def __init__(self, nfeat, nhid, dropout):
super(GCN2, self).__init__()
self.gc1 = DenseGCNConv(nfeat, nhid)
self.gc2 = DenseGCNConv(nhid, nhid)
self.dropout = dropout
self.classifier = nn.Linear(nhid * 2, 2)
def __init__(self,
num_features,
n_classes,
num_hidden,
num_hidden_layers,
dropout,
activation,
improved=True,
bias=True):
super(PDenseGCN, self).__init__()
# dropout
if dropout:
self.dropout = nn.Dropout(p=dropout)
else:
self.dropout = nn.Dropout(p=0.)
#activation
self.activation = activation
# input layer
self.conv_input = DenseGCNConv(num_features,
num_hidden,
improved=improved,
bias=bias)
# Hidden layers
self.layers = nn.ModuleList()
for _ in range(num_hidden_layers):
self.layers.append(
DenseGCNConv(num_hidden,
num_hidden,
improved=improved,
bias=bias))
# output layer
self.conv_output = DenseGCNConv(num_hidden,
n_classes,
improved=improved,
bias=bias)
def build_graph(self):
# entry GCN
self.entry_conv_first = DenseGCNConv(
in_channels=self.in_feature,
out_channels=self.hidden_feature,
)
self.entry_conv_block = DenseGCNConv(
in_channels=self.hidden_feature,
out_channels=self.hidden_feature,
)
self.entry_conv_last = DenseGCNConv(
in_channels=self.hidden_feature,
out_channels=self.out_feature,
)
self.gcn_hpool_layer = GcnHpoolSubmodel(
self.out_feature + self.hidden_feature * 2, self.h_hidden_feature,
self.h_out_feature, self.in_node, self.hidden_node, self.out_node
#self._hparams
)
self.pred_model = torch.nn.Sequential(
torch.nn.Linear(
2 * self.hidden_feature + 2 * self.h_hidden_feature +
self.h_out_feature + self.out_feature, self.h_hidden_feature),
#torch.nn.Linear( self.out_feature, self.h_hidden_feature),
torch.nn.ReLU(),
torch.nn.Linear(self.h_hidden_feature, self.h_out_feature))
class CoarsenBlock(torch.nn.Module):
def __init__(self, in_channels, assign_ratio):
super(CoarsenBlock, self).__init__()
self.gcn_att = DenseGCNConv(in_channels, 1, bias=True)
# self.att = torch.nn.Linear(in_channels,
# hidden)
self.assign_ratio = assign_ratio
def normalize_batch_adj(
self, adj
): # adj shape: batch_size * num_node * num_node, D^{-1/2} (A+I) D^{-1/2}
dim = adj.size()[1]
A = adj + torch.eye(dim, device=adj.device)
deg_inv_sqrt = A.sum(dim=-1).clamp(min=1).pow(-0.5)
newA = deg_inv_sqrt.unsqueeze(-1) * A * deg_inv_sqrt.unsqueeze(-2)
newA = (adj.sum(-1) > 0).float().unsqueeze(-1).to(adj.device) * newA
return newA
def reset_parameters(self):
self.gcn_att.reset_parameters()
def forward(self, x, adj, batch_num_nodes):
# alpha_vec = F.softmax(self.att(x).sum(-1), -1)
alpha_vec = F.sigmoid(torch.pow(self.gcn_att(x, adj),
2)).squeeze() # b*n*1 --> b*n
norm_adj = self.normalize_batch_adj(adj)
batch_size = x.size()[0]
cut_batch_num_nodes = batch_num_nodes
cut_value = torch.zeros_like(alpha_vec[:, 0])
for j in range(batch_size):
if cut_batch_num_nodes[j] > 1:
cut_batch_num_nodes[j] = torch.ceil(
cut_batch_num_nodes[j].float() * self.assign_ratio) + 1
# cut_value[j], _ = (-alpha_vec[j]).kthvalue(cut_batch_num_nodes[j], dim=-1)
temptopk, topk_ind = alpha_vec[j].topk(cut_batch_num_nodes[j],
dim=-1)
cut_value[j] = temptopk[-1]
else:
cut_value[j] = 0
# cut_alpha_vec = torch.mul( ((alpha_vec - torch.unsqueeze(cut_value, -1))>=0).float(), alpha_vec) # b * n
cut_alpha_vec = F.relu(alpha_vec - torch.unsqueeze(cut_value, -1))
S = torch.mul(norm_adj, cut_alpha_vec.unsqueeze(
1)) # repeat rows of cut_alpha_vec, #b * n * n
# temp_rowsum = torch.sum(S, -1).unsqueeze(-1).pow(-1)
# # temp_rowsum[temp_rowsum > 0] = 1.0 / temp_rowsum[temp_rowsum > 0]
# S = torch.mul(S, temp_rowsum) # row-wise normalization
S = F.normalize(S, p=1, dim=-1)
embedding_tensor = torch.matmul(torch.transpose(
S, 1, 2), x) # equals to torch.einsum('bij,bjk->bik',...)
