"""Module for graph transformation utilities."""
from collections.abc import Iterable, Mapping
from collections import defaultdict
import numpy as np
from scipy import sparse
from ._ffi.function import _init_api
from .base import dgl_warning, DGLError
from . import convert
from .heterograph import DGLHeteroGraph, DGLBlock
from .frame import Frame
from . import ndarray as nd
from . import backend as F
from . import utils, batch
from .partition import metis_partition_assignment
from .partition import partition_graph_with_halo
from .partition import metis_partition
# TO BE DEPRECATED
from ._deprecate.graph import DGLGraph as DGLGraphStale
__all__ = [
'line_graph',
'khop_adj',
'khop_graph',
'reverse',
'to_bidirected',
'to_bidirected_stale',
'add_reverse_edges',
'laplacian_lambda_max',
'knn_graph',
'segmented_knn_graph',
'add_edges',
'add_nodes',
'remove_edges',
'remove_nodes',
'add_self_loop',
'remove_self_loop',
'metapath_reachable_graph',
'compact_graphs',
'to_block',
'to_simple',
'to_simple_graph',
'as_immutable_graph',
'metis_partition_assignment',
'partition_graph_with_halo',
'metis_partition',
'as_heterograph']
def pairwise_squared_distance(x):
"""
x : (n_samples, n_points, dims)
return : (n_samples, n_points, n_points)
"""
x2s = F.sum(x * x, -1, True)
# assuming that __matmul__ is always implemented (true for PyTorch, MXNet and Chainer)
return x2s + F.swapaxes(x2s, -1, -2) - 2 * x @ F.swapaxes(x, -1, -2)
#pylint: disable=invalid-name
[docs]def knn_graph(x, k):
"""Construct a graph from a set of points according to k-nearest-neighbor (KNN)
and return.
The function transforms the coordinates/features of a point set
into a directed homogeneous graph. The coordinates of the point
set is specified as a matrix whose rows correspond to points and
columns correspond to coordinate/feature dimensions.
The nodes of the returned graph correspond to the points, where the predecessors
of each point are its k-nearest neighbors measured by the Euclidean distance.
If :attr:`x` is a 3D tensor, then each submatrix will be transformed
into a separate graph. DGL then composes the graphs into a large
graph of multiple connected components.
Parameters
----------
x : Tensor
The point coordinates. It can be either on CPU or GPU.
* If is 2D, ``x[i]`` corresponds to the i-th node in the KNN graph.
* If is 3D, ``x[i]`` corresponds to the i-th KNN graph and
``x[i][j]`` corresponds to the j-th node in the i-th KNN graph.
k : int
The number of nearest neighbors per node.
Returns
-------
DGLGraph
The constructred graph. The node IDs are in the same order as :attr:`x`.
The returned graph is on CPU, regardless of the context of input :attr:`x`.
Examples
--------
The following examples use PyTorch backend.
>>> import dgl
>>> import torch
When :attr:`x` is a 2D tensor, a single KNN graph is constructed.
>>> x = torch.tensor([[0.0, 0.0, 1.0],
... [1.0, 0.5, 0.5],
... [0.5, 0.2, 0.2],
... [0.3, 0.2, 0.4]])
>>> knn_g = dgl.knn_graph(x, 2) # Each node has two predecessors
>>> knn_g.edges()
>>> (tensor([0, 1, 2, 2, 2, 3, 3, 3]), tensor([0, 1, 1, 2, 3, 0, 2, 3]))
When :attr:`x` is a 3D tensor, DGL constructs multiple KNN graphs and
and then composes them into a graph of multiple connected components.
>>> x1 = torch.tensor([[0.0, 0.0, 1.0],
... [1.0, 0.5, 0.5],
... [0.5, 0.2, 0.2],
... [0.3, 0.2, 0.4]])
>>> x2 = torch.tensor([[0.0, 1.0, 1.0],
... [0.3, 0.3, 0.3],
... [0.4, 0.4, 1.0],
... [0.3, 0.8, 0.2]])
>>> x = torch.stack([x1, x2], dim=0)
>>> knn_g = dgl.knn_graph(x, 2) # Each node has two predecessors
>>> knn_g.edges()
(tensor([0, 1, 2, 2, 2, 3, 3, 3, 4, 5, 5, 5, 6, 6, 7, 7]),
tensor([0, 1, 1, 2, 3, 0, 2, 3, 4, 5, 6, 7, 4, 6, 5, 7]))
"""
if F.ndim(x) == 2:
x = F.unsqueeze(x, 0)
n_samples, n_points, _ = F.shape(x)
dist = pairwise_squared_distance(x)
k_indices = F.argtopk(dist, k, 2, descending=False)
dst = F.copy_to(k_indices, F.cpu())
src = F.zeros_like(dst) + F.reshape(F.arange(0, n_points), (1, -1, 1))
per_sample_offset = F.reshape(F.arange(0, n_samples) * n_points, (-1, 1, 1))
dst += per_sample_offset
src += per_sample_offset
dst = F.reshape(dst, (-1,))
src = F.reshape(src, (-1,))
adj = sparse.csr_matrix(
(F.asnumpy(F.zeros_like(dst) + 1), (F.asnumpy(dst), F.asnumpy(src))),
shape=(n_samples * n_points, n_samples * n_points))
return convert.from_scipy(adj)
#pylint: disable=invalid-name
[docs]def segmented_knn_graph(x, k, segs):
"""Construct multiple graphs from multiple sets of points according to
k-nearest-neighbor (KNN) and return.
Compared with :func:`dgl.knn_graph`, this allows multiple point sets with
different capacity. The points from different sets are stored contiguously
in the :attr:`x` tensor.
:attr:`segs` specifies the number of points in each point set. The
function constructs a KNN graph for each point set, where the predecessors
of each point are its k-nearest neighbors measured by the Euclidean distance.
DGL then composes all KNN graphs
into a graph with multiple connected components.
Parameters
----------
x : Tensor
Coordinates/features of points. Must be 2D. It can be either on CPU or GPU.
k : int
The number of nearest neighbors per node.
segs : list[int]
Number of points in each point set. The numbers in :attr:`segs`
must sum up to the number of rows in :attr:`x`.
Returns
-------
DGLGraph
The graph. The node IDs are in the same order as :attr:`x`.
The returned graph is on CPU, regardless of the context of input :attr:`x`.
Examples
--------
The following examples use PyTorch backend.
>>> import dgl
>>> import torch
In the example below, the first point set has three points
and the second point set has four points.
>>> # Features/coordinates of the first point set
>>> x1 = torch.tensor([[0.0, 0.5, 0.2],
... [0.1, 0.3, 0.2],
... [0.4, 0.2, 0.2]])
>>> # Features/coordinates of the second point set
>>> x2 = torch.tensor([[0.3, 0.2, 0.1],
... [0.5, 0.2, 0.3],
... [0.1, 0.1, 0.2],
... [0.6, 0.3, 0.3]])
>>> x = torch.cat([x1, x2], dim=0)
>>> segs = [x1.shape[0], x2.shape[0]]
>>> knn_g = dgl.segmented_knn_graph(x, 2, segs)
>>> knn_g.edges()
(tensor([0, 0, 1, 1, 1, 2, 3, 3, 4, 4, 5, 5, 6, 6]),
tensor([0, 1, 0, 1, 2, 2, 3, 5, 4, 6, 3, 5, 4, 6]))
"""
n_total_points, _ = F.shape(x)
offset = np.insert(np.cumsum(segs), 0, 0)
h_list = F.split(x, segs, 0)
dst = [
F.argtopk(pairwise_squared_distance(h_g), k, 1, descending=False) +
int(offset[i])
for i, h_g in enumerate(h_list)]
dst = F.cat(dst, 0)
src = F.arange(0, n_total_points).unsqueeze(1).expand(n_total_points, k)
dst = F.reshape(dst, (-1,))
src = F.reshape(src, (-1,))
adj = sparse.csr_matrix((F.asnumpy(F.zeros_like(dst) + 1), (F.asnumpy(dst), F.asnumpy(src))))
return convert.from_scipy(adj)
[docs]def to_bidirected(g, copy_ndata=False, readonly=None):
r"""Convert the graph to a bi-directional simple graph and return.
