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dmlc--dgl
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0.2.x
T
Zihao Ye 724aa0caf0 [Feature] FindEdge/FindEdges for Immutable Graph (#404) 
* fix rgcn tutorial

* small fix

* upd

* findedge/s

* upd

* upd

* upd

* upd

* add test

* remove redundancy

* upd

* upd

* upd

* upd

* add edge_subgraph

* explicit cast

* add test immutable subg

* reformat

* reformat

* fix bug

* upd
2019-02-27 15:32:32 +08:00

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"""Base graph class specialized for neural networks on graphs."""
from __future__ import absolute_import
from collections import defaultdict
import networkx as nx
import dgl
from .base import ALL, is_all, DGLError
from . import backend as F
from . import init
from .frame import FrameRef, Frame
from .graph_index import create_graph_index
from .runtime import ir, scheduler, Runtime
from . import utils
from .view import NodeView, EdgeView
from .udf import NodeBatch, EdgeBatch
__all__ = ['DGLGraph']
class DGLBaseGraph(object):
"""Base graph class.
DGL graph is always directional. Undirected graph can be represented using
two bi-directional edges.
Nodes are identified by consecutive integers starting from zero.
Edges can be specified by two end points (u, v) or the integer id assigned
when the edges are added. Edge IDs are automatically assigned by the order
of addition, i.e. the first edge being added has an ID of 0, the second
being 1, so on so forth.
Parameters
----------
graph : graph index, optional
Data to initialize graph.
"""
def __init__(self, graph):
self._graph = graph
def number_of_nodes(self):
"""Return the number of nodes in the graph.
Returns
-------
int
The number of nodes
"""
return self._graph.number_of_nodes()
def __len__(self):
"""Return the number of nodes in the graph."""
return self.number_of_nodes()
@property
def is_multigraph(self):
"""True if the graph is a multigraph, False otherwise.
"""
return self._graph.is_multigraph()
@property
def is_readonly(self):
"""True if the graph is readonly, False otherwise.
"""
return self._graph.is_readonly()
def number_of_edges(self):
"""Return the number of edges in the graph.
Returns
-------
int
The number of edges
"""
return self._graph.number_of_edges()
def has_node(self, vid):
"""Return True if the graph contains node `vid`.
Identical to `vid in G`.
Parameters
----------
vid : int
The node ID.
Returns
-------
bool
True if the node exists
Examples
--------
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.has_node(0)
True
>>> G.has_node(4)
False
Equivalently,
>>> 0 in G
True
See Also
--------
has_nodes
"""
return self._graph.has_node(vid)
def __contains__(self, vid):
"""Return True if the graph contains node `vid`.
Examples
--------
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> 0 in G
True
"""
return self._graph.has_node(vid)
def has_nodes(self, vids):
"""Return a 0-1 array ``a`` given the node ID array ``vids``.
``a[i]`` is 1 if the graph contains node ``vids[i]``, 0 otherwise.
Parameters
----------
vid : list or tensor
The array of node IDs.
Returns
-------
a : tensor
0-1 array indicating existence
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.has_nodes([0, 1, 2, 3, 4])
tensor([1, 1, 1, 0, 0])
See Also
--------
has_node
"""
vids = utils.toindex(vids)
rst = self._graph.has_nodes(vids)
return rst.tousertensor()
def has_edge_between(self, u, v):
"""Return True if the edge (u, v) is in the graph.
Parameters
----------
u : int
The source node ID.
v : int
The destination node ID.
Returns
-------
bool
True if the edge is in the graph, False otherwise.
Examples
--------
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edge(0, 1)
>>> G.has_edge_between(0, 1)
True
>>> G.has_edge_between(1, 0)
False
See Also
--------
has_edges_between
"""
return self._graph.has_edge_between(u, v)
def has_edges_between(self, u, v):
"""Return a 0-1 array `a` given the source node ID array `u` and
destination node ID array `v`.
`a[i]` is 1 if the graph contains edge `(u[i], v[i])`, 0 otherwise.
Parameters
----------
u : list, tensor
The source node ID array.
v : list, tensor
The destination node ID array.
Returns
-------
a : tensor
0-1 array indicating existence.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0], [1, 2]) # (0, 1), (0, 2)
Check if (0, 1), (0, 2), (1, 0), (2, 0) exist in the graph above:
>>> G.has_edges_between([0, 0, 1, 2], [1, 2, 0, 0])
tensor([1, 1, 0, 0])
See Also
--------
has_edge_between
"""
u = utils.toindex(u)
v = utils.toindex(v)
rst = self._graph.has_edges_between(u, v)
return rst.tousertensor()
def predecessors(self, v):
"""Return the predecessors of node `v` in the graph.
Node `u` is a predecessor of `v` if an edge `(u, v)` exist in the
graph.
Parameters
----------
v : int
The node.
Returns
-------
tensor
Array of predecessor node IDs.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([1, 2], [0, 0]) # (1, 0), (2, 0)
>>> G.predecessors(0)
tensor([1, 2])
See Also
--------
successors
"""
return self._graph.predecessors(v).tousertensor()
def successors(self, v):
"""Return the successors of node `v` in the graph.
Node `u` is a successor of `v` if an edge `(v, u)` exist in the
graph.
Parameters
----------
v : int
The node.
Returns
-------
tensor
Array of successor node IDs.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0], [1, 2]) # (0, 1), (0, 2)
>>> G.successors(0)
tensor([1, 2])
See Also
--------
predecessors
"""
return self._graph.successors(v).tousertensor()
def edge_id(self, u, v, force_multi=False):
"""Return the edge ID, or an array of edge IDs, between source node
`u` and destination node `v`.
Parameters
----------
u : int
The source node ID.
v : int
The destination node ID.
force_multi : bool
If False, will return a single edge ID if the graph is a simple graph.
If True, will always return an array.
Returns
-------
int or tensor
The edge ID if force_multi == True and the graph is a simple graph.
The edge ID array otherwise.
Examples
--------
The following example uses PyTorch backend.
For simple graphs:
>>> G = dgl.DGLGraph()
>>> G.add_node(3)
>>> G.add_edges([0, 0], [1, 2]) # (0, 1), (0, 2)
>>> G.edge_id(0, 2)
1
>>> G.edge_id(0, 1)
0
For multigraphs:
>>> G = dgl.DGLGraph(multigraph=True)
>>> G.add_nodes(3)
Adding edges (0, 1), (0, 2), (0, 1), (0, 2), so edge ID 0 and 2 both
connect from 0 and 1, while edge ID 1 and 3 both connect from 0 and 2.
>>> G.add_edges([0, 0, 0, 0], [1, 2, 1, 2])
>>> G.edge_id(0, 1)
tensor([0, 2])
See Also
--------
edge_ids
"""
idx = self._graph.edge_id(u, v)
return idx.tousertensor() if force_multi or self.is_multigraph else idx[0]
def edge_ids(self, u, v, force_multi=False):
"""Return all edge IDs between source node array `u` and destination
node array `v`.
Parameters
----------
u : list, tensor
The source node ID array.
v : list, tensor
The destination node ID array.
force_multi : bool
Whether to always treat the graph as a multigraph.
Returns
-------
tensor, or (tensor, tensor, tensor)
If the graph is a simple graph and `force_multi` is False, return
a single edge ID array `e`. `e[i]` is the edge ID between `u[i]`
and `v[i]`.
Otherwise, return three arrays `(eu, ev, e)`. `e[i]` is the ID
of an edge between `eu[i]` and `ev[i]`. All edges between `u[i]`
and `v[i]` are returned.
Notes
-----
If the graph is a simple graph, `force_multi` is False, and no edge
exist between some pairs of `u[i]` and `v[i]`, the result is undefined.
Examples
--------
The following example uses PyTorch backend.
For simple graphs:
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0], [1, 2]) # (0, 1), (0, 2)
>>> G.edge_ids([0, 0], [2, 1]) # get edge ID of (0, 2) and (0, 1)
>>> G.edge_ids([0, 0], [2, 1])
tensor([1, 0])
For multigraphs
>>> G = dgl.DGLGraph(multigraph=True)
>>> G.add_nodes(4)
>>> G.add_edges([0, 0, 0], [1, 1, 2]) # (0, 1), (0, 1), (0, 2)
Get all edges between (0, 1), (0, 2), (0, 3). Note that there is no
edge between 0 and 3:
>>> G.edge_ids([0, 0, 0], [1, 2, 3])
(tensor([0, 0, 0]), tensor([1, 1, 2]), tensor([0, 1, 2]))
See Also
--------
edge_id
"""
u = utils.toindex(u)
v = utils.toindex(v)
src, dst, eid = self._graph.edge_ids(u, v)
if force_multi or self.is_multigraph:
return src.tousertensor(), dst.tousertensor(), eid.tousertensor()
else:
return eid.tousertensor()
def find_edges(self, eid):
"""Given an edge ID array, return the source and destination node ID
array `s` and `d`. `s[i]` and `d[i]` are source and destination node
ID for edge `eid[i]`.
Parameters
----------
eid : list, tensor
The edge ID array.
Returns
-------
tensor
The source node ID array.
tensor
The destination node ID array.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0, 1], [1, 2, 2]) # (0, 1), (0, 2), (1, 2)
>>> G.find_edges([0, 2])
(tensor([0, 1]), tensor([1, 2]))
"""
eid = utils.toindex(eid)
src, dst, _ = self._graph.find_edges(eid)
return src.tousertensor(), dst.tousertensor()
def in_edges(self, v, form='uv'):
"""Return the inbound edges of the node(s).
Parameters
----------
v : int, list, tensor
The node(s).
form : str, optional
The return form. Currently support:
- 'all' : a tuple (u, v, eid)
- 'uv' : a pair (u, v), default
- 'eid' : one eid tensor
Returns
-------
A tuple of Tensors ``(eu, ev, eid)`` if ``form == 'all'``.
``eid[i]`` is the ID of an inbound edge to ``ev[i]`` from ``eu[i]``.
All inbound edges to ``v`` are returned.
A pair of Tensors (eu, ev) if form == 'uv'
``eu[i]`` is the source node of an inbound edge to ``ev[i]``.
All inbound edges to ``v`` are returned.
One Tensor if form == 'eid'
``eid[i]`` is ID of an inbound edge to any of the nodes in ``v``.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0, 1], [1, 2, 2]) # (0, 1), (0, 2), (1, 2)
For a single node:
>>> G.in_edges(2)
(tensor([0, 1]), tensor([2, 2]))
>>> G.in_edges(2, 'all')
(tensor([0, 1]), tensor([2, 2]), tensor([1, 2]))
>>> G.in_edges(2, 'eid')
tensor([1, 2])
For multiple nodes:
>>> G.in_edges([1, 2])
(tensor([0, 0, 1]), tensor([1, 2, 2]))
>>> G.in_edges([1, 2], 'all')
(tensor([0, 0, 1]), tensor([1, 2, 2]), tensor([0, 1, 2]))
"""
v = utils.toindex(v)
src, dst, eid = self._graph.in_edges(v)
if form == 'all':
return (src.tousertensor(), dst.tousertensor(), eid.tousertensor())
elif form == 'uv':
return (src.tousertensor(), dst.tousertensor())
elif form == 'eid':
return eid.tousertensor()
else:
raise DGLError('Invalid form:', form)
def out_edges(self, v, form='uv'):
"""Return the outbound edges of the node(s).
Parameters
----------
v : int, list, tensor
The node(s).
form : str, optional
The return form. Currently support:
- 'all' : a tuple (u, v, eid)
- 'uv' : a pair (u, v), default
- 'eid' : one eid tensor
Returns
-------
A tuple of Tensors ``(eu, ev, eid)`` if ``form == 'all'``.
``eid[i]`` is the ID of an outbound edge from ``eu[i]`` to ``ev[i]``.
All outbound edges from ``v`` are returned.
A pair of Tensors (eu, ev) if form == 'uv'
``ev[i]`` is the destination node of an outbound edge from ``eu[i]``.
All outbound edges from ``v`` are returned.
One Tensor if form == 'eid'
``eid[i]`` is ID of an outbound edge from any of the nodes in ``v``.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0, 1], [1, 2, 2]) # (0, 1), (0, 2), (1, 2)
For a single node:
>>> G.out_edges(0)
(tensor([0, 0]), tensor([1, 2]))
>>> G.out_edges(0, 'all')
(tensor([0, 0]), tensor([1, 2]), tensor([0, 1]))
>>> G.out_edges(0, 'eid')
tensor([0, 1])
For multiple nodes:
>>> G.out_edges([0, 1])
(tensor([0, 0, 1]), tensor([1, 2, 2]))
>>> G.out_edges([0, 1], 'all')
(tensor([0, 0, 1]), tensor([1, 2, 2]), tensor([0, 1, 2]))
"""
v = utils.toindex(v)
src, dst, eid = self._graph.out_edges(v)
if form == 'all':
return (src.tousertensor(), dst.tousertensor(), eid.tousertensor())
elif form == 'uv':
return (src.tousertensor(), dst.tousertensor())
elif form == 'eid':
return eid.tousertensor()
else:
raise DGLError('Invalid form:', form)
def all_edges(self, form='uv', order=None):
"""Return all the edges.
Parameters
----------
form : str, optional
The return form. Currently support:
- 'all' : a tuple (u, v, eid)
- 'uv' : a pair (u, v), default
- 'eid' : one eid tensor
order : string
The order of the returned edges. Currently support:
- 'srcdst' : sorted by their src and dst ids.
- 'eid' : sorted by edge Ids.
- None : the arbitrary order.
Returns
-------
A tuple of Tensors (u, v, eid) if form == 'all'
``eid[i]`` is the ID of an edge between ``u[i]`` and ``v[i]``.
All edges are returned.
A pair of Tensors (u, v) if form == 'uv'
An edge exists between ``u[i]`` and ``v[i]``.
If ``n`` edges exist between ``u`` and ``v``, then ``u`` and ``v`` as a pair
will appear ``n`` times.
One Tensor if form == 'eid'
``eid[i]`` is the ID of an edge in the graph.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0, 1], [1, 2, 2]) # (0, 1), (0, 2), (1, 2)
>>> G.all_edges()
(tensor([0, 0, 1]), tensor([1, 2, 2]))
>>> G.all_edges('all')
(tensor([0, 0, 1]), tensor([1, 2, 2]), tensor([0, 1, 2]))
"""
src, dst, eid = self._graph.edges(order)
if form == 'all':
return (src.tousertensor(), dst.tousertensor(), eid.tousertensor())
elif form == 'uv':
return (src.tousertensor(), dst.tousertensor())
elif form == 'eid':
return eid.tousertensor()
else:
raise DGLError('Invalid form:', form)
def in_degree(self, v):
"""Return the in-degree of node ``v``.
Parameters
----------
v : int
The node ID.
Returns
-------
int
The in-degree.
Examples
--------
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0, 1], [1, 2, 2]) # (0, 1), (0, 2), (1, 2)
>>> G.in_degree(2)
2
See Also
--------
in_degrees
"""
return self._graph.in_degree(v)
def in_degrees(self, v=ALL):
"""Return the array `d` of in-degrees of the node array `v`.
`d[i]` is the in-degree of node `v[i]`.
Parameters
----------
v : list, tensor, optional.
The node ID array. Default is to return the degrees of all the nodes.
Returns
-------
d : tensor
The in-degree array.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0, 1], [1, 2, 2]) # (0, 1), (0, 2), (1, 2)
>>> G.in_degrees([1, 2])
tensor([1, 2])
See Also
--------
in_degree
"""
if is_all(v):
v = utils.toindex(slice(0, self.number_of_nodes()))
else:
v = utils.toindex(v)
return self._graph.in_degrees(v).tousertensor()
def out_degree(self, v):
"""Return the out-degree of node `v`.
Parameters
----------
v : int
The node ID.
Returns
-------
int
The out-degree.
Examples
--------
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0, 1], [1, 2, 2]) # (0, 1), (0, 2), (1, 2)
>>> G.out_degree(0)
2
See Also
--------
out_degrees
"""
return self._graph.out_degree(v)
def out_degrees(self, v=ALL):
"""Return the array `d` of out-degrees of the node array `v`.
`d[i]` is the out-degree of node `v[i]`.
Parameters
----------
v : list, tensor
The node ID array. Default is to return the degrees of all the nodes.
Returns
-------
d : tensor
The out-degree array.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 0, 1], [1, 2, 2]) # (0, 1), (0, 2), (1, 2)
>>> G.out_degrees([0, 1])
tensor([2, 1])
See Also
--------
out_degree
"""
if is_all(v):
v = utils.toindex(slice(0, self.number_of_nodes()))
else:
v = utils.toindex(v)
return self._graph.out_degrees(v).tousertensor()
class DGLGraph(DGLBaseGraph):
"""Base graph class.
The graph stores nodes, edges and also their features.
DGL graph is always directional. Undirected graph can be represented using
two bi-directional edges.
Nodes are identified by consecutive integers starting from zero.
Edges can be specified by two end points (u, v) or the integer id assigned
when the edges are added. Edge IDs are automatically assigned by the order
of addition, i.e. the first edge being added has an ID of 0, the second
being 1, so on so forth.
Node and edge features are stored as a dictionary from the feature name
to the feature data (in tensor).
Parameters
----------
graph_data : graph data, optional
Data to initialize graph. Same as networkx's semantics.
node_frame : FrameRef, optional
Node feature storage.
edge_frame : FrameRef, optional
Edge feature storage.
multigraph : bool, optional
Whether the graph would be a multigraph (default: False)
readonly : bool, optional
Whether the graph structure is read-only (default: False).
Examples
--------
Create an empty graph with no nodes and edges.
>>> G = dgl.DGLGraph()
G can be grown in several ways.
**Nodes:**
Add N nodes:
>>> G.add_nodes(10) # 10 isolated nodes are added
**Edges:**
Add one edge at a time,
>>> G.add_edge(0, 1)
