def forward(self, x, edge_index):
edge_index, _ = remove_self_loops(edge_index)
# edge_index, _ = add_self_loops(edge_index, num_nodes=x.size(0))
out = self.fea_mlp(self.propagate(edge_index, x=x))
if self.BN is not None:
out = self.BN(out)
return out
def get_icosahedron_weights(nodes, depth):
"""Get the icosahedron laplacian list for a certain depth.
Args:
nodes (int): initial number of nodes.
depth (int): the depth of the UNet.
laplacian_type ["combinatorial", "normalized"]: the type of the laplacian.
Returns:
laps (list): increasing list of laplacians.
"""
edge_list = []
weight_list = []
order = icosahedron_order_calculator(nodes)
for _ in range(depth):
nodes = icosahedron_nodes_calculator(order)
order_initial = icosahedron_order_calculator(nodes)
coords = get_ico_coords(int(order_initial))
coords = torch.from_numpy(coords)
edge_index = knn_graph(coords, 6 if order else 5)
if order:
dist = torch.norm(coords[edge_index[0]] - coords[edge_index[1]],
p=2,
dim=1)
_, extra_idx = torch.topk(dist, 12)
edge_index[0, extra_idx] = edge_index[1, extra_idx]
edge_index, _ = remove_self_loops(edge_index)
edge_list.append(edge_index)
weight_list.append(None)
order -= 1
return edge_list[::-1], weight_list
def forward(self, x, edge_index):
x = x.unsqueeze(-1) if x.dim() == 1 else x
x = torch.mm(x, self.weight)
x = x.view(-1, self.heads, self.out_channels)
# Add self-loops to adjacency matrix.
edge_index, edge_attr = remove_self_loops(edge_index)
edge_index = add_self_loops(edge_index, num_nodes=x.size(0))
row, col = edge_index
# Compute attention coefficients.
alpha = torch.cat([x[row], x[col]], dim=-1)
alpha = (alpha * self.att_weight).sum(dim=-1)
alpha = F.leaky_relu(alpha, self.negative_slope)
alpha = softmax(alpha, row, num_nodes=x.size(0))
# Sample attention coefficients stochastically.
dropout = self.dropout if self.training else 0
alpha = F.dropout(alpha, p=dropout, training=True)
# Sum up neighborhoods.
out = alpha.view(-1, self.heads, 1) * x[col]
out = scatter_add(out, row, dim=0, dim_size=x.size(0))
if self.concat is True:
out = out.view(-1, self.heads * self.out_channels)
else:
out = out.sum(dim=1) / self.heads
if self.bias is not None:
out += self.bias
return out
def load_node_pair(adj, file_path, n_hop=10):
from os.path import join as pjoin
if file_path and os.path.exists(pjoin(file_path, 'pos_node_edge.pt')):
pos_neighbor = torch.load(pjoin(file_path, 'pos_node_edge.pt'))
neg_neighbor = torch.load(pjoin(file_path, 'neg_node_edge.pt'))
else:
adj = adj.to('cuda:8')
adj = adj > 0
neighbor = torch.mm(adj.float(), adj.float().t()) > 0
size = neighbor.size(1)
pos_neighbor = torch.zeros_like(neighbor)
sort_weight, indices = torch.sum(neighbor.float(), dim=0).sort()
min_count, max_count = int(size * 0.1), int(size * 0.9)
min_pos, max_pos = sort_weight[min_count], sort_weight[max_count]
min_count = (sort_weight < max(min_pos, 2)).sum()
max_count = (sort_weight <= max_pos).sum()
pos_select = indices[min_count:max_count]
pos_neighbor[:, pos_select] = neighbor[:, pos_select]
neg_neighbor = neighbor
for i in range(1, n_hop):
neg_neighbor = torch.mm(neg_neighbor.float(), neighbor.float()) > 0
neg_neighbor = ~neg_neighbor
pos_neighbor, _ = dense_to_sparse(pos_neighbor)
pos_neighbor = remove_self_loops(pos_neighbor)[0]
neg_neighbor, _ = dense_to_sparse(neg_neighbor)
pos_neighbor = pos_neighbor.cpu()
neg_neighbor = neg_neighbor.cpu()
if file_path:
torch.save(pos_neighbor, pjoin(file_path, 'pos_node_edge.pt'))
torch.save(neg_neighbor, pjoin(file_path, 'neg_node_edge.pt'))
return pos_neighbor, neg_neighbor
def process(self):
with open(self.raw_paths[0], 'r') as f:
graph_data = json.load(f)
mask = torch.zeros(len(graph_data['nodes']), dtype=torch.uint8)
for i in graph_data['nodes']:
