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model.py
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import random
from copy import deepcopy
import numpy as np
import scipy.sparse as sp
import torch
from scipy.sparse import csr_matrix
from sklearn.metrics import (accuracy_score, classification_report, f1_score,
precision_score, recall_score)
from torch import nn
from torch.nn import functional as nf
from dataloader import adj2graph, adj2graph_torch
from link_prediction_metric import evaluate_lp
from node_classification_metric import evaluate_clf
from utils import EarlyStopper, color_print, progress, randint_choice, shuffle
LABEL_EDGE_DROPOUT = 1
LABEL_GENERATE = 0
SAMPLE_RATE = (2, 3)
RATIO_NOISE = 0.1
def _generate_edge_dropout_graph(n_nodes, us, vs, ratio, device, return_matrix=False):
n = int(len(us) * (ratio + (random.random() - 0.5) * RATIO_NOISE))
indices = torch.randperm(len(us), device=device)[:n]
us = torch.tensor(us)[indices]
vs = torch.tensor(vs)[indices]
adj_mat = torch.zeros([n_nodes, n_nodes]).to(device)
adj_mat[us, vs] = 1
if return_matrix:
return adj_mat
return adj2graph_torch(adj_mat)
class LightGCN(nn.Module):
def __init__(self, n_nodes, graph, device, n_dim=64, n_layers=3, keep_prob=0.6, dropout=0):
super(LightGCN, self).__init__()
self.n_nodes = n_nodes
self.n_dim = n_dim
self.device = device
self.n_layers = n_layers
self.keep_prob = keep_prob
self.embeddings = torch.nn.Embedding(num_embeddings=self.n_nodes, embedding_dim=self.n_dim)
nn.init.normal_(self.embeddings.weight, std=0.1)
self.graph = graph
self.dropout = dropout
self.t_dropout = nn.Dropout(dropout)
def __dropout_x(self, x, keep_prob):
if not x.is_sparse:
return self.t_dropout(x)
size = x.size()
index = x.indices().t()
values = x.values()
random_index = torch.rand(len(values)) + keep_prob
random_index = random_index.int().bool()
index = index[random_index]
values = values[random_index] / keep_prob
g = torch.sparse.FloatTensor(index.t(), values, size)
return g
def __dropout(self, keep_prob, graph=None):
if graph is None:
graph = self.graph
return self.__dropout_x(graph, keep_prob)
def forward(self, training, graph=None, all_emb=None):
if graph is None:
graph = self.graph
if all_emb is None:
all_emb = self.embeddings.weight
emb_list = [all_emb]
g_dropped = self.__dropout(self.keep_prob, graph) if training and self.dropout else graph
for _ in range(self.n_layers):
all_emb = torch.sparse.mm(g_dropped, all_emb) if g_dropped.is_sparse else torch.mm(g_dropped, all_emb)
emb_list.append(all_emb)
emb_list = torch.stack(emb_list, dim=1)
light_out = torch.mean(emb_list, dim=1)
return light_out
class Generator(nn.Module):
def __init__(self, n_nodes, nodes, us, vs, device, n_dim=256, temperature=0.0001, lambda_new=0, lambda_count=0,
ssl_ratio=0.5, n_g_nodes=1200, init_rate=0.5):
super(Generator, self).__init__()
self.n_nodes = n_nodes
self.nodes = nodes
self.us = us
self.vs = vs
self.device = device
self.n_dim = n_dim
self.temperature = temperature
self.lambda_new = lambda_new
self.lambda_count = lambda_count
self.ssl_ratio = ssl_ratio
n_g_nodes = min(n_g_nodes, n_nodes)
self.n_g_nodes = n_g_nodes
self.g_nodes, self.o_us, self.o_vs, _, _ = self._partition_nodes()
self.n_candidate = n_g_nodes * n_g_nodes
self.n_target = int((len(us) - len(self.o_us)) * ssl_ratio)
self.new_indices = []
edges = {}
g_us, g_vs = [], []
_g_us, _g_vs = [], []
for u, v in zip(us, vs):
