"""Functions for extracting subgraphs.
The module only contains functions for extracting subgraphs deterministically.
For stochastic subgraph extraction, please see functions under :mod:`dgl.sampling`.
"""
from collections.abc import Mapping
from ._ffi.function import _init_api
from .base import DGLError, dgl_warning
from . import backend as F
from . import graph_index
from . import heterograph_index
from .heterograph import DGLHeteroGraph
from . import utils
from .utils import recursive_apply, context_of
__all__ = ['node_subgraph', 'edge_subgraph', 'node_type_subgraph', 'edge_type_subgraph',
'in_subgraph', 'out_subgraph', 'khop_in_subgraph', 'khop_out_subgraph']
[docs]def node_subgraph(graph, nodes, *, relabel_nodes=True, store_ids=True, output_device=None):
"""Return a subgraph induced on the given nodes.
A node-induced subgraph is a graph with edges whose endpoints are both in the
specified node set. In addition to extracting the subgraph, DGL also copies
the features of the extracted nodes and edges to the resulting graph. The copy
is *lazy* and incurs data movement only when needed.
If the graph is heterogeneous, DGL extracts a subgraph per relation and composes
them as the resulting graph. Thus, the resulting graph has the same set of relations
as the input one.
Parameters
----------
graph : DGLGraph
The graph to extract subgraphs from.
nodes : nodes or dict[str, nodes]
The nodes to form the subgraph. The allowed nodes formats are:
* Int Tensor: Each element is a node ID. The tensor must have the same device type
and ID data type as the graph's.
* iterable[int]: Each element is a node ID.
* Bool Tensor: Each :math:`i^{th}` element is a bool flag indicating whether
node :math:`i` is in the subgraph.
If the graph is homogeneous, one can directly pass the above formats.
Otherwise, the argument must be a dictionary with keys being node types
and values being the node IDs in the above formats.
relabel_nodes : bool, optional
If True, the extracted subgraph will only have the nodes in the specified node set
and it will relabel the nodes in order.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted edges in the ``edata`` of the
resulting graph under name ``dgl.EID``; if ``relabel_nodes`` is ``True``, it will
also store the raw IDs of the specified nodes in the ``ndata`` of the resulting
graph under name ``dgl.NID``.
output_device : Framework-specific device context object, optional
The output device. Default is the same as the input graph.
Returns
-------
G : DGLGraph
The subgraph.
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
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
Extract a subgraph from a homogeneous graph.
>>> g = dgl.graph(([0, 1, 2, 3, 4], [1, 2, 3, 4, 0])) # 5-node cycle
>>> sg = dgl.node_subgraph(g, [0, 1, 4])
>>> sg
Graph(num_nodes=3, num_edges=2,
ndata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)}
edata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.edges()
(tensor([0, 2]), tensor([1, 0]))
>>> sg.ndata[dgl.NID] # original node IDs
tensor([0, 1, 4])
>>> sg.edata[dgl.EID] # original edge IDs
tensor([0, 4])
Specify nodes using a boolean mask.
>>> nodes = torch.tensor([True, True, False, False, True]) # choose nodes [0, 1, 4]
>>> dgl.node_subgraph(g, nodes)
Graph(num_nodes=3, num_edges=2,
ndata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)}
edata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)})
The resulting subgraph also copies features from the parent graph.
>>> g.ndata['x'] = torch.arange(10).view(5, 2)
>>> sg = dgl.node_subgraph(g, [0, 1, 4])
>>> sg
Graph(num_nodes=3, num_edges=2,
ndata_schemes={'x': Scheme(shape=(2,), dtype=torch.int64),
'_ID': Scheme(shape=(), dtype=torch.int64)}
edata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.ndata['x']
tensor([[0, 1],
[2, 3],
[8, 9]])
Extract a subgraph from a hetergeneous graph.
>>> g = dgl.heterograph({
>>> ('user', 'plays', 'game'): ([0, 1, 1, 2], [0, 0, 2, 1]),
>>> ('user', 'follows', 'user'): ([0, 1, 1], [1, 2, 2])
>>> })
>>> sub_g = dgl.node_subgraph(g, {'user': [1, 2]})
>>> sub_g
Graph(num_nodes={'game': 0, 'user': 2},
num_edges={('user', 'follows', 'user'): 2, ('user', 'plays', 'game'): 0},
metagraph=[('user', 'user', 'follows'), ('user', 'game', 'plays')])
See Also
--------
edge_subgraph
"""
if graph.is_block:
raise DGLError('Extracting subgraph from a block graph is not allowed.')
