conv.py

import dgl
import dgl.function as fn
import torch
import torch.nn as nn
import torch.nn.functional as F
from dgl.nn.pytorch import SumPooling
from ogb.graphproppred.mol_encoder import AtomEncoder, BondEncoder


### GIN convolution along the graph structure
class GINConv(nn.Module):
    def __init__(self, emb_dim):
        """
        emb_dim (int): node embedding dimensionality
        """

        super(GINConv, self).__init__()

        self.mlp = nn.Sequential(
            nn.Linear(emb_dim, emb_dim),
            nn.BatchNorm1d(emb_dim),
            nn.ReLU(),
            nn.Linear(emb_dim, emb_dim),
        )
        self.eps = nn.Parameter(torch.Tensor([0]))

        self.bond_encoder = BondEncoder(emb_dim=emb_dim)

    def forward(self, g, x, edge_attr):
        with g.local_scope():
            edge_embedding = self.bond_encoder(edge_attr)
            g.ndata["x"] = x
            g.apply_edges(fn.copy_u("x", "m"))
            g.edata["m"] = F.relu(g.edata["m"] + edge_embedding)
            g.update_all(fn.copy_e("m", "m"), fn.sum("m", "new_x"))
            out = self.mlp((1 + self.eps) * x + g.ndata["new_x"])

            return out


### GCN convolution along the graph structure
class GCNConv(nn.Module):
    def __init__(self, emb_dim):
        """
        emb_dim (int): node embedding dimensionality
        """

        super(GCNConv, self).__init__()

        self.linear = nn.Linear(emb_dim, emb_dim)
        self.root_emb = nn.Embedding(1, emb_dim)
        self.bond_encoder = BondEncoder(emb_dim=emb_dim)

    def forward(self, g, x, edge_attr):
        with g.local_scope():
            x = self.linear(x)
            edge_embedding = self.bond_encoder(edge_attr)

            # Molecular graphs are undirected
            # g.out_degrees() is the same as g.in_degrees()
            degs = (g.out_degrees().float() + 1).to(x.device)
            norm = torch.pow(degs, -0.5).unsqueeze(-1)  # (N, 1)
            g.ndata["norm"] = norm
            g.apply_edges(fn.u_mul_v("norm", "norm", "norm"))

            g.ndata["x"] = x
            g.apply_edges(fn.copy_u("x", "m"))
            g.edata["m"] = g.edata["norm"] * F.relu(
                g.edata["m"] + edge_embedding
            )
            g.update_all(fn.copy_e("m", "m"), fn.sum("m", "new_x"))
            out = g.ndata["new_x"] + F.relu(
                x + self.root_emb.weight
            ) * 1.0 / degs.view(-1, 1)

            return out


### GNN to generate node embedding
class GNN_node(nn.Module):
    """
    Output:
        node representations
    """

    def __init__(
        self,
        num_layers,
        emb_dim,
        drop_ratio=0.5,
        JK="last",
        residual=False,
        gnn_type="gin",
    ):
        """
        num_layers (int): number of GNN message passing layers
        emb_dim (int): node embedding dimensionality
        """

        super(GNN_node, self).__init__()
        self.num_layers = num_layers
        self.drop_ratio = drop_ratio
        self.JK = JK
        ### add residual connection or not
        self.residual = residual

        if self.num_layers < 2:
            raise ValueError("Number of GNN layers must be greater than 1.")

        self.atom_encoder = AtomEncoder(emb_dim)

        ###List of GNNs
        self.convs = nn.ModuleList()
        self.batch_norms = nn.ModuleList()

        for layer in range(num_layers):
            if gnn_type == "gin":
                self.convs.append(GINConv(emb_dim))
            elif gnn_type == "gcn":
                self.convs.append(GCNConv(emb_dim))
            else:
                ValueError("Undefined GNN type called {}".format(gnn_type))

            self.batch_norms.append(nn.BatchNorm1d(emb_dim))

    def forward(self, g, x, edge_attr):
        ### computing input node embedding
        h_list = [self.atom_encoder(x)]
        for layer in range(self.num_layers):
            h = self.convs[layer](g, h_list[layer], edge_attr)
            h = self.batch_norms[layer](h)

            if layer == self.num_layers - 1:
                # remove relu for the last layer
                h = F.dropout(h, self.drop_ratio, training=self.training)
            else:
                h = F.dropout(
                    F.relu(h), self.drop_ratio, training=self.training
                )

            if self.residual:
                h += h_list[layer]

            h_list.append(h)

