Including convolutional layers causes my network not to train

Hi all,

I’m trying to create a message-passing neural network to perform regression over graphs, and am implementing a model I found in a paper working in a similar domain. One section of this model, after message-passing has occurred, involves upsampling the number of features each node contains by two 1x1 convolutions (conv1, conv2 in my code).

I’ve been facing an error; however, where if I include these convolutions my network fails to train at all. All predicted values are 0 (even in a dataset where all targets are 1). When I remove the convolutional layers and all of the associated squeezing/unsqueezing code, my network trains fine and can overfit on a tiny dataset, but when they are included the loss doesn’t increase or decrease at all.

I’m at a loss as to what’s going wrong - does anyone know what might be causing this?

from torch_geometric.nn import global_max_pool as gmp

embed_dim = 128

# TODO: Apply dropout

class BuildingBlock(torch.nn.Module):
    def __init__(self, in_channels, out_channels, dim=0):
        super(BuildingBlock, self).__init__()
        self.lin1 = Linear(in_channels, 256, dim)
        self.hidden = Linear(256, 128)
        self.lin2 = Linear(128, 128)
    def forward(self, x):
        x = F.relu(self.lin1(x))
        x = F.relu(self.hidden(x))
        x = F.dropout(x, 0.5)
        x = F.relu(self.lin2(x))
        return x

class PaliwalNet(torch.nn.Module):
    def __init__(self, t):
        super(PaliwalNet, self).__init__()
        self.embedding = Embedding(num_embeddings=len(distinct_features)+1, embedding_dim=embed_dim)
        self.MLP_V = BuildingBlock(embed_dim, 128)
        self.MLP_E = BuildingBlock(1, 128)
        self.message_passing_steps = nn.ModuleList()
        for i in range(t):
            self.message_passing_steps.append(PaliwalMP(embed_dim, embed_dim))
        self.conv1 = nn.Conv1d(128, 512, (1,1))
        self.conv2 = nn.Conv1d(512, 1024, (1,1))
        # FCNN for final prediction
        self.lin1 = Linear(1024, 512)
        self.lin2 = Linear(512, 512)
        self.lin3 = Linear(512, 256)
        self.lin4 = Linear(256, 256)
        self.lin5 = Linear(256, 128)
        self.lin6 = Linear(128, 1)

    def forward(self, data):
        x, edge_index, edge_attr, batch = data.x, data.edge_index, data.edge_attr, data.batch
        edge_index_u, edge_index_d = torch.split(edge_index, int(edge_index.shape[1]/2), dim=1)
        edge_attr_u, edge_attr_d = torch.split(edge_attr, int(edge_attr.shape[0]/2))
        # Generate learnable embeddings for node features
        x = x.squeeze(-1)
        x = self.embedding(x)
        # Embed node and edge features into high dimensional space
        x = self.MLP_V(x)
        edge_attr_u = self.MLP_E(edge_attr_u.float())
        edge_attr_d = self.MLP_E(edge_attr_d.float())
        for message_passing_step in self.message_passing_steps:
            x = message_passing_step(x, edge_index_u, edge_index_d, edge_attr_u, edge_attr_d)
        x = x.unsqueeze(-1).unsqueeze(-1)
        x = self.conv1(x)
        x = self.conv2(x)
        # Final prediction network
        x = x.squeeze(-1).squeeze(-1)
        g = gmp(x, batch)
        g = F.relu(self.lin1(g))
        g = F.relu(self.lin2(g))
        g = F.relu(self.lin3(g))
        g = F.relu(self.lin4(g))
        g = F.relu(self.lin5(g))
        g = F.relu(self.lin6(g))
        return g

Try to include batchnorm layer and activation layers in-between ur conv layers

Have just tried this, but no success sadly. Loss doesn’t change at all over training: image

I’m honestly not seeing what’s wrong with the code even tho I haven’t ran it for errors

Scan I see ur training loop?

Wait does ur dataset have negative values as targets?

The dataset only has 0’s and 1’s as targets. Having just reread the page for Conv1d, I suspect there might be an issue with the shape of my data being fed into the conv layer. Currently it’s in the form [n_nodes, 128] where n_nodes changes based on the input graph. It looks like the Conv1d expects [batch size, number of channels, sequence length], which I think in my case might be [1, 128, n_nodes]. Does that sound right?

Yah this is true
I totally forgot about that

Ah alright! I’ll try it out and let you know whether it works :slight_smile:

I totally overlooked the unsqueeze there

It’s working now - thanks so much for the help mate. I’ll need to go and figure out what it was trying to do before that was messing it up! image

Nice! :ok_hand:t2: Well I wasn’t really of much help but well… Ur welcome

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