if not isinstance(nodes, Mapping):
assert len(graph.ntypes) == 1, \
'need a dict of node type and IDs for graph with multiple node types'
nodes = {graph.ntypes[0]: nodes}
def _process_nodes(ntype, v):
if F.is_tensor(v) and F.dtype(v) == F.bool:
return F.astype(F.nonzero_1d(F.copy_to(v, graph.device)), graph.idtype)
else:
return utils.prepare_tensor(graph, v, 'nodes["{}"]'.format(ntype))
nodes = {ntype: _process_nodes(ntype, v) for ntype, v in nodes.items()}
device = context_of(nodes)
induced_nodes = [
nodes.get(ntype, F.copy_to(F.tensor([], graph.idtype), device))
for ntype in graph.ntypes]
sgi = graph._graph.node_subgraph(induced_nodes, relabel_nodes)
induced_edges = sgi.induced_edges
# (BarclayII) should not write induced_nodes = sgi.induced_nodes due to the same
# bug in #1453.
induced_nodes_or_device = induced_nodes if relabel_nodes else device
subg = _create_hetero_subgraph(
graph, sgi, induced_nodes_or_device, induced_edges, store_ids=store_ids)
return subg if output_device is None else subg.to(output_device)
DGLHeteroGraph.subgraph = utils.alias_func(node_subgraph)
[docs]def edge_subgraph(graph, edges, *, relabel_nodes=True, store_ids=True, output_device=None,
**deprecated_kwargs):
"""Return a subgraph induced on the given edges.
An edge-induced subgraph is equivalent to creating a new graph using the given
edges. In addition to extracting the subgraph, DGL also copies the features
of the extracted nodes and edges to the resulting graph. The copy is *lazy*
and incurs data movement only when needed.
If the graph is heterogeneous, DGL extracts a subgraph per relation and composes
them as the resulting graph. Thus, the resulting graph has the same set of relations
as the input one.
Parameters
----------
graph : DGLGraph
The graph to extract the subgraph from.
edges : edges or dict[(str, str, str), edges]
The edges to form the subgraph. The allowed edges formats are:
* Int Tensor: Each element is an edge ID. The tensor must have the same device type
and ID data type as the graph's.
* iterable[int]: Each element is an edge ID.
* Bool Tensor: Each :math:`i^{th}` element is a bool flag indicating whether
edge :math:`i` is in the subgraph.
If the graph is homogeneous, one can directly pass the above formats.
Otherwise, the argument must be a dictionary with keys being edge types
and values being the edge IDs in the above formats.
relabel_nodes : bool, optional
If True, it will remove the isolated nodes and relabel the incident nodes in the
extracted subgraph.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted edges in the ``edata`` of the
resulting graph under name ``dgl.EID``; if ``relabel_nodes`` is ``True``, it will
also store the raw IDs of the incident nodes in the ``ndata`` of the resulting
graph under name ``dgl.NID``.
output_device : Framework-specific device context object, optional
The output device. Default is the same as the input graph.
Returns
-------
G : DGLGraph
The subgraph.
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
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
Extract a subgraph from a homogeneous graph.
>>> g = dgl.graph(([0, 1, 2, 3, 4], [1, 2, 3, 4, 0])) # 5-node cycle
>>> sg = dgl.edge_subgraph(g, [0, 4])
>>> sg
Graph(num_nodes=3, num_edges=2,
ndata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)}
edata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.edges()
(tensor([0, 1]), tensor([2, 0]))
>>> sg.ndata[dgl.NID] # original node IDs
tensor([0, 4, 1])
>>> sg.edata[dgl.EID] # original edge IDs
tensor([0, 4])
Extract a subgraph without node relabeling.
>>> sg = dgl.edge_subgraph(g, [0, 4], relabel_nodes=False)
>>> sg
Graph(num_nodes=5, num_edges=2,
ndata_schemes={}
edata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.edges()
(tensor([0, 4]), tensor([1, 0]))
Specify edges using a boolean mask.
>>> nodes = torch.tensor([True, False, False, False, True]) # choose edges [0, 4]
>>> dgl.edge_subgraph(g, nodes)
Graph(num_nodes=3, num_edges=2,
ndata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)}
edata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)})
The resulting subgraph also copies features from the parent graph.
>>> g.ndata['x'] = torch.arange(10).view(5, 2)
>>> sg = dgl.edge_subgraph(g, [0, 4])
>>> sg
Graph(num_nodes=3, num_edges=2,
ndata_schemes={'x': Scheme(shape=(2,), dtype=torch.int64),
'_ID': Scheme(shape=(), dtype=torch.int64)}
edata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.ndata[dgl.NID]
tensor([0, 4, 1])
>>> sg.ndata['x']
tensor([[0, 1],
[8, 9],
[2, 3]])
Extract a subgraph from a hetergeneous graph.
>>> g = dgl.heterograph({
>>> ('user', 'plays', 'game'): ([0, 1, 1, 2], [0, 0, 2, 1]),
>>> ('user', 'follows', 'user'): ([0, 1, 1], [1, 2, 2])
>>> })
>>> sub_g = dgl.edge_subgraph(g, {('user', 'follows', 'user'): [1, 2],
... ('user', 'plays', 'game'): [2]})
>>> print(sub_g)
Graph(num_nodes={'game': 1, user': 2},
num_edges={('user', 'follows', 'user'): 2, ('user', 'plays', 'game'): 1},
metagraph=[('user', 'user', 'follows'), ('user', 'game', 'plays')])
See Also
--------
node_subgraph
"""
if len(deprecated_kwargs) != 0:
dgl_warning(
"Key word argument preserve_nodes is deprecated. Use relabel_nodes instead.")
