def test_convert_scipy():
index = torch.tensor([[0, 0, 1, 2, 2], [0, 2, 1, 0, 1]])
value = torch.Tensor([1, 2, 4, 1, 3])
N = 3
out = from_scipy(to_scipy(index, value, N, N))
assert out[0].tolist() == index.tolist()
assert out[1].tolist() == value.tolist()
def mm(indexA, valueA, indexB, valueB, m, k, n):
assert valueA.dtype == valueB.dtype
if indexA.is_cuda:
return torch_sparse.spspmm_cuda.spspmm(indexA, valueA, indexB, valueB,
m, k, n)
A = to_scipy(indexA, valueA, m, k)
B = to_scipy(indexB, valueB, k, n)
C = A.dot(B).tocoo().tocsr().tocoo() # Force coalesce.
indexC, valueC = from_scipy(C)
return indexC, valueC
def create_sparse_H(H: torch.Tensor):
# H: 2 x nnz
# return H: N x N
import numpy as np
import scipy.sparse as sp
import torch
import torch_sparse
# M = H[1].max() + 1
H = sp.csr_matrix((torch.ones_like(H[0]), H.tolist()))
N, M = H.shape
Dv = sp.spdiags(np.power(H.sum(1).reshape(-1), -0.5), 0, N, N)
De = sp.spdiags(np.power(H.sum(0).reshape(-1), -1.), 0, M, M)
Hv = Dv * H * De * H.transpose() * Dv # V x V, for HGNN
(row, col), value = torch_sparse.from_scipy(Hv)
# Hv = Hv.tocoo()
# row, col, value = Hv.row, Hv.col, Hv.data
H = torch.sparse.FloatTensor(torch.stack((row, col)), value,
(N, N)).float() # V x V
return H
def transpose(index, value, m, n):
"""Transposes dimensions 0 and 1 of a sparse tensor.
Args:
index (:class:`LongTensor`): The index tensor of sparse matrix.
value (:class:`Tensor`): The value tensor of sparse matrix.
m (int): The first dimension of sparse matrix.
n (int): The second dimension of sparse matrix.
:rtype: (:class:`LongTensor`, :class:`Tensor`)
"""
if value.dim() == 1 and not value.is_cuda:
mat = to_scipy(index, value, m, n).tocsc()
(col, row), value = from_scipy(mat)
index = torch.stack([row, col], dim=0)
return index, value
row, col = index
index = torch.stack([col, row], dim=0)
index, value = coalesce(index, value, n, m)
return index, value
def transpose(index, value, m, n, coalesced=True):
"""Transposes dimensions 0 and 1 of a sparse tensor.
Args:
index (:class:`LongTensor`): The index tensor of sparse matrix.
value (:class:`Tensor`): The value tensor of sparse matrix.
m (int): The first dimension of corresponding dense matrix.
n (int): The second dimension of corresponding dense matrix.
coalesced (bool, optional): If set to :obj:`False`, will not coalesce
the output. (default: :obj:`True`)
:rtype: (:class:`LongTensor`, :class:`Tensor`)
"""
if value.dim() == 1 and not value.is_cuda:
mat = to_scipy(index, value, m, n).tocsc()
(col, row), value = from_scipy(mat)
index = torch.stack([row, col], dim=0)
return index, value
row, col = index
index = torch.stack([col, row], dim=0)
if coalesced:
index, value = coalesce(index, value, n, m)
return index, value
def initialise(X, Y, G, args, unseen=None):
"""
initialises model, optimiser, normalises graph, and features
arguments:
X, Y, G: the entire dataset (with graph, features, labels)
args: arguments
unseen: if not None, remove these nodes from hypergraphs
returns:
a tuple with model details (UniGNN, optimiser)
"""
G = G.copy()
if unseen is not None:
unseen = set(unseen)
# remove unseen nodes
for e, vs in G.items():
G[e] = list(set(vs) - unseen)
if args.add_self_loop:
Vs = set(range(X.shape[0]))