mask[i['id']] = 1 if i['val'] else (2 if i['test'] else 0)
train_mask, val_mask, test_mask = mask == 0, mask == 1, mask == 2
row, col = [], []
for i in graph_data['links']:
row.append(i['source'])
col.append(i['target'])
edge_index = torch.stack([torch.tensor(row), torch.tensor(col)], dim=0)
edge_index, _ = remove_self_loops(edge_index)
edge_index, _ = coalesce(edge_index, num_nodes=mask.size(0))
x = torch.from_numpy(np.load(self.raw_paths[1])).float()
with open(self.raw_paths[2], 'r') as f:
y_data = json.load(f)
y = []
for i in range(len(y_data)):
y.append(y_data[str(i)])
y = torch.tensor(y, dtype=torch.float)
data = Data(x=x, edge_index=edge_index, y=y)
data.train_mask = train_mask
data.val_mask = val_mask
data.test_mask = test_mask
data = data if self.pre_transform is None else self.pre_transform(data)
data, slices = self.collate([data])
torch.save((data, slices), self.processed_paths[0])
def forward(self,
x,
edge_index,
size=None,
return_attention_weights=False):
""""""
if size is None and torch.is_tensor(x):
edge_index, _ = remove_self_loops(edge_index)
edge_index, _ = add_self_loops(edge_index,
num_nodes=x.size(self.node_dim))
if torch.is_tensor(x):
x = torch.matmul(x, self.weight)
else:
x = (None if x[0] is None else torch.matmul(x[0], self.weight),
None if x[1] is None else torch.matmul(x[1], self.weight))
out = self.propagate(edge_index,
size=size,
x=x,
return_attention_weights=return_attention_weights)
if return_attention_weights:
alpha, self.alpha = self.alpha, None
return out, alpha
else:
return out
def pool_edge(cluster, edge_index, edge_attr=None):
num_nodes = cluster.size(0)
edge_index = cluster[edge_index.view(-1)].view(2, -1)
edge_index, edge_attr = remove_self_loops(edge_index, edge_attr)
edge_index, edge_attr = coalesce(edge_index, edge_attr, num_nodes,
num_nodes)
return edge_index, edge_attr
def __call__(self, data):
edge_index, edge_attr = data.edge_index, data.edge_attr
n = data.num_nodes
fill = 1e16
value = edge_index.new_full((edge_index.size(1), ),
fill,
dtype=torch.float)
index, value = spspmm(edge_index, value, edge_index, value, n, n, n)
index, value = remove_self_loops(index, value)
edge_index = torch.cat([edge_index, index], dim=1)
if edge_attr is None:
data.edge_index, _ = coalesce(edge_index, None, n, n)
else:
value = value.view(-1, *[1 for _ in range(edge_attr.dim() - 1)])
value = value.expand(-1, *list(edge_attr.size())[1:])
edge_attr = torch.cat([edge_attr, value], dim=0)
data.edge_index, edge_attr = coalesce(edge_index,
edge_attr,
n,
n,
op='min',
fill_value=fill)
edge_attr[edge_attr >= fill] = 0
data.edge_attr = edge_attr
return data
def __init__(self, name, num_fixed_features, use_rand_feats):
# Write path
self.path = osp.join(osp.dirname(osp.realpath(__file__)), '..', 'data',
name)
self.edges, self.objects, self.weights = load_edge_list(
self.path, False)
num_nodes = len(self.objects)
self.feats = torch.randn(num_nodes,
num_fixed_features,
requires_grad=False)
perm = torch.randperm(self.feats.size(0))
perm_idx = perm[:num_nodes]
feats = self.feats[perm_idx]
G = nx.Graph()
G.add_edges_from(self.edges)
edge_index = torch.tensor(list(G.edges)).t().contiguous()
edge_index, _ = remove_self_loops(edge_index)
if use_rand_feats:
self.num_features = num_fixed_features
self.dataset = Data(edge_index=edge_index, x=feats)
else:
adj_mat = torch.Tensor(nx.to_numpy_matrix(G))
self.dataset = Data(edge_index=edge_index, x=adj_mat)
self.num_features = num_nodes
self.reconstruction_loss = None
def structured_negative_sampling_feasible(
edge_index: Tensor,
num_nodes: Optional[int] = None,
contains_neg_self_loops: bool = True) -> bool:
r"""Returns :obj:`True` if
:meth:`~torch_geometric.utils.structured_negative_sampling` is feasible
on the graph given by :obj:`edge_index`.