relabel_nodes = not deprecated_kwargs.get('preserve_nodes')
if graph.is_block and relabel_nodes:
raise DGLError('Extracting subgraph from a block graph is not allowed.')
if not isinstance(edges, Mapping):
assert len(graph.canonical_etypes) == 1, \
'need a dict of edge type and IDs for graph with multiple edge types'
edges = {graph.canonical_etypes[0]: edges}
def _process_edges(etype, e):
if F.is_tensor(e) and F.dtype(e) == F.bool:
return F.astype(F.nonzero_1d(F.copy_to(e, graph.device)), graph.idtype)
else:
return utils.prepare_tensor(graph, e, 'edges["{}"]'.format(etype))
edges = {graph.to_canonical_etype(etype): e for etype, e in edges.items()}
edges = {etype: _process_edges(etype, e) for etype, e in edges.items()}
device = context_of(edges)
induced_edges = [
edges.get(cetype, F.copy_to(F.tensor([], graph.idtype), device))
for cetype in graph.canonical_etypes]
sgi = graph._graph.edge_subgraph(induced_edges, not relabel_nodes)
induced_nodes_or_device = sgi.induced_nodes if relabel_nodes else device
subg = _create_hetero_subgraph(
graph, sgi, induced_nodes_or_device, induced_edges, store_ids=store_ids)
return subg if output_device is None else subg.to(output_device)
DGLHeteroGraph.edge_subgraph = utils.alias_func(edge_subgraph)
[docs]def in_subgraph(graph, nodes, *, relabel_nodes=False, store_ids=True, output_device=None):
"""Return the subgraph induced on the inbound edges of all the edge types of the
given nodes.
An in subgraph is equivalent to creating a new graph using the incoming edges of the
given nodes. In addition to extracting the subgraph, DGL also copies the features of
the extracted nodes and edges to the resulting graph. The copy is *lazy* and incurs
data movement only when needed.
If the graph is heterogeneous, DGL extracts a subgraph per relation and composes
them as the resulting graph. Thus, the resulting graph has the same set of relations
as the input one.
Parameters
----------
graph : DGLGraph
The input graph.
nodes : nodes or dict[str, nodes]
The nodes to form the subgraph. The allowed nodes formats are:
* Int Tensor: Each element is a node ID. The tensor must have the same device type
and ID data type as the graph's.
* iterable[int]: Each element is a node ID.
If the graph is homogeneous, one can directly pass the above formats.
Otherwise, the argument must be a dictionary with keys being node types
and values being the node IDs in the above formats.
relabel_nodes : bool, optional
If True, it will remove the isolated nodes and relabel the rest nodes in the
extracted subgraph.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted edges in the ``edata`` of the
resulting graph under name ``dgl.EID``; if ``relabel_nodes`` is ``True``, it will
also store the raw IDs of the extracted nodes in the ``ndata`` of the resulting
graph under name ``dgl.NID``.
output_device : Framework-specific device context object, optional
The output device. Default is the same as the input graph.
Returns
-------
DGLGraph
The subgraph.
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
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
Extract a subgraph from a homogeneous graph.
>>> g = dgl.graph(([0, 1, 2, 3, 4], [1, 2, 3, 4, 0])) # 5-node cycle
>>> g.edata['w'] = torch.arange(10).view(5, 2)
>>> sg = dgl.in_subgraph(g, [2, 0])
>>> sg
Graph(num_nodes=5, num_edges=2,
ndata_schemes={}
edata_schemes={'w': Scheme(shape=(2,), dtype=torch.int64),
'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.edges()
(tensor([1, 4]), tensor([2, 0]))
>>> sg.edata[dgl.EID] # original edge IDs
tensor([1, 4])
>>> sg.edata['w'] # also extract the features
tensor([[2, 3],
[8, 9]])
Extract a subgraph with node labeling.
>>> sg = dgl.in_subgraph(g, [2, 0], relabel_nodes=True)
>>> sg
Graph(num_nodes=4, num_edges=2,
ndata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64}
edata_schemes={'w': Scheme(shape=(2,), dtype=torch.int64),
'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.edges()
(tensor([1, 3]), tensor([2, 0]))
>>> sg.edata[dgl.EID] # original edge IDs
tensor([1, 4])
>>> sg.ndata[dgl.NID] # original node IDs
tensor([0, 1, 2, 4])
Extract a subgraph from a heterogeneous graph.