For an input graph :math:`G`, return a new graph :math:`G'` such that an edge
:math:`(u, v)\in G'` if and only if there exists an edge :math:`(u, v)\in G` or
an edge :math:`(v, u)\in G`. The resulting graph :math:`G'` is a simple graph,
meaning there is no parallel edge.
The operation only works for edges whose two endpoints belong to the same node type.
DGL will raise error if the input graph is heterogeneous and contains edges
with different types of endpoints.
Parameters
----------
g : DGLGraph
The input graph.
copy_ndata: bool, optional
If True, the node features of the bidirected graph are copied from the
original graph. If False, the bidirected graph will not have any node features.
(Default: False)
readonly : bool
**DEPRECATED**.
Returns
-------
DGLGraph
The bidirected graph
Notes
-----
If :attr:`copy_ndata` is True, the resulting graph will share the node feature
tensors with the input graph. Hence, users should try to avoid in-place operations
which will be visible to both graphs.
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
The following examples use PyTorch backend.
>>> import dgl
>>> import torch as th
>>> g = dgl.graph((th.tensor([0, 1, 2]), th.tensor([1, 2, 0])))
>>> bg1 = dgl.to_bidirected(g)
>>> bg1.edges()
(tensor([0, 1, 2, 1, 2, 0]), tensor([1, 2, 0, 0, 1, 2]))
The graph already have i->j and j->i
>>> g = dgl.graph((th.tensor([0, 1, 2, 0]), th.tensor([1, 2, 0, 2])))
>>> bg1 = dgl.to_bidirected(g)
>>> bg1.edges()
(tensor([0, 1, 2, 1, 2, 0]), tensor([1, 2, 0, 0, 1, 2]))
**Heterogeneous graphs with Multiple Edge Types**
>>> g = dgl.heterograph({
... ('user', 'wins', 'user'): (th.tensor([0, 2, 0, 2]), th.tensor([1, 1, 2, 0])),
... ('user', 'follows', 'user'): (th.tensor([1, 2, 1]), th.tensor([2, 1, 1]))
... })
>>> bg1 = dgl.to_bidirected(g)
>>> bg1.edges(etype='wins')
(tensor([0, 0, 1, 1, 2, 2]), tensor([1, 2, 0, 2, 0, 1]))
>>> bg1.edges(etype='follows')
(tensor([1, 1, 2]), tensor([1, 2, 1]))
"""
if readonly is not None:
dgl_warning("Parameter readonly is deprecated" \
"There will be no difference between readonly and non-readonly DGLGraph")
for c_etype in g.canonical_etypes:
if c_etype[0] != c_etype[2]:
assert False, "to_bidirected is not well defined for " \
"unidirectional bipartite graphs" \
", but {} is unidirectional bipartite".format(c_etype)
assert g.is_multigraph is False, "to_bidirected only support simple graph"
g = add_reverse_edges(g, copy_ndata=copy_ndata, copy_edata=False)
g = to_simple(g, return_counts=None, copy_ndata=copy_ndata, copy_edata=False)
return g
[docs]def add_reverse_edges(g, readonly=None, copy_ndata=True,
copy_edata=False, ignore_bipartite=False):
r"""Add an reversed edge for each edge in the input graph and return a new graph.
For a graph with edges :math:`(i_1, j_1), \cdots, (i_n, j_n)`, this
function creates a new graph with edges
:math:`(i_1, j_1), \cdots, (i_n, j_n), (j_1, i_1), \cdots, (j_n, i_n)`.
The operation only works for edges whose two endpoints belong to the same node type.
DGL will raise error if the input graph is heterogeneous and contains edges
with different types of endpoints. If :attr:`ignore_bipartite` is true, DGL will
ignore those edges instead.
Parameters
----------
g : DGLGraph
The input graph.
readonly : bool, default to be True
Deprecated. There will be no difference between readonly and non-readonly
copy_ndata: bool, optional
If True, the node features of the new graph are copied from
the original graph. If False, the new graph will not have any
node features.
(Default: True)
copy_edata: bool, optional
If True, the features of the reversed edges will be identical to
the original ones."
If False, the new graph will not have any edge features.
(Default: False)
ignore_bipartite: bool, optional
If True, unidirectional bipartite graphs are ignored and
no error is raised. If False, an error will be raised if
an edge type of the input heterogeneous graph is for a unidirectional
bipartite graph.
Returns
-------
DGLGraph
The graph with reversed edges added.
Notes
-----
If :attr:`copy_ndata` is True, the resulting graph will share the node feature
tensors with the input graph. Hence, users should try to avoid in-place operations
which will be visible to both graphs. On the contrary, the two graphs do not share
the same edge feature storage.
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
**Homogeneous graphs**
>>> g = dgl.graph((th.tensor([0, 0]), th.tensor([0, 1])))
>>> bg1 = dgl.add_reverse_edges(g)
>>> bg1.edges()
(tensor([0, 0, 0, 1]), tensor([0, 1, 0, 0]))
**Heterogeneous graphs**
>>> g = dgl.heterograph({
>>> ('user', 'wins', 'user'): (th.tensor([0, 2, 0, 2, 2]), th.tensor([1, 1, 2, 1, 0])),
>>> ('user', 'plays', 'game'): (th.tensor([1, 2, 1]), th.tensor([2, 1, 1])),
>>> ('user', 'follows', 'user'): (th.tensor([1, 2, 1), th.tensor([0, 0, 0]))
>>> })
>>> g.nodes['game'].data['hv'] = th.ones(3, 1)
>>> g.edges['wins'].data['h'] = th.tensor([0, 1, 2, 3, 4])
The :func:`add_reverse_edges` operation is applied to the edge type
``('user', 'wins', 'user')`` and the edge type ``('user', 'follows', 'user')``.
The edge type ``('user', 'plays', 'game')`` is ignored. Both the node features and
edge features are shared.
>>> bg = dgl.add_reverse_edges(g, copy_ndata=True,
copy_edata=True, ignore_bipartite=True)
>>> bg.edges(('user', 'wins', 'user'))
(tensor([0, 2, 0, 2, 2, 1, 1, 2, 1, 0]), tensor([1, 1, 2, 1, 0, 0, 2, 0, 2, 2]))
>>> bg.edges(('user', 'follows', 'user'))
(tensor([1, 2, 1, 0, 0, 0]), tensor([0, 0, 0, 1, 2, 1]))
>>> bg.edges(('user', 'plays', 'game'))
(th.tensor([1, 2, 1]), th.tensor([2, 1, 1]))
>>> bg.nodes['game'].data['hv']
tensor([0, 0, 0])
>>> bg.edges[('user', 'wins', 'user')].data['h']
th.tensor([0, 1, 2, 3, 4, 0, 1, 2, 3, 4])
"""
if readonly is not None:
dgl_warning("Parameter readonly is deprecated" \
"There will be no difference between readonly and non-readonly DGLGraph")
# get node cnt for each ntype
num_nodes_dict = {}
for ntype in g.ntypes:
num_nodes_dict[ntype] = g.number_of_nodes(ntype)
canonical_etypes = g.canonical_etypes
num_nodes_dict = {ntype: g.number_of_nodes(ntype) for ntype in g.ntypes}
# fast path
if ignore_bipartite is False:
subgs = {}
for c_etype in canonical_etypes:
if c_etype[0] != c_etype[2]:
assert False, "add_reverse_edges is not well defined for " \
"unidirectional bipartite graphs" \
", but {} is unidirectional bipartite".format(c_etype)
u, v = g.edges(form='uv', order='eid', etype=c_etype)
subgs[c_etype] = (F.cat([u, v], dim=0), F.cat([v, u], dim=0))
new_g = convert.heterograph(subgs, num_nodes_dict=num_nodes_dict)
else:
subgs = {}
for c_etype in canonical_etypes:
if c_etype[0] != c_etype[2]:
u, v = g.edges(form='uv', order='eid', etype=c_etype)
subgs[c_etype] = (u, v)
else:
u, v = g.edges(form='uv', order='eid', etype=c_etype)
subgs[c_etype] = (F.cat([u, v], dim=0), F.cat([v, u], dim=0))
new_g = convert.heterograph(subgs, num_nodes_dict=num_nodes_dict)
# handle features
if copy_ndata:
node_frames = utils.extract_node_subframes(g, None)
utils.set_new_frames(new_g, node_frames=node_frames)
if copy_edata:
# find indices
eids = []
for c_etype in canonical_etypes:
eid = F.copy_to(F.arange(0, g.number_of_edges(c_etype)), new_g.device)
if c_etype[0] != c_etype[2]:
eids.append(eid)
else:
eids.append(F.cat([eid, eid], 0))
edge_frames = utils.extract_edge_subframes(g, eids)
utils.set_new_frames(new_g, edge_frames=edge_frames)
return new_g
[docs]def line_graph(g, backtracking=True, shared=False):
"""Return the line graph of this graph.