:obj:`~torch_geometric.utils.structured_negative_sampling` is infeasible
if atleast one node is connected to all other nodes.
Args:
edge_index (LongTensor): The edge indices.
num_nodes (int, optional): The number of nodes, *i.e.*
:obj:`max_val + 1` of :attr:`edge_index`. (default: :obj:`None`)
contains_neg_self_loops (bool, optional): If set to
:obj:`False`, sampled negative edges will not contain self loops.
(default: :obj:`True`)
:rtype: bool
"""
num_nodes = maybe_num_nodes(edge_index, num_nodes)
max_num_neighbors = num_nodes
edge_index = coalesce(edge_index, num_nodes=num_nodes)
if not contains_neg_self_loops:
edge_index, _ = remove_self_loops(edge_index)
max_num_neighbors -= 1 # Reduce number of valid neighbors
deg = degree(edge_index[0], num_nodes)
# True if there exists no node that is connected to all other nodes.
return bool(torch.all(deg < max_num_neighbors))
def recon_loss1(self, z, edge_index, batch):
EPS = 1e-15
MAX_LOGSTD = 10
r"""Given latent variables :obj:`z`, computes the binary cross
entropy loss for positive edges :obj:`pos_edge_index` and negative
sampled edges.
Args:
z (Tensor): The latent space :math:`\mathbf{Z}`.
pos_edge_index (LongTensor): The positive edges to train against.
"""
recon_adj = self.edge_recon(z, edge_index)
pos_loss = -torch.log(
recon_adj + EPS).mean()
# Do not include self-loops in negative samples
pos_edge_index, _ = remove_self_loops(edge_index)
pos_edge_index, _ = add_self_loops(pos_edge_index)
neg_edge_index = negative_sampling(pos_edge_index, z.size(0)) #random thingggg
neg_loss = -torch.log(1 -
self.edge_recon(z, neg_edge_index) +
EPS).mean()
return pos_loss + neg_loss
def forward(self, x, edge_index, size=None):
if size is None and torch.is_tensor(x):
edge_index, _ = remove_self_loops(edge_index)
edge_index, _ = add_self_loops(edge_index,
num_nodes=x.size(self.node_dim))
self.cache["edge_index"] = edge_index
if torch.is_tensor(x):
x = torch.matmul(x, self.weight)
else:
x = (None if x[0] is None else torch.matmul(x[0], self.weight),
None if x[1] is None else torch.matmul(x[1], self.weight))
propagated = self.propagate(edge_index, size=size, x=x)
if self.training:
att_neg_list = []
for _ in range(self.num_neg_samples_per_edge):
edge_j, edge_i, edge_k = structured_negative_sampling(
edge_index=edge_index,
num_nodes=x.size(0),
)
x_j, x_k = x[edge_j], x[edge_k]
att_neg = self.get_unnormalized_attention(x_j, x_k)
att_neg_list.append(att_neg)
self.cache["att_neg"] = torch.stack(att_neg_list,
dim=-1) # [E, heads, num_neg]
return propagated
def test_attr():
model.eval()
accs = []
m = ['train_mask', 'val_mask', 'test_mask']
i = 0
for _, mask in data('train_mask', 'val_mask', 'test_mask'):
if (m[i] == 'train_mask') :
x, pos_edge_index = data.x, data.train_pos_edge_index
_edge_index, _ = remove_self_loops(pos_edge_index)