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): ([0, 1, 1, 2], [0, 0, 2, 1]),
... ('user', 'follows', 'user'): ([0, 1, 1], [1, 2, 2])})
>>> sub_g = g.in_subgraph({'user': [2], 'game': [2]})
>>> sub_g
Graph(num_nodes={'game': 3, 'user': 3},
num_edges={('user', 'plays', 'game'): 1, ('user', 'follows', 'user'): 2},
metagraph=[('user', 'game', 'plays'), ('user', 'user', 'follows')])
See also
--------
out_subgraph
"""
if graph.is_block:
raise DGLError('Extracting subgraph of a block graph is not allowed.')
if not isinstance(nodes, dict):
if len(graph.ntypes) > 1:
raise DGLError("Must specify node type when the graph is not homogeneous.")
nodes = {graph.ntypes[0] : nodes}
nodes = utils.prepare_tensor_dict(graph, nodes, 'nodes')
device = context_of(nodes)
nodes_all_types = [
F.to_dgl_nd(nodes.get(ntype, F.copy_to(F.tensor([], graph.idtype), device)))
for ntype in graph.ntypes]
sgi = _CAPI_DGLInSubgraph(graph._graph, nodes_all_types, relabel_nodes)
induced_nodes_or_device = sgi.induced_nodes if relabel_nodes else device
induced_edges = sgi.induced_edges
subg = _create_hetero_subgraph(
graph, sgi, induced_nodes_or_device, induced_edges, store_ids=store_ids)
return subg if output_device is None else subg.to(output_device)
DGLHeteroGraph.in_subgraph = utils.alias_func(in_subgraph)
[docs]def out_subgraph(graph, nodes, *, relabel_nodes=False, store_ids=True, output_device=None):
"""Return the subgraph induced on the outbound edges of all the edge types of the
given nodes.
An out subgraph is equivalent to creating a new graph using the outcoming edges of
the given nodes. In addition to extracting the subgraph, DGL also copies the features
of the extracted nodes and edges to the resulting graph. The copy is *lazy* and incurs
data movement only when needed.
If the graph is heterogeneous, DGL extracts a subgraph per relation and composes
them as the resulting graph. Thus, the resulting graph has the same set of relations
as the input one.
Parameters
----------
graph : DGLGraph
The input graph.
nodes : nodes or dict[str, nodes]
The nodes to form the subgraph. The allowed nodes formats are:
* Int Tensor: Each element is a node ID. The tensor must have the same device type
and ID data type as the graph's.
* iterable[int]: Each element is a node ID.
If the graph is homogeneous, one can directly pass the above formats.
Otherwise, the argument must be a dictionary with keys being node types
and values being the node IDs in the above formats.
relabel_nodes : bool, optional
If True, it will remove the isolated nodes and relabel the rest nodes in the
extracted subgraph.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted edges in the ``edata`` of the
resulting graph under name ``dgl.EID``; if ``relabel_nodes`` is ``True``, it will
also store the raw IDs of the extracted nodes in the ``ndata`` of the resulting
graph under name ``dgl.NID``.
output_device : Framework-specific device context object, optional
The output device. Default is the same as the input graph.
Returns
-------
DGLGraph
The subgraph.
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
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
Extract a subgraph from a homogeneous graph.
>>> g = dgl.graph(([0, 1, 2, 3, 4], [1, 2, 3, 4, 0])) # 5-node cycle
>>> g.edata['w'] = torch.arange(10).view(5, 2)
>>> sg = dgl.out_subgraph(g, [2, 0])
>>> sg
Graph(num_nodes=5, num_edges=2,
ndata_schemes={}
edata_schemes={'w': Scheme(shape=(2,), dtype=torch.int64),
'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.edges()
(tensor([2, 0]), tensor([3, 1]))
>>> sg.edata[dgl.EID] # original edge IDs
tensor([2, 0])
>>> sg.edata['w'] # also extract the features
tensor([[4, 5],
[0, 1]])
Extract a subgraph with node labeling.
>>> sg = dgl.out_subgraph(g, [2, 0], relabel_nodes=True)
>>> sg
Graph(num_nodes=4, num_edges=2,
ndata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)}
edata_schemes={'w': Scheme(shape=(2,), dtype=torch.int64),
'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.edges()
(tensor([2, 0]), tensor([3, 1]))
>>> sg.edata[dgl.EID] # original edge IDs
tensor([2, 0])
>>> sg.ndata[dgl.NID] # original node IDs
tensor([0, 1, 2, 3])
Extract a subgraph from a heterogeneous graph.
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): ([0, 1, 1, 2], [0, 0, 2, 1]),
... ('user', 'follows', 'user'): ([0, 1, 1], [1, 2, 2])})
>>> sub_g = g.out_subgraph({'user': [1]})
>>> sub_g
Graph(num_nodes={'game': 3, 'user': 3},
num_edges={('user', 'plays', 'game'): 2, ('user', 'follows', 'user'): 2},
metagraph=[('user', 'game', 'plays'), ('user', 'user', 'follows')])
See also
--------
in_subgraph
"""
if graph.is_block:
raise DGLError('Extracting subgraph of a block graph is not allowed.')
if not isinstance(nodes, dict):
if len(graph.ntypes) > 1:
raise DGLError("Must specify node type when the graph is not homogeneous.")
nodes = {graph.ntypes[0] : nodes}
nodes = utils.prepare_tensor_dict(graph, nodes, 'nodes')
device = context_of(nodes)
nodes_all_types = [
F.to_dgl_nd(nodes.get(ntype, F.copy_to(F.tensor([], graph.idtype), device)))
for ntype in graph.ntypes]
sgi = _CAPI_DGLOutSubgraph(graph._graph, nodes_all_types, relabel_nodes)
induced_nodes_or_device = sgi.induced_nodes if relabel_nodes else device
induced_edges = sgi.induced_edges
subg = _create_hetero_subgraph(
graph, sgi, induced_nodes_or_device, induced_edges, store_ids=store_ids)
return subg if output_device is None else subg.to(output_device)
DGLHeteroGraph.out_subgraph = utils.alias_func(out_subgraph)
[docs]def khop_in_subgraph(graph, nodes, k, *, relabel_nodes=True, store_ids=True, output_device=None):
"""Return the subgraph induced by k-hop in-neighborhood of the specified node(s).