or multiple edges,
>>> G.add_edges([1, 2, 3], [3, 4, 5]) # three edges: 1->3, 2->4, 3->5
or multiple edges starting from the same node,
>>> G.add_edges(4, [7, 8, 9]) # three edges: 4->7, 4->8, 4->9
or multiple edges pointing to the same node,
>>> G.add_edges([2, 6, 8], 5) # three edges: 2->5, 6->5, 8->5
or multiple edges using tensor type
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> G.add_edges(th.tensor([3, 4, 5]), 1) # three edges: 3->1, 4->1, 5->1
NOTE: Removing nodes and edges is not supported by DGLGraph.
**Features:**
Both nodes and edges can have feature data. Features are stored as
key/value pair. The key must be hashable while the value must be tensor
type. Features are batched on the first dimension.
Use G.ndata to get/set features for all nodes.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.ndata['x'] = th.zeros((3, 5)) # init 3 nodes with zero vector(len=5)
>>> G.ndata
{'x' : tensor([[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]])}
Use G.nodes to get/set features for some nodes.
>>> G.nodes[[0, 2]].data['x'] = th.ones((2, 5))
>>> G.ndata
{'x' : tensor([[1., 1., 1., 1., 1.],
[0., 0., 0., 0., 0.],
[1., 1., 1., 1., 1.]])}
Similarly, use G.edata and G.edges to get/set features for edges.
>>> G.add_edges([0, 1], 2) # 0->2, 1->2
>>> G.edata['y'] = th.zeros((2, 4)) # init 2 edges with zero vector(len=4)
>>> G.edata
{'y' : tensor([[0., 0., 0., 0.],
[0., 0., 0., 0.]])}
>>> G.edges[1, 2].data['y'] = th.ones((1, 4))
>>> G.edata
{'y' : tensor([[0., 0., 0., 0.],
[1., 1., 1., 1.]])}
Note that each edge is assigned a unique id equal to its adding
order. So edge 1->2 has id=1. DGL supports directly use edge id
to access edge features.
>>> G.edges[0].data['y'] += 2.
>>> G.edata
{'y' : tensor([[2., 2., 2., 2.],
[1., 1., 1., 1.]])}
**Message Passing:**
One common operation for updating node features is message passing,
where the source nodes send messages through edges to the destinations.
With :class:`DGLGraph`, we can do this with :func:`send` and :func:`recv`.
In the example below, the source nodes add 1 to their node features as
the messages and send the messages to the destinations.
>>> # Define the function for sending messages.
>>> def send_source(edges): return {'m': edges.src['x'] + 1}
>>> # Set the function defined to be the default message function.
>>> G.register_message_func(send_source)
>>> # Send messages through all edges.
>>> G.send(G.edges())
Just like you need to go to your mailbox for retrieving mails, the destination
nodes also need to receive the messages and potentially update their features.
>>> # Define a function for summing messages received and replacing the original feature.
>>> def simple_reduce(nodes): return {'x': nodes.mailbox['m'].sum(1)}
>>> # Set the function defined to be the default message reduce function.
>>> G.register_reduce_func(simple_reduce)
>>> # All existing edges have node 2 as the destination.
>>> # Receive the messages for node 2 and update its feature.
>>> G.recv(v=2)
>>> G.ndata
{'x': tensor([[1., 1., 1., 1., 1.],
[0., 0., 0., 0., 0.],
[3., 3., 3., 3., 3.]])} # 3 = (1 + 1) + (0 + 1)
For more examples about message passing, please read our tutorials.
"""
def __init__(self,
graph_data=None,
node_frame=None,
edge_frame=None,
multigraph=False,
readonly=False):
# graph
super(DGLGraph, self).__init__(create_graph_index(graph_data, multigraph, readonly))
# node and edge frame
if node_frame is None:
self._node_frame = FrameRef(Frame(num_rows=self.number_of_nodes()))
else:
self._node_frame = node_frame
if edge_frame is None:
self._edge_frame = FrameRef(Frame(num_rows=self.number_of_edges()))
else:
self._edge_frame = edge_frame
# message indicator:
# if self._msg_index[eid] == 1, then edge eid has message
self._msg_index = utils.zero_index(size=self.number_of_edges())
# message frame
self._msg_frame = FrameRef(Frame(num_rows=self.number_of_edges()))
# set initializer for message frame
self._msg_frame.set_initializer(init.zero_initializer)
# registered functions
self._message_func = None
self._reduce_func = None
self._apply_node_func = None
self._apply_edge_func = None
def add_nodes(self, num, data=None):
"""Add multiple new nodes.
Parameters
----------
num : int
Number of nodes to be added.
data : dict, optional
Feature data of the added nodes.
Notes
-----
If new nodes are added with features, and any of the old nodes
do not have some of the feature fields, those fields are filled
by initializers defined with ``set_n_initializer`` (default filling
with zeros).
Examples
--------
>>> G = dgl.DGLGraph()
>>> g.add_nodes(2)
>>> g.number_of_nodes()
2
>>> g.add_nodes(3)
>>> g.number_of_nodes()
5
Adding new nodes with features:
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g.add_nodes(2, {'x': th.ones(2, 4)}) # default zero initializer
>>> g.ndata['x']
tensor([[0., 0., 0., 0.],
[0., 0., 0., 0.],
[0., 0., 0., 0.],
[0., 0., 0., 0.],
[0., 0., 0., 0.],
[1., 1., 1., 1.],
[1., 1., 1., 1.]])
"""
self._graph.add_nodes(num)
if data is None:
# Initialize feature placeholders if there are features existing
self._node_frame.add_rows(num)
else:
self._node_frame.append(data)
def add_edge(self, u, v, data=None):
"""Add one new edge between u and v.
Parameters
----------
u : int
The source node ID. Must exist in the graph.
v : int
The destination node ID. Must exist in the graph.
data : dict, optional
Feature data of the added edges.
Notes
-----
If new edges are added with features, and any of the old edges
do not have some of the feature fields, those fields are filled
by initializers defined with ``set_e_initializer`` (default filling
with zeros).
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edge(0, 1)
Adding new edge with features
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> G.add_edge(0, 2, {'x': th.ones(1, 4)})
>>> G.edges()
(tensor([0, 0]), tensor([1, 2]))
>>> G.edata['x']
tensor([[0., 0., 0., 0.],
[1., 1., 1., 1.]])
>>> G.edges[0, 2].data['x']
tensor([[1., 1., 1., 1.]])
See Also
--------
add_edges
"""
self._graph.add_edge(u, v)
if data is None:
# Initialize feature placeholders if there are features existing
self._edge_frame.add_rows(1)
else:
self._edge_frame.append(data)
# resize msg_index and msg_frame
self._msg_index = self._msg_index.append_zeros(1)
self._msg_frame.add_rows(1)
def add_edges(self, u, v, data=None):
"""Add multiple edges for list of source nodes u and destination nodes
v. A single edge is added between every pair of ``u[i]`` and ``v[i]``.
Parameters
----------
u : list, tensor
The source node IDs. All nodes must exist in the graph.
v : list, tensor
The destination node IDs. All nodes must exist in the graph.
data : dict, optional
Feature data of the added edges.
Notes
-----
If new edges are added with features, and any of the old edges
do not have some of the feature fields, those fields are filled
by initializers defined with ``set_e_initializer`` (default filling
with zeros).
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(4)
>>> G.add_edges([0, 2], [1, 3]) # add edges (0, 1) and (2, 3)
Adding new edges with features
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> G.add_edges([1, 3], [2, 0], {'x': th.ones(2, 4)}) # (1, 2), (3, 0)
>>> G.edata['x']
tensor([[0., 0., 0., 0.],
[0., 0., 0., 0.],
[1., 1., 1., 1.],
[1., 1., 1., 1.]])
See Also
--------
add_edge
"""
u = utils.toindex(u)
v = utils.toindex(v)
self._graph.add_edges(u, v)
num = max(len(u), len(v))
if data is None:
# Initialize feature placeholders if there are features existing
# NOTE: use max due to edge broadcasting syntax
self._edge_frame.add_rows(num)
else:
self._edge_frame.append(data)
# initialize feature placeholder for messages
self._msg_index = self._msg_index.append_zeros(num)
self._msg_frame.add_rows(num)
def clear(self):
"""Remove all nodes and edges, as well as their features, from the
graph.
Examples
--------
>>> G = dgl.DGLGraph()
>>> G.add_nodes(4)
>>> G.add_edges([0, 1, 2, 3], [1, 2, 3, 0])
>>> G.number_of_nodes()
4
>>> G.number_of_edges()
4
>>> G.clear()
>>> G.number_of_nodes()
0
>>> G.number_of_edges()
0
"""
self._graph.clear()
self._node_frame.clear()
self._edge_frame.clear()
self._msg_index = utils.zero_index(0)
self._msg_frame.clear()
