How to use DGL with Binary Classification Problem?

I’m new to DGL and also to GCN. I’m having a set of graphs with associate binary labels (0 or 1). I implemented a classifier by following the DGL tutorial ( and ended up with around 70% testing accuracy. However, the tutorial problem is a multiclass one, my one is a binary one. So, could anyone please help me to figure out the areas I need to modify in my classifier to work well with binary classification situations?

I think you just need to set n_classes to be 2 in Classifier.

Yes. Thank you mufeili. That’s true. I used n_classes=2 when I’m building the mentioned classifier. But I wanted to know, how to use binary cross-entropy as the loss function with a Sigmoid output layer?

This is how I implemented so far.

#Create model
classifier_model = Classifier(1, 256, 1)
loss_func = nn.BCELoss()
optimizer = optim.Adam(classifier_model.parameters(), lr=0.001)

epoch_losses = []
for epoch in range(10):
    epoch_loss = 0
    for iter, (bg, label) in enumerate(train_data_loader):
        prediction = classifier_model(bg)
        loss = loss_func(torch.sigmoid(prediction), label.float())
        epoch_loss += loss.detach().item()
    epoch_loss /= (iter + 1)
    print('Epoch {}, loss {:.4f}'.format(epoch, epoch_loss))

total = 0
y_pred = []
y_true = []

with torch.no_grad():
    for data in test_data_loader:
        graphs, labels = data
        outputs = torch.softmax(classifier_model(graphs), 1)
        _, predicted = torch.max(, 1)
        total += labels.size(0)

#Print results
print("Accuracy: %.2f%%" % ((accuracy_score(y_true, y_pred, normalize=False)) / total * 100))
print("Precision: %.2f%%" % (metrics.precision_score(y_true, y_pred) * 100))
print("Recall: %.2f%%" % (metrics.recall_score(y_true, y_pred) * 100))
print("F1-Score: %.2f%%" % (metrics.f1_score(y_true, y_pred) * 100))`

However, my model performs as follows.

    Accuracy: 55.56%
    Precision: 0.00%
    Recall: 0.00%
    F1-Score: 0.00%

Can anyone please tell me where I did the mistake?

I’d suggest use BCEWithLogitsLoss rather than BCELoss as the latter one can have issues for numerical stability. As for the model performance, you need to check the following issues:

  1. How balanced is your dataset? What proportion of the dataset are positive/negative?
  2. Did you try tunning the hyperparameters?
  3. How did you initialize node features?

I tried with BCEWithLogitsLoss but getting the same results.

  1. It’s 50%, 50% data source for both label 0 and 1

  2. I did some tuning, but my problem is when I use nn.CrossEntropyLoss() as the loss function with n_classes as 2, I’m getting following performance. But it’s nothing with BCEWithLogitsLoss or BCELoss. Do I need to any modifications in the classifier itself? I’m using the same which is mentioned in the tutorial.

    #performance when CrossEntropyLoss is used as the loss function (epoch = 100)
    Accuracy: 88.89%
    Precision: 100.00%
    Recall: 75.00%
    F1-Score: 85.71%

This is the classifier code:

    class Classifier(nn.Module):
        def __init__(self, in_dim, hidden_dim, n_classes):
            super(Classifier, self).__init__()

        self.layers = nn.ModuleList([
            GCN(in_dim, hidden_dim, F.relu),
            GCN(hidden_dim, hidden_dim, F.relu),
            GCN(hidden_dim, hidden_dim, F.relu),
            GCN(hidden_dim, hidden_dim, F.relu)])
        self.classify = nn.Linear(hidden_dim, n_classes)
        self.dropout = nn.Dropout(p=0.2)

    def forward(self, g):
        # For undirected graphs, in_degree is the same as
        # out_degree.
        h = g.in_degrees().view(-1, 1).float()
        for conv in self.layers:
            h = conv(g, h)
        g.ndata['h'] = h
        hg = dgl.mean_nodes(g, 'h')
        return self.classify(hg)
  1. node features are in a N*d matrix (N- no of nodes, d- node features). All nodes doesn’t carry all features, in that case it will represent with 0 values. Also, the d is not same for all the graphs. It’s changing (N is also the same). In following code line I’m assigning matrix to the graphs using DGL library.
    g.ndata['features'] = torch.Tensor(list(X)) #X is the N*d feature matrix and it's a numpy array

Since I’m getting good results with Cross-entropy I’m highly trusted that the classifier need to be changed little bit to work with BCELoss(). But I couldn’t find how to do that. Plz help.

Could you please try printing the shape & value of your prediction and labels and also check the result returned by BCEWithLogitsLoss?