We can expand a set of nodes by including the predecessors of them. From a
specified node set, a k-hop in subgraph is obtained by first repeating the node set
expansion for k times and then creating a node induced subgraph. In addition to
extracting the subgraph, DGL also copies the features of the extracted nodes and
edges to the resulting graph. The copy is *lazy* and incurs data movement only
when needed.
If the graph is heterogeneous, DGL extracts a subgraph per relation and composes
them as the resulting graph. Thus the resulting graph has the same set of relations
as the input one.
Parameters
----------
graph : DGLGraph
The input graph.
nodes : nodes or dict[str, nodes]
The starting node(s) to expand. The allowed formats are:
* Int: ID of a single node.
* Int Tensor: Each element is a node ID. The tensor must have the same device
type and ID data type as the graph's.
* iterable[int]: Each element is a node ID.
If the graph is homogeneous, one can directly pass the above formats.
Otherwise, the argument must be a dictionary with keys being node types
and values being the node IDs in the above formats.
k : int
The number of hops.
relabel_nodes : bool, optional
If True, it will remove the isolated nodes and relabel the rest nodes in the
extracted subgraph.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted edges in the ``edata`` of the
resulting graph under name ``dgl.EID``; if ``relabel_nodes`` is ``True``, it will
also store the raw IDs of the extracted nodes in the ``ndata`` of the resulting
graph under name ``dgl.NID``.
output_device : Framework-specific device context object, optional
The output device. Default is the same as the input graph.
Returns
-------
DGLGraph
The subgraph.
Tensor or dict[str, Tensor], optional
The new IDs of the input :attr:`nodes` after node relabeling. This is returned
only when :attr:`relabel_nodes` is True. It is in the same form as :attr:`nodes`.
Notes
-----
When k is 1, the result subgraph is different from the one obtained by
:func:`dgl.in_subgraph`. The 1-hop in subgraph also includes the edges
among the neighborhood.
Examples
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
Extract a two-hop subgraph from a homogeneous graph.
>>> g = dgl.graph(([1, 1, 2, 3, 4], [0, 2, 0, 4, 2]))
>>> g.edata['w'] = torch.arange(10).view(5, 2)
>>> sg, inverse_indices = dgl.khop_in_subgraph(g, 0, k=2)
>>> sg
Graph(num_nodes=4, num_edges=4,
ndata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)}
edata_schemes={'w': Scheme(shape=(2,), dtype=torch.int64),
'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.edges()
(tensor([1, 1, 2, 3]), tensor([0, 2, 0, 2]))
>>> sg.edata[dgl.EID] # original edge IDs
tensor([0, 1, 2, 4])
>>> sg.edata['w'] # also extract the features
tensor([[0, 1],
[2, 3],
[4, 5],
[8, 9]])
>>> inverse_indices
tensor([0])
Extract a subgraph from a heterogeneous graph.
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): ([0, 1, 1, 2], [0, 0, 2, 1]),
... ('user', 'follows', 'user'): ([0, 1, 1], [1, 2, 2])})
>>> sg, inverse_indices = dgl.khop_in_subgraph(g, {'game': 0}, k=2)
>>> sg
Graph(num_nodes={'game': 1, 'user': 2},
num_edges={('user', 'follows', 'user'): 1, ('user', 'plays', 'game'): 2},
metagraph=[('user', 'user', 'follows'), ('user', 'game', 'plays')])
>>> inverse_indices
{'game': tensor([0])}
See also
--------
khop_out_subgraph
"""
if graph.is_block:
raise DGLError('Extracting subgraph of a block graph is not allowed.')