def clear_cache(self):
"""Clear all cached graph structures such as adjmat.
By default, all graph structure related sparse matrices (e.g. adjmat, incmat)
are cached so they could be reused with the cost of extra memory consumption.
This function can be used to clear the cached matrices if memory is an issue.
"""
self._graph.clear_cache()
def to_networkx(self, node_attrs=None, edge_attrs=None):
"""Convert to networkx graph.
The edge id will be saved as the 'id' edge attribute.
Parameters
----------
node_attrs : iterable of str, optional
The node attributes to be copied.
edge_attrs : iterable of str, optional
The edge attributes to be copied.
Returns
-------
networkx.DiGraph
The nx graph
Examples
--------
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = DGLGraph()
>>> g.add_nodes(5, {'n1': th.randn(5, 10)})
>>> g.add_edges([0,1,3,4], [2,4,0,3], {'e1': th.randn(4, 6)})
>>> nxg = g.to_networkx(node_attrs=['n1'], edge_attrs=['e1'])
"""
nx_graph = self._graph.to_networkx()
if node_attrs is not None:
for nid, attr in nx_graph.nodes(data=True):
feat_dict = self.get_n_repr(nid)
attr.update({key: F.squeeze(feat_dict[key], 0) for key in node_attrs})
if edge_attrs is not None:
for _, _, attr in nx_graph.edges(data=True):
eid = attr['id']
feat_dict = self.get_e_repr(eid)
attr.update({key: F.squeeze(feat_dict[key], 0) for key in edge_attrs})
return nx_graph
def from_networkx(self, nx_graph, node_attrs=None, edge_attrs=None):
"""Convert from networkx graph.
If 'id' edge attribute exists, the edge will be added follows
the edge id order. Otherwise, order is undefined.
Parameters
----------
nx_graph : networkx.DiGraph
If the node labels of ``nx_graph`` are not consecutive
integers, its nodes will be relabeled using consecutive integers.
The new node ordering will inherit that of ``sorted(nx_graph.nodes())``
node_attrs : iterable of str, optional
The node attributes needs to be copied.
edge_attrs : iterable of str, optional
The edge attributes needs to be copied.
Examples
--------
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> import networkx as nx
>>> nxg = nx.DiGraph()
>>> nxg.add_edge(0, 1, id=0, e1=5, e2=th.zeros(4))
>>> nxg.add_edge(2, 3, id=2, e1=6, e2=th.ones(4))
>>> nxg.add_edge(1, 2, id=1, e1=2, e2=th.full((4,), 2))
>>> g = dgl.DGLGraph()
>>> g.from_networkx(nxg, edge_attrs=['e1', 'e2'])
>>> g.edata['e1']
tensor([5, 2, 6])
>>> g.edata['e2']
tensor([[0., 0., 0., 0.],
[2., 2., 2., 2.],
[1., 1., 1., 1.]])
"""
# Relabel nodes using consecutive integers
nx_graph = nx.convert_node_labels_to_integers(nx_graph, ordering='sorted')
# With to_directed we will get a directed version of the original networkx
# graph, with the original nodes, edges and their attributes preserved.
# This is particularly helpful when we are also converting the edge attributes
# as the reversed edges (u, v) will be created with the same attributes as the
# original edges (v, u).
if not nx_graph.is_directed():
nx_graph = nx_graph.to_directed()
self.clear()
self._graph.from_networkx(nx_graph)
self._node_frame.add_rows(self.number_of_nodes())
self._edge_frame.add_rows(self.number_of_edges())
self._msg_index = utils.zero_index(self.number_of_edges())
self._msg_frame.add_rows(self.number_of_edges())
# copy attributes
def _batcher(lst):
if F.is_tensor(lst[0]):
return F.cat([F.unsqueeze(x, 0) for x in lst], dim=0)
else:
return F.tensor(lst)
if node_attrs is not None:
# mapping from feature name to a list of tensors to be concatenated
attr_dict = defaultdict(list)
for nid in range(self.number_of_nodes()):
for attr in node_attrs:
attr_dict[attr].append(nx_graph.nodes[nid][attr])
for attr in node_attrs:
self._node_frame[attr] = _batcher(attr_dict[attr])
if edge_attrs is not None:
has_edge_id = 'id' in next(iter(nx_graph.edges(data=True)))[-1]
# mapping from feature name to a list of tensors to be concatenated
attr_dict = defaultdict(lambda: [None] * self.number_of_edges())
# each defaultdict value is initialized to be a list of None
# None here serves as placeholder to be replaced by feature with
# corresponding edge id
if has_edge_id:
num_edges = self.number_of_edges()
for _, _, attrs in nx_graph.edges(data=True):
if attrs['id'] >= num_edges:
raise DGLError('Expect the pre-specified edge ids to be'
' smaller than the number of edges --'
' {}, got {}.'.format(num_edges, attrs['id']))
for key in edge_attrs:
attr_dict[key][attrs['id']] = attrs[key]
else:
# XXX: assuming networkx iteration order is deterministic
# so the order is the same as graph_index.from_networkx
for eid, (_, _, attrs) in enumerate(nx_graph.edges(data=True)):
for key in edge_attrs:
attr_dict[key][eid] = attrs[key]
for attr in edge_attrs:
for val in attr_dict[attr]:
if val is None:
raise DGLError('Not all edges have attribute {}.'.format(attr))
self._edge_frame[attr] = _batcher(attr_dict[attr])
def from_scipy_sparse_matrix(self, spmat):
""" Convert from scipy sparse matrix.
Parameters
----------
spmat : scipy sparse matrix
The graph's adjacency matrix
Examples
--------
>>> from scipy.sparse import coo_matrix
>>> row = np.array([0, 3, 1, 0])
>>> col = np.array([0, 3, 1, 2])
>>> data = np.array([4, 5, 7, 9])
>>> a = coo_matrix((data, (row, col)), shape=(4, 4))
>>> g = dgl.DGLGraph()
>>> g.from_scipy_sparse_matrix(a)
"""
self.clear()
self._graph.from_scipy_sparse_matrix(spmat)
self._node_frame.add_rows(self.number_of_nodes())
self._edge_frame.add_rows(self.number_of_edges())
self._msg_index = utils.zero_index(self.number_of_edges())
self._msg_frame.add_rows(self.number_of_edges())
def node_attr_schemes(self):
"""Return the node feature schemes.
Each feature scheme is a named tuple that stores the shape and data type
of the node feature
Returns
-------
dict of str to schemes
The schemes of node feature columns.
Examples
--------
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.ndata['x'] = torch.zeros((3,5))
>>> G.node_attr_schemes()
{'x': Scheme(shape=(5,), dtype=torch.float32)}
"""
return self._node_frame.schemes
def edge_attr_schemes(self):
"""Return the edge feature schemes.
Each feature scheme is a named tuple that stores the shape and data type
of the node feature
Returns
-------
dict of str to schemes
The schemes of edge feature columns.
Examples
--------
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 1], 2) # 0->2, 1->2
>>> G.edata['y'] = th.zeros((2, 4))
>>> G.edge_attr_schemes()
{'y': Scheme(shape=(4,), dtype=torch.float32)}
"""
return self._edge_frame.schemes
def set_n_initializer(self, initializer, field=None):
"""Set the initializer for empty node features.
Initializer is a callable that returns a tensor given the shape, data type
and device context.
When a subset of the nodes are assigned a new feature, initializer is
used to create feature for rest of the nodes.
Parameters
----------
initializer : callable
The initializer.
field : str, optional
The feature field name. Default is set an initializer for all the
feature fields.
Examples
--------
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
Set initializer for all node features
>>> G.set_n_initializer(dgl.init.zero_initializer)
Set feature for partial nodes
>>> G.nodes[[0, 2]].data['x'] = th.ones((2, 5))
>>> G.ndata
{'x' : tensor([[1., 1., 1., 1., 1.],
[0., 0., 0., 0., 0.],
[1., 1., 1., 1., 1.]])}
Note
-----
User defined initializer must follow the signature of
:func:`dgl.init.base_initializer() <dgl.init.base_initializer>`
"""
self._node_frame.set_initializer(initializer, field)
def set_e_initializer(self, initializer, field=None):
"""Set the initializer for empty edge features.
Initializer is a callable that returns a tensor given the shape, data
type and device context.
When a subset of the edges are assigned a new feature, initializer is
used to create feature for rest of the edges.
Parameters
----------
initializer : callable
The initializer.
field : str, optional
The feature field name. Default is set an initializer for all the
feature fields.
Examples
--------
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 1], 2) # 0->2, 1->2
Set initializer for edge features
>>> G.set_e_initializer(dgl.init.zero_initializer)
Set feature for partial edges
>>> G.edges[1, 2].data['y'] = th.ones((1, 4))