new_adj = torch.matmul(torch.matmul(torch.transpose(S, 1, 2), adj),
S) # batched matrix multiply
return embedding_tensor, new_adj, S
class Coarsening(torch.nn.Module):
def __init__(self, dataset, hidden, ratio=0.25): # we only use 1 layer for coarsening
super(Coarsening, self).__init__()
# self.embed_block1 = GNNBlock(dataset.num_features, hidden, hidden)
self.embed_block1 = DenseGCNConv(dataset.num_features, hidden)
self.coarse_block1 = CoarsenBlock(hidden, ratio)
self.embed_block2 = DenseGCNConv(hidden, dataset.num_features)
self.jump = JumpingKnowledge(mode='cat')
self.lin1 = Linear(hidden + dataset.num_features, hidden)
self.lin2 = Linear(hidden, dataset.num_classes)
def reset_parameters(self):
self.embed_block1.reset_parameters()
self.coarse_block1.reset_parameters()
self.jump.reset_parameters()
self.lin1.reset_parameters()
self.lin2.reset_parameters()
def forward(self, data, epsilon=0.01, opt_epochs=100):
x, adj, mask = data.x, data.adj, data.mask
batch_num_nodes = data.mask.sum(-1)
x1 = F.relu(self.embed_block1(x, adj, mask, add_loop=True))
# xs = [x1.mean(dim=1)]
coarse_x, new_adj, S = self.coarse_block1(x1, adj, batch_num_nodes)
xs = [coarse_x.mean(dim=1)]
x2 = F.tanh(self.embed_block2(coarse_x, new_adj, mask, add_loop=True))
xs.append(x2.mean(dim=1))
opt_loss = 0.0
for i in range(len(x)):
x3 = self.get_nonzero_rows(x[i])
x4 = self.get_nonzero_rows(x2[i])
# if x3.size()[0]==0 or x4.size()[0]==0:
# continue
# opt_loss += sinkhorn_loss_default(x3, x4, epsilon, niter=opt_epochs).float()
opt_loss += sinkhorn_loss_default(x3, x2[i], epsilon, niter=opt_epochs)
return xs, new_adj, S, opt_loss
def predict(self, xs):
x = self.jump(xs)
x = F.relu(self.lin1(x))
x = F.dropout(x, p=0.5, training=self.training)
x = self.lin2(x)
return F.log_softmax(x, dim=-1)