is_mapping = isinstance(nodes, Mapping)
if not is_mapping:
assert len(graph.ntypes) == 1, \
'need a dict of node type and IDs for graph with multiple node types'
nodes = {graph.ntypes[0]: nodes}
for nty, nty_nodes in nodes.items():
nodes[nty] = utils.prepare_tensor(graph, nty_nodes, 'nodes["{}"]'.format(nty))
last_hop_nodes = nodes
k_hop_nodes_ = [last_hop_nodes]
device = context_of(nodes)
place_holder = F.copy_to(F.tensor([], dtype=graph.idtype), device)
for _ in range(k):
current_hop_nodes = {nty: [] for nty in graph.ntypes}
for cetype in graph.canonical_etypes:
srctype, _, dsttype = cetype
in_nbrs, _ = graph.in_edges(last_hop_nodes.get(dsttype, place_holder), etype=cetype)
current_hop_nodes[srctype].append(in_nbrs)
for nty in graph.ntypes:
if len(current_hop_nodes[nty]) == 0:
current_hop_nodes[nty] = place_holder
continue
current_hop_nodes[nty] = F.unique(F.cat(current_hop_nodes[nty], dim=0))
k_hop_nodes_.append(current_hop_nodes)
last_hop_nodes = current_hop_nodes
k_hop_nodes = dict()
inverse_indices = dict()
for nty in graph.ntypes:
k_hop_nodes[nty], inverse_indices[nty] = F.unique(F.cat([
hop_nodes.get(nty, place_holder)
for hop_nodes in k_hop_nodes_], dim=0), return_inverse=True)
sub_g = node_subgraph(graph, k_hop_nodes, relabel_nodes=relabel_nodes, store_ids=store_ids)
if output_device is not None:
sub_g = sub_g.to(output_device)
if relabel_nodes:
if is_mapping:
seed_inverse_indices = dict()
for nty in nodes:
seed_inverse_indices[nty] = F.slice_axis(
inverse_indices[nty], axis=0, begin=0, end=len(nodes[nty]))
else:
seed_inverse_indices = F.slice_axis(
inverse_indices[nty], axis=0, begin=0, end=len(nodes[nty]))
if output_device is not None:
seed_inverse_indices = recursive_apply(
seed_inverse_indices, lambda x: F.copy_to(x, output_device))
return sub_g, seed_inverse_indices
else:
return sub_g
DGLHeteroGraph.khop_in_subgraph = utils.alias_func(khop_in_subgraph)
[docs]def khop_out_subgraph(graph, nodes, k, *, relabel_nodes=True, store_ids=True, output_device=None):
"""Return the subgraph induced by k-hop out-neighborhood of the specified node(s).
We can expand a set of nodes by including the successors of them. From a
specified node set, a k-hop out subgraph is obtained by first repeating the node set
expansion for k times and then creating a node induced subgraph. In addition to
extracting the subgraph, DGL also copies the features of the extracted nodes and
edges to the resulting graph. The copy is *lazy* and incurs data movement only
when needed.
If the graph is heterogeneous, DGL extracts a subgraph per relation and composes
them as the resulting graph. Thus the resulting graph has the same set of relations
as the input one.
Parameters
----------
graph : DGLGraph
The input graph.
nodes : nodes or dict[str, nodes]
The starting node(s) to expand. The allowed formats are:
* Int: ID of a single node.
* Int Tensor: Each element is a node ID. The tensor must have the same device
type and ID data type as the graph's.
* iterable[int]: Each element is a node ID.
If the graph is homogeneous, one can directly pass the above formats.
Otherwise, the argument must be a dictionary with keys being node types
and values being the node IDs in the above formats.
k : int
The number of hops.
relabel_nodes : bool, optional
If True, it will remove the isolated nodes and relabel the rest nodes in the
extracted subgraph.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted edges in the ``edata`` of the
resulting graph under name ``dgl.EID``; if ``relabel_nodes`` is ``True``, it will
also store the raw IDs of the extracted nodes in the ``ndata`` of the resulting
graph under name ``dgl.NID``.
output_device : Framework-specific device context object, optional
The output device. Default is the same as the input graph.
Returns
-------
DGLGraph
The subgraph.
Tensor or dict[str, Tensor], optional
The new IDs of the input :attr:`nodes` after node relabeling. This is returned
only when :attr:`relabel_nodes` is True. It is in the same form as :attr:`nodes`.
Notes
-----
When k is 1, the result subgraph is different from the one obtained by
:func:`dgl.out_subgraph`. The 1-hop out subgraph also includes the edges
among the neighborhood.
Examples
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
Extract a two-hop subgraph from a homogeneous graph.
>>> g = dgl.graph(([0, 2, 0, 4, 2], [1, 1, 2, 3, 4]))
>>> g.edata['w'] = torch.arange(10).view(5, 2)
>>> sg, inverse_indices = dgl.khop_out_subgraph(g, 0, k=2)
>>> sg
Graph(num_nodes=4, num_edges=4,
ndata_schemes={'_ID': Scheme(shape=(), dtype=torch.int64)}
edata_schemes={'w': Scheme(shape=(2,), dtype=torch.int64),
'_ID': Scheme(shape=(), dtype=torch.int64)})
>>> sg.edges()
(tensor([0, 0, 2, 2]), tensor([1, 2, 1, 3]))
>>> sg.edata[dgl.EID] # original edge IDs
tensor([0, 2, 1, 4])
>>> sg.edata['w'] # also extract the features
tensor([[0, 1],
[4, 5],
[2, 3],
[8, 9]])
>>> inverse_indices
tensor([0])
Extract a subgraph from a heterogeneous graph.
