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import torch
import torch.nn.functional as F
import torch.nn as nn
from torch_geometric.utils import degree
from .models_misc import mlp
from ogb.graphproppred.mol_encoder import AtomEncoder, BondEncoder
from ogb.utils.features import get_atom_feature_dims, get_bond_feature_dims
def multi_class_accuracy(y_hat, y, reduction='sum'):
pred = y_hat.max(1)[1]
if reduction == 'sum':
acc = pred.eq(y).sum().float()
elif reduction == 'mean':
acc = pred.eq(y).mean().float()
else:
raise NotImplementedError('Reduction {} not currently implemented.'.format(reduction))
return acc
def global_add_pool_sparse(x, batch):
#-------------- global sum pooling
index = torch.stack([batch, torch.tensor(list(range(batch.shape[0])), device=x.device)], 0)
x_sparse = torch.sparse.FloatTensor(index, x, torch.Size([torch.max(batch)+1, x.shape[0], x.shape[1]]))
return torch.sparse.sum(x_sparse, 1).to_dense()
def global_mean_pool_sparse(x, batch):
#-------------- global average pooling
index = torch.stack([batch, torch.tensor(list(range(batch.shape[0])), device=x.device)], 0)
x_sparse = torch.sparse.FloatTensor(index, x, torch.Size([torch.max(batch)+1, x.shape[0], x.shape[1]]))
graph_sizes = degree(batch).float()
graph_sizes[graph_sizes==0.0] = 1.0
return torch.sparse.sum(x_sparse, 1).to_dense() / graph_sizes.unsqueeze(1)
class DiscreteEmbedding(torch.nn.Module):
def __init__(self, encoder_name, d_in_features, d_in_encoder, d_out_encoder, **kwargs):
super(DiscreteEmbedding, self).__init__()
#-------------- various different embedding layers
kwargs['init'] = None if 'init' not in kwargs else kwargs['init']
self.encoder_name = encoder_name
# d_in_features: input feature size (e.g. if already one hot encoded),
# d_in_encoder: number of unique values that will be encoded (size of embedding vocabulary)
#-------------- fill embedding with zeros
if encoder_name == 'zero_encoder':
self.encoder = zero_encoder(d_out_encoder)
d_out = d_out_encoder
#-------------- linear pojection
elif encoder_name == 'linear':
self.encoder = nn.Linear(d_in_features, d_out_encoder, bias=True)
d_out = d_out_encoder
#-------------- mlp
elif encoder_name == 'mlp':
self.encoder = mlp(d_in_features,
d_out_encoder,
d_out_encoder,
kwargs['seed'],
kwargs['activation_mlp'],
kwargs['bn_mlp'])
d_out = d_out_encoder
#-------------- multi hot encoding of categorical data
elif encoder_name == 'one_hot_encoder':
self.encoder = one_hot_encoder(d_in_encoder)
d_out = sum(d_in_encoder)
#-------------- embedding of categorical data (linear projection without bias of one hot encodings)
elif encoder_name == 'embedding':
self.encoder = multi_embedding(d_in_encoder, d_out_encoder, kwargs['aggr'], kwargs['init'])
if kwargs['aggr'] == 'concat':
d_out = len(d_in_encoder) * d_out_encoder
else:
d_out = d_out_encoder
#-------------- for ogb: multi hot encoding of node features
elif encoder_name == 'atom_one_hot_encoder':
full_atom_feature_dims = get_atom_feature_dims() if kwargs['features_scope'] == 'full' else get_atom_feature_dims()[:2]
self.encoder = one_hot_encoder(full_atom_feature_dims)
d_out = sum(full_atom_feature_dims)
#-------------- for ogb: multi hot encoding of edge features
elif encoder_name == 'bond_one_hot_encoder':
full_bond_feature_dims = get_bond_feature_dims() if kwargs['features_scope'] == 'full' else get_bond_feature_dims()[:2]
self.encoder = one_hot_encoder(full_bond_feature_dims)
d_out = sum(full_bond_feature_dims)
#-------------- for ogb: embedding of node features
elif encoder_name == 'atom_encoder':
self.encoder = AtomEncoder(d_out_encoder)
d_out = d_out_encoder
#-------------- for ogb: embedding of edge features
elif encoder_name == 'bond_encoder':
self.encoder = BondEncoder(emb_dim = d_out_encoder)
d_out = d_out_encoder