The line graph ``L(G)`` of a given graph ``G`` is defined as another graph where
the nodes in ``L(G)`` maps to the edges in ``G``. For any pair of edges ``(u, v)``
and ``(v, w)`` in ``G``, the corresponding node of edge ``(u, v)`` in ``L(G)`` will
have an edge connecting to the corresponding node of edge ``(v, w)``.
Parameters
----------
g : DGLGraph
Input graph. Must be homogeneous.
backtracking : bool, optional
If False, the line graph node corresponding to edge ``(u, v)`` will not have
an edge connecting to the line graph node corresponding to edge ``(v, u)``.
Default: True.
shared : bool, optional
Whether to copy the edge features of the original graph as the node features
of the result line graph.
Returns
-------
G : DGLGraph
The line graph of this graph.
Notes
-----
* If :attr:`shared` is True, the node features of the resulting graph share the same
storage with the edge features of the input graph. Hence, users should try to
avoid in-place operations which will be visible to both graphs.
* The function supports input graph on GPU but copies it to CPU during computation.
* This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
Assume that the graph has the following adjacency matrix: ::
A = [[0, 0, 1],
[1, 0, 1],
[1, 1, 0]]
>>> g = dgl.graph(([0, 1, 1, 2, 2],[2, 0, 2, 0, 1]), 'user', 'follows')
>>> lg = g.line_graph()
>>> lg
Graph(num_nodes=5, num_edges=8,
ndata_schemes={}
edata_schemes={})
>>> lg.edges()
(tensor([0, 0, 1, 2, 2, 3, 4, 4]), tensor([3, 4, 0, 3, 4, 0, 1, 2]))
>>> lg = g.line_graph(backtracking=False)
>>> lg
Graph(num_nodes=5, num_edges=4,
ndata_schemes={}
edata_schemes={})
>>> lg.edges()
(tensor([0, 1, 2, 4]), tensor([4, 0, 3, 1]))
"""
assert g.is_homogeneous, \
'only homogeneous graph is supported'
dev = g.device
lg = DGLHeteroGraph(_CAPI_DGLHeteroLineGraph(g._graph.copy_to(nd.cpu()), backtracking))
lg = lg.to(dev)
if shared:
new_frames = utils.extract_edge_subframes(g, None)
utils.set_new_frames(lg, node_frames=new_frames)
return lg
DGLHeteroGraph.line_graph = utils.alias_func(line_graph)
[docs]def khop_adj(g, k):
"""Return the matrix of :math:`A^k` where :math:`A` is the adjacency matrix of the graph
:math:`g`.
The returned matrix is a 32-bit float dense matrix on CPU. The graph must be homogeneous.
Parameters
----------
g : DGLGraph
The input graph.
k : int
The :math:`k` in :math:`A^k`.
Returns
-------
Tensor
The returned tensor.
Examples
--------
>>> import dgl
>>> g = dgl.graph(([0,1,2,3,4,0,1,2,3,4], [0,1,2,3,4,1,2,3,4,0]))
>>> dgl.khop_adj(g, 1)
tensor([[1., 0., 0., 0., 1.],
[1., 1., 0., 0., 0.],
[0., 1., 1., 0., 0.],
[0., 0., 1., 1., 0.],
[0., 0., 0., 1., 1.]])
>>> dgl.khop_adj(g, 3)
tensor([[1., 0., 1., 3., 3.],
[3., 1., 0., 1., 3.],
[3., 3., 1., 0., 1.],
[1., 3., 3., 1., 0.],
[0., 1., 3., 3., 1.]])
"""
assert g.is_homogeneous, \
'only homogeneous graph is supported'
adj_k = g.adj(scipy_fmt=g.formats()['created'][0]) ** k
return F.tensor(adj_k.todense().astype(np.float32))
[docs]def khop_graph(g, k, copy_ndata=True):
"""Return the graph whose edges connect the :attr:`k`-hop neighbors of the original graph.
More specifically, an edge from node ``u`` and node ``v`` exists in the new graph if
and only if a path with length :attr:`k` exists from node ``u`` to node ``v`` in the
original graph.
The adjacency matrix of the returned graph is :math:`A^k`
(where :math:`A` is the adjacency matrix of :math:`g`).
Parameters
----------
g : DGLGraph
The input graph.
k : int
The :math:`k` in `k`-hop graph.
copy_ndata: bool, optional
If True, the node features of the new graph are copied from the
original graph.
If False, the new graph will not have any node features.
(Default: True)
Returns
-------
DGLGraph
The returned graph.
Notes
-----
If :attr:`copy_ndata` is True, the resulting graph will share the node feature
tensors with the input graph. Hence, users should try to avoid in-place operations
which will be visible to both graphs.
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
Below gives an easy example:
>>> import dgl
>>> g = dgl.graph(([0, 1], [1, 2]))
>>> g_2 = dgl.transform.khop_graph(g, 2)
>>> print(g_2.edges())
(tensor([0]), tensor([2]))
A more complicated example:
>>> import dgl
>>> g = dgl.graph(([0,1,2,3,4,0,1,2,3,4], [0,1,2,3,4,1,2,3,4,0]))
>>> dgl.khop_graph(g, 1)
DGLGraph(num_nodes=5, num_edges=10,
ndata_schemes={}
edata_schemes={})
>>> dgl.khop_graph(g, 3)
DGLGraph(num_nodes=5, num_edges=40,
ndata_schemes={}
edata_schemes={})
"""
assert g.is_homogeneous, \
'only homogeneous graph is supported'
n = g.number_of_nodes()
adj_k = g.adj(transpose=True, scipy_fmt=g.formats()['created'][0]) ** k
adj_k = adj_k.tocoo()
multiplicity = adj_k.data
row = np.repeat(adj_k.row, multiplicity)
col = np.repeat(adj_k.col, multiplicity)
# TODO(zihao): we should support creating multi-graph from scipy sparse matrix
# in the future.
new_g = convert.graph((row, col), num_nodes=n)
# handle ndata
if copy_ndata:
node_frames = utils.extract_node_subframes(g, None)
utils.set_new_frames(new_g, node_frames=node_frames)
return new_g
[docs]def reverse(g, copy_ndata=True, copy_edata=False, *, share_ndata=None, share_edata=None):
r"""Return a new graph with every edges being the reverse ones in the input graph.
The reverse (also called converse, transpose) of a graph with edges
:math:`(i_1, j_1), (i_2, j_2), \cdots` of type ``(U, E, V)`` is a new graph with edges
:math:`(j_1, i_1), (j_2, i_2), \cdots` of type ``(V, E, U)``.
The returned graph shares the data structure with the original graph, i.e. dgl.reverse
will not create extra storage for the reversed graph.
Parameters
----------
g : DGLGraph
The input graph.
copy_ndata: bool, optional
If True, the node features of the reversed graph are copied from the
original graph. If False, the reversed graph will not have any node features.
(Default: True)
copy_edata: bool, optional
If True, the edge features of the reversed graph are copied from the
original graph. If False, the reversed graph will not have any edge features.
(Default: False)
Return
------
DGLGraph
The reversed graph.
Notes
-----
If :attr:`copy_ndata` or :attr:`copy_edata` is True,
the resulting graph will share the node or edge feature
tensors with the input graph. Hence, users should try to avoid in-place operations
which will be visible to both graphs.
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
**Homogeneous graphs**
Create a graph to reverse.
>>> import dgl
>>> import torch as th
>>> g = dgl.graph((th.tensor([0, 1, 2]), th.tensor([1, 2, 0])))
>>> g.ndata['h'] = th.tensor([[0.], [1.], [2.]])
>>> g.edata['h'] = th.tensor([[3.], [4.], [5.]])
Reverse the graph.
>>> rg = dgl.reverse(g, copy_edata=True)
>>> rg.ndata['h']
tensor([[0.],
[1.],
[2.]])
The i-th edge in the reversed graph corresponds to the i-th edge in the
original graph. When :attr:`copy_edata` is True, they have the same features.