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): ([0, 1, 1, 2], [0, 0, 2, 1]),
... ('user', 'follows', 'user'): ([0, 1], [1, 3])})
>>> sg, inverse_indices = dgl.khop_out_subgraph(g, {'user': 0}, k=2)
>>> sg
Graph(num_nodes={'game': 2, 'user': 3},
num_edges={('user', 'follows', 'user'): 2, ('user', 'plays', 'game'): 2},
metagraph=[('user', 'user', 'follows'), ('user', 'game', 'plays')])
>>> inverse_indices
{'user': tensor([0])}
See also
--------
khop_in_subgraph
"""
if graph.is_block:
raise DGLError('Extracting subgraph of a block graph is not allowed.')
is_mapping = isinstance(nodes, Mapping)
if not is_mapping:
assert len(graph.ntypes) == 1, \
'need a dict of node type and IDs for graph with multiple node types'
nodes = {graph.ntypes[0]: nodes}
for nty, nty_nodes in nodes.items():
nodes[nty] = utils.prepare_tensor(graph, nty_nodes, 'nodes["{}"]'.format(nty))
last_hop_nodes = nodes
k_hop_nodes_ = [last_hop_nodes]
device = context_of(nodes)
place_holder = F.copy_to(F.tensor([], dtype=graph.idtype), device)
for _ in range(k):
current_hop_nodes = {nty: [] for nty in graph.ntypes}
for cetype in graph.canonical_etypes:
srctype, _, dsttype = cetype
_, out_nbrs = graph.out_edges(last_hop_nodes.get(
srctype, place_holder), etype=cetype)
current_hop_nodes[dsttype].append(out_nbrs)
for nty in graph.ntypes:
if len(current_hop_nodes[nty]) == 0:
current_hop_nodes[nty] = place_holder
continue
current_hop_nodes[nty] = F.unique(F.cat(current_hop_nodes[nty], dim=0))
k_hop_nodes_.append(current_hop_nodes)
last_hop_nodes = current_hop_nodes
k_hop_nodes = dict()
inverse_indices = dict()
for nty in graph.ntypes:
k_hop_nodes[nty], inverse_indices[nty] = F.unique(F.cat([
hop_nodes.get(nty, place_holder)
for hop_nodes in k_hop_nodes_], dim=0), return_inverse=True)
sub_g = node_subgraph(graph, k_hop_nodes, relabel_nodes=relabel_nodes, store_ids=store_ids)
if output_device is not None:
sub_g = sub_g.to(output_device)
if relabel_nodes:
if is_mapping:
seed_inverse_indices = dict()
for nty in nodes:
seed_inverse_indices[nty] = F.slice_axis(
inverse_indices[nty], axis=0, begin=0, end=len(nodes[nty]))
else:
seed_inverse_indices = F.slice_axis(
inverse_indices[nty], axis=0, begin=0, end=len(nodes[nty]))
if output_device is not None:
seed_inverse_indices = recursive_apply(
seed_inverse_indices, lambda x: F.copy_to(x, output_device))
return sub_g, seed_inverse_indices
else:
return sub_g
DGLHeteroGraph.khop_out_subgraph = utils.alias_func(khop_out_subgraph)
[docs]def node_type_subgraph(graph, ntypes, output_device=None):
"""Return the subgraph induced on given node types.
A node-type-induced subgraph contains all the nodes of the given subset of
the node types of a graph and any edges whose endpoints are both in this subset.
In addition to extracting the subgraph, DGL also copies the features of the
extracted nodes and edges to the resulting graph.
The copy is *lazy* and incurs data movement only when needed.
Parameters
----------
graph : DGLGraph
The graph to extract subgraphs from.
ntypes : list[str]
The type names of the nodes in the subgraph.
output_device : Framework-specific device context object, optional
The output device. Default is the same as the input graph.
Returns
-------
G : DGLGraph
The subgraph.
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
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
Instantiate a heterograph.
>>> g = dgl.heterograph({
>>> ('user', 'plays', 'game'): ([0, 1, 1, 2], [0, 0, 2, 1]),
>>> ('user', 'follows', 'user'): ([0, 1, 1], [1, 2, 2])
>>> })
>>> # Set node features
>>> g.nodes['user'].data['h'] = torch.tensor([[0.], [1.], [2.]])
Get subgraphs.
>>> sub_g = g.node_type_subgraph(['user'])
>>> print(sub_g)
Graph(num_nodes=3, num_edges=3,
ndata_schemes={'h': Scheme(shape=(1,), dtype=torch.float32)}
edata_schemes={})
Get the extracted node features.
>>> sub_g.nodes['user'].data['h']
tensor([[0.],
[1.],
[2.]])
See Also
--------
edge_type_subgraph
"""
ntid = [graph.get_ntype_id(ntype) for ntype in ntypes]
stids, dtids, etids = graph._graph.metagraph.edges('eid')
stids, dtids, etids = stids.tonumpy(), dtids.tonumpy(), etids.tonumpy()
etypes = []
for stid, dtid, etid in zip(stids, dtids, etids):
if stid in ntid and dtid in ntid:
etypes.append(graph.canonical_etypes[etid])
if len(etypes) == 0:
raise DGLError('There are no edges among nodes of the specified types.')
return edge_type_subgraph(graph, etypes, output_device=output_device)
DGLHeteroGraph.node_type_subgraph = utils.alias_func(node_type_subgraph)
[docs]def edge_type_subgraph(graph, etypes, output_device=None):
"""Return the subgraph induced on given edge types.
An edge-type-induced subgraph contains all the edges of the given subset of
the edge types of a graph. It also contains all nodes of a particular type
if some nodes of the type are incident to these edges.
