def run_model(args):
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
use_equiv = args.decoder == 'equiv'
# Collect data and schema
schema, data_original, dl = load_data(args.dataset,
use_edge_data=args.use_edge_data,
use_other_edges=args.use_other_edges,
use_node_attrs=args.use_node_attrs,
node_val=args.node_val)
data, in_dims = select_features(data_original, schema, args.feats_type)
data = data.to(device)
# Precompute data indices
indices_identity, indices_transpose = data.calculate_indices()
# Get target relations and create data structure for embeddings
target_rel_ids = dl.links_test['data'].keys()
target_rels = [schema.relations[rel_id] for rel_id in target_rel_ids]
target_ents = schema.entities
# Get relations used by decoder
if use_equiv:
output_rels = schema.relations
else:
output_rels = {rel.id: rel for rel in target_rels}
data_embedding = SparseMatrixData.make_entity_embeddings(
target_ents, args.embedding_dim)
data_embedding.to(device)
# Get training and validation positive samples now
train_pos_heads, train_pos_tails = dict(), dict()
val_pos_heads, val_pos_tails = dict(), dict()
for target_rel_id in target_rel_ids:
train_val_pos = get_train_valid_pos(dl, target_rel_id)
train_pos_heads[target_rel_id], train_pos_tails[target_rel_id], \
val_pos_heads[target_rel_id], val_pos_tails[target_rel_id] = train_val_pos
# Get additional indices to be used when making predictions
pred_idx_matrices = {}
for target_rel in target_rels:
if args.pred_indices == 'train':
train_neg_head, train_neg_tail = get_train_neg(
dl, target_rel.id, tail_weighted=args.tail_weighted)
pred_idx_matrices[target_rel.id] = make_target_matrix(
target_rel, train_pos_heads[target_rel.id],
train_pos_tails[target_rel.id], train_neg_head, train_neg_tail,
device)
elif args.pred_indices == 'train_neg':
# Get negative samples twice
train_neg_head1, train_neg_tail1 = get_train_neg(
dl, target_rel.id, tail_weighted=args.tail_weighted)
train_neg_head2, train_neg_tail2 = get_train_neg(
dl, target_rel.id, tail_weighted=args.tail_weighted)
pred_idx_matrices[target_rel.id] = make_target_matrix(
target_rel, train_neg_head1, train_neg_tail1, train_neg_head2,
train_neg_tail2, device)
elif args.pred_indices == 'none':
pred_idx_matrices[target_rel.id] = None
# Create network and optimizer
net = EquivLinkPredictor(schema,
in_dims,
layers=args.layers,
embedding_dim=args.embedding_dim,
embedding_entities=target_ents,
output_rels=output_rels,
activation=eval('nn.%s()' % args.act_fn),
final_activation=nn.Identity(),
dropout=args.dropout,
pool_op=args.pool_op,
norm_affine=args.norm_affine,
norm_embed=args.norm_embed,
in_fc_layer=args.in_fc_layer,
decode=args.decoder)
net.to(device)
optimizer = torch.optim.Adam(net.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
# Set up logging and checkpointing
if args.wandb_log_run:
wandb.init(config=args,
settings=wandb.Settings(start_method='fork'),
project="EquivariantHGN_LP",
entity='danieltlevy')
wandb.watch(net, log='all', log_freq=args.wandb_log_param_freq)
print(args)
print("Number of parameters: {}".format(count_parameters(net)))
run_name = args.dataset + '_' + str(args.run)
if args.wandb_log_run and wandb.run.name is not None:
run_name = run_name + '_' + str(wandb.run.name)
if args.checkpoint_path != '':
checkpoint_path = args.checkpoint_path
else:
checkpoint_path = f"checkpoint/checkpoint_{run_name}.pt"
print("Checkpoint Path: " + checkpoint_path)
val_metric_best = -1e10
# training
loss_func = nn.BCELoss()
progress = tqdm(range(args.epoch), desc="Epoch 0", position=0, leave=True)
for epoch in progress:
net.train()
# Make target matrix and labels to train on
if use_equiv:
# Target is same as input
target_schema = schema
data_target = data.clone()
else:
# Target is just target relation
target_schema = DataSchema(schema.entities, target_rels)
