import torch from torch_geometric.nn import MessagePassing from torch_geometric.nn import global_mean_pool, global_add_pool import torch.nn.functional as F from torch_geometric.utils import add_self_loops, degree allowable_features = { 'node_type' : [0,1,2], 'num_inverted_predecessors' : [0,1,2] } def get_node_feature_dims(): return list(map(len, [ allowable_features['node_type'] ])) full_node_feature_dims = get_node_feature_dims() class NodeEncoder(torch.nn.Module): def __init__(self, emb_dim): super(NodeEncoder, self).__init__() self.node_type_embedding = torch.nn.Embedding(full_node_feature_dims[0], emb_dim) torch.nn.init.xavier_uniform_(self.node_type_embedding.weight.data) def forward(self, x): # First feature is node type, second feature is inverted predecessor x_embedding = self.node_type_embedding(x[:, 0]) #for i in range(1, x.shape[1]): #print(x_embedding,x_embedding.shape) x_embedding = torch.cat((x_embedding, x[:,1].reshape(-1,1)), dim=1) return x_embedding class GCNConv(MessagePassing): def __init__(self, in_emb_dim, out_emb_dim): super(GCNConv, self).__init__(aggr='add') self.linear = torch.nn.Linear(in_emb_dim, out_emb_dim) def forward(self, x, edge_index): edge_index, _ = add_self_loops(edge_index, num_nodes=x.size(0)) x = self.linear(x) 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, norm=norm) def message(self, x_j, norm): return norm.view(-1, 1) * x_j def update(self, aggr_out): return aggr_out class GNN_node(torch.nn.Module): """ Output: node representations """ def __init__(self, node_encoder, num_layer, input_dim, emb_dim, gnn_type='gcn'): ''' 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.node_emb_size = input_dim self.node_encoder = node_encoder ###List of GNNs self.convs = torch.nn.ModuleList() self.batch_norms = torch.nn.ModuleList() self.convs.append(GCNConv(input_dim, emb_dim)) self.batch_norms.append(torch.nn.BatchNorm1d(emb_dim)) for layer in range(1, num_layer): self.convs.append(GCNConv(emb_dim, emb_dim)) self.batch_norms.append(torch.nn.BatchNorm1d(emb_dim)) def forward(self, batched_data): # gate_type, node_type, edge_index = batched_data.gate_type, batched_data.node_type, batched_data.edge_index edge_index = batched_data.edge_index x = torch.cat([batched_data.node_type.reshape(-1, 1), batched_data.num_inverted_predecessors.reshape(-1, 1)], dim=1) h = self.node_encoder(x) for layer in range(self.num_layer): h = self.convs[layer](h, edge_index) h = self.batch_norms[layer](h) if layer != self.num_layer - 1: h = F.relu(h) return h class GNN(torch.nn.Module): def __init__(self, node_encoder, n_classes, input_dim, num_layer = 2, emb_dim = 128,gnn_type = 'gcn',graph_pooling = "mean"): super(GNN, self).__init__() self.num_layer = num_layer self.emb_dim = emb_dim self.graph_pooling = graph_pooling self.hidden_dim = emb_dim self.n_classes = n_classes self.gnn_node = GNN_node(node_encoder,num_layer,input_dim,emb_dim,gnn_type = gnn_type) self.pool = global_mean_pool self.fc1 = torch.nn.Linear(emb_dim, emb_dim) self.graph_pred_linear = torch.nn.Linear(emb_dim, self.n_classes) def forward(self, batched_data): h_node = self.gnn_node(batched_data) h_graph = self.pool(h_node, batched_data.batch) h_graph = F.relu(self.fc1(h_graph)) prediction = self.graph_pred_linear(h_graph) return prediction