def get_nonzero_rows(self, M):# M is a matrix
# row_ind = M.sum(-1).nonzero().squeeze() #nonzero has bugs in Pytorch 1.2.0.........
#So we use other methods to take place of it
MM, MM_ind = M.sum(-1).sort()
N = (M.sum(-1)>0).sum()
return M[MM_ind[:N]]
def __repr__(self):
return self.__class__.__name__
def __init__(self, in_channels, assign_ratio):
super(CoarsenBlock, self).__init__()
self.gcn_att = DenseGCNConv(in_channels, 1, bias=True)
# self.att = torch.nn.Linear(in_channels,
# hidden)
self.assign_ratio = assign_ratio
def __init__(self, in_channels, hidden_channels, out_channels):
super(GNNBlock, self).__init__()
self.conv1 = DenseGCNConv(in_channels, hidden_channels)
self.conv2 = DenseGCNConv(hidden_channels, out_channels)
self.lin = torch.nn.Linear(hidden_channels + out_channels,
out_channels)
def __init__(self, nfeat, nhid, dropout):
super(GCN1, self).__init__()
self.gc1 = DenseGCNConv(nfeat, nhid)
self.gc2 = DenseGCNConv(nhid, nhid)
self.dropout = dropout
self.classifier = nn.Linear(nhid * 2, 2)
self.attention = nn.Linear(nhid, 8)
self.node_classifier = nn.Linear(nhid, 2)
def __init__(self, hparams):
super(GVAE, self).__init__()
self.hparams = hparams
if hparams.pool_type == 'stat':
# since stat moments x4
self.prepool_dim = hparams.hidden_dim // 4
else:
self.prepool_dim = hparams.hidden_dim
# encoding layers
if hparams.gnn_type == 'gcn':
self.gcn_1 = DenseGCNConv(hparams.input_dim, hparams.hidden_dim)
self.gcn_2 = DenseGCNConv(hparams.hidden_dim, hparams.hidden_dim)
self.gcn_31 = DenseGCNConv(hparams.hidden_dim, self.prepool_dim)
self.gcn_32 = DenseGCNConv(hparams.hidden_dim, self.prepool_dim)
elif hparams.gnn_type == 'sage':
self.gcn_1 = gnn_modules.DenseSAGEConv(hparams.input_dim,
hparams.hidden_dim)
self.gcn_2 = gnn_modules.DenseSAGEConv(hparams.hidden_dim,
hparams.hidden_dim)
self.gcn_31 = gnn_modules.DenseSAGEConv(hparams.hidden_dim,
self.prepool_dim)
self.gcn_32 = gnn_modules.DenseSAGEConv(hparams.hidden_dim,
self.prepool_dim)
self.fc2 = nn.Linear(hparams.hidden_dim, hparams.bottle_dim)
# decoding layers
self.fc3 = nn.Linear(hparams.bottle_dim,
hparams.node_dim * hparams.input_dim)
self.fc4 = nn.Linear(hparams.node_dim * hparams.input_dim,
hparams.node_dim * hparams.input_dim)
# energy prediction
self.regfc1 = nn.Linear(hparams.bottle_dim, 20)
self.regfc2 = nn.Linear(20, 1)
# diff pool
if hparams.pool_type == 'diff':
self.gcn_diff = DenseGCNConv(hparams.hidden_dim, 1)
if hparams.n_gpus > 0:
self.dev_type = 'cuda'
if hparams.n_gpus == 0:
self.dev_type = 'cpu'
self.eps = 1e-5
def __init__(self, dataset, hidden, ratio=0.25): # we only use 1 layer for coarsening
super(Coarsening, self).__init__()
# self.embed_block1 = GNNBlock(dataset.num_features, hidden, hidden)
self.embed_block1 = DenseGCNConv(dataset.num_features, hidden)
self.coarse_block1 = CoarsenBlock(hidden, ratio)
self.embed_block2 = DenseGCNConv(hidden, dataset.num_features)
self.jump = JumpingKnowledge(mode='cat')
self.lin1 = Linear(hidden + dataset.num_features, hidden)
self.lin2 = Linear(hidden, dataset.num_classes)
def __init__(self, dataset, hidden, num_layers=2, ratio=0.5):
super(MultiLayerCoarsening, self).__init__()
self.embed_block1 = DenseGCNConv(dataset.num_features, hidden)
self.coarse_block1 = CoarsenBlock(hidden, ratio)
self.embed_block2 = DenseGCNConv(hidden, dataset.num_features)
# self.embed_block2 = GNNBlock(hidden, hidden, dataset.num_features)
self.num_layers = num_layers
self.jump = JumpingKnowledge(mode='cat')
