""" Graph Attention Networks Paper: https://arxiv.org/abs/1710.10903 Code: https://github.com/PetarV-/GAT GAT with batch processing """ import argparse import numpy as np import time import mxnet as mx from mxnet import gluon from dgl import DGLGraph from dgl.data import register_data_args, load_data def elu(data): return mx.nd.LeakyReLU(data, act_type='elu') def gat_message(edges): return {'ft': edges.src['ft'], 'a2': edges.src['a2']} class GATReduce(gluon.Block): def __init__(self, attn_drop): super(GATReduce, self).__init__() if attn_drop: self.attn_drop = gluon.nn.Dropout(attn_drop) else: self.attn_drop = 0 def forward(self, nodes): a1 = mx.nd.expand_dims(nodes.data['a1'], 1) # shape (B, 1, 1) a2 = nodes.mailbox['a2'] # shape (B, deg, 1) ft = nodes.mailbox['ft'] # shape (B, deg, D) # attention a = a1 + a2 # shape (B, deg, 1) e = mx.nd.softmax(mx.nd.LeakyReLU(a)) if self.attn_drop != 0.0: e = self.attn_drop(e) return {'accum': mx.nd.sum(e * ft, axis=1)} # shape (B, D) class GATFinalize(gluon.Block): def __init__(self, headid, indim, hiddendim, activation, residual): super(GATFinalize, self).__init__() self.headid = headid self.activation = activation self.residual = residual self.residual_fc = None if residual: if indim != hiddendim: self.residual_fc = gluon.nn.Dense(hiddendim, use_bias=False) def forward(self, nodes): ret = nodes.data['accum'] if self.residual: if self.residual_fc is not None: ret = self.residual_fc(nodes.data['h']) + ret else: ret = nodes.data['h'] + ret return {'head%d' % self.headid : self.activation(ret)} class GATPrepare(gluon.Block): def __init__(self, indim, hiddendim, drop): super(GATPrepare, self).__init__() self.fc = gluon.nn.Dense(hiddendim) if drop: self.drop = gluon.nn.Dropout(drop) else: self.drop = 0 self.attn_l = gluon.nn.Dense(1, use_bias=False) self.attn_r = gluon.nn.Dense(1, use_bias=False) def forward(self, feats): h = feats if self.drop != 0.0: h = self.drop(h) ft = self.fc(h) a1 = self.attn_l(ft) a2 = self.attn_r(ft) return {'h': h, 'ft': ft, 'a1': a1, 'a2': a2} class GAT(gluon.Block): def __init__(self, g, num_layers, in_dim, num_hidden, num_classes, num_heads, activation, in_drop, attn_drop, residual): super(GAT, self).__init__() self.g = g self.num_layers = num_layers self.num_heads = num_heads self.prp = gluon.nn.Sequential() self.red = gluon.nn.Sequential() self.fnl = gluon.nn.Sequential() # input projection (no residual) for hid in range(num_heads): self.prp.add(GATPrepare(in_dim, num_hidden, in_drop)) self.red.add(GATReduce(attn_drop)) self.fnl.add(GATFinalize(hid, in_dim, num_hidden, activation, False)) # hidden layers for l in range(num_layers - 1): for hid in range(num_heads): # due to multi-head, the in_dim = num_hidden * num_heads self.prp.add(GATPrepare(num_hidden * num_heads, num_hidden, in_drop)) self.red.add(GATReduce(attn_drop)) self.fnl.add(GATFinalize(hid, num_hidden * num_heads, num_hidden, activation, residual)) # output projection self.prp.add(GATPrepare(num_hidden * num_heads, num_classes, in_drop)) self.red.add(GATReduce(attn_drop)) self.fnl.add(GATFinalize(0, num_hidden * num_heads, num_classes, activation, residual)) # sanity check assert len(self.prp) == self.num_layers * self.num_heads + 1 assert len(self.red) == self.num_layers * self.num_heads + 1 assert len(self.fnl) == self.num_layers * self.num_heads + 1 def forward(self, features): last = features for l in range(self.num_layers): for hid in