>>> G.edata
{'y' : tensor([[0., 0., 0., 0.],
[1., 1., 1., 1.]])}
Note
-----
User defined initializer must follow the signature of
:func:`dgl.init.base_initializer() <dgl.init.base_initializer>`
"""
self._edge_frame.set_initializer(initializer, field)
@property
def nodes(self):
"""Return a node view that can used to set/get feature data.
Examples
--------
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
Get nodes in graph G:
>>> G.nodes()
tensor([0, 1, 2])
Get feature dictionary of all nodes:
>>> G.nodes[:].data
{}
The above can be abbreviated as
>>> G.ndata
{}
Init all 3 nodes with zero vector(len=5)
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> G.ndata['x'] = th.zeros((3, 5))
>>> G.ndata['x']
{'x' : tensor([[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]])}
Use G.nodes to get/set features for some nodes.
>>> G.nodes[[0, 2]].data['x'] = th.ones((2, 5))
>>> G.ndata
{'x' : tensor([[1., 1., 1., 1., 1.],
[0., 0., 0., 0., 0.],
[1., 1., 1., 1., 1.]])}
See Also
--------
dgl.DGLGraph.ndata
"""
return NodeView(self)
@property
def ndata(self):
"""Return the data view of all the nodes.
DGLGraph.ndata is an abbreviation of DGLGraph.nodes[:].data
See Also
--------
dgl.DGLGraph.nodes
"""
return self.nodes[:].data
@property
def edges(self):
"""Return a edges view that can used to set/get feature data.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edges([0, 1], 2) # 0->2, 1->2
Get edges in graph G:
>>> G.edges()
(tensor([0, 1]), tensor([2, 2]))
Get feature dictionary of all edges:
>>> G.edges[:].data
{}
The above can be abbreviated as
>>> G.edata
{}
Init 2 edges with zero vector(len=4)
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> G.edata['y'] = th.zeros((2, 4))
>>> G.edata
{'y' : tensor([[0., 0., 0., 0.],
[0., 0., 0., 0.]])}
Use G.edges to get/set features for some edges.
>>> G.edges[1, 2].data['y'] = th.ones((1, 4))
>>> G.edata
{'y' : tensor([[0., 0., 0., 0.],
[1., 1., 1., 1.]])}
See Also
--------
dgl.DGLGraph.edata
"""
return EdgeView(self)
@property
def edata(self):
"""Return the data view of all the edges.
DGLGraph.data is an abbreviation of DGLGraph.edges[:].data
See Also
--------
dgl.DGLGraph.edges
"""
return self.edges[:].data
def set_n_repr(self, data, u=ALL, inplace=False):
"""Set node(s) representation.
`data` is a dictionary from the feature name to feature tensor. Each tensor
is of shape (B, D1, D2, ...), where B is the number of nodes to be updated,
and (D1, D2, ...) be the shape of the node representation tensor. The
length of the given node ids must match B (i.e, len(u) == B).
All update will be done out of place to work with autograd unless the
inplace flag is true.
Parameters
----------
data : dict of tensor
Node representation.
u : node, container or tensor
The node(s).
inplace : bool
If True, update will be done in place, but autograd will break.
"""
# sanity check
if not utils.is_dict_like(data):
raise DGLError('Expect dictionary type for feature data.'
' Got "%s" instead.' % type(data))
if is_all(u):
num_nodes = self.number_of_nodes()
else:
u = utils.toindex(u)
num_nodes = len(u)
for key, val in data.items():
nfeats = F.shape(val)[0]
if nfeats != num_nodes:
raise DGLError('Expect number of features to match number of nodes (len(u)).'
' Got %d and %d instead.' % (nfeats, num_nodes))
# set
if is_all(u):
for key, val in data.items():
self._node_frame[key] = val
else:
self._node_frame.update_rows(u, data, inplace=inplace)
def get_n_repr(self, u=ALL):
"""Get node(s) representation.
The returned feature tensor batches multiple node features on the first dimension.
Parameters
----------
u : node, container or tensor
The node(s).
Returns
-------
dict
Representation dict from feature name to feature tensor.
"""
if len(self.node_attr_schemes()) == 0:
return dict()
if is_all(u):
return dict(self._node_frame)
else:
u = utils.toindex(u)
return self._node_frame.select_rows(u)
def pop_n_repr(self, key):
"""Get and remove the specified node repr.
Parameters
----------
key : str
The attribute name.
Returns
-------
Tensor
The popped representation
"""
return self._node_frame.pop(key)
def set_e_repr(self, data, edges=ALL, inplace=False):
"""Set edge(s) representation.
`data` is a dictionary from the feature name to feature tensor. Each tensor
is of shape (B, D1, D2, ...), where B is the number of edges to be updated,
and (D1, D2, ...) be the shape of the edge representation tensor.
All update will be done out of place to work with autograd unless the
inplace flag is true.
Parameters
----------
data : tensor or dict of tensor
Edge representation.
edges : edges
Edges can be a pair of endpoint nodes (u, v), or a
tensor of edge ids. The default value is all the edges.
inplace : bool
If True, update will be done in place, but autograd will break.
"""
# parse argument
if is_all(edges):
eid = ALL
elif isinstance(edges, tuple):
u, v = edges
u = utils.toindex(u)
v = utils.toindex(v)
# Rewrite u, v to handle edge broadcasting and multigraph.
_, _, eid = self._graph.edge_ids(u, v)
else:
eid = utils.toindex(edges)
# sanity check
if not utils.is_dict_like(data):
raise DGLError('Expect dictionary type for feature data.'
' Got "%s" instead.' % type(data))
if is_all(eid):
num_edges = self.number_of_edges()
else:
eid = utils.toindex(eid)
num_edges = len(eid)
for key, val in data.items():
nfeats = F.shape(val)[0]
if nfeats != num_edges:
raise DGLError('Expect number of features to match number of edges.'
' Got %d and %d instead.' % (nfeats, num_edges))
# set
if is_all(eid):
# update column
for key, val in data.items():
self._edge_frame[key] = val
else:
# update row
self._edge_frame.update_rows(eid, data, inplace=inplace)
def get_e_repr(self, edges=ALL):
"""Get node(s) representation.
Parameters
----------
edges : edges
Edges can be a pair of endpoint nodes (u, v), or a
tensor of edge ids. The default value is all the edges.
Returns
-------
dict
Representation dict
"""
if len(self.edge_attr_schemes()) == 0:
return dict()
# parse argument
if is_all(edges):
eid = ALL
elif isinstance(edges, tuple):
u, v = edges
u = utils.toindex(u)
v = utils.toindex(v)
# Rewrite u, v to handle edge broadcasting and multigraph.
_, _, eid = self._graph.edge_ids(u, v)
else:
eid = utils.toindex(edges)
if is_all(eid):
return dict(self._edge_frame)
else:
eid = utils.toindex(eid)
return self._edge_frame.select_rows(eid)
def pop_e_repr(self, key):
"""Get and remove the specified edge repr.
Parameters
----------
key : str
The attribute name.
Returns
-------
Tensor
The popped representation
"""
return self._edge_frame.pop(key)
def register_message_func(self, func):
"""Register global message function.
Once registered, ``func`` will be used as the default
message function in message passing operations, including
:func:`send`, :func:`send_and_recv`, :func:`pull`,
:func:`push`, :func:`update_all`.
Parameters
----------
func : callable
Message function on the edge. The function should be
an :mod:`Edge UDF <dgl.udf>`.
See Also
--------
send
send_and_recv
pull
push
update_all
"""
self._message_func = func
def register_reduce_func(self, func):
"""Register global message reduce function.
Once registered, ``func`` will be used as the default
message reduce function in message passing operations, including
:func:`recv`, :func:`send_and_recv`, :func:`push`, :func:`pull`,
:func:`update_all`.
Parameters
----------
func : callable
Reduce function on the node. The function should be
a :mod:`Node UDF <dgl.udf>`.
See Also
--------
recv
send_and_recv
push
pull
update_all
"""
self._reduce_func = func
def register_apply_node_func(self, func):
"""Register global node apply function.
Once registered, ``func`` will be used as the default apply
node function. Related operations include :func:`apply_nodes`,
:func:`recv`, :func:`send_and_recv`, :func:`push`, :func:`pull`,
:func:`update_all`.
Parameters
----------
func : callable
Apply function on the nodes. The function should be
a :mod:`Node UDF <dgl.udf>`.
See Also
--------
apply_nodes
register_apply_edge_func
"""
self._apply_node_func = func
def register_apply_edge_func(self, func):
"""Register global edge apply function.
Once registered, ``func`` will be used as the default apply