#-------------- no embedding, use as is
elif encoder_name == 'None':
self.encoder = None
d_out = d_in_features
else:
raise NotImplementedError('Encoder {} is not currently supported.'.format(encoder_name))
self.d_out = d_out
return
def forward(self, x):
x = x.unsqueeze(-1) if x.dim() == 1 else x
if self.encoder is not None:
x = x.float() if self.encoder_name == 'linear' or self.encoder_name == 'mlp' else x.long()
return self.encoder(x)
else:
return x.float()
class multi_embedding(torch.nn.Module):
def __init__(self, d_in, d_out, aggr = 'concat', init=None):
super(multi_embedding, self).__init__()
#-------------- embedding of multiple categorical features. Summation or concatenation of the embeddings is allowed
self.d_in = d_in
self.aggr = aggr
self.encoder = []
for i in range(len(d_in)):
self.encoder.append(nn.Embedding(d_in[i], d_out))
if init == 'zeros':
print('### INITIALIZING EMBEDDING TO ZERO ###')
torch.nn.init.constant_(self.encoder[i].weight.data, 0)
else:
torch.nn.init.xavier_uniform_(self.encoder[-1].weight.data)
self.encoder = nn.ModuleList(self.encoder)
return
def forward(self, tensor):
for i in range(tensor.shape[1]):
embedding_i = self.encoder[i](tensor[:,i])
if self.aggr == 'concat':
embedding = torch.cat((embedding, embedding_i),1) if i>0 else embedding_i
elif self.aggr == 'sum':
embedding = embedding + embedding_i if i>0 else embedding_i
else:
raise NotImplementedError('multi embedding aggregation {} is not currently supported.'.format(self.aggr))
return embedding
class one_hot_encoder(torch.nn.Module):
def __init__(self, d_in):
super(one_hot_encoder, self).__init__()
self.d_in = d_in
return
def forward(self, tensor):
for i in range(tensor.shape[1]):
onehot_i = torch.zeros((tensor.shape[0], self.d_in[i]), device=tensor.device)
onehot_i.scatter_(1, tensor[:,i:i+1], 1)
onehot = torch.cat((onehot, onehot_i), 1) if i>0 else onehot_i
return onehot
def __repr__(self):
return '{}({})'.format(self.__class__.__name__, self.d_in)
class zero_encoder(torch.nn.Module):
def __init__(self, d_out):
super(zero_encoder, self).__init__()
self.d_out = d_out
return
def forward(self, tensor):
return torch.zeros((tensor.shape[0], self.d_out), device=tensor.device)
def __repr__(self):
return '{}({})'.format(self.__class__.__name__, self.d_out)
class central_encoder(nn.Module):
def __init__(self, nb_encoder, d_ef, extend=True):
super(central_encoder, self).__init__()
#-------------- For the neighbor aggregation: central node embedding
#-------------- This is a way to create a dummy variable that represents self loops.
#-------------- Useful when working with edge features or GSN-e
#-------------- Two ways are allowed: extra dummy variable (one hot or embedding) or a vector filled with zeros
self.extend = extend
self.nb_encoder = nb_encoder
if self.extend:
print('##### EXTENDING EDGE FEATURE DIMENSIONS #####')
if 'one_hot_encoder' in nb_encoder:
if self.extend:
self.encoder = DiscreteEmbedding('one_hot_encoder', 1, [d_ef+1], None)
self.d_out = d_ef+1
else:
self.d_out = d_ef
else:
self.d_out = d_ef
if self.extend:
self.encoder = DiscreteEmbedding('embedding', None, [1], d_ef, aggr='sum')
else:
pass
return
def forward(self, x_nb, num_nodes):
if 'one_hot_encoder' in self.nb_encoder:
if self.extend:
zero_extension = torch.zeros((x_nb.shape[0], 1), device=x_nb.device)
x_nb = torch.cat((zero_extension, x_nb), -1)
x_central = torch.zeros((num_nodes,1), device=x_nb.device).long()
x_central = self.encoder(x_central)
else:
x_central = torch.zeros((num_nodes, self.d_out), device=x_nb.device)
else:
if self.extend:
x_central = torch.zeros((num_nodes,1), device=x_nb.device).long()
x_central = self.encoder(x_central)
else:
x_central = torch.zeros((num_nodes, self.d_out), device=x_nb.device)
return x_central, x_nb
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