self.lin1 = Linear(hidden + dataset.num_features, hidden)
self.lin2 = Linear(hidden, dataset.num_classes)
def __init__(self, nfeat, nhid, dropout):
super(GCN, self).__init__()
self.gc1 = DenseGCNConv(nfeat, nhid)
self.gc2 = DenseGCNConv(nhid, nhid)
self.gc3 = DenseGCNConv(nfeat, nhid)
self.gc4 = DenseGCNConv(nhid, nhid)
self.dropout = dropout
self.number_attention = 1
self.classifier = nn.Linear(nhid * self.number_attention, 2)
# self.classifier2 = nn.Linear(nhid*self.number_attention, 2)
self.node_classifier = nn.Linear(nhid, 2)
self.attention = nn.Linear(nhid, self.number_attention)
class Block(torch.nn.Module):
def __init__(self, in_channels, hidden_channels, out_channels):
super(Block, self).__init__()
self.conv1 = DenseGCNConv(in_channels, hidden_channels)
self.conv2 = DenseGCNConv(hidden_channels, hidden_channels)
self.lin = nn.Linear(hidden_channels + hidden_channels, out_channels)
def reset_parameters(self):
self.conv1.reset_parameters()
self.conv2.reset_parameters()
self.lin.reset_parameters()
def forward(self, x, adj, mask=None, add_loop=True):
x1 = F.relu(self.conv1(x, adj, mask, add_loop))
x2 = F.relu(self.conv2(x1, adj, mask, add_loop))
out = self.lin(torch.cat((x1, x2), -1))
return out
class GNNBlock(torch.nn.Module): #2 layer GCN block
def __init__(self, in_channels, hidden_channels, out_channels):
super(GNNBlock, self).__init__()
self.conv1 = DenseGCNConv(in_channels, hidden_channels)
self.conv2 = DenseGCNConv(hidden_channels, out_channels)
self.lin = torch.nn.Linear(hidden_channels + out_channels,
out_channels)
# self.lin1 = torch.nn.Linear(hidden_channels, out_channels)
def reset_parameters(self):
self.conv1.reset_parameters()
self.conv2.reset_parameters()
self.lin.reset_parameters()
def forward(self, x, adj, mask=None, add_loop=True):
x1 = F.relu(self.conv1(x, adj, mask, add_loop))
x2 = F.relu(self.conv2(x1, adj, mask, add_loop))
return self.lin(torch.cat([x1, x2], dim=-1))
def __init__(self, in_feature, hidden_feature, out_feature, in_node,
hidden_node, out_node):
super(GcnHpoolSubmodel, self).__init__()
#self._hparams = hparams_lib.copy_hparams(hparams)
#self.build_graph(in_feature, hidden_feature, out_feature, in_node, hidden_node, out_node)
self.reset_parameters()
#self._device = torch.device(self._hparams.device)
self.pool_tensor = None
# # embedding blocks
#
# self.embed_conv_first = GCNConv(
# in_channels=in_feature,
# out_channels=hidden_feature,
# )
# self.embed_conv_block = GCNConv(
# in_channels=hidden_feature,
# out_channels=hidden_feature,
# )
# self.embed_conv_last = GCNConv(
# in_channels=hidden_feature,
# out_channels=out_feature,
# )
# embedding blocks
self.embed_conv_first = DenseGCNConv(
in_channels=in_feature,
out_channels=hidden_feature,
)
self.embed_conv_block = DenseGCNConv(
in_channels=hidden_feature,
out_channels=hidden_feature,
)
self.embed_conv_last = DenseGCNConv(
in_channels=hidden_feature,
out_channels=out_feature,
)
# pooling blocks
self.pool_conv_first = DenseGCNConv(
in_channels=in_node,
out_channels=hidden_node,
)
self.pool_conv_block = DenseGCNConv(
in_channels=hidden_node,
out_channels=hidden_node,
)
self.pool_conv_last = DenseGCNConv(
in_channels=hidden_node,
out_channels=out_node,
)
self.pool_linear = torch.nn.Linear(hidden_node * 2 + out_node,
out_node)
def test_dense_gcn_conv():
channels = 16
sparse_conv = GCNConv(channels, channels)
dense_conv = DenseGCNConv(channels, channels)
assert dense_conv.__repr__() == 'DenseGCNConv(16, 16)'