edge function in :func:`apply_edges`.
Parameters
----------
func : callable
Apply function on the edge. The function should be
an :mod:`Edge UDF <dgl.udf>`.
See Also
--------
apply_edges
register_apply_node_func
"""
self._apply_edge_func = func
def apply_nodes(self, func="default", v=ALL, inplace=False):
"""Apply the function on the nodes to update their features.
If None is provided for ``func``, nothing will happen.
Parameters
----------
func : callable or None, optional
Apply function on the nodes. The function should be
a :mod:`Node UDF <dgl.udf>`.
v : int, iterable of int, tensor, optional
The node (ids) on which to apply ``func``. The default
value is all the nodes.
inplace : bool, optional
If True, update will be done in place, but autograd will break.
Examples
--------
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(3)
>>> g.ndata['x'] = th.ones(3, 1)
>>> # Increment the node feature by 1.
>>> def increment_feature(nodes): return {'x': nodes.data['x'] + 1}
>>> g.apply_nodes(func=increment_feature, v=[0, 2]) # Apply func to nodes 0, 2
>>> g.ndata
{'x': tensor([[2.],
[1.],
[2.]])}
See Also
--------
register_apply_node_func
apply_edges
"""
if func == "default":
func = self._apply_node_func
if is_all(v):
v = utils.toindex(slice(0, self.number_of_nodes()))
else:
v = utils.toindex(v)
with ir.prog() as prog:
scheduler.schedule_apply_nodes(graph=self,
v=v,
apply_func=func,
inplace=inplace)
Runtime.run(prog)
def apply_edges(self, func="default", edges=ALL, inplace=False):
"""Apply the function on the edges to update their features.
If None is provided for ``func``, nothing will happen.
Parameters
----------
func : callable, optional
Apply function on the edge. The function should be
an :mod:`Edge UDF <dgl.udf>`.
edges : valid edges type, optional
Edges on which to apply ``func``. See :func:`send` for valid
edges type. Default is all the edges.
inplace: bool, optional
If True, update will be done in place, but autograd will break.
Notes
-----
On multigraphs, if :math:`u` and :math:`v` are specified, then all the edges
between :math:`u` and :math:`v` will be updated.
Examples
--------
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(3)
>>> g.add_edges([0, 1], [1, 2]) # 0 -> 1, 1 -> 2
>>> g.edata['y'] = th.ones(2, 1)
>>> # Doubles the edge feature.
>>> def double_feature(edges): return {'y': edges.data['y'] * 2}
>>> g.apply_edges(func=double_feature, edges=0) # Apply func to the first edge.
>>> g.edata
{'y': tensor([[2.], # 2 * 1
[1.]])}
See Also
--------
apply_nodes
"""
if func == "default":
func = self._apply_edge_func
assert func is not None
if is_all(edges):
u, v, _ = self._graph.edges()
eid = utils.toindex(slice(0, self.number_of_edges()))
elif isinstance(edges, tuple):
u, v = edges
u = utils.toindex(u)
v = utils.toindex(v)
# Rewrite u, v to handle edge broadcasting and multigraph.
u, v, eid = self._graph.edge_ids(u, v)
else:
eid = utils.toindex(edges)
u, v, _ = self._graph.find_edges(eid)
with ir.prog() as prog:
scheduler.schedule_apply_edges(graph=self,
u=u,
v=v,
eid=eid,
apply_func=func,
inplace=inplace)
Runtime.run(prog)
def group_apply_edges(self, group_by, func, edges=ALL, inplace=False):
"""Group the edges by nodes and apply the function on the grouped edges to
update their features.
Parameters
----------
group_by : str
Specify how to group edges. Expected to be either 'src' or 'dst'
func : callable
Apply function on the edge. The function should be
an :mod:`Edge UDF <dgl.udf>`. The input of `Edge UDF` should
be (bucket_size, degrees, *feature_shape), and
return the dict with values of the same shapes.
edges : valid edges type, optional
Edges on which to group and apply ``func``. See :func:`send` for valid
edges type. Default is all the edges.
inplace: bool, optional
If True, update will be done in place, but autograd will break.
Notes
-----
On multigraphs, if :math:`u` and :math:`v` are specified, then all the edges
between :math:`u` and :math:`v` will be updated.
Examples
--------
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(4)
>>> g.add_edges(0, [1, 2, 3])
>>> g.add_edges(1, [2, 3])
>>> g.add_edges(2, [2, 3])
>>> g.edata['feat'] = th.randn((g.number_of_edges(), 1))
>>> # Softmax over the out edges of each node
>>> # Second dimension of edges.data is the degree dimension
>>> def softmax_feat(edges): return {'norm_feat': th.softmax(edges.data['feat'], dim=1)}
>>> g.group_apply_edges(func=softmax_feat, group_by='src') # Apply func to the first edge.
>>> u, v, eid = g.out_edges(1, form='all')
>>> in_feat = g.edata['feat'][eid]
>>> out_feat = g.edata['norm_feat'][eid]
>>> print(out_feat - th.softmax(in_feat, 0))
tensor([[0.],
[0.]])
See Also
--------
apply_edges
"""
assert func is not None
if group_by not in ('src', 'dst'):
raise DGLError("Group_by should be either src or dst")
if is_all(edges):
u, v, _ = self._graph.edges()
eid = utils.toindex(slice(0, self.number_of_edges()))
elif isinstance(edges, tuple):
u, v = edges
u = utils.toindex(u)
v = utils.toindex(v)
# Rewrite u, v to handle edge broadcasting and multigraph.
u, v, eid = self._graph.edge_ids(u, v)
else:
eid = utils.toindex(edges)
u, v, _ = self._graph.find_edges(eid)
with ir.prog() as prog:
scheduler.schedule_group_apply_edge(graph=self,
u=u,
v=v,
eid=eid,
apply_func=func,
group_by=group_by,
inplace=inplace)
Runtime.run(prog)
def send(self, edges=ALL, message_func="default"):
"""Send messages along the given edges.
``edges`` can be any of the following types:
* ``int`` : Specify one edge using its edge id.
* ``pair of int`` : Specify one edge using its endpoints.
* ``int iterable`` / ``tensor`` : Specify multiple edges using their edge ids.
* ``pair of int iterable`` / ``pair of tensors`` :
Specify multiple edges using their endpoints.
The UDF returns messages on the edges and can be later fetched in
the destination node's ``mailbox``. Receiving will consume the messages.
See :func:`recv` for example.
If multiple ``send`` are triggered on the same edge without ``recv``. Messages
generated by the later ``send`` will overwrite previous messages.
Parameters
----------
edges : valid edges type, optional
Edges on which to apply ``message_func``. Default is sending along all
the edges.
message_func : callable
Message function on the edges. The function should be
an :mod:`Edge UDF <dgl.udf>`.
Notes
-----
On multigraphs, if :math:`u` and :math:`v` are specified, then the messages will be sent
along all edges between :math:`u` and :math:`v`.
Examples
--------
See the *message passing* example in :class:`DGLGraph` or :func:`recv`.
"""
if message_func == "default":
message_func = self._message_func
if is_all(edges):
eid = utils.toindex(slice(0, self.number_of_edges()))
u, v, _ = self._graph.edges()
elif isinstance(edges, tuple):
u, v = edges
u = utils.toindex(u)
v = utils.toindex(v)
# Rewrite u, v to handle edge broadcasting and multigraph.
u, v, eid = self._graph.edge_ids(u, v)
else:
eid = utils.toindex(edges)
u, v, _ = self._graph.find_edges(eid)
if len(eid) == 0:
# no edge to be triggered
return
with ir.prog() as prog:
scheduler.schedule_send(graph=self, u=u, v=v, eid=eid,
message_func=message_func)
Runtime.run(prog)
def recv(self,
v=ALL,
reduce_func="default",
apply_node_func="default",
inplace=False):
"""Receive and reduce incoming messages and update the features of node(s) :math:`v`.
Optionally, apply a function to update the node features after receive.
* `reduce_func` will be skipped for nodes with no incoming message.
* If all ``v`` have no incoming message, this will downgrade to an :func:`apply_nodes`.
* If some ``v`` have no incoming message, their new feature value will be calculated
by the column initializer (see :func:`set_n_initializer`). The feature shapes and
dtypes will be inferred.
The node features will be updated by the result of the ``reduce_func``.
Messages are consumed once received.
The provided UDF maybe called multiple times so it is recommended to provide
function with no side effect.
Parameters
----------
v : node, container or tensor, optional
The node to be updated. Default is receiving all the nodes.
reduce_func : callable, optional
Reduce function on the node. The function should be
a :mod:`Node UDF <dgl.udf>`.