edges[(u, v)] = 1
for idx in range(self.n_candidate):
i, j = idx // n_g_nodes, idx % n_g_nodes
if (self.g_nodes[i], self.g_nodes[j]) not in edges:
self.new_indices.append(idx)
else:
g_us.append(i)
g_vs.append(j)
_g_us.append(self.g_nodes[i])
_g_vs.append(self.g_nodes[j])
self.g_us = np.array(g_us)
self.g_vs = np.array(g_vs)
self._g_us = np.array(_g_us)
self._g_vs = np.array(_g_vs)
assert len(g_us) == len(self._g_us) and len(g_vs) == len(self._g_vs)
self.g_mat = csr_matrix((np.ones_like(self.g_us), (self.g_us, self.g_vs)),
shape=(n_g_nodes, n_g_nodes)).toarray()
n_all = n_nodes * n_nodes
color_print(f'Existing Edges: {len(us)} / {n_all} = {len(us) / n_all * 100:.2f}%')
color_print(f'Candidate Edges: {self.n_candidate} / {n_all} = {self.n_candidate / n_all * 100:.2f}%')
color_print(f'New Edges: {len(self.new_indices)} / {n_all} = {len(self.new_indices) / n_all * 100:.2f}%')
if init_rate >= 0:
n_existing_edges = int(self.n_target * init_rate)
n_new_edges = int(self.n_target * (1 - init_rate))
weight_existing = n_existing_edges / (self.n_candidate - len(self.new_indices))
weight_new = n_new_edges / len(self.new_indices)
weights = torch.ones(self.n_candidate).to(device) * weight_existing
weights[self.new_indices] = weight_new
self.weights = nn.Parameter(weights)
else:
self.weights = nn.Parameter(torch.rand(self.n_candidate).to(device))
def _partition_nodes(self):
if self.n_g_nodes >= self.n_nodes:
g_nodes, o_us, o_vs, g_us, g_vs = self.nodes, [], [], self.us, self.vs
else:
degree = {}
for u in self.us:
degree[u] = degree.get(u, 0) + 1
for v in self.vs:
degree[v] = degree.get(v, 0) + 1
g_nodes = list(x[0] for x in sorted(degree.items(), key=lambda x: x[1], reverse=True)[:self.n_g_nodes])
g_nodes_set = set(g_nodes)
o_us, o_vs = [], []
g_us, g_vs = [], []
for u, v in zip(self.us, self.vs):
if u not in g_nodes_set or v not in g_nodes_set:
o_us.append(u)
o_vs.append(v)
else:
g_us.append(u)
g_vs.append(v)
color_print(f'Nodes (g_nodes + o_nodes): {len(g_nodes)} + {self.n_nodes - self.n_g_nodes} = {self.n_nodes}')
color_print(f'Edges (g_edges + o_edges): {len(g_us)} + {len(o_us)} = {len(self.us)}')
return np.array(g_nodes), np.array(o_us), np.array(o_vs), np.array(g_us), np.array(g_vs)
def forward(self):
noises = torch.rand(self.n_candidate, device=self.device)
matrix = self.weights - noises
matrix = torch.sigmoid(matrix / self.temperature)
return matrix
def generate_g_graph(self, make_binary=False):
g_matrix = self.forward().view(self.n_g_nodes, self.n_g_nodes)
if make_binary:
g_matrix[g_matrix >= 0.5] = 1
g_matrix[g_matrix != 1] = 0
return adj2graph_torch(g_matrix)
def generate_g_edge_dropout_graph(self):
return _generate_edge_dropout_graph(self.n_g_nodes, self.g_us, self.g_vs, self.ssl_ratio, self.device)
def generate_adj_graph(self):
matrix = self.forward().view(self.n_g_nodes, self.n_g_nodes)
idx = torch.zeros_like(matrix)
idx[matrix >= 0.5] = 1
u_idx, v_idx = idx.to_sparse().indices().tolist()
us = self.g_nodes[u_idx]
vs = self.g_nodes[v_idx]
mat = csr_matrix((np.ones_like(us), (us, vs)), shape=(self.n_nodes, self.n_nodes))
if len(self.o_us):
keep_idx = randint_choice(len(self.o_us), size=int(len(self.o_us) * self.ssl_ratio), replace=False)
us = self.o_us[keep_idx]
vs = self.o_vs[keep_idx]
mat += csr_matrix((np.ones_like(us), (us, vs)), shape=(self.n_nodes, self.n_nodes))
return adj2graph(mat).to(self.device), adj2graph_torch(matrix).to(self.device)
