Embeddings in graph classification

Hi all,

Question: What is the proper way of storing embeddings outside of GPU and only loading to GPU the ones beings used, without repetition, during training?

Context: I am using a biological knowledge graph. When I am predicting something like a GENE-DRUG interaction, I sample a n-hops subgraph around this node pair, and then classify the subgraph. My goal is to do graph batching. I am starting with 1-hop subgraph, which usually has around 600 nodes and 30k edges. The whole graph has over 300.000 nodes.

Lets suppose that my batch has 2 subgraphs of 600 nodes each, and they have 100 nodes in common. Where do I store the embeddings so that backpropagation updates the embeddings properly and GPU memory is not wasted?

  1. In the node?
  2. In the dataloader?
  3. In the model?

Thanks you so much for your time! I have been reading the documentation for a while and cant figure it out. If it is not a big deal, would you please write a quick example like the one below?

import dgl.nn.pytorch as dglnn
import torch.nn as nn
import torch

class Classifier(nn.Module):
    def __init__(self, in_dim, hidden_dim, n_classes):
        super(Classifier, self).__init__()
        self.conv1 = dglnn.GraphConv(in_dim, hidden_dim)
        self.conv2 = dglnn.GraphConv(hidden_dim, hidden_dim)
        self.classify = nn.Linear(hidden_dim, n_classes)

    def forward(self, g, h):
        # Apply graph convolution and activation.
        h = F.relu(self.conv1(g, h))
        h = F.relu(self.conv2(g, h))
        with g.local_scope():
            g.ndata['h'] = h
            # Calculate graph representation by average readout.
            hg = dgl.mean_nodes(g, 'h')
            return self.classify(hg)

import dgl.data
dataset = dgl.data.GINDataset('MUTAG', False)

from dgl.dataloading import GraphDataLoader
dataloader = GraphDataLoader(

import torch.nn.functional as F

# Only an example, 7 is the input feature size
model = Classifier(7, 20, 5)
opt = torch.optim.Adam(model.parameters())
for epoch in range(20):
    for batched_graph, labels in dataloader:
        feats = batched_graph.ndata['attr']
        logits = model(batched_graph, feats)
        loss = F.cross_entropy(logits, labels)

Would DistEmbedding be the solution?

def initializer(shape, dtype):
    arr = th.zeros(shape, dtype=dtype)
    arr.uniform_(-1, 1)
    return arr

emb = dgl.distributed.DistEmbedding(g.number_of_nodes(), 10, init_func=initializer)
optimizer = dgl.distributed.SparseAdagrad([emb], lr=0.001)
for blocks in dataloader:
    feats = emb(nids)
    loss = F.sum(feats + 1, 0)

I don’t think DistEmbedding is relevant here unless you are doing distributed training. You may initialize the embeddings of all nodes with nn.Embedding and put it on CPU. Every time you have a new batch of subgraphs, you can retrieve the embeddings of the corresponding nodes and put them on GPU.

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