        ### Different implementations of Jk-concat
        if self.JK == "last":
            node_representation = h_list[-1]
        elif self.JK == "sum":
            node_representation = 0
            for layer in range(self.num_layers):
                node_representation += h_list[layer]

        return node_representation


### Virtual GNN to generate node embedding
class GNN_node_Virtualnode(nn.Module):
    """
    Output:
        node representations
    """

    def __init__(
        self,
        num_layers,
        emb_dim,
        drop_ratio=0.5,
        JK="last",
        residual=False,
        gnn_type="gin",
    ):
        """
        num_layers (int): number of GNN message passing layers
        emb_dim (int): node embedding dimensionality
        """

        super(GNN_node_Virtualnode, self).__init__()
        self.num_layers = num_layers
        self.drop_ratio = drop_ratio
        self.JK = JK
        ### add residual connection or not
        self.residual = residual

        if self.num_layers < 2:
            raise ValueError("Number of GNN layers must be greater than 1.")

        self.atom_encoder = AtomEncoder(emb_dim)

        ### set the initial virtual node embedding to 0.
        self.virtualnode_embedding = nn.Embedding(1, emb_dim)
        nn.init.constant_(self.virtualnode_embedding.weight.data, 0)

        ### List of GNNs
        self.convs = nn.ModuleList()
        ### batch norms applied to node embeddings
        self.batch_norms = nn.ModuleList()

        ### List of MLPs to transform virtual node at every layer
        self.mlp_virtualnode_list = nn.ModuleList()

        for layer in range(num_layers):
            if gnn_type == "gin":
                self.convs.append(GINConv(emb_dim))
            elif gnn_type == "gcn":
                self.convs.append(GCNConv(emb_dim))
            else:
                ValueError("Undefined GNN type called {}".format(gnn_type))

            self.batch_norms.append(nn.BatchNorm1d(emb_dim))

        for layer in range(num_layers - 1):
            self.mlp_virtualnode_list.append(
                nn.Sequential(
                    nn.Linear(emb_dim, emb_dim),
                    nn.BatchNorm1d(emb_dim),
                    nn.ReLU(),
                    nn.Linear(emb_dim, emb_dim),
                    nn.BatchNorm1d(emb_dim),
                    nn.ReLU(),
                )
            )
        self.pool = SumPooling()

    def forward(self, g, x, edge_attr):
        ### virtual node embeddings for graphs
        virtualnode_embedding = self.virtualnode_embedding(
            torch.zeros(g.batch_size).to(x.dtype).to(x.device)
        )

        h_list = [self.atom_encoder(x)]
        batch_id = dgl.broadcast_nodes(
            g, torch.arange(g.batch_size).to(x.device)
        )
        for layer in range(self.num_layers):
            ### add message from virtual nodes to graph nodes
            h_list[layer] = h_list[layer] + virtualnode_embedding[batch_id]

            ### Message passing among graph nodes
            h = self.convs[layer](g, h_list[layer], edge_attr)
            h = self.batch_norms[layer](h)
            if layer == self.num_layers - 1:
                # remove relu for the last layer
                h = F.dropout(h, self.drop_ratio, training=self.training)
            else:
                h = F.dropout(
                    F.relu(h), self.drop_ratio, training=self.training
                )

            if self.residual:
                h = h + h_list[layer]

            h_list.append(h)

            ### update the virtual nodes
            if layer < self.num_layers - 1:
                ### add message from graph nodes to virtual nodes
                virtualnode_embedding_temp = (
                    self.pool(g, h_list[layer]) + virtualnode_embedding
                )
                ### transform virtual nodes using MLP
                virtualnode_embedding_temp = self.mlp_virtualnode_list[layer](
                    virtualnode_embedding_temp
                )

                if self.residual:
                    virtualnode_embedding = virtualnode_embedding + F.dropout(
                        virtualnode_embedding_temp,
                        self.drop_ratio,
                        training=self.training,
                    )
                else:
                    virtualnode_embedding = F.dropout(
                        virtualnode_embedding_temp,
                        self.drop_ratio,
                        training=self.training,
                    )

        ### Different implementations of Jk-concat
        if self.JK == "last":
            node_representation = h_list[-1]
        elif self.JK == "sum":
            node_representation = 0
            for layer in range(self.num_layers):
                node_representation += h_list[layer]

        return node_representation