def mm_backwardcorrect_sparse_embed(sparseX: FloatTensor,
denseY: paddle.fluid.dygraph.core.VarBase):
update_inds = sparseX.indices[0]
updates = paddle.nn.functional.embedding(
sparseX.indices[1], denseY, sparse=False) * sparseX.values.view(-1, 1)
ret_Mat2 = paddle.scatter_nd(paddle.reshape(update_inds, (-1, 1)), updates,
(sparseX.shape[0], denseY.shape[1]))
return paddorch.convertTensor(ret_Mat2)
def linear(input, weight, bias=None):
if input.shape[-1]!=weight.shape[0]:
weight=paddle.transpose(weight,[1,0])
layer_obj=fluid.dygraph.Linear(input.shape[-1],weight.shape[1])
fluid.layers.assign(weight,layer_obj.weight)
if bias is not None:
fluid.layers.assign(bias, layer_obj.bias)
return paddorch.convertTensor(layer_obj(input.astype("float32")))
def _add_undirected_graph_positional_embedding(g, hidden_size, retry=10):
# We use eigenvectors of normalized graph laplacian as vertex features.
# It could be viewed as a generalization of positional embedding in the
# attention is all you need paper.
# Recall that the eignvectors of normalized laplacian of a line graph are cos/sin functions.
# See section 2.4 of http://www.cs.yale.edu/homes/spielman/561/2009/lect02-09.pdf
n = g.number_of_nodes()
adj = g.adjacency_matrix_scipy(transpose=False,
return_edge_ids=False).astype(float)
norm = sparse.diags(dgl.backend.asnumpy(g.in_degrees()).clip(1)**-0.5,
dtype=float)
laplacian = norm * adj * norm
k = min(n - 2, hidden_size)
x = eigen_decomposision(n, k, laplacian, hidden_size, retry)
g.ndata["pos_undirected"] = torch.convertTensor(x)
return g
def from_dlpack(dlpack):
tensor_from_dlpack = fluid.core.from_dlpack(dlpack)
place = tensor_from_dlpack._place()
if True: # "win" in platform: # CPU env
if "int32" in str(tensor_from_dlpack):
return paddorch.convertTensor(
paddle.to_tensor(np.array(tensor_from_dlpack), dtype="int32"))
else:
return paddorch.Tensor(
paddle.to_tensor(np.array(tensor_from_dlpack)))
else:
with paddle.fluid.dygraph.guard(place=place):
tensor_from_dlpack.__class__ = paddle.fluid.LoDTensor
ret = paddle.Tensor(tensor_from_dlpack)
if "int32" in str(tensor_from_dlpack):
ret = paddle.to_tensor(ret, dtype="int32")
tensor_from_dlpack.__class__ = paddle.fluid.core_avx.Tensor
return ret
def test_finetune(epoch, valid_loader, model, output_layer, criterion, sw,
opt):
n_batch = len(valid_loader)
model.eval()
output_layer.eval()
epoch_loss_meter = AverageMeter()
epoch_f1_meter = AverageMeter()
for idx, batch in enumerate(valid_loader):
graph_q, y = batch
bsz = graph_q.batch_size
# ===================forward=====================
with torch.no_grad():
feat_q = model(graph_q)
assert feat_q.shape == (graph_q.batch_size, opt.hidden_size)
out = output_layer(feat_q)
loss = torch.convertTensor(criterion(out, y))
preds = out.argmax(dim=1)
f1 = f1_score(y.cpu().numpy(), preds.cpu().numpy(), average="micro")
# ===================meters=====================
epoch_loss_meter.update(loss.item(), bsz)
epoch_f1_meter.update(f1, bsz)
global_step = (epoch + 1) * n_batch
sw.add_scalar("ft_loss/valid", epoch_loss_meter.avg, global_step)
sw.add_scalar("ft_f1/valid", epoch_f1_meter.avg, global_step)
print(opt.model_folder)
print(
f"Epoch {epoch}, loss {epoch_loss_meter.avg:.3f}, f1 {epoch_f1_meter.avg:.3f}"
)
return epoch_loss_meter.avg, epoch_f1_meter.avg
def normalize(input, p=2, dim=1, eps=1e-12, out=None):
return torch.convertTensor( input/paddle.norm(input,p,axis=dim,keepdim=True))
import paddorch
arr = paddorch.convertTensor(1.0 / paddorch.arange(1, 30))
print(arr)