>>> rg.edges()
(tensor([1, 2, 0]), tensor([0, 1, 2]))
>>> rg.edata['h']
tensor([[3.],
[4.],
[5.]])
**Heterogenenous graphs**
>>> g = dgl.heterograph({
... ('user', 'follows', 'user'): (th.tensor([0, 2]), th.tensor([1, 2])),
... ('user', 'plays', 'game'): (th.tensor([1, 2, 1]), th.tensor([2, 1, 1]))
... })
>>> g.nodes['game'].data['hv'] = th.ones(3, 1)
>>> g.edges['plays'].data['he'] = th.zeros(3, 1)
The resulting graph will have edge types
``('user', 'follows', 'user)`` and ``('game', 'plays', 'user')``.
>>> rg = dgl.reverse(g, copy_ndata=True)
>>> rg
Graph(num_nodes={'game': 3, 'user': 3},
num_edges={('user', 'follows', 'user'): 2, ('game', 'plays', 'user'): 3},
metagraph=[('user', 'user'), ('game', 'user')])
>>> rg.edges(etype='follows')
(tensor([1, 2]), tensor([0, 2]))
>>> rg.edges(etype='plays')
(tensor([2, 1, 1]), tensor([1, 2, 1]))
>>> rg.nodes['game'].data['hv']
tensor([[1.],
[1.],
[1.]])
>>> rg.edges['plays'].data
{}
"""
if share_ndata is not None:
dgl_warning('share_ndata argument has been renamed to copy_ndata.')
copy_ndata = share_ndata
if share_edata is not None:
dgl_warning('share_edata argument has been renamed to copy_edata.')
copy_edata = share_edata
if g.is_block:
# TODO(0.5 release, xiangsx) need to handle BLOCK
# currently reversing a block results in undefined behavior
raise DGLError('Reversing a block graph is not supported.')
gidx = g._graph.reverse()
new_g = DGLHeteroGraph(gidx, g.ntypes, g.etypes)
# handle ndata
if copy_ndata:
# for each ntype
for ntype in g.ntypes:
new_g.nodes[ntype].data.update(g.nodes[ntype].data)
# handle edata
if copy_edata:
# for each etype
for utype, etype, vtype in g.canonical_etypes:
new_g.edges[vtype, etype, utype].data.update(
g.edges[utype, etype, vtype].data)
return new_g
DGLHeteroGraph.reverse = utils.alias_func(reverse)
def to_simple_graph(g):
"""Convert the graph to a simple graph with no multi-edge.
DEPRECATED: renamed to dgl.to_simple
Parameters
----------
g : DGLGraph
The input graph.
Returns
-------
DGLGraph
A simple graph.
Notes
-----
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
"""
dgl_warning('dgl.to_simple_graph is renamed to dgl.to_simple in v0.5.')
return to_simple(g)
def to_bidirected_stale(g, readonly=True):
"""NOTE: this function only works on the deprecated
:class:`dgl.DGLGraphStale` object.
Convert the graph to a bidirected graph.
The function generates a new graph with no node/edge feature.
If g has an edge for ``(u, v)`` but no edge for ``(v, u)``, then the
returned graph will have both ``(u, v)`` and ``(v, u)``.
If the input graph is a multigraph (there are multiple edges from node u to node v),
the returned graph isn't well defined.
Parameters
----------
g : DGLGraphStale
The input graph.
readonly : bool
Whether the returned bidirected graph is readonly or not.
(Default: True)
Notes
-----
Please make sure g is a simple graph, otherwise the return value is undefined.
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Returns
-------
DGLGraph
Examples
--------
The following two examples use PyTorch backend, one for non-multi graph
and one for multi-graph.
>>> g = dgl._deprecate.graph.DGLGraph()
>>> g.add_nodes(2)
>>> g.add_edges([0, 0], [0, 1])
>>> bg1 = dgl.to_bidirected_stale(g)
>>> bg1.edges()
(tensor([0, 1, 0]), tensor([0, 0, 1]))
"""
if readonly:
newgidx = _CAPI_DGLToBidirectedImmutableGraph(g._graph)
else:
newgidx = _CAPI_DGLToBidirectedMutableGraph(g._graph)
return DGLGraphStale(newgidx)
[docs]def laplacian_lambda_max(g):
"""Return the largest eigenvalue of the normalized symmetric Laplacian of a graph.
If the graph is batched from multiple graphs, return the list of the largest eigenvalue
for each graph instead.
Parameters
----------
g : DGLGraph
The input graph, it must be a bi-directed homogeneous graph, i.e., every edge
should have an accompanied reverse edge in the graph.
The graph can be batched from multiple graphs.
Returns
-------
list[float]
A list where the i-th item indicates the largest eigenvalue
of i-th graph in :attr:`g`.
In the case where the function takes a single graph, it will return a list
consisting of a single element.
Examples
--------
>>> import dgl
>>> g = dgl.graph(([0, 1, 2, 3, 4, 0, 1, 2, 3, 4], [1, 2, 3, 4, 0, 4, 0, 1, 2, 3]))
>>> dgl.laplacian_lambda_max(g)
[1.809016994374948]
"""
g_arr = batch.unbatch(g)
rst = []
for g_i in g_arr:
n = g_i.number_of_nodes()
adj = g_i.adj(scipy_fmt=g_i.formats()['created'][0]).astype(float)
norm = sparse.diags(F.asnumpy(g_i.in_degrees()).clip(1) ** -0.5, dtype=float)
laplacian = sparse.eye(n) - norm * adj * norm
rst.append(sparse.linalg.eigs(laplacian, 1, which='LM',
return_eigenvectors=False)[0].real)
return rst
[docs]def add_nodes(g, num, data=None, ntype=None):
r"""Add the given number of nodes to the graph and return a new graph.
The new nodes will have IDs starting from ``g.num_nodes(ntype)``.
Parameters
----------
num : int
The number of nodes to add.
data : dict[str, Tensor], optional
Feature data of the added nodes. The keys are feature names
while the values are feature data.
ntype : str, optional
The node type name. Can be omitted if there is
only one type of nodes in the graph.
Return
------
DGLGraph
The graph with newly added nodes.
Notes
-----
* For features in :attr:`g` but not in :attr:`data`,
DGL assigns zero features for the newly added nodes.
* For feature in :attr:`data` but not in :attr:`g`, DGL assigns zero features
for the existing nodes in the graph.
* This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
**Homogeneous Graphs**
>>> g = dgl.graph((torch.tensor([0, 1]), torch.tensor([1, 2])))
>>> g.num_nodes()
3
>>> g = dgl.add_nodes(g, 2)
>>> g.num_nodes()
5
If the graph has some node features and new nodes are added without
features, their features will be filled with zeros.
>>> g.ndata['h'] = torch.ones(5, 1)
>>> g = dgl.add_nodes(g, 1)
>>> g.ndata['h']
tensor([[1.], [1.], [1.], [1.], [1.], [0.]])
Assign features for the new nodes.
>>> g = dgl.add_nodes(g, 1, {'h': torch.ones(1, 1), 'w': torch.ones(1, 1)})
>>> g.ndata['h']
tensor([[1.], [1.], [1.], [1.], [1.], [0.], [1.]])
Since :attr:`data` contains new feature fields, the features for existing nodes
will be filled with zeros.
>>> g.ndata['w']
tensor([[0.], [0.], [0.], [0.], [0.], [0.], [1.]])
**Heterogeneous Graphs**
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): (torch.tensor([0, 1, 1, 2]),
... torch.tensor([0, 0, 1, 1])),
... ('developer', 'develops', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))
... })
>>> g.num_nodes('user')
3
>>> g = dgl.add_nodes(g, 2, ntype='user')
>>> g.num_nodes('user')
5
See Also
--------
remove_nodes
add_edges
remove_edges
"""
g = g.clone()
g.add_nodes(num, data=data, ntype=ntype)
return g
[docs]def add_edges(g, u, v, data=None, etype=None):
r"""Add the edges to the graph and return a new graph.
The i-th new edge will be from ``u[i]`` to ``v[i]``. The IDs of the new
edges will start from ``g.num_edges(etype)``.
