# code form https://github.com/snap-stanford/ogb/blob/master/examples/graphproppred/code2/gnn.py import torch from torch_geometric.nn import MessagePassing from torch_geometric.nn import global_add_pool, global_mean_pool, global_max_pool, GlobalAttention, Set2Set import torch.nn.functional as F from torch_geometric.nn.inits import uniform from src.model.conv import GNN_node, GNN_node_Virtualnode from torch_scatter import scatter_mean class GNN(torch.nn.Module): def __init__(self, num_vocab, max_seq_len, node_encoder, num_layer = 5, emb_dim = 300, gnn_type = 'gin', virtual_node = True, residual = False, drop_ratio = 0.5, JK = "last", graph_pooling = "mean", num_class=0, edge_attr_dim=2): ''' num_tasks (int): number of labels to be predicted virtual_node (bool): whether to add virtual node or not ''' super(GNN, self).__init__() self.num_class = num_class # if we do classification self.num_layer = num_layer self.drop_ratio = drop_ratio self.JK = JK self.emb_dim = emb_dim self.num_vocab = num_vocab self.max_seq_len = max_seq_len self.graph_pooling = graph_pooling if self.num_layer < 2: raise ValueError("Number of GNN layers must be greater than 1.") ### GNN to generate node embeddings if virtual_node: self.gnn_node = GNN_node_Virtualnode(num_layer, emb_dim, node_encoder, JK = JK, drop_ratio = drop_ratio, residual = residual, gnn_type = gnn_type, edge_attr_dim=edge_attr_dim) else: self.gnn_node = GNN_node(num_layer, emb_dim, node_encoder, JK = JK, drop_ratio = drop_ratio, residual = residual, gnn_type = gnn_type, edge_attr_dim=edge_attr_dim) ### Pooling function to generate whole-graph embeddings if self.graph_pooling == "sum": self.pool = global_add_pool elif self.graph_pooling == "mean": self.pool = global_mean_pool elif self.graph_pooling == "max": self.pool = global_max_pool elif self.graph_pooling == "attention": self.pool = GlobalAttention(gate_nn = 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, 1))) elif self.graph_pooling == "set2set": self.pool = Set2Set(emb_dim, processing_steps = 2) else: raise ValueError("Invalid graph pooling type.") self.graph_pred_linear_list = torch.nn.ModuleList() if self.num_class > 0: if graph_pooling == "set2set": self.graph_pred_linear = torch.nn.Linear(2*self.emb_dim, self.num_class) else: self.graph_pred_linear = torch.nn.Linear(self.emb_dim, self.num_class) else: if graph_pooling == "set2set": for i in range(max_seq_len): self.graph_pred_linear_list.append(torch.nn.Linear(2*emb_dim, self.num_vocab)) else: if self.num_vocab == 1: self.graph_pred_linear_list.append(torch.nn.Sequential( torch.nn.Linear(emb_dim, self.num_vocab), torch.nn.ReLU())) else: for i in range(max_seq_len): self.graph_pred_linear_list.append(torch.nn.Linear(emb_dim, self.num_vocab)) def forward(self, batched_data): ''' Return: A list of predictions. i-th element represents prediction at i-th position of the sequence. ''' h_node = self.gnn_node(batched_data) h_graph = self.pool(h_node, batched_data.batch) if self.num_class > 0: return self.graph_pred_linear(h_graph) pred_list = [] for i in range(self.max_seq_len): pred_list.append(self.graph_pred_linear_list[i](h_graph)) return pred_list if __name__ == '__main__': pass