# Ensure same weights and bias.
dense_conv.weight = sparse_conv.weight
dense_conv.bias = sparse_conv.bias
x = torch.randn((5, channels))
edge_index = torch.tensor([[0, 0, 1, 1, 2, 2, 3, 4],
[1, 2, 0, 2, 0, 1, 4, 3]])
sparse_out = sparse_conv(x, edge_index)
assert sparse_out.size() == (5, channels)
x = torch.cat([x, x.new_zeros(1, channels)], dim=0).view(2, 3, channels)
adj = torch.Tensor([
[
[0, 1, 1],
[1, 0, 1],
[1, 1, 0],
],
[
[0, 1, 0],
[1, 0, 0],
[0, 0, 0],
],
])
mask = torch.tensor([[1, 1, 1], [1, 1, 0]], dtype=torch.uint8)
dense_out = dense_conv(x, adj, mask)
assert dense_out.size() == (2, 3, channels)
assert dense_out[1, 2].abs().sum().item() == 0
dense_out = dense_out.view(6, channels)[:-1]
assert torch.allclose(sparse_out, dense_out, atol=1e-04)
def test_dense_gcn_conv_with_broadcasting():
batch_size, num_nodes, channels = 8, 3, 16
conv = DenseGCNConv(channels, channels)
x = torch.randn(batch_size, num_nodes, channels)
adj = torch.Tensor([
[0, 1, 1],
[1, 0, 1],
[1, 1, 0],
])
assert conv(x, adj).size() == (batch_size, num_nodes, channels)
mask = torch.tensor([1, 1, 1], dtype=torch.uint8)
assert conv(x, adj, mask).size() == (batch_size, num_nodes, channels)
def __init__(self,
input_dim=3,
hidden_dim=16,
embedding_dim=32,
output_dim_id=len(class_to_id),
output_dim_p4=4,
dropout_rate=0.5,
convlayer="sgconv",
space_dim=2,
nearest=3):
super(PFNet5, self).__init__()
self.input_dim = input_dim
act = nn.LeakyReLU
self.inp = nn.Sequential(
nn.Linear(input_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, embedding_dim),
act(),
)
self.conv = DenseGCNConv(embedding_dim, embedding_dim)
self.nn1 = nn.Sequential(
nn.Linear(embedding_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, output_dim_id),
)
self.nn2 = nn.Sequential(
nn.Linear(embedding_dim + output_dim_id, hidden_dim),
act(),
nn.Linear(hidden_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, hidden_dim),
act(),
nn.Linear(hidden_dim, output_dim_p4),
)
def test_gcn():
x_len, x_dim = 100, 1000
x = np.random.randn(x_len, x_dim)
adj = sps.rand(x_len, x_len, density=0.1)
edge_index = np.array(adj.nonzero())
gcn = SparseGCN(x_dim, x_dim)
print(x[7].mean(), np.linalg.norm(x))
start = time.time()
out = gcn.forward(x, edge_index)
print(time.time() - start)
print(out[7].mean(), np.linalg.norm(out), sps.linalg.norm(gcn.w))
gcn1 = DenseGCNConv(x_dim, x_dim, improved=True, bias=False)
adj = adj > 0
out = gcn1(torch.tensor(x, dtype=torch.float),
torch.tensor(adj.toarray(), dtype=torch.float))
print(out[0, 7].mean(), out.norm(), gcn1.weight.norm())
def __init__(self,
num_nodes,
input_dim,
output_dim,
lstm_hidden_size,
lstm_num_layers,
batch_size,
gnn_hidden_size,
lstm_dropout=0,
**kwargs):
super(GNNLSTM, self).__init__()
self.num_nodes = num_nodes
self.input_dim = input_dim
self.lstm_hidden_size = lstm_hidden_size
self.lstm_num_layers = lstm_num_layers
self.gnn_hidden_size = gnn_hidden_size
self.lstm_dropout = lstm_dropout
self.output_dim = output_dim
self.batch_size = batch_size
if 'target_node' in kwargs.keys():
self.target_node = kwargs['target_node']
else:
self.target_node = None
# LSTM layers definition
self.graph_lstm = GraphLSTM(num_nodes=num_nodes,
input_dim=input_dim,
hidden_size=lstm_hidden_size,
num_layers=lstm_num_layers,
batch_size=batch_size,