pos_edge_index_with_self_loops, _ = add_self_loops(_edge_index,
num_nodes=x.size(0))
neg_edge_index = negative_sampling(
edge_index=pos_edge_index_with_self_loops, num_nodes=x.size(0),
num_neg_samples=pos_edge_index.size(1))
else:
pos_edge_index, neg_edge_index = [
index for _, index in data("{}_pos_edge_index".format(m[i].split("_")[0]),
"{}_neg_edge_index".format(m[i].split("_")[0]))
]
_, logits, _ = model(pos_edge_index, neg_edge_index)
pred = logits[mask].max(1)[1]
macro = f1_score((data.y[mask]).cpu().numpy(), pred.cpu().numpy(),average='macro')
accs.append(macro)
i+=1
return accs
def forward(self, x, pos, edge_index):
edge_index, _ = remove_self_loops(edge_index)
self.define_message(x)
if self.x_is_none:
return self.propagate(edge_index, pos=pos)
else:
return self.propagate(edge_index, x=x, pos=pos[0])
def __norm__(self,
edge_index,
num_nodes: Optional[int],
edge_weight: OptTensor,
normalization: Optional[str],
lambda_max,
dtype: Optional[int] = None,
batch: OptTensor = None):
edge_index, edge_weight = remove_self_loops(edge_index, edge_weight)
edge_index, edge_weight = get_laplacian(edge_index, edge_weight,
normalization, dtype,
num_nodes)
if batch is not None and lambda_max.numel() > 1:
lambda_max = lambda_max[batch[edge_index[0]]]
edge_weight = (2.0 * edge_weight) / lambda_max
edge_weight.masked_fill_(edge_weight == float('inf'), 0)
edge_index, edge_weight = add_self_loops(edge_index,
edge_weight,
fill_value=-1.,
num_nodes=num_nodes)
assert edge_weight is not None
return edge_index, edge_weight
def forward(self,
x,
edge_index,
edge_attr,
weight,
bias,
edge_encoder_w,
edge_encoder_b,
size=None):
""""""
if size is None and torch.is_tensor(x):
edge_index, _ = remove_self_loops(edge_index)
edge_index, _ = add_self_loops(edge_index, num_nodes=x.size(0))
# add features to self-loop edges
self_loop_attr = torch.zeros(x.size(0), self.edge_in_channels)
self_loop_attr[:, 7] = 1 # for bio dataset
self_loop_attr = self_loop_attr.to(edge_attr.device).to(
edge_attr.dtype)
edge_attr = torch.cat((edge_attr, self_loop_attr), dim=0)
edge_emb = F.linear(edge_attr, edge_encoder_w, edge_encoder_b)
x = torch.matmul(x, weight)
return self.propagate(edge_index,
size=size,
x=x,
bias=bias,
edge_attr=edge_emb)
def forward(self, x: Union[OptTensor, PairOptTensor],
pos: Union[Tensor, PairTensor],
normal: Union[Tensor, PairTensor],
edge_index: Adj) -> Tensor: # yapf: disable
""""""
if not isinstance(x, tuple):
x: PairOptTensor = (x, None)
if isinstance(pos, Tensor):
pos: PairTensor = (pos, pos)
if isinstance(normal, Tensor):
normal: PairTensor = (normal, normal)
if self.add_self_loops:
if isinstance(edge_index, Tensor):
edge_index, _ = remove_self_loops(edge_index)
edge_index, _ = add_self_loops(edge_index,
num_nodes=pos[1].size(0))