def generate_edge_dropout_graph(self):
g_keep_idx = randint_choice(len(self.g_us), size=int(len(self.g_us) * self.ssl_ratio), replace=False)
g_us = self.g_us[g_keep_idx]
g_vs = self.g_vs[g_keep_idx]
g_ratings = np.ones_like(g_us, dtype=np.float32)
g_adj_mat = sp.csr_matrix((g_ratings, (g_us, g_vs)), shape=(self.n_g_nodes, self.n_g_nodes))
o_keep_idx = randint_choice(len(self.o_us), size=int(len(self.o_us) * self.ssl_ratio), replace=False)
o_us = self.o_us[o_keep_idx]
o_vs = self.o_vs[o_keep_idx]
us = np.concatenate([self._g_us[g_keep_idx], o_us])
vs = np.concatenate([self._g_vs[g_keep_idx], o_vs])
ratings = np.ones_like(us, dtype=np.float32)
adj_mat = sp.csr_matrix((ratings, (us, vs)), shape=(self.n_nodes, self.n_nodes))
return adj2graph(adj_mat).to(self.device), adj2graph(g_adj_mat).to(self.device)
def reg_loss(self):
weights = self.weights
edge_count_loss = (weights.abs().sum() - self.n_target).abs()
new_edge_loss = weights[self.new_indices].abs().sum()
return edge_count_loss * self.lambda_count + new_edge_loss * self.lambda_new
def loss(self, discriminator, batch_size):
scores = []
labels = []
for _ in range(batch_size):
graph = self.generate_g_graph()
score = discriminator.forward(graph, False)
scores.append(score)
labels.append(LABEL_EDGE_DROPOUT)
scores = torch.cat(scores)
labels = torch.FloatTensor(labels).to(self.device)
loss = discriminator.loss_fn(scores, labels) + self.reg_loss()
return loss, scores.mean()
def warmup(self, batch_size):
reg_loss = []
for _ in range(batch_size):
reg_loss.append(self.reg_loss())
reg_loss = torch.stack(reg_loss).mean()
return reg_loss
class Discriminator(nn.Module):
def __init__(self, n_nodes, device, n_dim):
super(Discriminator, self).__init__()
self.device = device
self.gcn = LightGCN(n_nodes, None, device, n_dim)
self.gcn.embeddings.weight.requires_grad_(False)
self.linear = nn.Sequential(
nn.Linear(n_dim * 2, n_dim),
nn.Sigmoid(),
nn.Linear(n_dim, n_dim),
nn.Dropout(0.1),
nn.Sigmoid(),
nn.Linear(n_dim, 1),
nn.Sigmoid()
)
self.loss_fn = nn.BCEWithLogitsLoss()
def forward(self, graph, training):
all_embeddings = self.gcn.forward(training, graph)
graph_embedding = torch.cat([torch.sum(all_embeddings, dim=0), torch.max(all_embeddings, dim=0)[0]])
return self.linear(graph_embedding)
def loss(self, graphs, labels):
scores = []
for graph in graphs:
scores.append(self.forward(graph, True))
scores = torch.cat(scores)
labels = torch.FloatTensor(labels).to(self.device)
return self.loss_fn(scores, labels)
def evaluate(self, graphs, labels, acc_only=True):
scores = []
for graph in graphs:
scores.append(self.forward(graph, True).item())
scores = np.array(scores)
median = 0.5
index_pos = scores >= median
index_neg = scores < median
scores[index_pos] = 1
scores[index_neg] = 0
accuracy = accuracy_score(labels, scores)
if not acc_only:
precision = precision_score(labels, scores, zero_division=0.0)
recall = recall_score(labels, scores, zero_division=0.0)
f1 = f1_score(labels, scores, zero_division=0.0)
report = classification_report(labels, scores, zero_division=0.0)
return accuracy, precision, recall, f1, report
return accuracy
class GCL(nn.Module):
def __init__(self, n_nodes, nodes, all_neighbors, us, vs, graph, device, dataset, n_dim,
temperature=0.5, lambda_ssl=1, lambda_bpr=1, lambda_reg=0.0001, node_features=None):
super(GCL, self).__init__()
self.n_nodes = n_nodes
self.nodes = nodes
