrug.core.Configurable>`.

import torch
from torch import nn
from torch.nn import functional as F
from torch.utils import data as torch_data

from torchdrug import core, layers, datasets, metrics
from torchdrug.core import Registry as R

@R.register("models.VGCN")
class VariationalGraphConvolutionalNetwork(nn.Module, core.Configurable):

    def __init__(self, input_dim, hidden_dims, beta=0, batch_norm=False,
                 activation="relu"):
        super(VariationalGraphConvolutionalNetwork, self).__init__()
        self.input_dim = input_dim
        self.output_dim = hidden_dims[-1]
        self.dims = [input_dim] + list(hidden_dims)
        self.beta = beta

        self.layers = nn.ModuleList()
        for i in range(len(self.dims) - 2):
            self.layers.append(
                layers.GraphConv(self.dims[i], self.dims[i + 1], None,
                                 batch_norm, activation)
            )
        self.layers.append(
            layers.GraphConv(self.dims[-2], self.dims[-1] * 2, None, False, None)
        )

The definition is similar to most other torch models, except two points. First, the decoration line @R.register("models.VGCN") registers the model in the library with the name models.VGCN. This enables the model to be dumped into string format and reconstructed later. Second, self.input_dim and self.output_dim are set to inform other models that connect to it.

Then we implement the forward function. The forward function takes 4 arguments, graph(s), node input feature(s), the global loss and the global metric. The advanatage of these global variables is that they enable implementation of losses in a distributed, module-centric manner.

We compute the variational regularization loss, and add it to the global loss and the global metric.

def reparameterize(self, mu, log_sigma):
    if self.training:
        z = mu + torch.rand_like(mu) * log_sigma.exp()
    else:
        z = mu
    return z

def forward(self, graph, input, all_loss=None, metric=None):
    x = input
    for layer in self.layers:
        x = layer(graph, x)
    mu, log_sigma = x.chunk(2, dim=-1)
    node_feature = self.reparameterize(mu, log_sigma)

    if all_loss is not None and self.beta > 0:
        loss = 0.5 * (mu ** 2 + log_sigma.exp() ** 2 - 2 * log_sigma - 1)
        loss = loss.sum(dim=-1).mean()
        all_loss += loss * self.beta
        metric["variational regularization loss"] = loss

    return {
        "node_feature": node_feature
    }

Here we explicitly return a dict to indicate the type of our representations. The dict may also contain other representations, such edge representations or graph representations.

Link Prediction Task

Here we show how to implement the link prediction task for VGAE.

Generally, a task in TorchDrug contains 4 functions, predict(), target(), forward and evaluate(). Such interfaces empower us to seamlessly switch between different devices, such as CPUs, GPUs or even the distributed setting.

Among the above functions, predict() and target() compute the prediction and the ground truth for a batch respectively. forward() compute the training loss, while evaluate() compute the evaluation metrics.

Optionally, one can also implement preprocess() function, which performs arbitrary operations based on the dataset.

In the case of VGAE, we first compute the undirected training graph in preprocess(). In predict(), we perform negative sampling, and predict the logits for both positive and negative edges. In target(), we return the ground truth label for edges. evaluate() computes the area under ROC curve for the predictions.

@R.register("tasks.LinkPrediction")
class LinkPrediction(tasks.Task, core.Configurable):

    def __init__(self, model):
        super(LinkPrediction, self).__init__()
        self.model = model

    def preprocess(self, train_set, valid_set, test_set):
        dataset = train_set.dataset
        graph = dataset.graph
        train_graph = dataset.graph.edge_mask(train_set.indices)

        # flip the edges to make the graph undirected
        edge_list = train_graph.edge_list.repeat(2, 1)
        edge_list[train_graph.num_edge:, :2] = edge_list[train_graph.num_edge:, :2] \
                                               .flip(1)
        index = torch.arange(train_graph.num_edge, device=self.device) \
                .repeat(2, 1).t().flatten()
        data_dict, meta_dict = train_graph.data_mask(edge_index=index)
        train_graph = type(train_graph)(
            edge_list, edge_weight=train_graph.edge_weight[index],
            num_node=train_graph.num_node, num_edge=train_graph.num_edge * 2,
            meta_dict=meta_dict, **data_dict
        )

        self.register_buffer("train_graph", train_graph)
        self.num_node = dataset.num_node

    def forward(self, batch):
        all_loss = torch.tensor(0, dtype=torch.float32, device=self.device)
        metric = {}

        pred = self.predict(batch, all_loss, metric)
        target = self.target(batch)
        metric.update(self.evaluate(pred, target))

        loss = F.binary_cross_entropy_with_logits(pred, target)
        metric["bce loss"] = loss

        all_loss += loss

        return all_loss, metric

    def predict(self, batch, all_loss=None, metric=None):
        neg_batch = torch.randint(self.num_node, batch.shape, device=self.device)
        batch = torch.cat([batch, neg_batch])
        node_in, node_out = batch.t()

        output = self.model(self.train_graph, self.train_graph.node_feature.float(),
                            all_loss, metric)
        node_feature = output["node_feature"]
        pred = torch.einsum("bd, bd -> b",
                            node_feature[node_in], node_feature[node_out])
        return pred

    def target(self, batch):
        batch_size = len(batch)
        target = torch.zeros(batch_size * 2, device=self.device)
        target[:batch_size] = 1
        return target

    def evaluate(self, pred, target):
        roc = metrics.area_under_roc(pred, target)
        return {
            "AUROC": roc
        }

Put Them Together

Let's put all the ingredients together. Since the original Cora is a node classification dataset, we apply a wrapper to make it compatible with link prediction.

class CoraLinkPrediction(datasets.Cora):

    def __getitem__(self, index):
        return self.graph.edge_list[index]

    def __len__(self):
        return self.graph.num_edge

dataset = CoraLinkPrediction("~/node-datasets/")
lengths = [int(0.8 * len(dataset)), int(0.1 * len(dataset))]
lengths += [len(dataset) - sum(lengths)]
train_set, valid_set, test_set = torch_data.random_split(dataset, lengths)

model = VariationalGraphConvolutionalNetwork(dataset.node_feature_dim, [128, 16],
                                             beta=1e-3, batch_norm=True)
task = LinkPrediction(model)

optimizer = torch.optim.Adam(task.parameters(), lr=1e-2)
solver = core.Engine(task, train_set, valid_set, test_set, optimizer, gpus=[0],
                     batch_size=len(train_set))
solver.train(num_epoch=200)
solver.evaluate("valid")

The result may look like

AUROC: 0.898589