elif isinstance(edge_index, SparseTensor):
edge_index = set_diag(edge_index)
# propagate_type: (x: PairOptTensor, pos: PairTensor, normal: PairTensor) # noqa
out = self.propagate(edge_index,
x=x,
pos=pos,
normal=normal,
size=None)
if self.global_nn is not None:
out = self.global_nn(out)
return out
def forward(self,
x,
edge_index,
size=None,
edge_weights=None,
return_alpha=False):
self.return_alpha = return_alpha
if size is None and torch.is_tensor(x):
edge_index, edge_weights = remove_self_loops(
edge_index, edge_weights)
edge_index, edge_weights = add_self_loops(edge_index,
edge_weight=edge_weights,
num_nodes=x.size(
self.node_dim))
self.edge_weights = edge_weights
if torch.is_tensor(x):
x = torch.matmul(x, self.weight)
else:
x = (None if x[0] is None else torch.matmul(x[0], self.weight),
None if x[1] is None else torch.matmul(x[1], self.weight))
if self.return_alpha:
return self.propagate(edge_index, size=size,
x=x), self.alpha, edge_index
return self.propagate(edge_index, size=size, x=x)
def barabasi_albert_graph(num_nodes, num_edges):
r"""Returns the :obj:`edge_index` of a Barabasi-Albert preferential
attachment model, where a graph of :obj:`num_nodes` nodes grows by
attaching new nodes with :obj:`num_edges` edges that are preferentially
attached to existing nodes with high degree.
Args:
num_nodes (int): The number of nodes.
num_edges (int): The number of edges from a new node to existing nodes.
"""
assert num_edges > 0 and num_edges < num_nodes
row, col = torch.arange(num_edges), torch.randperm(num_edges)
for i in range(num_edges, num_nodes):
row = torch.cat([row, torch.full((num_edges, ), i, dtype=torch.long)])
choice = np.random.choice(torch.cat([row, col]).numpy(), num_edges)
col = torch.cat([col, torch.from_numpy(choice)])
edge_index = torch.stack([row, col], dim=0)
edge_index, _ = remove_self_loops(edge_index)
edge_index = to_undirected(edge_index, num_nodes=num_nodes)
return edge_index
def forward(self, x, edge_index):
""""""
edge_index, _ = remove_self_loops(edge_index)
edge_index, _ = add_self_loops(edge_index, num_nodes=x.size(0))
x = torch.mm(x, self.weight).view(-1, self.heads, self.out_channels)
return self.propagate(edge_index, x=x, num_nodes=x.size(0))
def forward(self, x, edge_index, pseudo):
""""""
# See https://github.com/shchur/gnn-benchmark for the reference
# TensorFlow implementation.
edge_index, _ = remove_self_loops(edge_index)
edge_index = add_self_loops(edge_index, num_nodes=x.size(0))
x = x.unsqueeze(-1) if x.dim() == 1 else x
pseudo = pseudo.unsqueeze(-1) if pseudo.dim() == 1 else pseudo
row, col = edge_index
F, (E, D) = x.size(0), pseudo.size()
gaussian = -0.5 * (pseudo.view(E, 1, D) - self.mu.view(1, F, D))**2
gaussian = torch.exp(gaussian / (1e-14 + self.sigma.view(1, F, D)**2))
gaussian = gaussian.prod(dim=-1)