Parameters
----------
u : int, Tensor or iterable[int]
Source node IDs, ``u[i]`` gives the source node for the i-th new edge.
v : int, Tensor or iterable[int]
Destination node IDs, ``v[i]`` gives the destination node for the i-th new edge.
data : dict[str, Tensor], optional
Feature data of the added edges. The keys are feature names
while the values are feature data.
etype : str or (str, str, str), optional
The type names of the edges. The allowed type name formats are:
* ``(str, str, str)`` for source node type, edge type and destination node type.
* or one ``str`` edge type name if the name can uniquely identify a
triplet format in the graph.
Can be omitted if the graph has only one type of edges.
Return
------
DGLGraph
The graph with newly added edges.
Notes
-----
* If the end nodes of the given edges do not exist in :attr:`g`,
:func:`dgl.add_nodes` is invoked to add those nodes.
The node features of the new nodes will be filled with zeros.
* For features in :attr:`g` but not in :attr:`data`,
DGL assigns zero features for the newly added nodes.
* For feature in :attr:`data` but not in :attr:`g`, DGL assigns zero features
for the existing nodes in the graph.
* This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
**Homogeneous Graphs**
>>> g = dgl.graph((torch.tensor([0, 1]), torch.tensor([1, 2])))
>>> g.num_edges()
2
>>> g = dgl.add_edges(g, torch.tensor([1, 3]), torch.tensor([0, 1]))
>>> g.num_edges()
4
Since ``u`` or ``v`` contains a non-existing node ID, the nodes are
added implicitly.
>>> g.num_nodes()
4
If the graph has some edge features and new edges are added without
features, their features will be filled with zeros.
>>> g.edata['h'] = torch.ones(4, 1)
>>> g = dgl.add_edges(g, torch.tensor([1]), torch.tensor([1]))
>>> g.edata['h']
tensor([[1.], [1.], [1.], [1.], [0.]])
You can also assign features for the new edges in adding new edges.
>>> g = dgl.add_edges(g, torch.tensor([0, 0]), torch.tensor([2, 2]),
... {'h': torch.tensor([[1.], [2.]]), 'w': torch.ones(2, 1)})
>>> g.edata['h']
tensor([[1.], [1.], [1.], [1.], [0.], [1.], [2.]])
Since :attr:`data` contains new feature fields, the features for old edges
will be filled with zeros.
>>> g.edata['w']
tensor([[0.], [0.], [0.], [0.], [0.], [1.], [1.]])
**Heterogeneous Graphs**
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): (torch.tensor([0, 1, 1, 2]),
... torch.tensor([0, 0, 1, 1])),
... ('developer', 'develops', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))
... })
>>> g.number_of_edges('plays')
4
>>> g = dgl.add_edges(g, torch.tensor([3]), torch.tensor([3]), etype='plays')
>>> g.number_of_edges('plays')
5
See Also
--------
add_nodes
remove_nodes
remove_edges
"""
g = g.clone()
g.add_edges(u, v, data=data, etype=etype)
return g
[docs]def remove_edges(g, eids, etype=None, store_ids=False):
r"""Remove the specified edges and return a new graph.
Also delete the features of the edges. The edges must exist in the graph.
The resulting graph has the same number of the nodes as the input one,
even if some nodes become isolated after the the edge removal.
Parameters
----------
eids : int, Tensor, iterable[int]
The IDs of the edges to remove.
etype : str or (str, str, str), optional
The type names of the edges. The allowed type name formats are:
* ``(str, str, str)`` for source node type, edge type and destination node type.
* or one ``str`` edge type name if the name can uniquely identify a
triplet format in the graph.
Can be omitted if the graph has only one type of edges.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted nodes and edges in the ``ndata``
and ``edata`` of the resulting graph under name ``dgl.NID`` and ``dgl.EID``,
respectively.
Return
------
DGLGraph
The graph with edges deleted.
Notes
-----
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
>>> import dgl
>>> import torch
**Homogeneous Graphs**
>>> g = dgl.graph((torch.tensor([0, 0, 2]), torch.tensor([0, 1, 2])))
>>> g.edata['he'] = torch.arange(3).float().reshape(-1, 1)
>>> g = dgl.remove_edges(g, torch.tensor([0, 1]))
>>> g
Graph(num_nodes=3, num_edges=1,
ndata_schemes={}
edata_schemes={'he': Scheme(shape=(1,), dtype=torch.float32)})
>>> g.edges('all')
(tensor([2]), tensor([2]), tensor([0]))
>>> g.edata['he']
tensor([[2.]])
**Heterogeneous Graphs**
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): (torch.tensor([0, 1, 1, 2]),
... torch.tensor([0, 0, 1, 1])),
... ('developer', 'develops', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))
... })
>>> g = dgl.remove_edges(g, torch.tensor([0, 1]), 'plays')
>>> g.edges('all', etype='plays')
(tensor([0, 1]), tensor([0, 0]), tensor([0, 1]))
See Also
--------
add_nodes
add_edges
remove_nodes
"""
g = g.clone()
g.remove_edges(eids, etype=etype, store_ids=store_ids)
return g
[docs]def remove_nodes(g, nids, ntype=None, store_ids=False):
r"""Remove the specified nodes and return a new graph.
Also delete the features. Edges that connect from/to the nodes will be
removed as well. After the removal, DGL re-labels the remaining nodes and edges
with IDs from 0.
Parameters
----------
nids : int, Tensor, iterable[int]
The nodes to be removed.
ntype : str, optional
The type of the nodes to remove. Can be omitted if there is
only one node type in the graph.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted nodes and edges in the ``ndata``
and ``edata`` of the resulting graph under name ``dgl.NID`` and ``dgl.EID``,
respectively.
Return
------
DGLGraph
The graph with nodes deleted.
Notes
-----
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
>>> import dgl
>>> import torch
**Homogeneous Graphs**
>>> g = dgl.graph((torch.tensor([0, 0, 2]), torch.tensor([0, 1, 2])))
>>> g.ndata['hv'] = torch.arange(3).float().reshape(-1, 1)
>>> g.edata['he'] = torch.arange(3).float().reshape(-1, 1)
>>> g = dgl.remove_nodes(g, torch.tensor([0, 1]))
>>> g
Graph(num_nodes=1, num_edges=1,
ndata_schemes={'hv': Scheme(shape=(1,), dtype=torch.float32)}
edata_schemes={'he': Scheme(shape=(1,), dtype=torch.float32)})
>>> g.ndata['hv']
tensor([[2.]])
>>> g.edata['he']
tensor([[2.]])
**Heterogeneous Graphs**
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): (torch.tensor([0, 1, 1, 2]),
... torch.tensor([0, 0, 1, 1])),
... ('developer', 'develops', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))
... })
>>> g = dgl.remove_nodes(g, torch.tensor([0, 1]), ntype='game')
>>> g.num_nodes('user')
3
>>> g.num_nodes('game')
0
>>> g.num_edges('plays')
0
See Also
--------
add_nodes
add_edges
remove_edges
"""
g = g.clone()
g.remove_nodes(nids, ntype=ntype, store_ids=store_ids)
return g
[docs]def add_self_loop(g, etype=None):
r"""Add self-loops for each node in the graph and return a new graph.
Parameters
----------
g : DGLGraph
The graph.
etype : str or (str, str, str), optional
The type names of the edges. The allowed type name formats are:
* ``(str, str, str)`` for source node type, edge type and destination node type.
* or one ``str`` edge type name if the name can uniquely identify a
triplet format in the graph.
Can be omitted if the graph has only one type of edges.
Return
------
DGLGraph
The graph with self-loops.
Notes
-----
* The function only supports homogeneous graphs or heterogeneous graphs but
the relation graph specified by the :attr:`etype` argument is homogeneous.
* The function adds self-loops regardless of whether they already exist or not.
If one wishes to have exactly one self-loop for every node,
call :func:`remove_self_loop` before invoking :func:`add_self_loop`.
* Features of the new edges (self-loop edges) will be filled with zeros.
* This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
>>> import dgl
>>> import torch
**Homogeneous Graphs**
>>> g = dgl.graph((torch.tensor([0, 0, 2]), torch.tensor([2, 1, 0])))
>>> g.ndata['hv'] = torch.arange(3).float().reshape(-1, 1)
>>> g.edata['he'] = torch.arange(3).float().reshape(-1, 1)
>>> g = dgl.add_self_loop(g)
>>> g
Graph(num_nodes=3, num_edges=6,
ndata_schemes={'hv': Scheme(shape=(1,), dtype=torch.float32)}
edata_schemes={'he': Scheme(shape=(1,), dtype=torch.float32)})
>>> g.edata['he']
tensor([[0.],
[1.],
[2.],
[0.],
[0.],
[0.]])