data_target = SparseMatrixData(target_schema)
labels_train = torch.Tensor([]).to(device)
for target_rel in target_rels:
train_neg_head, train_neg_tail = get_train_neg(
dl, target_rel.id, tail_weighted=args.tail_weighted)
train_matrix = make_target_matrix(target_rel,
train_pos_heads[target_rel.id],
train_pos_tails[target_rel.id],
train_neg_head, train_neg_tail,
device)
data_target[target_rel.id] = train_matrix
labels_train_rel = train_matrix.values.squeeze()
labels_train = torch.cat([labels_train, labels_train_rel])
# Make prediction
if use_equiv:
idx_id_tgt, idx_trans_tgt = data_target.calculate_indices()
output_data = net(data, indices_identity, indices_transpose,
data_embedding, data_target, idx_id_tgt,
idx_trans_tgt)
else:
output_data = net(data, indices_identity, indices_transpose,
data_embedding, data_target)
logits_combined = torch.Tensor([]).to(device)
for target_rel in target_rels:
logits_rel = output_data[target_rel.id].values.squeeze()
logits_combined = torch.cat([logits_combined, logits_rel])
logp = torch.sigmoid(logits_combined)
train_loss = loss_func(logp, labels_train)
# autograd
optimizer.zero_grad()
train_loss.backward()
optimizer.step()
# Update logging
progress.set_description(f"Epoch {epoch}")
progress.set_postfix(loss=train_loss.item())
wandb_log = {'Train Loss': train_loss.item(), 'epoch': epoch}
# Evaluate on validation set
net.eval()
if epoch % args.val_every == 0:
with torch.no_grad():
net.eval()
left = torch.Tensor([]).to(device)
right = torch.Tensor([]).to(device)
labels_val = torch.Tensor([]).to(device)
valid_masks = {}
for target_rel in target_rels:
if args.val_neg == '2hop':
valid_neg_head, valid_neg_tail = get_valid_neg_2hop(
dl, target_rel.id)
elif args.val_neg == 'randomtw':
valid_neg_head, valid_neg_tail = get_valid_neg(
dl, target_rel.id, tail_weighted=True)
else:
valid_neg_head, valid_neg_tail = get_valid_neg(
dl, target_rel.id)
valid_matrix_full = make_target_matrix(
target_rel, val_pos_heads[target_rel.id],
val_pos_tails[target_rel.id], valid_neg_head,
valid_neg_tail, device)
valid_matrix, left_rel, right_rel, labels_val_rel = coalesce_matrix(
valid_matrix_full)
left = torch.cat([left, left_rel])
right = torch.cat([right, right_rel])
labels_val = torch.cat([labels_val, labels_val_rel])
if use_equiv:
# Add in additional prediction indices
pred_idx_matrix = pred_idx_matrices[target_rel.id]
if pred_idx_matrix is None:
valid_combined_matrix = valid_matrix
valid_mask = torch.arange(
valid_matrix.nnz()).to(device)
else:
valid_combined_matrix, valid_mask = combine_matrices(
valid_matrix, pred_idx_matrix)
valid_masks[target_rel.id] = valid_mask
data_target[target_rel.id] = valid_combined_matrix
else:
data_target[target_rel.id] = valid_matrix
if use_equiv:
data_target.zero_()
idx_id_val, idx_trans_val = data_target.calculate_indices()
output_data = net(data, indices_identity,
indices_transpose, data_embedding,
data_target, idx_id_val, idx_trans_val)
else:
output_data = net(data, indices_identity,
indices_transpose, data_embedding,
data_target)
logits_combined = torch.Tensor([]).to(device)
for target_rel in target_rels:
logits_rel_full = output_data[
target_rel.id].values.squeeze()
if use_equiv:
logits_rel = logits_rel_full[valid_masks[
target_rel.id]]
else:
logits_rel = logits_rel_full
logits_combined = torch.cat([logits_combined, logits_rel])
logp = torch.sigmoid(logits_combined)
val_loss = loss_func(logp, labels_val).item()
wandb_log.update({'val_loss': val_loss})
left = left.cpu().numpy()
right = right.cpu().numpy()
edge_list = np.concatenate(
[left.reshape((1, -1)),
right.reshape((1, -1))], axis=0)
res = dl.evaluate(edge_list,
logp.cpu().numpy(),
labels_val.cpu().numpy())
val_roc_auc = res['roc_auc']
val_mrr = res['MRR']
wandb_log.update(res)
print("\nVal Loss: {:.3f} Val ROC AUC: {:.3f} Val MRR: {:.3f}".