# Normalize gaussians in edge dimension.
gaussian_mean = scatter_add(gaussian, row, dim=0, dim_size=x.size(0))
gaussian = gaussian / (1e-14 + gaussian_mean[row]).view(E, F)
out = scatter_add(x[col] * gaussian, row, dim=0, dim_size=x.size(0))
out = self.lin(out)
return out
def forward(self, x, edge_index, return_attention_weights=False):
""""""
if torch.is_tensor(x):
x = self.lin(x)
x = (x, x)
else:
x = (self.lin(x[0]), self.lin(x[1]))
edge_index, _ = remove_self_loops(edge_index)
edge_index, _ = add_self_loops(edge_index,
num_nodes=x[1].size(self.node_dim))
out = self.propagate(edge_index,
x=x,
return_attention_weights=return_attention_weights)
if self.concat:
out = out.view(-1, self.heads * self.out_channels)
else:
out = out.mean(dim=1)
if self.bias is not None:
out = out + self.bias
if return_attention_weights:
alpha, self.__alpha__ = self.__alpha__, None
return out, (edge_index, alpha)
else:
return out
def process(self):
for s, split in enumerate(['train', 'valid', 'test']):
path = osp.join(self.raw_dir, '{}_graph.json').format(split)
with open(path, 'r') as f:
G = nx.DiGraph(json_graph.node_link_graph(json.load(f)))
x = np.load(osp.join(self.raw_dir, '{}_feats.npy').format(split))
x = torch.from_numpy(x).to(torch.float)
y = np.load(osp.join(self.raw_dir, '{}_labels.npy').format(split))
y = torch.from_numpy(y).to(torch.float)
data_list = []
path = osp.join(self.raw_dir, '{}_graph_id.npy').format(split)
idx = torch.from_numpy(np.load(path)).to(torch.long)
idx = idx - idx.min()
for i in range(idx.max().item() + 1):
mask = idx == i
G_s = G.subgraph(mask.nonzero().view(-1).tolist())
edge_index = torch.tensor(list(G_s.edges)).t().contiguous()
edge_index = edge_index - edge_index.min()
edge_index, _ = remove_self_loops(edge_index)
data = Data(edge_index=edge_index, x=x[mask], y=y[mask])
if self.pre_filter is not None and not self.pre_filter(data):
continue
if self.pre_transform is not None:
data = self.pre_transform(data)
data_list.append(data)
torch.save(self.collate(data_list), self.processed_paths[s])
def forward(self, x, edge_index, mask=None, edge_weight=None, size=None):
edge_index, _ = remove_self_loops(edge_index)
if mask is not None:
x = x * mask
h = x
return self.propagate(edge_index, size=size, x=x, h=h,
edge_weight=edge_weight)
def norm(edge_index, num_nodes, edge_weight, dtype=None):
edge_index, _ = remove_self_loops(edge_index)
if edge_weight is None:
edge_weight = torch.ones((edge_index.size(1), ),
dtype=dtype,
device=edge_index.device)
row, col = edge_index
deg = scatter_add(edge_weight, row, dim=0, dim_size=num_nodes)
deg_inv_sqrt = deg.pow(-0.5)
deg_inv_sqrt[deg_inv_sqrt == float('inf')] = 0
edge_index, edge_weight = add_self_loops(edge_index, edge_weight, 0,
num_nodes)
row, col = edge_index
expand_deg = torch.zeros((edge_weight.size(0), ),
dtype=dtype,
device=edge_index.device)
expand_deg[-num_nodes:] = torch.ones((num_nodes, ),
dtype=dtype,
device=edge_index.device)
return edge_index, expand_deg - deg_inv_sqrt[
row] * edge_weight * deg_inv_sqrt[col]
def forward(self, x, edge_index, size=None):
x_l = x_r = x
alpha_l = (x_l * self.att_l).sum(dim=-1)
alpha_r = (x_r * self.att_r).sum(dim=-1)
# print(alpha_l.shape)
# print(alpha_r.shape)
if self.add_self_loops:
if isinstance(edge_index, Tensor):
num_nodes = x_l.size(0)
if x_r is not None:
num_nodes = min(num_nodes, x_r.size(0))
if size is not None:
num_nodes = min(size[0], size[1])
edge_index, _ = remove_self_loops(edge_index)
edge_index, _ = add_self_loops(edge_index, num_nodes=num_nodes)
elif isinstance(edge_index, SparseTensor):
edge_index = set_diag(edge_index)
if isinstance(edge_index, SparseTensor):
self.degree = edge_index.sum(dim=0)
else:
_, col = edge_index[0], edge_index[1]
self.degree = degree(col)
theta = self.get_relu_coefs(x, edge_index)
self.theta = theta.view(-1, self.channels, 2 * self.k)
out = self.propagate(edge_index,
x=(x_l, x_r),
alpha=(alpha_l, alpha_r),
size=size)
return out
def forward(self, x, edge_index):
edge_index, _ = remove_self_loops(edge_index)
edge_index = add_self_loops(edge_index, num_nodes=x.size(0))
x = x.unsqueeze(-1) if x.dim() == 1 else x
row, col = edge_index
if self.pool == 'mean':
out = torch.matmul(x, self.weight)
if self.bias is not None:
out = out + self.bias
out = self.act(out)
out = scatter_mean(out[col], row, dim=0, dim_size=out.size(0))
elif self.pool == 'max':
out = torch.matmul(x, self.weight)
if self.bias is not None:
out = out + self.bias
out = self.act(out)
out, _ = scatter_max(out[col], row, dim=0, dim_size=out.size(0))
elif self.pool == 'add':
x = torch.matmul(x, self.weight)
if self.bias is not None:
out = out + self.bias
out = self.act(out)
out = scatter_add(x[col], row, dim=0, dim_size=x.size(0))
else:
print('pooling not defined!')