self.nodes_tensor = torch.tensor(self.nodes, device=device)
self.all_neighbors = all_neighbors
self.us = us
self.vs = vs
self.graph = graph
self.device = device
self.dataset = dataset
self.temperature = temperature
self.lambda_ssl = lambda_ssl
self.lambda_bpr = lambda_bpr
self.lambda_reg = lambda_reg
self.gcn = LightGCN(n_nodes, graph, device, n_dim)
if node_features:
color_print('Using node features to init lgn with dim =', n_dim)
for node in node_features:
self.gcn.embeddings.weight.data[node] = torch.FloatTensor(node_features[node]).to(device)
self.to(device)
def get_all_embeddings(self, training, graph=None):
return self.gcn.forward(training, graph)
def forward(self, training, graph1, graph2, nodes=None):
# ========================= ssl loss ========================= #
all_embeddings1 = self.get_all_embeddings(training, graph1)
all_embeddings2 = self.get_all_embeddings(training, graph2)
if nodes is not None:
all_embeddings1 = all_embeddings1[nodes]
all_embeddings2 = all_embeddings2[nodes]
normalize_all_embeddings1 = nf.normalize(all_embeddings1, 1)
normalize_all_embeddings2 = nf.normalize(all_embeddings2, 1)
pos_score = torch.sum(normalize_all_embeddings1 * normalize_all_embeddings2, dim=1)
ttl_score = torch.matmul(normalize_all_embeddings1, normalize_all_embeddings2.t())
pos_score = torch.exp(pos_score / self.temperature)
ttl_score = torch.sum(torch.exp(ttl_score / self.temperature), dim=1)
ssl_loss = -torch.sum(torch.log(pos_score / ttl_score))
# ========================= bpr loss ========================= #
if nodes is None:
nodes = self.nodes_tensor
node_list = []
pos_list = []
neg_list = []
for u in nodes.tolist():
pos_list.extend(self.all_neighbors[u])
for _ in range(len(self.all_neighbors[u])):
node_list.append(u)
while True:
neg = random.choice(self.nodes)
if neg in self.all_neighbors[u]:
continue
else:
neg_list.append(neg)
break
node_list = torch.tensor(node_list, device=self.device)
pos_list = torch.tensor(pos_list, device=self.device)
neg_list = torch.tensor(neg_list, device=self.device)
embeddings = self.get_all_embeddings(True, self.graph)
u_embeddings = embeddings[node_list]
v_embeddings = embeddings[pos_list]
n_embeddings = embeddings[neg_list]
u_emb0 = self.gcn.embeddings(node_list)
v_emb0 = self.gcn.embeddings(pos_list)
n_emb0 = self.gcn.embeddings(neg_list)
reg_loss = (1 / 2) * (u_emb0.norm(2).pow(2) +
v_emb0.norm(2).pow(2) +
n_emb0.norm(2).pow(2)) / float(nodes.size(0))
pos_scores = torch.mul(u_embeddings, v_embeddings)
pos_scores = torch.sum(pos_scores, dim=1)
neg_scores = torch.mul(u_embeddings, n_embeddings)
neg_scores = torch.sum(neg_scores, dim=1)
bpr_loss = torch.mean(torch.nn.functional.softplus(neg_scores - pos_scores))
return ssl_loss * self.lambda_ssl + bpr_loss * self.lambda_bpr + reg_loss * self.lambda_reg
def do_valid(self, valid_edges):
model = {}
embeddings = self.get_all_embeddings(False).detach().cpu().numpy()
for i, embedding in enumerate(embeddings):
model[i] = embedding
mrr, _ = evaluate_lp(f'data/{self.dataset}', model, test_data=valid_edges)
return mrr
def get_embeddings(self):
embeddings = self.get_all_embeddings(False).detach().cpu().numpy()
model = {i: embedding for i, embedding in enumerate(embeddings)}
return model
class GACN(nn.Module):
def __init__(self, n_nodes, nodes, all_neighbors, graph, device, dataset, args, node_features=None):
super(GACN, self).__init__()