**Heterogeneous Graphs**
>>> g = dgl.heterograph({
... ('user', 'follows', 'user'): (torch.tensor([1, 2]),
... torch.tensor([0, 1])),
... ('user', 'plays', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))})
>>> g = dgl.add_self_loop(g, etype='follows')
>>> g
Graph(num_nodes={'user': 3, 'game': 2},
num_edges={('user', 'plays', 'game'): 2, ('user', 'follows', 'user'): 5},
metagraph=[('user', 'user'), ('user', 'game')])
"""
etype = g.to_canonical_etype(etype)
if etype[0] != etype[2]:
raise DGLError(
'add_self_loop does not support unidirectional bipartite graphs: {}.' \
'Please make sure the types of head node and tail node are identical.' \
''.format(etype))
nodes = g.nodes(etype[0])
new_g = add_edges(g, nodes, nodes, etype=etype)
return new_g
DGLHeteroGraph.add_self_loop = utils.alias_func(add_self_loop)
[docs]def remove_self_loop(g, etype=None):
r""" Remove self-loops for each node in the graph and return a new graph.
Parameters
----------
g : DGLGraph
The graph.
etype : str or (str, str, str), optional
The type names of the edges. The allowed type name formats are:
* ``(str, str, str)`` for source node type, edge type and destination node type.
* or one ``str`` edge type name if the name can uniquely identify a
triplet format in the graph.
Can be omitted if the graph has only one type of edges.
Notes
-----
If a node has multiple self-loops, remove them all. Do nothing for nodes without
self-loops.
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
---------
>>> import dgl
>>> import torch
**Homogeneous Graphs**
>>> g = dgl.graph((torch.tensor([0, 0, 0, 1]), torch.tensor([1, 0, 0, 2])))
>>> g.edata['he'] = torch.arange(4).float().reshape(-1, 1)
>>> g = dgl.remove_self_loop(g)
>>> g
Graph(num_nodes=3, num_edges=2,
edata_schemes={'he': Scheme(shape=(2,), dtype=torch.float32)})
>>> g.edata['he']
tensor([[0.],[3.]])
**Heterogeneous Graphs**
>>> g = dgl.heterograph({
... ('user', 'follows', 'user'): (torch.tensor([0, 1, 1, 1, 2]),
... torch.tensor([0, 0, 1, 1, 1])),
... ('user', 'plays', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))
... })
>>> g = dgl.remove_self_loop(g, etype='follows')
>>> g.num_nodes('user')
3
>>> g.num_nodes('game')
2
>>> g.num_edges('follows')
2
>>> g.num_edges('plays')
2
See Also
--------
add_self_loop
"""
etype = g.to_canonical_etype(etype)
if etype[0] != etype[2]:
raise DGLError(
'remove_self_loop does not support unidirectional bipartite graphs: {}.' \
'Please make sure the types of head node and tail node are identical.' \
''.format(etype))
u, v = g.edges(form='uv', order='eid', etype=etype)
self_loop_eids = F.tensor(F.nonzero_1d(u == v), dtype=F.dtype(u))
new_g = remove_edges(g, self_loop_eids, etype=etype)
return new_g
DGLHeteroGraph.remove_self_loop = utils.alias_func(remove_self_loop)
[docs]def compact_graphs(graphs, always_preserve=None, copy_ndata=True, copy_edata=True):
"""Given a list of graphs with the same set of nodes, find and eliminate the common
isolated nodes across all graphs.
This function requires the graphs to have the same set of nodes (i.e. the node types
must be the same, and the number of nodes of each node type must be the same). The
metagraph does not have to be the same.
It finds all the nodes that have zero in-degree and zero out-degree in all the given
graphs, and eliminates them from all the graphs.
Useful for graph sampling where you have a giant graph but you only wish to perform
message passing on a smaller graph with a (tiny) subset of nodes.
Parameters
----------
graphs : DGLGraph or list[DGLGraph]
The graph, or list of graphs.
All graphs must be on CPU.
All graphs must have the same set of nodes.
always_preserve : Tensor or dict[str, Tensor], optional
If a dict of node types and node ID tensors is given, the nodes of given
node types would not be removed, regardless of whether they are isolated.
If a Tensor is given, DGL assumes that all the graphs have one (same) node type.
copy_ndata: bool, optional
If True, the node features of the returned graphs are copied from the
original graphs.
If False, the returned graphs will not have any node features.
(Default: True)
copy_edata: bool, optional
If True, the edge features of the reversed graph are copied from the
original graph.
If False, the reversed graph will not have any edge features.
(Default: True)
Returns
-------
DGLGraph or list[DGLGraph]
The compacted graph or list of compacted graphs.
Each returned graph would have a feature ``dgl.NID`` containing the mapping
of node IDs for each type from the compacted graph(s) to the original graph(s).
Note that the mapping is the same for all the compacted graphs.
All the returned graphs are on CPU.
Notes
-----
This function currently requires that the same node type of all graphs should have
the same node type ID, i.e. the node types are *ordered* the same.
If :attr:`copy_edata` is True, the resulting graph will share the edge feature
tensors with the input graph. Hence, users should try to avoid in-place operations
which will be visible to both graphs.
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
The following code constructs a bipartite graph with 20 users and 10 games, but
only user #1 and #3, as well as game #3 and #5, have connections:
>>> g = dgl.heterograph({('user', 'plays', 'game'): ([1, 3], [3, 5])},
>>> {'user': 20, 'game': 10})
The following would compact the graph above to another bipartite graph with only
two users and two games.
>>> new_g, induced_nodes = dgl.compact_graphs(g)
>>> induced_nodes
{'user': tensor([1, 3]), 'game': tensor([3, 5])}
The mapping tells us that only user #1 and #3 as well as game #3 and #5 are kept.
Furthermore, the first user and second user in the compacted graph maps to
user #1 and #3 in the original graph. Games are similar.
One can verify that the edge connections are kept the same in the compacted graph.
>>> new_g.edges(form='all', order='eid', etype='plays')
(tensor([0, 1]), tensor([0, 1]), tensor([0, 1]))
When compacting multiple graphs, nodes that do not have any connections in any
of the given graphs are removed. So if you compact ``g`` and the following ``g2``
graphs together:
>>> g2 = dgl.heterograph({('user', 'plays', 'game'): ([1, 6], [6, 8])},
>>> {'user': 20, 'game': 10})
>>> (new_g, new_g2), induced_nodes = dgl.compact_graphs([g, g2])
>>> induced_nodes
{'user': tensor([1, 3, 6]), 'game': tensor([3, 5, 6, 8])}
Then one can see that user #1 from both graphs, users #3 from the first graph, as
well as user #6 from the second graph, are kept. Games are similar.
Similarly, one can also verify the connections:
>>> new_g.edges(form='all', order='eid', etype='plays')
(tensor([0, 1]), tensor([0, 1]), tensor([0, 1]))
>>> new_g2.edges(form='all', order='eid', etype='plays')
(tensor([0, 2]), tensor([2, 3]), tensor([0, 1]))
"""
return_single = False
if not isinstance(graphs, Iterable):
graphs = [graphs]
return_single = True
if len(graphs) == 0:
return []
if graphs[0].is_block:
raise DGLError('Compacting a block graph is not allowed.')
assert all(g.device == F.cpu() for g in graphs), 'all the graphs must be on CPU'
# Ensure the node types are ordered the same.
# TODO(BarclayII): we ideally need to remove this constraint.
ntypes = graphs[0].ntypes
idtype = graphs[0].idtype
device = graphs[0].device
for g in graphs:
assert ntypes == g.ntypes, \
("All graphs should have the same node types in the same order, got %s and %s" %
ntypes, g.ntypes)
assert idtype == g.idtype, "Expect graph data type to be {}, but got {}".format(
idtype, g.idtype)
assert device == g.device, "Expect graph device to be {}, but got {}".format(
device, g.device)
# Process the dictionary or tensor of "always preserve" nodes
if always_preserve is None:
always_preserve = {}
elif not isinstance(always_preserve, Mapping):
if len(ntypes) > 1:
raise ValueError("Node type must be given if multiple node types exist.")