format(val_loss, val_roc_auc, val_mrr))
if args.val_metric == 'loss':
val_metric = -val_loss
elif args.val_metric == 'roc_auc':
val_metric = val_roc_auc
elif args.val_metric == 'mrr':
val_metric = val_mrr
if val_metric > val_metric_best:
val_metric_best = val_metric
print("New best, saving")
torch.save(
{
'epoch': epoch,
'net_state_dict': net.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
'train_loss': train_loss.item(),
'val_loss': val_loss,
'val_roc_auc': val_roc_auc,
'val_mrr': val_mrr
}, checkpoint_path)
if args.wandb_log_run:
wandb.summary["val_roc_auc_best"] = val_roc_auc
wandb.summary["val_mrr_best"] = val_mrr
wandb.summary["val_loss_best"] = val_loss
wandb.summary["epoch_best"] = epoch
wandb.summary["train_loss_best"] = train_loss.item()
wandb.save(checkpoint_path)
if args.wandb_log_run:
wandb.log(wandb_log)
# Evaluate on test set
if args.evaluate:
for target_rel in target_rels:
print("Evaluating Target Rel " + str(target_rel.id))
checkpoint = torch.load(checkpoint_path, map_location=device)
net.load_state_dict(checkpoint['net_state_dict'])
net.eval()
# Target is same as input
data_target = data.clone()
with torch.no_grad():
left_full, right_full, test_labels_full = get_test_neigh_from_file(
dl, args.dataset, target_rel.id)
test_matrix_full = make_target_matrix_test(
target_rel, left_full, right_full, test_labels_full,
device)
test_matrix, left, right, test_labels = coalesce_matrix(
test_matrix_full)
if use_equiv:
test_combined_matrix, test_mask = combine_matrices(
test_matrix, train_matrix)
data_target[target_rel.id] = test_combined_matrix
data_target.zero_()
idx_id_tst, idx_trans_tst = data_target.calculate_indices()
data_out = net(data, indices_identity, indices_transpose,
data_embedding, data_target, idx_id_tst,
idx_trans_tst)
logits_full = data_out[target_rel.id].values.squeeze()
logits = logits_full[test_mask]
else:
data_target[target_rel.id] = test_matrix
data_out = net(data, indices_identity, indices_transpose,
data_embedding, data_target)
logits_full = data_out[target_rel.id].values.squeeze()
logits = logits_full
pred = torch.sigmoid(logits).cpu().numpy()
left = left.cpu().numpy()
right = right.cpu().numpy()
edge_list = np.vstack((left, right))
edge_list_full = np.vstack((left_full, right_full))
file_path = f"test_out/{run_name}.txt"
gen_file_for_evaluate(dl,
edge_list_full,
edge_list,
pred,
target_rel.id,
file_path=file_path)
def run_model(args):
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
if args.lgnn:
load_data_fn = load_data_flat
else:
load_data_fn = load_data
schema, schema_out, data, data_target, labels, \
train_val_test_idx, dl = load_data_fn(args.dataset,
use_edge_data=args.use_edge_data,
use_node_attrs=args.use_node_attr,
feats_type=args.feats_type)
target_entity_id = 0 # True for all current NC datasets
data, in_dims = select_features(data, schema, args.feats_type,
target_entity_id)
if args.multi_label:
labels = torch.FloatTensor(labels).to(device)
else:
labels = torch.LongTensor(labels).to(device)
train_idx = train_val_test_idx['train_idx']
train_idx = np.sort(train_idx)
val_idx = train_val_test_idx['val_idx']
val_idx = np.sort(val_idx)
test_idx = train_val_test_idx['test_idx']
test_idx = np.sort(test_idx)
data = data.to(device)
data_embedding = SparseMatrixData.make_entity_embeddings(
schema.entities, args.embedding_dim)
data_embedding.to(device)
indices_identity, indices_transpose = data.calculate_indices()
data_target = data_target.to(device)
num_classes = dl.labels_train['num_classes']
net = AlternatingHGN(schema,
in_dims,
width=args.width,
depth=args.depth,
embedding_dim=args.embedding_dim,
activation=eval('nn.%s()' % args.act_fn),
final_activation=nn.Identity(),
dropout=args.dropout,
output_dim=num_classes,
norm=args.norm,