n_dim, ssl_ratio, lambda_new, lambda_count, n_g_nodes, temperature, st, init_rate = \
args.n_dim, args.ssl_ratio, args.lambda_new, args.lambda_count, args.n_g_nodes, args.temperature, \
args.st, args.init_rate
self.n_nodes = n_nodes
self.nodes = nodes
self.all_neighbors = all_neighbors
self.graph = graph
self.device = device
self.dataset = dataset
self.n_dim = n_dim
self.ssl_ratio = ssl_ratio
self.st = st
self.degree_map = {}
us, vs = [], []
for node, neighbors in all_neighbors.items():
self.degree_map[node] = len(neighbors)
if len(neighbors) > 0:
us.extend([node] * len(neighbors))
vs.extend(neighbors)
self.us = np.array(us)
self.vs = np.array(vs)
self.generator = Generator(n_nodes, nodes, self.us, self.vs, device, n_dim, temperature, lambda_new,
lambda_count, ssl_ratio, n_g_nodes, init_rate)
self.g_nodes = torch.tensor(self.generator.g_nodes).to(self.device)
self.discriminator = Discriminator(self.generator.n_g_nodes, device, n_dim)
self.gcl = GCL(n_nodes, nodes, all_neighbors, self.us, self.vs, graph, device, dataset, n_dim,
args.cl_temperature, args.cl_lambda_ssl, args.cl_lambda_bpr, args.cl_lambda_reg, node_features)
self.to(device)
self.eval()
def prepare_discriminator_data(self, n_samples):
graphs, labels = [], []
for i in range(n_samples):
if i % SAMPLE_RATE[1] < SAMPLE_RATE[0]:
graphs.append(self.generator.generate_g_edge_dropout_graph())
labels.append(LABEL_EDGE_DROPOUT)
else:
graphs.append(self.generator.generate_g_graph(make_binary=True))
labels.append(LABEL_GENERATE)
return graphs, labels
def do_train(self, args, valid_edges):
optimizer_params = {'params': filter(lambda param: param.requires_grad, self.generator.parameters()),
'lr': args.lr_g}
if args.wd_g:
optimizer_params['weight_decay'] = args.wd_g
optimizer_g = torch.optim.Adam(**optimizer_params)
optimizer_params = {'params': self.discriminator.linear.parameters(), 'lr': args.lr_d}
if args.wd_d:
optimizer_params['weight_decay'] = args.wd_d
optimizer_d = torch.optim.Adam(**optimizer_params)
optimizer_params = {'params': self.gcl.gcn.parameters(), 'lr': args.lr_cl}
if args.wd_cl:
optimizer_params['weight_decay'] = args.wd_cl
optimizer_cl = torch.optim.Adam(**optimizer_params)
outer_early_stopper = EarlyStopper(
args.patience,
lambda: deepcopy(self.state_dict()),
_print=color_print)
for epoch in range(1, args.n_epoch + 1):
color_print('\n# ************** Begin: Train Discriminator ************** #')
self.generator.eval()
self.discriminator.linear.train()
self.gcl.gcn.eval()
self.discriminator.gcn.embeddings.weight = torch.nn.Parameter(
self.gcl.gcn.embeddings.weight[self.g_nodes])
data_iter = progress(range(1, args.n_epoch_d + 1))
for epoch_d in data_iter:
loss_list = []
for _ in range(args.iter_d):
with torch.no_grad():
graphs, labels = self.prepare_discriminator_data(args.bs_d)
graphs, labels = shuffle(graphs, labels)
loss = self.discriminator.loss(graphs, labels)
optimizer_d.zero_grad()
loss.backward()
optimizer_d.step()
loss_list.append(loss.item())
if epoch_d % args.ri_d == 0:
data_iter.write(f'[Iter {epoch}] [Discriminator] [Epoch {epoch_d}] '
f'loss = {np.nanmean(loss_list)}')
data_iter.close()
# color_print('# ============== End: Train Discriminator ============== #')
color_print('\n# ************** Begin: Train CL ************** #')
self.generator.eval()
self.discriminator.linear.eval()
self.gcl.gcn.train()
data_iter = progress(range(1, args.n_epoch_cl + 1))