# only add self-loop to those are orginally un-self-looped
# TODO:maybe we should remove some repeated self-loops?
for edge, nodes in G.items():
if len(nodes) == 1 and nodes[0] in Vs:
Vs.remove(nodes[0])
for v in Vs:
G[f'self-loop-{v}'] = [v]
N, M = X.shape[0], len(G)
indptr, indices, data = [0], [], []
for e, vs in G.items():
indices += vs
data += [1] * len(vs)
indptr.append(len(indices))
H = sp.csc_matrix((data, indices, indptr), shape=(N, M),
dtype=int).tocsr() # V x E
degV = torch.from_numpy(H.sum(1)).view(-1, 1).float()
degE2 = torch.from_numpy(H.sum(0)).view(-1, 1).float()
(row, col), value = torch_sparse.from_scipy(H)
V, E = row, col
from torch_scatter import scatter
assert args.first_aggregate in (
'mean', 'sum'), 'use `mean` or `sum` for first-stage aggregation'
degE = scatter(degV[V], E, dim=0, reduce=args.first_aggregate)
degE = degE.pow(-0.5)
degV = degV.pow(-0.5)
degV[degV.isinf(
)] = 1 # when not added self-loop, some nodes might not be connected with any edge
V, E = V.cuda(), E.cuda()
args.degV = degV.cuda()
args.degE = degE.cuda()
args.degE2 = degE2.pow(-1.).cuda()
nfeat, nclass = X.shape[1], len(Y.unique())
nlayer = args.nlayer
nhid = args.nhid
nhead = args.nhead
# UniGNN and optimiser
if args.model_name == 'UniGCNII':
model = UniGCNII(args, nfeat, nhid, nclass, nlayer, nhead, V, E)
optimiser = torch.optim.Adam([
dict(params=model.reg_params, weight_decay=0.01),
dict(params=model.non_reg_params, weight_decay=5e-4)
],
lr=0.01)
elif args.model_name == 'HyperGCN':
args.fast = True
dataset = args.dataset_dict
model = HyperGCN(args, nfeat, nhid, nclass, nlayer, dataset['n'],
dataset['hypergraph'], dataset['features'])
optimiser = optim.Adam(model.parameters(), lr=0.01, weight_decay=5e-4)
else:
model = UniGNN(args, nfeat, nhid, nclass, nlayer, nhead, V, E)
p1, p2, p3, = [], [], [] # 用于设置不同的层使用不同的学习率
for n, p in model.named_parameters():
print(n, p.shape)
if '.lam' in n:
p2.append(p)
elif '.mul' in n:
p3.append(p)
else:
p1.append(p)
optimiser = optim.Adam([{
'params': p1,
'weight_decay': 5e-4,
'lr': 0.01
}, {
'params': p2,
'weight_decay': args.wd_sw,
'lr': args.lr_sw
}, {
'params': p3,
'weight_decay': args.wd_mul,
'lr': args.lr_mul
}])
#optimiser= optim.Adam(model.parameters(), lr=0.01, weight_decay=5e-4)
model.cuda()
return model, optimiser
import torch
from torch_sparse import to_scipy, from_scipy, coalesce
def transpose(index, value, m, nm coalesce=True):
"""Transposes dimensions 0 and 1 of a sparse tensor.
Args:
index (:class:`LongTensor`): The index tensor of sparse matrix.
value (:class:`Tensor`): The value tensor of sparse matrix.
m (int): The first dimension of corresponding dense matrix.
n (int): The second dimension of corresponding dense matrix.
coalesce (bool, optional): To return coalesced index and value or not (default: :obj:`True`)
:rtype: (:class:`LongTensor`, :class:`Tensor`)
"""
if value.dim() == 1 and not value.is_cuda:
mat = to_scipy(index, value, m, n).tocsc()
(col, row), value = from_scipy(mat)
index = torch.stack([row, col], dim=0)
return index, value
row, col = index
index = torch.stack([col, row], dim=0)
if coalesce:
index, value = coalesce(index, value, n, m)
return index, value