pool_op=args.pool_op,
norm_affine=args.norm_affine,
norm_out=args.norm_out)
net.to(device)
optimizer = torch.optim.Adam(net.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
if args.wandb_log_run:
wandb.init(config=args,
settings=wandb.Settings(start_method='fork'),
project="EquivariantHGN_NC",
entity='danieltlevy')
wandb.watch(net, log='all', log_freq=args.wandb_log_param_freq)
print(args)
print("Number of parameters: {}".format(count_parameters(net)))
run_name = args.dataset + '_' + str(args.run)
if args.wandb_log_run and wandb.run.name is not None:
run_name = run_name + '_' + str(wandb.run.name)
if args.checkpoint_path != '':
checkpoint_path = args.checkpoint_path
else:
checkpoint_path = f"checkpoint/checkpoint_{run_name}.pt"
print("Checkpoint Path: " + checkpoint_path)
progress = tqdm(range(args.epoch), desc="Epoch 0", position=0, leave=True)
# training loop
net.train()
val_micro_best = 0
for epoch in progress:
# training
net.train()
optimizer.zero_grad()
logits = net(data, data_embedding).squeeze()
logp = regr_fcn(logits, args.multi_label)
train_loss = loss_fcn(logp[train_idx], labels[train_idx],
args.multi_label)
train_loss.backward()
optimizer.step()
if args.multi_label:
train_micro, train_macro = f1_scores_multi(
logits[train_idx], dl.labels_train['data'][train_idx])
else:
train_micro, train_macro = f1_scores(logits[train_idx],
labels[train_idx])
with torch.no_grad():
progress.set_description(f"Epoch {epoch}")
progress.set_postfix(loss=train_loss.item(), micr=train_micro)
wandb_log = {
'Train Loss': train_loss.item(),
'Train Micro': train_micro,
'Train Macro': train_macro
}
if epoch % args.val_every == 0:
# validation
net.eval()
logits = net(data, data_embedding).squeeze()
logp = regr_fcn(logits, args.multi_label)
val_loss = loss_fcn(logp[val_idx], labels[val_idx],
args.multi_label)
if args.multi_label:
val_micro, val_macro = f1_scores_multi(
logits[val_idx], dl.labels_train['data'][val_idx])
else:
val_micro, val_macro = f1_scores(logits[val_idx],
labels[val_idx])
print("\nVal Loss: {:.3f} Val Micro-F1: {:.3f} \
Val Macro-F1: {:.3f}".format(val_loss, val_micro, val_macro))
wandb_log.update({
'Val Loss': val_loss.item(),
'Val Micro-F1': val_micro,
'Val Macro-F1': val_macro
})
if val_micro > val_micro_best:
val_micro_best = val_micro
print("New best, saving")
torch.save(
{
'epoch': epoch,
'net_state_dict': net.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
'train_loss': train_loss.item(),
'train_micro': train_micro,
'train_macro': train_macro,
'val_loss': val_loss.item(),
'val_micro': val_micro,
'val_macro': val_macro
}, checkpoint_path)
if args.wandb_log_run:
wandb.run.summary["val_micro_best"] = val_micro
wandb.run.summary["val_macro_best"] = val_macro
wandb.run.summary["val_loss_best"] = val_loss.item()
wandb.run.summary["epoch_best"] = epoch
wandb.run.summary["train_loss_best"] = train_loss.item(
)
wandb.run.summary['train_micro_best'] = train_micro
wandb.run.summary['train_macro_best'] = train_macro
wandb.save(checkpoint_path)
if epoch % args.wandb_log_loss_freq == 0:
if args.wandb_log_run:
wandb.log(wandb_log, step=epoch)
# testing with evaluate_results_nc
if args.evaluate:
checkpoint = torch.load(checkpoint_path)
net.load_state_dict(checkpoint['net_state_dict'])
net.eval()
test_logits = []
with torch.no_grad():
logits = net(data, data_embedding).squeeze()
test_logits = logits[test_idx]
if args.multi_label:
pred = (test_logits.cpu().numpy() > 0).astype(int)
else:
pred = test_logits.cpu().numpy().argmax(axis=1)
onehot = np.eye(num_classes, dtype=np.int32)
file_path = f"test_out/{run_name}.txt"
dl.gen_file_for_evaluate(test_idx=test_idx,
label=pred,
file_path=file_path,
multi_label=args.multi_label)
if not args.multi_label:
pred = onehot[pred]
print(dl.evaluate(pred))