dropout=lstm_dropout)
# GNN layers definition
self.gcn = DenseGCNConv(in_channels=lstm_num_layers * lstm_hidden_size,
out_channels=gnn_hidden_size)
# MLP definition
self.mlp = nn.Sequential(nn.Linear(gnn_hidden_size, 512), nn.ReLU(),
nn.Linear(512, 256), nn.ReLU(),
nn.Linear(256, 64), nn.ReLU(),
nn.Linear(64, output_dim))
def __init__(self, in_dim, out_dim, act, p):
super(GCN, self).__init__()
self.act = act
self.drop = nn.Dropout(p=p) if p > 0.0 else nn.Identity()
self.gcn = DenseGCNConv(in_dim, out_dim, improved=True)
class MultiLayerCoarsening(torch.nn.Module):
def __init__(self, dataset, hidden, num_layers=2, ratio=0.5):
super(MultiLayerCoarsening, self).__init__()
self.embed_block1 = DenseGCNConv(dataset.num_features, hidden)
self.coarse_block1 = CoarsenBlock(hidden, ratio)
self.embed_block2 = DenseGCNConv(hidden, dataset.num_features)
# self.embed_block2 = GNNBlock(hidden, hidden, dataset.num_features)
self.num_layers = num_layers
self.jump = JumpingKnowledge(mode='cat')
self.lin1 = Linear( hidden *num_layers, hidden)
self.lin2 = Linear(hidden, dataset.num_classes)
def reset_parameters(self):
self.embed_block1.reset_parameters()
self.coarse_block1.reset_parameters()
self.jump.reset_parameters()
self.lin1.reset_parameters()
self.lin2.reset_parameters()
def forward(self, data, epsilon=0.01, opt_epochs=100):
x, adj, mask = data.x, data.adj, data.mask
batch_num_nodes = data.mask.sum(-1)
new_adjs = [adj]
Ss = []
x1 = F.relu(self.embed_block1(x, adj, mask, add_loop=True))
# xs = [x1.mean(dim=1)]
xs = []
coarse_x, new_adj, S = self.coarse_block1(x1, adj, batch_num_nodes)
new_adjs.append(new_adj)
Ss.append(S)
# x2 = F.relu(self.embed_block1(coarse_x, new_adj, mask, add_loop=True))
xs.append(coarse_x.mean(dim=1))
x2 = self.embed_block2(coarse_x, new_adj, mask,
add_loop=True) # should not add ReLu, otherwise x2 could be all zero.
# xs.append(x2.mean(dim=1))
for i in range(self.num_layers-1):
x1 = F.relu(self.embed_block1(F.relu(x2), new_adj, mask, add_loop=True))
coarse_x, new_adj, S = self.coarse_block1(x1, new_adj, batch_num_nodes)
new_adjs.append(new_adj)
Ss.append(S)
xs.append(coarse_x.mean(dim=1))
x2 = self.embed_block2(coarse_x, new_adj, mask, add_loop=True)#should not add ReLu, otherwise x2 could be all zero.
# xs.append(x2.mean(dim=1))
opt_loss = 0.0
for i in range(len(x)):
x3 = self.get_nonzero_rows(x[i])
x4 = self.get_nonzero_rows(x2[i])
if x3.size()[0]==0:
continue
if x4.size()[0]==0:
opt_loss += sinkhorn_loss_default(x3, x2[i], epsilon, niter=opt_epochs).float()
continue
opt_loss += sinkhorn_loss_default(x3, x4, epsilon, niter=opt_epochs).float()
return xs, new_adjs, Ss, opt_loss
def get_nonzero_rows(self, M):# M is a matrix
# row_ind = M.sum(-1).nonzero().squeeze() #nonzero has bugs in Pytorch 1.2.0.........
#So we use other methods to take place of it
MM, MM_ind = torch.abs(M.sum(-1)).sort()
N = (torch.abs(M.sum(-1))>0).sum()
return M[MM_ind[:N]]
def predict(self, xs):
x = self.jump(xs)
x = F.relu(self.lin1(x))
x = F.dropout(x, p=0.5, training=self.training)
x = self.lin2(x)
return F.log_softmax(x, dim=-1)
def test(self, train_z, train_y, test_z, test_y, solver='lbfgs',
multi_class='auto', *args, **kwargs):
r"""Evaluates latent space quality via a logistic regression downstream
task."""