In addition to extracting the subgraph, DGL also copies the features of the
extracted nodes and edges to the resulting graph.
The copy is *lazy* and incurs data movement only when needed.
Parameters
----------
graph : DGLGraph
The graph to extract subgraphs from.
etypes : list[str] or list[(str, str, str)]
The type names of the edges in the subgraph. The allowed type name
formats are:
* ``(str, str, str)`` for source node type, edge type and destination node type.
* or one ``str`` for the edge type name if the name can uniquely identify a
triplet format in the graph.
output_device : Framework-specific device context object, optional
The output device. Default is the same as the input graph.
Returns
-------
G : DGLGraph
The subgraph.
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
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
Instantiate a heterograph.
>>> g = dgl.heterograph({
>>> ('user', 'plays', 'game'): ([0, 1, 1, 2], [0, 0, 2, 1]),
>>> ('user', 'follows', 'user'): ([0, 1, 1], [1, 2, 2])
>>> })
>>> # Set edge features
>>> g.edges['follows'].data['h'] = torch.tensor([[0.], [1.], [2.]])
Get subgraphs.
>>> sub_g = g.edge_type_subgraph(['follows'])
>>> sub_g
Graph(num_nodes=3, num_edges=3,
ndata_schemes={}
edata_schemes={'h': Scheme(shape=(1,), dtype=torch.float32)})
Get the shared edge features.
>>> sub_g.edges['follows'].data['h']
tensor([[0.],
[1.],
[2.]])
See Also
--------
node_type_subgraph
"""
etype_ids = [graph.get_etype_id(etype) for etype in etypes]
# meta graph is homogeneous graph, still using int64
meta_src, meta_dst, _ = graph._graph.metagraph.find_edges(utils.toindex(etype_ids, "int64"))
rel_graphs = [graph._graph.get_relation_graph(i) for i in etype_ids]
meta_src = meta_src.tonumpy()
meta_dst = meta_dst.tonumpy()
ntypes_invmap = {n: i for i, n in enumerate(set(meta_src) | set(meta_dst))}
mapped_meta_src = [ntypes_invmap[v] for v in meta_src]
mapped_meta_dst = [ntypes_invmap[v] for v in meta_dst]
node_frames = [graph._node_frames[i] for i in ntypes_invmap]
edge_frames = [graph._edge_frames[i] for i in etype_ids]
induced_ntypes = [graph._ntypes[i] for i in ntypes_invmap]
induced_etypes = [graph._etypes[i] for i in etype_ids] # get the "name" of edge type
num_nodes_per_induced_type = [graph.number_of_nodes(ntype) for ntype in induced_ntypes]
metagraph = graph_index.from_edge_list((mapped_meta_src, mapped_meta_dst), True)
# num_nodes_per_type should be int64
hgidx = heterograph_index.create_heterograph_from_relations(
metagraph, rel_graphs, utils.toindex(num_nodes_per_induced_type, "int64"))
hg = DGLHeteroGraph(hgidx, induced_ntypes, induced_etypes, node_frames, edge_frames)
return hg if output_device is None else hg.to(output_device)
DGLHeteroGraph.edge_type_subgraph = utils.alias_func(edge_type_subgraph)
#################### Internal functions ####################
def _create_hetero_subgraph(parent, sgi, induced_nodes_or_device, induced_edges_or_device,
store_ids=True):
"""Internal function to create a subgraph.
Parameters
----------
parent : DGLGraph
The parent DGLGraph.
sgi : HeteroSubgraphIndex
Subgraph object returned by CAPI.
induced_nodes_or_device : list[Tensor] or device or None
Induced node IDs or the device. Will store it as the dgl.NID ndata unless it
is None, which means the induced node IDs are the same as the parent node IDs.
If a device is given, the features will be copied to the given device.
induced_edges_or_device : list[Tensor] or device or None
Induced edge IDs. Will store it as the dgl.EID ndata unless it
is None, which means the induced edge IDs are the same as the parent edge IDs.
If a device is given, the features will be copied to the given device.
store_ids : bool
If True and induced_nodes is not None, it will store the raw IDs of the extracted
nodes in the ``ndata`` of the resulting graph under name ``dgl.NID``.
If True and induced_edges is not None, it will store the raw IDs of the extracted
edges in the ``edata`` of the resulting graph under name ``dgl.EID``.
Returns
-------
DGLGraph
Graph
"""
# (BarclayII) Giving a device argument to induced_nodes_or_device is necessary for
# UVA subgraphing, where the node features are not sliced but the device changed.
# Not having this will give us a subgraph on GPU but node features on CPU if we don't
# relabel the nodes.
node_frames = utils.extract_node_subframes(parent, induced_nodes_or_device, store_ids)
edge_frames = utils.extract_edge_subframes(parent, induced_edges_or_device, store_ids)
hsg = DGLHeteroGraph(sgi.graph, parent.ntypes, parent.etypes)
utils.set_new_frames(hsg, node_frames=node_frames, edge_frames=edge_frames)
return hsg
_init_api("dgl.subgraph")