Retrieve entire node embedding from minibatch training

Hi I am doing minibatch training on my own dataset. I am following this tutorial:

but I need the node embeddings for all the nodes in the entire graph.

For traditional link prediction task with global training, for example, this tutorial:
we can use the following

node_embeddings = model.sage(graph, node_features)

But in minibatch training, model.sage takes (blocks, feature) instead of (graph, feature). I think I have to do something like node_embedding = model.sage(blocks, feature) where, this time, blocks = [blocks[0], blocks[1]] and blocks[0] and blocks[1] are from the entire graph. We convert the entire graph to appropriate blocks and feed to the forward function of sage.

Does that make sense? If it makes sense, how do I convert g (the entire graph) to the appropriate blocks. If not, how can I get the the embeddings for every node in g. What I did was something like:

    def forward(self, blocks, x, global_item_embedding_dic, global_user_embedding_dic, epoc_count):
        x = self.conv1(blocks[0], x)
        x = {k: F.relu(v) for k, v in x.items()}
        x = self.conv2(blocks[1], x)
        if epoc_count == num_epoch - 1:
            item_emb = x['item'].detach().numpy().tolist()
            user_emb = x['user'].detach().numpy().tolist()
            item_id_list = list(blocks[1].dstnodes['item'].data[dgl.NID].numpy())
            user_id_list = list(blocks[1].dstnodes['user'].data[dgl.NID].numpy())
            for iid, emb in zip(item_id_list, item_emb):
                global_item_embedding_dic[iid] = emb
            for uid, emb in zip(user_id_list, user_emb):
                global_user_embedding_dic[uid] = emb
        return x, global_item_embedding_dic, global_user_embedding_dic

item_tuple_list = [ (k,v) for k,v in global_item_embedding_dic.items()]
item_tuple_list = sorted(item_tuple_list)
item_tuple_list = [v for (k,v) in item_tuple_list]
item_feat_tensor = torch.FloatTensor(item_tuple_list)

user_tuple_list = [ (k,v) for k,v in global_user_embedding_dic.items()]
user_tuple_list = sorted(user_tuple_list)
user_tuple_list = [v for (k,v) in user_tuple_list]
user_feat_tensor = torch.FloatTensor(user_tuple_list)
node_embeddings = {'user':user_feat_tensor, 'item':item_feat_tensor}

In each minibatch in the final epoc, I use global dictionary and update embedding for each node, and eventually sort the features to get a 2*2 tensor for final embeddings.

Please share some thoughts, thanks in advance!

Hi, in mini-batch training, each iteration computes a subset of node embeddings, so to retrieve the entire node embedding, you need to maintain a list, append the embeddings computed at each iteration, and concatenate them all at the end. Below is a pseudo code:

g = ...   # Graph data
model = ...  # GraphSAGE model 
all_node_ids = torch.arange(g.num_nodes())
dataloader = dgl.dataloading.DataLoader(
    all_node_ids,     # compute embeddings for all the nodes
    ...               # other arguments
    shuffle=False,    # remember to set this to False so you can just concatenate embeddings at the end
)  # Dataloader that generates 

all_embeddings = []
for blocks in dataloader:
    embed = model(blocks, ...)
# Concatenate them all
all_embeddings =

This topic was automatically closed 30 days after the last reply. New replies are no longer allowed.