clf = LogisticRegression(solver=solver, multi_class=multi_class, *args,
**kwargs).fit(train_z.detach().cpu().numpy(),
train_y.detach().cpu().numpy())
return clf.score(test_z.detach().cpu().numpy(),
test_y.detach().cpu().numpy())
def __repr__(self):
return self.__class__.__name__
def __init__(self):
super(Net, self).__init__()
self.conv1 = DenseGCNConv(dataset.num_node_features, 16)
self.conv2 = DenseGCNConv(16, dataset.num_classes)
class MultiLayerCoarsening(torch.nn.Module):
def __init__(self, dataset, hidden, num_layers=2, ratio=0.5):
super(MultiLayerCoarsening, self).__init__()
self.embed_block1 = DenseGCNConv(dataset.num_features, hidden)
self.coarse_block1 = CoarsenBlock(hidden, ratio)
self.embed_block2 = DenseGCNConv(hidden, dataset.num_features)
# self.embed_block2 = GNNBlock(hidden, hidden, dataset.num_features)
self.num_layers = num_layers
self.jump = JumpingKnowledge(mode='cat')
self.lin1 = Linear(hidden + dataset.num_features, hidden)
self.lin2 = Linear(hidden, dataset.num_classes)
def reset_parameters(self):
self.embed_block1.reset_parameters()
self.coarse_block1.reset_parameters()
self.embed_block2.reset_parameters()
self.jump.reset_parameters()
self.lin1.reset_parameters()
self.lin2.reset_parameters()
def forward(self, data, epsilon=0.01, opt_epochs=100):
x, adj, mask = data.x, data.adj, data.mask
batch_num_nodes = data.mask.sum(-1)
new_adjs = [adj]
Ss = []
x1 = F.relu(self.embed_block1(x, adj, mask, add_loop=True))
xs = [x1.mean(dim=1)]
new_adj = adj
coarse_x = x1
# coarse_x, new_adj, S = self.coarse_block1(x1, adj, batch_num_nodes)
# new_adjs.append(new_adj)
# Ss.append(S)
for i in range(self.num_layers):
coarse_x, new_adj, S = self.coarse_block1(coarse_x, new_adj,
batch_num_nodes)
new_adjs.append(new_adj)
Ss.append(S)
x2 = self.embed_block2(
coarse_x, new_adj, mask, add_loop=True
) #should not add ReLu, otherwise x2 could be all zero.
xs.append(x2.mean(dim=1))
opt_loss = 0.0
for i in range(len(x)):
x3 = self.get_nonzero_rows(x[i])
x4 = self.get_nonzero_rows(x2[i])
if x3.size()[0] == 0:
continue
if x4.size()[0] == 0:
# opt_loss += sinkhorn_loss_default(x3, x2[i], epsilon, niter=opt_epochs).float()
continue
opt_loss += sinkhorn_loss_default(x3,
x4,
epsilon,
niter=opt_epochs).float()
return xs, new_adjs, Ss, opt_loss
def get_nonzero_rows(self, M): # M is a matrix
# row_ind = M.sum(-1).nonzero().squeeze() #nonzero has bugs in Pytorch 1.2.0.........
#So we use other methods to take place of it
MM, MM_ind = torch.abs(M.sum(-1)).sort()
N = (torch.abs(M.sum(-1)) > 0).sum()
return M[MM_ind[:N]]
def predict(self, xs):
x = self.jump(xs)
x = F.relu(self.lin1(x))
x = F.dropout(x, p=0.5, training=self.training)
x = self.lin2(x)
return F.log_softmax(x, dim=-1)
def __repr__(self):
return self.__class__.__name__