range(self.num_heads): i = l * self.num_heads + hid # prepare self.g.set_n_repr(self.prp[i](last)) # message passing self.g.update_all(gat_message, self.red[i], self.fnl[i]) # merge all the heads last = mx.nd.concat( *[self.g.pop_n_repr('head%d' % hid) for hid in range(self.num_heads)], dim=1) # output projection self.g.set_n_repr(self.prp[-1](last)) self.g.update_all(gat_message, self.red[-1], self.fnl[-1]) return self.g.pop_n_repr('head0') def evaluate(model, features, labels, mask): logits = model(features) logits = logits[mask].asnumpy().squeeze() val_labels = labels[mask].asnumpy().squeeze() max_index = np.argmax(logits, axis=1) accuracy = np.sum(np.where(max_index == val_labels, 1, 0)) / len(val_labels) return accuracy def main(args): # load and preprocess dataset data = load_data(args) features = mx.nd.array(data.features) labels = mx.nd.array(data.labels) mask = mx.nd.array(np.where(data.train_mask == 1)) test_mask = mx.nd.array(np.where(data.test_mask == 1)) val_mask = mx.nd.array(np.where(data.val_mask == 1)) in_feats = features.shape[1] n_classes = data.num_labels n_edges = data.graph.number_of_edges() if args.gpu < 0: ctx = mx.cpu() else: ctx = mx.gpu(args.gpu) features = features.as_in_context(ctx) labels = labels.as_in_context(ctx) mask = mask.as_in_context(ctx) test_mask = test_mask.as_in_context(ctx) val_mask = val_mask.as_in_context(ctx) # create graph g = data.graph # add self-loop g.remove_edges_from(g.selfloop_edges()) g = DGLGraph(g) g.add_edges(g.nodes(), g.nodes()) # create model model = GAT(g, args.num_layers, in_feats, args.num_hidden, n_classes, args.num_heads, elu, args.in_drop, args.attn_drop, args.residual) model.initialize(ctx=ctx) # use optimizer trainer = gluon.Trainer(model.collect_params(), 'adam', {'learning_rate': args.lr}) dur = [] for epoch in range(args.epochs): if epoch >= 3: t0 = time.time() # forward with mx.autograd.record(): logits = model(features) loss = mx.nd.softmax_cross_entropy(logits[mask].squeeze(), labels[mask].squeeze()) loss.backward() trainer.step(mask.shape[0]) if epoch >= 3: dur.append(time.time() - t0) print("Epoch {:05d} | Loss {:.4f} | Time(s) {:.4f} | ETputs(KTEPS) {:.2f}".format( epoch, loss.asnumpy()[0], np.mean(dur), n_edges / np.mean(dur) / 1000)) if epoch % 100 == 0: val_accuracy = evaluate(model, features, labels, val_mask) print("Validation Accuracy {:.4f}".format(val_accuracy)) test_accuracy = evaluate(model, features, labels, test_mask) print("Test Accuracy {:.4f}".format(test_accuracy)) if __name__ == '__main__': parser = argparse.ArgumentParser(description='GAT') register_data_args(parser) parser.add_argument("--gpu", type=int, default=-1, help="Which GPU to use. Set -1 to use CPU.") parser.add_argument("--epochs", type=int, default=1000, help="number of training epochs") parser.add_argument("--num-heads", type=int, default=8, help="number of attentional heads to use") parser.add_argument("--num-layers", type=int, default=1, help="number of hidden layers") parser.add_argument("--num-hidden", type=int, default=8, help="size of hidden units") parser.add_argument("--residual", action="store_false", help="use residual connection") parser.add_argument("--in-drop", type=float, default=.6, help="input feature dropout") parser.add_argument("--attn-drop", type=float, default=.6, help="attention dropout") parser.add_argument("--lr", type=float, default=0.005, help="learning rate") args = parser.parse_args() print(args) main(args)