early_stopper = EarlyStopper(args.patience_cl, lambda: deepcopy(self.gcl.state_dict()))
for epoch_cl in data_iter:
graph1, g_graph1 = self.generator.generate_adj_graph()
graph2, g_graph2 = self.generator.generate_edge_dropout_graph()
with torch.no_grad():
score1 = self.discriminator.forward(g_graph1, False).item()
score2 = self.discriminator.forward(g_graph2, False).item()
if abs(score2 - score1) > self.st:
continue
nodes = None
batch_nodes = None
if args.bs_cl < self.n_nodes:
nodes = self.nodes.copy()
random.shuffle(nodes)
nodes = torch.tensor(nodes).to(device=self.device)
loss_list = []
for i in range(0, self.n_nodes, args.bs_cl):
if nodes is not None:
batch_nodes = nodes[i:i + args.bs_cl]
loss = self.gcl.forward(training=True, graph1=graph1, graph2=graph2, nodes=batch_nodes)
optimizer_cl.zero_grad()
loss.backward()
optimizer_cl.step()
loss_list.append(loss.item())
if epoch_cl % args.ri_cl == 0:
if args.task == 'lp':
self.gcl.gcn.eval()
with torch.no_grad():
score = self.gcl.do_valid(
valid_edges if args.n_valid >= len(valid_edges) else random.sample(valid_edges, args.n_valid))
self.gcl.gcn.train()
data_iter.write(f'[Iter {epoch}] [Contrastive Learning] [Epoch {epoch_cl}] '
f'loss = {np.nanmean(loss_list)}, mrr = {score}')
if not early_stopper.update(score):
break
else:
data_iter.write(f'[Iter {epoch}] [Contrastive Learning] [Epoch {epoch_cl}] '
f'loss = {np.nanmean(loss_list)}')
data_iter.close()
if args.task == 'lp' and early_stopper.best_model:
self.gcl.load_state_dict(early_stopper.best_model)
if args.task == 'lp':
if not outer_early_stopper.update(early_stopper.best_score):
break
# color_print('# ============== End: Train CL ============== #')
color_print('\n# ************** Begin: Train Generator ************** #')
self.generator.train()
self.discriminator.linear.eval()
self.gcl.gcn.eval()
data_iter = progress(range(1, args.n_epoch_g + 1))
for epoch_g in data_iter:
loss_list, score_list = [], []
for _ in range(args.iter_g):
loss, score = self.generator.loss(self.discriminator, args.bs_g)
optimizer_g.zero_grad()
loss.backward()
optimizer_g.step()
loss_list.append(loss.item())
score_list.append(score.item())
if epoch_g % args.ri_g == 0:
data_iter.write(f'[Iter {epoch}] [Generator] [Epoch {epoch_g}] '
f'loss = {np.nanmean(loss_list)}')
data_iter.close()
# color_print('# ============== End: Train Generator ============== #
if outer_early_stopper.best_model:
self.load_state_dict(outer_early_stopper.best_model)
model = self.gcl.get_embeddings()
if args.task == 'lp':
print('=======================================================================')
print(f'Evaluating GACN in link prediction task on {self.dataset}.')
print('-----------------------------------------------------------------------')
mrr, recall_50 = evaluate_lp(f'data/{self.dataset}', model)
color_print(f'MRR: {mrr}')
color_print(f'Recall_50: {recall_50}')
elif args.task == 'clf':
evaluate_clf(self.dataset, model)
def generate_graph(self):
with torch.no_grad():
self.generator.eval()
g_matrix = self.generator.forward().view(self.generator.n_g_nodes, self.generator.n_g_nodes)
g_matrix[g_matrix >= 0.5] = 1
g_matrix[g_matrix != 1] = 0
g_matrix = g_matrix.detach().cpu().tolist()
self.generator.train()
neighbors = {}
for node, neighbor_prob in zip(self.nodes, g_matrix):
neighbors[node] = []
for i, v in enumerate(neighbor_prob):
if v == 1:
neighbors[node].append(self.nodes[i])
return neighbors