arr[arr > 0.1] = 0.0
print(arr)
arr[paddorch.isfinite(arr)] = 1.0
print(arr)
arr[paddorch.isinf(arr)] = 2.0
print(arr)
arr = paddorch.convertTensor(1.0 / paddorch.arange(1, 31)).view(-1, 5, 2)
print("before", arr)
arr[:, 2, :] = 999
print("after", arr)
def train_finetune(
epoch,
train_loader,
model,
output_layer,
criterion,
optimizer,
output_layer_optimizer,
sw,
opt,
):
"""
one epoch training for moco
"""
n_batch = len(train_loader)
model.train()
output_layer.train()
batch_time = AverageMeter()
data_time = AverageMeter()
loss_meter = AverageMeter()
f1_meter = AverageMeter()
epoch_loss_meter = AverageMeter()
epoch_f1_meter = AverageMeter()
prob_meter = AverageMeter()
graph_size = AverageMeter()
max_num_nodes = 0
max_num_edges = 0
end = time.time()
for idx, batch in enumerate(train_loader):
data_time.update(time.time() - end)
graph_q, y = batch
graph_q.to(torch.device(opt.gpu))
y = y.to(torch.device(opt.gpu))
bsz = graph_q.batch_size
# ===================forward=====================
feat_q = model(graph_q)
assert feat_q.shape == (graph_q.batch_size, opt.hidden_size)
out = output_layer(feat_q)
loss = torch.convertTensor(criterion(out, y))
# ===================backward=====================
optimizer.zero_grad()
output_layer_optimizer.zero_grad()
loss.backward()
# torch.nn.utils.clip_grad_value_(model.parameters(), 1)
# torch.nn.utils.clip_grad_value_(output_layer.parameters(), 1)
global_step = epoch * n_batch + idx
lr_this_step = opt.learning_rate * warmup_linear(
global_step / (opt.epochs * n_batch), 0.1)
# if lr_this_step is not None:
# optimizer.set_lr(lr_this_step)
# output_layer_optimizer.set_lr(lr_this_step)
optimizer.step()
output_layer_optimizer.step()
preds = out.argmax(dim=1)
f1 = f1_score(y.cpu().numpy(), preds.cpu().numpy(), average="micro")
# ===================meters=====================
f1_meter.update(f1, bsz)
epoch_f1_meter.update(f1, bsz)
loss_meter.update(loss.item(), bsz)
epoch_loss_meter.update(loss.item(), bsz)
graph_size.update(graph_q.number_of_nodes() / bsz, bsz)
max_num_nodes = max(max_num_nodes, graph_q.number_of_nodes())
max_num_edges = max(max_num_edges, graph_q.number_of_edges())
batch_time.update(time.time() - end)
end = time.time()
# print info
if (idx + 1) % opt.print_freq == 0:
mem = psutil.virtual_memory()
# print(f'{idx:8} - {mem.percent:5} - {mem.free/1024**3:10.2f} - {mem.available/1024**3:10.2f} - {mem.used/1024**3:10.2f}')
# mem_used.append(mem.used/1024**3)
print("Train: [{0}][{1}/{2}]\t"
"BT {batch_time.val:.3f} ({batch_time.avg:.3f})\t"
"DT {data_time.val:.3f} ({data_time.avg:.3f})\t"
"loss {loss.val:.3f} ({loss.avg:.3f})\t"
"f1 {f1.val:.3f} ({f1.avg:.3f})\t"
"GS {graph_size.val:.3f} ({graph_size.avg:.3f})\t"
"mem {mem:.3f}".format(
epoch,
idx + 1,
n_batch,
batch_time=batch_time,
data_time=data_time,
loss=loss_meter,
f1=f1_meter,
graph_size=graph_size,
mem=mem.used / 1024**3,
))
# print(out[0].abs().max())
# tensorboard logger
if (idx + 1) % opt.tb_freq == 0:
sw.add_scalar("ft_loss", loss_meter.avg, global_step)
sw.add_scalar("ft_f1", f1_meter.avg, global_step)
sw.add_scalar("graph_size", graph_size.avg, global_step)
sw.add_scalar("lr", lr_this_step, global_step)
sw.add_scalar("graph_size/max", max_num_nodes, global_step)
sw.add_scalar("graph_size/max_edges", max_num_edges, global_step)
# sw.add_scalar(
# "learning_rate", optimizer.param_groups[0]["lr"], global_step
# )
loss_meter.reset()
f1_meter.reset()
graph_size.reset()
max_num_nodes, max_num_edges = 0, 0
return epoch_loss_meter.avg, epoch_f1_meter.avg