apply_node_func : callable
Apply function on the nodes. The function should be
a :mod:`Node UDF <dgl.udf>`.
inplace: bool, optional
If True, update will be done in place, but autograd will break.
Examples
--------
Create a graph object for demo.
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(3)
>>> g.ndata['x'] = th.tensor([[1.], [2.], [3.]])
>>> g.add_edges([0, 1], [1, 2])
>>> # Define the function for sending node features as messages.
>>> def send_source(edges): return {'m': edges.src['x']}
>>> # Set the function defined to be the default message function.
>>> g.register_message_func(send_source)
>>> # Sum the messages received and use this to replace the original node feature.
>>> def simple_reduce(nodes): return {'x': nodes.mailbox['m'].sum(1)}
>>> # Set the function defined to be the default message reduce function.
>>> g.register_reduce_func(simple_reduce)
Send and receive messages. Note that although node :math:`0` has no incoming edges,
its feature gets changed from :math:`1` to :math:`0` as it is also included in
``g.nodes()``.
>>> g.send(g.edges())
>>> g.recv(g.nodes())
>>> g.ndata['x']
tensor([[0.],
[1.],
[2.]])
Once messages are received, one will need another call of :func:`send` again before
another call of :func:`recv`. Otherwise, nothing will happen.
>>> g.recv(g.nodes())
>>> g.ndata['x']
tensor([[0.],
[1.],
[2.]])
"""
if reduce_func == "default":
reduce_func = self._reduce_func
if apply_node_func == "default":
apply_node_func = self._apply_node_func
assert reduce_func is not None
if is_all(v):
v = F.arange(0, self.number_of_nodes())
elif isinstance(v, int):
v = [v]
v = utils.toindex(v)
if len(v) == 0:
# no vertex to be triggered.
return
with ir.prog() as prog:
scheduler.schedule_recv(graph=self,
recv_nodes=v,
reduce_func=reduce_func,
apply_func=apply_node_func,
inplace=inplace)
Runtime.run(prog)
def send_and_recv(self,
edges,
message_func="default",
reduce_func="default",
apply_node_func="default",
inplace=False):
"""Send messages along edges and let destinations receive them.
Optionally, apply a function to update the node features after receive.
This is a convenient combination for performing
``send(self, self.edges, message_func)`` and
``recv(self, dst, reduce_func, apply_node_func)``, where ``dst``
are the destinations of the ``edges``.
Parameters
----------
edges : valid edges type
Edges on which to apply ``func``. See :func:`send` for valid
edges type.
message_func : callable, optional
Message function on the edges. The function should be
an :mod:`Edge UDF <dgl.udf>`.
reduce_func : callable, optional
Reduce function on the node. The function should be
a :mod:`Node UDF <dgl.udf>`.
apply_node_func : callable, optional
Apply function on the nodes. The function should be
a :mod:`Node UDF <dgl.udf>`.
inplace: bool, optional
If True, update will be done in place, but autograd will break.
Examples
--------
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(3)
>>> g.ndata['x'] = th.tensor([[1.], [2.], [3.]])
>>> g.add_edges([0, 1], [1, 2])
>>> # Define the function for sending node features as messages.
>>> def send_source(edges): return {'m': edges.src['x']}
>>> # Set the function defined to be the default message function.
>>> g.register_message_func(send_source)
>>> # Sum the messages received and use this to replace the original node feature.
>>> def simple_reduce(nodes): return {'x': nodes.mailbox['m'].sum(1)}
>>> # Set the function defined to be the default message reduce function.
>>> g.register_reduce_func(simple_reduce)
Send and receive messages.
>>> g.send_and_recv(g.edges())
>>> g.ndata['x']
tensor([[1.],
[1.],
[2.]])
Note that the feature of node :math:`0` remains the same as it has no
incoming edges.
Notes
-----
On multigraphs, if u and v are specified, then the messages will be sent
and received along all edges between u and v.
See Also
--------
send
recv
"""
if message_func == "default":
message_func = self._message_func
if reduce_func == "default":
reduce_func = self._reduce_func
if apply_node_func == "default":
apply_node_func = self._apply_node_func
assert message_func is not None
assert reduce_func is not None
if isinstance(edges, tuple):
u, v = edges
u = utils.toindex(u)
v = utils.toindex(v)
# Rewrite u, v to handle edge broadcasting and multigraph.
u, v, eid = self._graph.edge_ids(u, v)
else:
eid = utils.toindex(edges)
u, v, _ = self._graph.find_edges(eid)
if len(u) == 0:
# no edges to be triggered
return
with ir.prog() as prog:
scheduler.schedule_snr(graph=self,
edge_tuples=(u, v, eid),
message_func=message_func,
reduce_func=reduce_func,
apply_func=apply_node_func,
inplace=inplace)
Runtime.run(prog)
def pull(self,
v,
message_func="default",
reduce_func="default",
apply_node_func="default",
inplace=False):
"""Pull messages from the node(s)' predecessors and then update their features.
Optionally, apply a function to update the node features after receive.
* `reduce_func` will be skipped for nodes with no incoming message.
* If all ``v`` have no incoming message, this will downgrade to an :func:`apply_nodes`.
* If some ``v`` have no incoming message, their new feature value will be calculated
by the column initializer (see :func:`set_n_initializer`). The feature shapes and
dtypes will be inferred.
Parameters
----------
v : int, iterable of int, or tensor
The node(s) to be updated.
message_func : callable, optional
Message function on the edges. The function should be
an :mod:`Edge UDF <dgl.udf>`.
reduce_func : callable, optional
Reduce function on the node. The function should be
a :mod:`Node UDF <dgl.udf>`.
apply_node_func : callable, optional
Apply function on the nodes. The function should be
a :mod:`Node UDF <dgl.udf>`.
inplace: bool, optional
If True, update will be done in place, but autograd will break.
Examples
--------
Create a graph for demo.
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(3)
>>> g.ndata['x'] = th.tensor([[0.], [1.], [2.]])
Use the built-in message function :func:`~dgl.function.copy_src` for copying
node features as the message.
>>> m_func = dgl.function.copy_src('x', 'm')
>>> g.register_message_func(m_func)
Use the built-int message reducing function :func:`~dgl.function.sum`, which
sums the messages received and replace the old node features with it.
>>> m_reduce_func = dgl.function.sum('m', 'x')
>>> g.register_reduce_func(m_reduce_func)
As no edges exist, nothing happens.
>>> g.pull(g.nodes())
>>> g.ndata['x']
tensor([[0.],
[1.],
[2.]])
Add edges ``0 -> 1, 1 -> 2``. Pull messages for the node :math:`2`.
>>> g.add_edges([0, 1], [1, 2])
>>> g.pull(2)
>>> g.ndata['x']
tensor([[0.],
[1.],
[1.]])
The feature of node :math:`2` changes but the feature of node :math:`1`
remains the same as we did not :func:`pull` (and reduce) messages for it.
See Also
--------
push
"""
if message_func == "default":
message_func = self._message_func
if reduce_func == "default":
reduce_func = self._reduce_func
if apply_node_func == "default":
apply_node_func = self._apply_node_func
assert message_func is not None
assert reduce_func is not None
v = utils.toindex(v)
if len(v) == 0:
return
with ir.prog() as prog:
scheduler.schedule_pull(graph=self,
pull_nodes=v,
message_func=message_func,
reduce_func=reduce_func,
apply_func=apply_node_func,
inplace=inplace)
Runtime.run(prog)
def push(self,
u,
message_func="default",
reduce_func="default",
apply_node_func="default",
inplace=False):
"""Send message from the node(s) to their successors and update them.
Optionally, apply a function to update the node features after receive.
Parameters
----------
u : int, iterable of int, or tensor
The node(s) to push messages out.
message_func : callable, optional
Message function on the edges. The function should be
an :mod:`Edge UDF <dgl.udf>`.
reduce_func : callable, optional
Reduce function on the node. The function should be
a :mod:`Node UDF <dgl.udf>`.
apply_node_func : callable, optional
Apply function on the nodes. The function should be
a :mod:`Node UDF <dgl.udf>`.
inplace: bool, optional
If True, update will be done in place, but autograd will break.
Examples
--------
Create a graph for demo.
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(3)