always_preserve = {ntypes[0]: always_preserve}
always_preserve = utils.prepare_tensor_dict(graphs[0], always_preserve, 'always_preserve')
always_preserve_nd = []
for ntype in ntypes:
nodes = always_preserve.get(ntype, None)
if nodes is None:
nodes = F.copy_to(F.tensor([], idtype), device)
always_preserve_nd.append(F.to_dgl_nd(nodes))
# Compact and construct heterographs
new_graph_indexes, induced_nodes = _CAPI_DGLCompactGraphs(
[g._graph for g in graphs], always_preserve_nd)
induced_nodes = [F.from_dgl_nd(nodes) for nodes in induced_nodes]
new_graphs = [
DGLHeteroGraph(new_graph_index, graph.ntypes, graph.etypes)
for new_graph_index, graph in zip(new_graph_indexes, graphs)]
if copy_ndata:
for g, new_g in zip(graphs, new_graphs):
node_frames = utils.extract_node_subframes(g, induced_nodes)
utils.set_new_frames(new_g, node_frames=node_frames)
if copy_edata:
for g, new_g in zip(graphs, new_graphs):
edge_frames = utils.extract_edge_subframes(g, None)
utils.set_new_frames(new_g, edge_frames=edge_frames)
if return_single:
new_graphs = new_graphs[0]
return new_graphs
[docs]def to_block(g, dst_nodes=None, include_dst_in_src=True):
"""Convert a graph into a bipartite-structured *block* for message passing.
A block is a graph consisting of two sets of nodes: the
*source* nodes and *destination* nodes. The source and destination nodes can have multiple
node types. All the edges connect from source nodes to destination nodes.
Specifically, the source nodes and destination nodes will have the same node types as the
ones in the original graph. DGL maps each edge ``(u, v)`` with edge type
``(utype, etype, vtype)`` in the original graph to the edge with type
``etype`` connecting from node ID ``u`` of type ``utype`` in the source side to node
ID ``v`` of type ``vtype`` in the destination side.
For blocks returned by :func:`to_block`, the destination nodes of the block will only
contain the nodes that have at least one inbound edge of any type. The source nodes
of the block will only contain the nodes that appear in the destination nodes, as well
as the nodes that have at least one outbound edge connecting to one of the destination nodes.
The destination nodes are specified by the :attr:`dst_nodes` argument if it is not None.
Parameters
----------
graph : DGLGraph
The graph.
dst_nodes : Tensor or dict[str, Tensor], optional
The list of destination nodes.
If a tensor is given, the graph must have only one node type.
If given, it must be a superset of all the nodes that have at least one inbound
edge. An error will be raised otherwise.
include_dst_in_src : bool
If False, do not include destination nodes in source nodes.
(Default: True)
Returns
-------
DGLBlock
The new graph describing the block.
The node IDs induced for each type in both sides would be stored in feature
``dgl.NID``.
The edge IDs induced for each type would be stored in feature ``dgl.EID``.
Raises
------
DGLError
If :attr:`dst_nodes` is specified but it is not a superset of all the nodes that
have at least one inbound edge.
If :attr:`dst_nodes` is not None, and :attr:`g` and :attr:`dst_nodes`
are not in the same context.
Notes
-----
:func:`to_block` is most commonly used in customizing neighborhood sampling
for stochastic training on a large graph. Please refer to the user guide
:ref:`guide-minibatch` for a more thorough discussion about the methodology
of stochastic training.
See also :func:`create_block` for more flexible construction of blocks.
Examples
--------
Converting a homogeneous graph to a block as described above:
>>> g = dgl.graph(([1, 2], [2, 3]))
>>> block = dgl.to_block(g, torch.LongTensor([3, 2]))
The destination nodes would be exactly the same as the ones given: [3, 2].
>>> induced_dst = block.dstdata[dgl.NID]
>>> induced_dst
tensor([3, 2])
The first few source nodes would also be exactly the same as
the ones given. The rest of the nodes are the ones necessary for message passing
into nodes 3, 2. This means that the node 1 would be included.
>>> induced_src = block.srcdata[dgl.NID]
>>> induced_src
tensor([3, 2, 1])
You can notice that the first two nodes are identical to the given nodes as well as
the destination nodes.
The induced edges can also be obtained by the following:
>>> block.edata[dgl.EID]
tensor([2, 1])
This indicates that edge (2, 3) and (1, 2) are included in the result graph. You can
verify that the first edge in the block indeed maps to the edge (2, 3), and the
second edge in the block indeed maps to the edge (1, 2):
>>> src, dst = block.edges(order='eid')
>>> induced_src[src], induced_dst[dst]
(tensor([2, 1]), tensor([3, 2]))
The destination nodes specified must be a superset of the nodes that have edges connecting
to them. For example, the following will raise an error since the destination nodes
does not contain node 3, which has an edge connecting to it.
>>> g = dgl.graph(([1, 2], [2, 3]))
>>> dgl.to_block(g, torch.LongTensor([2])) # error
Converting a heterogeneous graph to a block is similar, except that when specifying
the destination nodes, you have to give a dict:
>>> g = dgl.heterograph({('A', '_E', 'B'): ([1, 2], [2, 3])})
If you don't specify any node of type A on the destination side, the node type ``A``
in the block would have zero nodes on the destination side.
>>> block = dgl.to_block(g, {'B': torch.LongTensor([3, 2])})
>>> block.number_of_dst_nodes('A')
0
>>> block.number_of_dst_nodes('B')
2
>>> block.dstnodes['B'].data[dgl.NID]
tensor([3, 2])
The source side would contain all the nodes on the destination side:
>>> block.srcnodes['B'].data[dgl.NID]
tensor([3, 2])
As well as all the nodes that have connections to the nodes on the destination side:
>>> block.srcnodes['A'].data[dgl.NID]
tensor([2, 1])
See also
--------
create_block
"""
if dst_nodes is None:
# Find all nodes that appeared as destinations
dst_nodes = defaultdict(list)
for etype in g.canonical_etypes:
_, dst = g.edges(etype=etype)
dst_nodes[etype[2]].append(dst)
dst_nodes = {ntype: F.unique(F.cat(values, 0)) for ntype, values in dst_nodes.items()}
elif not isinstance(dst_nodes, Mapping):
# dst_nodes is a Tensor, check if the g has only one type.
if len(g.ntypes) > 1:
raise DGLError(
'Graph has more than one node type; please specify a dict for dst_nodes.')
dst_nodes = {g.ntypes[0]: dst_nodes}
dst_node_ids = [
utils.toindex(dst_nodes.get(ntype, []), g._idtype_str).tousertensor(
ctx=F.to_backend_ctx(g._graph.ctx))
for ntype in g.ntypes]
dst_node_ids_nd = [F.to_dgl_nd(nodes) for nodes in dst_node_ids]
for d in dst_node_ids_nd:
if g._graph.ctx != d.ctx:
raise ValueError('g and dst_nodes need to have the same context.')
new_graph_index, src_nodes_nd, induced_edges_nd = _CAPI_DGLToBlock(
g._graph, dst_node_ids_nd, include_dst_in_src)
# The new graph duplicates the original node types to SRC and DST sets.
new_ntypes = (g.ntypes, g.ntypes)
new_graph = DGLBlock(new_graph_index, new_ntypes, g.etypes)
assert new_graph.is_unibipartite # sanity check
src_node_ids = [F.from_dgl_nd(src) for src in src_nodes_nd]
edge_ids = [F.from_dgl_nd(eid) for eid in induced_edges_nd]
node_frames = utils.extract_node_subframes_for_block(g, src_node_ids, dst_node_ids)
edge_frames = utils.extract_edge_subframes(g, edge_ids)
utils.set_new_frames(new_graph, node_frames=node_frames, edge_frames=edge_frames)
return new_graph
def _coalesce_edge_frame(g, edge_maps, counts, aggregator):
r"""Coalesce edge features of duplicate edges via given aggregator in g.
Parameters
----------
g : DGLGraph
The input graph.
edge_maps : List[Tensor]
The edge mapping corresponding to each edge type in g.
counts : List[Tensor]
The number of duplicated edges from the original graph for each edge type.
aggregator : str
Indicates how to coalesce edge features, could be ``arbitrary``, ``sum``
or ``mean``.
Returns
-------
List[Frame]
The frames corresponding to each edge type.
