# code from https://github.com/snap-stanford/ogb/blob/master/examples/graphproppred/code2/conv.py import torch from torch_geometric.nn import MessagePassing import torch.nn.functional as F from torch_geometric.nn import global_mean_pool, global_add_pool from torch_geometric.utils import degree import math ### GIN convolution along the graph structure class GINConv(MessagePassing): def __init__(self, emb_dim, edge_attr_dim): ''' emb_dim (int): node embedding dimensionality ''' super(GINConv, self).__init__(aggr = "add") self.mlp = torch.nn.Sequential(torch.nn.Linear(emb_dim, 2*emb_dim), torch.nn.BatchNorm1d(2*emb_dim), torch.nn.ReLU(), torch.nn.Linear(2*emb_dim, emb_dim)) self.eps = torch.nn.Parameter(torch.Tensor([0])) # edge_attr is two dimensional after augment_edge transformation self.edge_encoder = torch.nn.Linear(edge_attr_dim, emb_dim) def forward(self, x, edge_index, edge_attr): edge_embedding = self.edge_encoder(edge_attr) out = self.mlp((1 + self.eps) *x + self.propagate(edge_index, x=x, edge_attr=edge_embedding)) return out def message(self, x_j, edge_attr): return F.relu(x_j + edge_attr) def update(self, aggr_out): return aggr_out ### GCN convolution along the graph structure class GCNConv(MessagePassing): def __init__(self, emb_dim, edge_attr_dim): super(GCNConv, self).__init__(aggr='add') self.linear = torch.nn.Linear(emb_dim, emb_dim) self.root_emb = torch.nn.Embedding(1, emb_dim) # edge_attr is two dimensional after augment_edge transformation self.edge_encoder = torch.nn.Linear(edge_attr_dim, emb_dim) def forward(self, x, edge_index, edge_attr): x = self.linear(x) edge_embedding = self.edge_encoder(edge_attr) row, col = edge_index #edge_weight = torch.ones((edge_index.size(1), ), device=edge_index.device) deg = degree(row, x.size(0), dtype = x.dtype) + 1 deg_inv_sqrt = deg.pow(-0.5) deg_inv_sqrt[deg_inv_sqrt == float('inf')] = 0 norm = deg_inv_sqrt[row] * deg_inv_sqrt[col] return self.propagate(edge_index, x=x, edge_attr = edge_embedding, norm=norm) + F.relu(x + self.root_emb.weight) * 1./deg.view(-1,1) def message(self, x_j, edge_attr, norm): return norm.view(-1, 1) * F.relu(x_j + edge_attr) def update(self, aggr_out): return aggr_out ### GNN to generate node embedding class GNN_node(torch.nn.Module): """ Output: node representations """ def __init__(self, num_layer, emb_dim, node_encoder, drop_ratio = 0.5, JK = "last", residual = False, gnn_type = 'gin', edge_attr_dim=2): ''' emb_dim (int): node embedding dimensionality num_layer (int): number of GNN message passing layers ''' super(GNN_node, self).__init__() self.num_layer = num_layer self.drop_ratio = drop_ratio self.JK = JK ### add residual connection or not self.residual = residual if self.num_layer < 2: raise ValueError("Number of GNN layers must be greater than 1.") self.node_encoder = node_encoder ###List of GNNs self.convs = torch.nn.ModuleList() self.batch_norms = torch.nn.ModuleList() for layer in range(num_layer): if gnn_type == 'gin': self.convs.append(GINConv(emb_dim, edge_attr_dim)) elif gnn_type == 'gcn': self.convs.append(GCNConv(emb_dim, edge_attr_dim)) else: ValueError('Undefined GNN type called {}'.format(gnn_type)) self.batch_norms.append(torch.nn.BatchNorm1d(emb_dim)) def forward(self, batched_data): x, edge_index, edge_attr, node_depth, batch = batched_data.x, batched_data.edge_index, batched_data.edge_attr, batched_data.node_depth, batched_data.batch ### computing input node embedding h_list = [self.node_encoder(x, node_depth.view(-1,))] for layer in range(self.num_layer): h = self.convs[layer](h_list[layer], edge_index, edge_attr) h = self.batch_norms[layer](h) if layer == self.num_layer - 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_layer): node_representation += h_list[layer] return node_representation ### Virtual GNN to generate node embedding class GNN_node_Virtualnode(torch.nn.Module): """ Output: node representations """ def __init__(self, num_layer, emb_dim, node_encoder, drop_ratio = 0.5, JK = "last", residual = False, gnn_type = 'gin', edge_attr_dim=2): ''' emb_dim (int): node embedding dimensionality ''' super(GNN_node_Virtualnode, self).__init__() self.num_layer = num_layer self.drop_ratio = drop_ratio self.JK = JK ### add residual connection or not self.residual = residual if self.num_layer < 2: raise ValueError("Number of GNN layers must be greater than 1.") self.node_encoder = node_encoder ### set the initial virtual node embedding to 0. self.virtualnode_embedding = torch.nn.Embedding(1, emb_dim) torch.nn.init.constant_(self.virtualnode_embedding.weight.data, 0) ### List of GNNs self.convs = torch.nn.ModuleList() ### batch norms applied to node embeddings self.batch_norms = torch.nn.ModuleList() ### List of MLPs to transform virtual node at every layer self.mlp_virtualnode_list = torch.nn.ModuleList() for layer in range(num_layer): if gnn_type == 'gin': self.convs.append(GINConv(emb_dim, edge_attr_dim)) elif gnn_type == 'gcn': self.convs.append(GCNConv(emb_dim, edge_attr_dim)) else: ValueError('Undefined GNN type called {}'.format(gnn_type)) self.batch_norms.append(torch.nn.BatchNorm1d(emb_dim)) for layer in range(num_layer - 1): self.mlp_virtualnode_list.append(torch.nn.Sequential(torch.nn.Linear(emb_dim, 2*emb_dim), torch.nn.BatchNorm1d(2*emb_dim), torch.nn.ReLU(), \ torch.nn.Linear(2*emb_dim, emb_dim), torch.nn.BatchNorm1d(emb_dim), torch.nn.ReLU())) def forward(self, batched_data): x, edge_index, edge_attr, node_depth, batch = batched_data.x, batched_data.edge_index, batched_data.edge_attr, batched_data.node_depth, batched_data.batch ### virtual node embeddings for graphs virtualnode_embedding = self.virtualnode_embedding(torch.zeros(batch[-1].item() + 1).to(edge_index.dtype).to(edge_index.device)) h_list = [self.node_encoder(x, node_depth.view(-1,))] for layer in range(self.num_layer): ### add message from virtual nodes to graph nodes h_list[layer] = h_list[layer] + virtualnode_embedding[batch] ### Message passing among graph nodes h = self.convs[layer](h_list[layer], edge_index, edge_attr) h = self.batch_norms[layer](h) if layer == self.num_layer - 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_layer - 1: ### add message from graph nodes to virtual nodes virtualnode_embedding_temp = global_add_pool(h_list[layer], batch) + virtualnode_embedding ### transform virtual nodes using MLP if self.residual: virtualnode_embedding = virtualnode_embedding + F.dropout(self.mlp_virtualnode_list[layer](virtualnode_embedding_temp), self.drop_ratio, training = self.training) else: virtualnode_embedding = F.dropout(self.mlp_virtualnode_list[layer](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_layer): node_representation += h_list[layer] return node_representation if __name__ == "__main__": pass