if self.normalize:
out = F.normalize(out, p=2, dim=-1)
return out
def compat_matrix_edge_idx(edge_idx, labels):
"""
c x c compatibility matrix, where c is number of classes
H[i,j] is proportion of endpoints that are class j
of edges incident to class i nodes
"Generalizing GNNs Beyond Homophily"
treats negative labels as unlabeled
"""
edge_index = remove_self_loops(edge_idx)[0]
src_node, targ_node = edge_index[0, :], edge_index[1, :]
labeled_nodes = (labels[src_node] >= 0) * (labels[targ_node] >= 0)
label = labels.squeeze()
c = label.max() + 1
H = torch.zeros((c, c)).to(edge_index.device)
src_label = label[src_node[labeled_nodes]]
targ_label = label[targ_node[labeled_nodes]]
label_idx = torch.cat((src_label.unsqueeze(0), targ_label.unsqueeze(0)),
axis=0)
for k in range(c):
sum_idx = torch.where(src_label == k)[0]
add_idx = targ_label[sum_idx]
scatter_add(torch.ones_like(add_idx).to(H.dtype),
add_idx,
out=H[k, :],
dim=-1)
H = H / torch.sum(H, axis=1, keepdims=True)
return H
def forward(self, x, edge_index):
edge_index, _ = remove_self_loops(edge_index)
deg = degree(edge_index[1 if self.flow == 'source_to_target' else 0],
x.size(0), dtype=torch.long)
deg.clamp_(max=self.max_degree)
if not self.root_weight:
edge_index, _ = add_self_loops(edge_index,
num_nodes=x.size(self.node_dim))
h = self.propagate(edge_index, x=x)
out = x.new_empty(list(x.size())[:-1] + [self.out_channels])
for i in deg.unique().tolist():
idx = (deg == i).nonzero().view(-1)
r = self.rel_lins[i](h.index_select(self.node_dim, idx))
if self.root_weight:
r = r + self.root_lins[i](x.index_select(self.node_dim, idx))
out.index_copy_(self.node_dim, idx, r)
return out
def forward(self, x, edge_index, edge_attr=None):
""""""
x = x.unsqueeze(-1) if x.dim() == 1 else x
edge_index, edge_attr = remove_self_loops(edge_index, edge_attr)
if edge_attr is None:
edge_attr = x.new_ones((edge_index.size(1), ))
assert edge_attr.dim() == 1 and edge_attr.numel() == edge_index.size(1)
# Add self-loops to adjacency matrix.
edge_index = add_self_loops(edge_index, x.size(0))
loop_value = x.new_full((x.size(0), ), 1 if not self.improved else 2)
edge_attr = torch.cat([edge_attr, loop_value], dim=0)
# Normalize adjacency matrix.
row, col = edge_index
deg = scatter_add(edge_attr, row, dim=0, dim_size=x.size(0))
deg = deg.pow(-0.5)
deg[deg == float('inf')] = 0
edge_attr = deg[row] * edge_attr * deg[col]
# Perform the convolution.
out = torch.mm(x, self.weight)
out = spmm(edge_index, edge_attr, out.size(0), out)
if self.bias is not None:
out = out + self.bias
return out