"""
if aggregator == 'arbitrary':
eids = []
for i in range(len(g.canonical_etypes)):
feat_idx = F.asnumpy(edge_maps[i])
_, indices = np.unique(feat_idx, return_index=True)
eids.append(F.zerocopy_from_numpy(indices))
edge_frames = utils.extract_edge_subframes(g, eids)
elif aggregator in ['sum', 'mean']:
edge_frames = []
for i in range(len(g.canonical_etypes)):
feat_idx = edge_maps[i]
_, indices = np.unique(F.asnumpy(feat_idx), return_index=True)
_num_rows = len(indices)
_data = {}
for key, col in g._edge_frames[i]._columns.items():
data = col.data
new_data = F.scatter_add(data, feat_idx, _num_rows)
if aggregator == 'mean':
norm = F.astype(counts[i], F.dtype(data))
norm = F.reshape(norm, (F.shape(norm)[0],) + (1,) * (F.ndim(data) - 1))
new_data /= norm
_data[key] = new_data
newf = Frame(data=_data, num_rows=_num_rows)
edge_frames.append(newf)
else:
raise DGLError("Aggregator {} not regonized, cannot coalesce edge feature in the "
"specified way".format(aggregator))
return edge_frames
[docs]def to_simple(g,
return_counts='count',
writeback_mapping=False,
copy_ndata=True,
copy_edata=False,
aggregator='arbitrary'):
r"""Convert a graph to a simple graph without parallel edges and return.
For a heterogeneous graph with multiple edge types, DGL treats edges with the same
edge type and endpoints as parallel edges and removes them.
Optionally, one can get the the number of parallel edges by specifying the
:attr:`return_counts` argument. To get the a mapping from the edge IDs in the
input graph to the edge IDs in the resulting graph, set :attr:`writeback_mapping`
to true.
Parameters
----------
g : DGLGraph
The input graph. Must be on CPU.
return_counts : str, optional
If given, the count of each edge in the original graph
will be stored as edge features under the name
``return_counts``. The old features with the same name will be replaced.
(Default: "count")
writeback_mapping: bool, optional
If True, return an extra write-back mapping for each edge
type. The write-back mapping is a tensor recording
the mapping from the edge IDs in the input graph to
the edge IDs in the result graph. If the graph is
heterogeneous, DGL returns a dictionary of edge types and such
tensors.
If False, only the simple graph is returned.
(Default: False)
copy_ndata: bool, optional
If True, the node features of the simple graph are copied
from the original graph.
If False, the simple graph will not have any node features.
(Default: True)
copy_edata: bool, optional
If True, the edge features of the simple graph are copied
from the original graph. If there exists duplicate edges between
two nodes (u, v), the feature of the edge is the aggregation
of edge feature of duplicate edges.
If False, the simple graph will not have any edge features.
(Default: False)
aggregator: str, optional
Indicate how to coalesce edge feature of duplicate edges.
If ``arbitrary``, select one of the duplicate edges' feature.
If ``sum``, compute the summation of duplicate edges' feature.
If ``mean``, compute the average of duplicate edges' feature.
(Default: ``arbitrary``)
Returns
-------
DGLGraph
The graph.
tensor or dict of tensor
The writeback mapping. Only when ``writeback_mapping`` is True.
Notes
-----
If :attr:`copy_ndata` is True, the resulting graph will share the node feature
tensors with the input graph. Hence, users should try to avoid in-place operations
which will be visible to both graphs.
This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
**Homogeneous Graphs**
Create a graph for demonstrating to_simple API.
In the original graph, there are multiple edges between 1 and 2.
>>> import dgl
>>> import torch as th
>>> g = dgl.graph((th.tensor([0, 1, 2, 1]), th.tensor([1, 2, 0, 2])))
>>> g.ndata['h'] = th.tensor([[0.], [1.], [2.]])
>>> g.edata['h'] = th.tensor([[3.], [4.], [5.], [6.]])
Convert the graph to a simple graph. The return counts is
stored in the edge feature 'cnt' and the writeback mapping
is returned in a tensor.
>>> sg, wm = dgl.to_simple(g, return_counts='cnt', writeback_mapping=True)
>>> sg.ndata['h']
tensor([[0.],
[1.],
[2.]])
>>> u, v, eid = sg.edges(form='all')
>>> u
tensor([0, 1, 2])
>>> v
tensor([1, 2, 0])
>>> eid
tensor([0, 1, 2])
>>> sg.edata['cnt']
tensor([1, 2, 1])
>>> wm
tensor([0, 1, 2, 1])
>>> 'h' in g.edata
False
**Heterogeneous Graphs**
>>> g = dgl.heterograph({
... ('user', 'wins', 'user'): (th.tensor([0, 2, 0, 2, 2]), th.tensor([1, 1, 2, 1, 0])),
... ('user', 'plays', 'game'): (th.tensor([1, 2, 1]), th.tensor([2, 1, 1]))
... })
>>> g.nodes['game'].data['hv'] = th.ones(3, 1)
>>> g.edges['plays'].data['he'] = th.zeros(3, 1)
The return counts is stored in the default edge feature 'count' for each edge type.
>>> sg, wm = dgl.to_simple(g, copy_ndata=False, writeback_mapping=True)
>>> sg
Graph(num_nodes={'game': 3, 'user': 3},
num_edges={('user', 'wins', 'user'): 4, ('game', 'plays', 'user'): 3},
metagraph=[('user', 'user'), ('game', 'user')])
>>> sg.edges(etype='wins')
(tensor([0, 2, 0, 2]), tensor([1, 1, 2, 0]))
>>> wm[('user', 'wins', 'user')]
tensor([0, 1, 2, 1, 3])
>>> sg.edges(etype='plays')
(tensor([2, 1, 1]), tensor([1, 2, 1]))
>>> wm[('user', 'plays', 'game')]
tensor([0, 1, 2])
>>> 'hv' in sg.nodes['game'].data
False
>>> 'he' in sg.edges['plays'].data
False
>>> sg.edata['count']
{('user', 'wins', 'user'): tensor([1, 2, 1, 1])
('user', 'plays', 'game'): tensor([1, 1, 1])}
"""
assert g.device == F.cpu(), 'the graph must be on CPU'
if g.is_block:
raise DGLError('Cannot convert a block graph to a simple graph.')
simple_graph_index, counts, edge_maps = _CAPI_DGLToSimpleHetero(g._graph)
simple_graph = DGLHeteroGraph(simple_graph_index, g.ntypes, g.etypes)
counts = [F.from_dgl_nd(count) for count in counts]
edge_maps = [F.from_dgl_nd(edge_map) for edge_map in edge_maps]
if copy_ndata:
node_frames = utils.extract_node_subframes(g, None)
utils.set_new_frames(simple_graph, node_frames=node_frames)
if copy_edata:
new_edge_frames = _coalesce_edge_frame(g, edge_maps, counts, aggregator)
utils.set_new_frames(simple_graph, edge_frames=new_edge_frames)
if return_counts is not None:
for count, canonical_etype in zip(counts, g.canonical_etypes):
simple_graph.edges[canonical_etype].data[return_counts] = count
if writeback_mapping:
# single edge type
if len(edge_maps) == 1:
return simple_graph, edge_maps[0]
# multiple edge type
else:
wb_map = {}
for edge_map, canonical_etype in zip(edge_maps, g.canonical_etypes):
wb_map[canonical_etype] = edge_map
return simple_graph, wb_map
return simple_graph
DGLHeteroGraph.to_simple = utils.alias_func(to_simple)
def as_heterograph(g, ntype='_U', etype='_E'): # pylint: disable=unused-argument
"""Convert a DGLGraph to a DGLHeteroGraph with one node and edge type.
DEPRECATED: DGLGraph and DGLHeteroGraph have been merged. This function will
do nothing and can be removed safely in all cases.
"""
dgl_warning('DEPRECATED: DGLGraph and DGLHeteroGraph have been merged in v0.5.\n'
'\tdgl.as_heterograph will do nothing and can be removed safely in all cases.')
return g
def as_immutable_graph(hg):
"""Convert a DGLHeteroGraph with one node and edge type into a DGLGraph.
DEPRECATED: DGLGraph and DGLHeteroGraph have been merged. This function will
do nothing and can be removed safely in all cases.
"""
dgl_warning('DEPRECATED: DGLGraph and DGLHeteroGraph have been merged in v0.5.\n'
'\tdgl.as_immutable_graph will do nothing and can be removed safely in all cases.')
return hg
_init_api("dgl.transform")