>>> g.ndata['x'] = th.tensor([[1.], [2.], [3.]])
Use the built-in message function :func:`~dgl.function.copy_src` for copying
node features as the message.
>>> m_func = dgl.function.copy_src('x', 'm')
>>> g.register_message_func(m_func)
Use the built-int message reducing function :func:`~dgl.function.sum`, which
sums the messages received and replace the old node features with it.
>>> m_reduce_func = dgl.function.sum('m', 'x')
>>> g.register_reduce_func(m_reduce_func)
As no edges exist, nothing happens.
>>> g.push(g.nodes())
>>> g.ndata['x']
tensor([[1.],
[2.],
[3.]])
Add edges ``0 -> 1, 1 -> 2``. Send messages from the node :math:`1`. and update.
>>> g.add_edges([0, 1], [1, 2])
>>> g.push(1)
>>> g.ndata['x']
tensor([[1.],
[2.],
[2.]])
The feature of node :math:`2` changes but the feature of node :math:`1`
remains the same as we did not :func:`push` for node :math:`0`.
See Also
--------
pull
"""
if message_func == "default":
message_func = self._message_func
if reduce_func == "default":
reduce_func = self._reduce_func
if apply_node_func == "default":
apply_node_func = self._apply_node_func
assert message_func is not None
assert reduce_func is not None
u = utils.toindex(u)
if len(u) == 0:
return
with ir.prog() as prog:
scheduler.schedule_push(graph=self,
u=u,
message_func=message_func,
reduce_func=reduce_func,
apply_func=apply_node_func,
inplace=inplace)
Runtime.run(prog)
def update_all(self,
message_func="default",
reduce_func="default",
apply_node_func="default"):
"""Send messages through all edges and update all nodes.
Optionally, apply a function to update the node features after receive.
This is a convenient combination for performing
``send(self, self.edges(), message_func)`` and
``recv(self, self.nodes(), reduce_func, apply_node_func)``.
Parameters
----------
message_func : callable, optional
Message function on the edges. The function should be
an :mod:`Edge UDF <dgl.udf>`.
reduce_func : callable, optional
Reduce function on the node. The function should be
a :mod:`Node UDF <dgl.udf>`.
apply_node_func : callable, optional
Apply function on the nodes. The function should be
a :mod:`Node UDF <dgl.udf>`.
See Also
--------
send
recv
"""
if message_func == "default":
message_func = self._message_func
if reduce_func == "default":
reduce_func = self._reduce_func
if apply_node_func == "default":
apply_node_func = self._apply_node_func
assert message_func is not None
assert reduce_func is not None
with ir.prog() as prog:
scheduler.schedule_update_all(graph=self,
message_func=message_func,
reduce_func=reduce_func,
apply_func=apply_node_func)
Runtime.run(prog)
def prop_nodes(self,
nodes_generator,
message_func="default",
reduce_func="default",
apply_node_func="default"):
"""Propagate messages using graph traversal by triggering
:func:`pull()` on nodes.
The traversal order is specified by the ``nodes_generator``. It generates
node frontiers, which is a list or a tensor of nodes. The nodes in the
same frontier will be triggered together, while nodes in different frontiers
will be triggered according to the generating order.
Parameters
----------
node_generators : iterable, each element is a list or a tensor of node ids
The generator of node frontiers. It specifies which nodes perform
:func:`pull` at each timestep.
message_func : callable, optional
Message function on the edges. The function should be
an :mod:`Edge UDF <dgl.udf>`.
reduce_func : callable, optional
Reduce function on the node. The function should be
a :mod:`Node UDF <dgl.udf>`.
apply_node_func : callable, optional
Apply function on the nodes. The function should be
a :mod:`Node UDF <dgl.udf>`.
Examples
--------
Create a graph for demo.
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(4)
>>> g.ndata['x'] = th.tensor([[1.], [2.], [3.], [4.]])
>>> g.add_edges([0, 1, 1, 2], [1, 2, 3, 3])
Prepare message function and message reduce function for demo.
>>> def send_source(edges): return {'m': edges.src['x']}
>>> g.register_message_func(send_source)
>>> def simple_reduce(nodes): return {'x': nodes.mailbox['m'].sum(1)}
>>> g.register_reduce_func(simple_reduce)
First pull messages for nodes :math:`1, 2` with edges ``0 -> 1`` and
``1 -> 2``; and then pull messages for node :math:`3` with edges
``1 -> 3`` and ``2 -> 3``.
>>> g.prop_nodes([[1, 2], [3]])
>>> g.ndata['x']
tensor([[1.],
[1.],
[2.],
[3.]])
In the first stage, we pull messages for nodes :math:`1, 2`.
The feature of node :math:`1` is replaced by that of node :math:`0`, i.e. 1
The feature of node :math:`2` is replaced by that of node :math:`1`, i.e. 2.
Both of the replacement happen simultaneously.
In the second stage, we pull messages for node :math:`3`.
The feature of node :math:`3` becomes the sum of node :math:`1`'s feature and
:math:`2`'s feature, i.e. 1 + 2 = 3.
See Also
--------
prop_edges
"""
for node_frontier in nodes_generator:
self.pull(node_frontier, message_func, reduce_func, apply_node_func)
def prop_edges(self,
edges_generator,
message_func="default",
reduce_func="default",
apply_node_func="default"):
"""Propagate messages using graph traversal by triggering
:func:`send_and_recv()` on edges.
The traversal order is specified by the ``edges_generator``. It generates
edge frontiers. The edge frontiers should be of *valid edges type*.
See :func:`send` for more details.
Edges in the same frontier will be triggered together, while edges in
different frontiers will be triggered according to the generating order.
Parameters
----------
edges_generator : generator
The generator of edge frontiers.
message_func : callable, optional
Message function on the edges. The function should be
an :mod:`Edge UDF <dgl.udf>`.
reduce_func : callable, optional
Reduce function on the node. The function should be
a :mod:`Node UDF <dgl.udf>`.
apply_node_func : callable, optional
Apply function on the nodes. The function should be
a :mod:`Node UDF <dgl.udf>`.
Examples
--------
Create a graph for demo.
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(4)
>>> g.ndata['x'] = th.tensor([[1.], [2.], [3.], [4.]])
>>> g.add_edges([0, 1, 1, 2], [1, 2, 3, 3])
Prepare message function and message reduce function for demo.
>>> def send_source(edges): return {'m': edges.src['x']}
>>> g.register_message_func(send_source)
>>> def simple_reduce(nodes): return {'x': nodes.mailbox['m'].sum(1)}
>>> g.register_reduce_func(simple_reduce)
First propagate messages for edges ``0 -> 1``, ``1 -> 3`` and then
propagate messages for edges ``1 -> 2``, ``2 -> 3``.
>>> g.prop_edges([([0, 1], [1, 3]), ([1, 2], [2, 3])])
>>> g.ndata['x']
tensor([[1.],
[1.],
[1.],
[3.]])
In the first stage, the following happens simultaneously.
- The feature of node :math:`1` is replaced by that of
node :math:`0`, i.e. 1.
- The feature of node :math:`3` is replaced by that of
node :math:`1`, i.e. 2.
In the second stage, the following happens simultaneously.
- The feature of node :math:`2` is replaced by that of
node :math:`1`, i.e. 1.
- The feature of node :math:`3` is replaced by that of
node :math:`2`, i.e. 3.
See Also
--------
prop_nodes
"""
for edge_frontier in edges_generator:
self.send_and_recv(edge_frontier, message_func, reduce_func, apply_node_func)
def subgraph(self, nodes):
"""Return the subgraph induced on given nodes.
Parameters
----------
nodes : list, or iterable
A node ID array to construct subgraph.
All nodes must exist in the graph.
Returns
-------
G : DGLSubGraph
The subgraph.
The nodes are relabeled so that node `i` in the subgraph is mapped
to node `nodes[i]` in the original graph.
The edges are also relabeled.
One can retrieve the mapping from subgraph node/edge ID to parent
node/edge ID via `parent_nid` and `parent_eid` properties of the
subgraph.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(5)
>>> G.add_edges([0, 1, 2, 3, 4], [1, 2, 3, 4, 0]) # 5-node cycle
>>> SG = G.subgraph([0, 1, 4])
>>> SG.nodes()
tensor([0, 1, 2])
>>> SG.edges()
(tensor([0, 2]), tensor([1, 0]))
>>> SG.parent_nid
tensor([0, 1, 4])
>>> SG.parent_eid
tensor([0, 4])
See Also
--------
DGLSubGraph
subgraphs
edge_subgraph
"""
from . import subgraph
induced_nodes = utils.toindex(nodes)
sgi = self._graph.node_subgraph(induced_nodes)
return subgraph.DGLSubGraph(self, sgi.induced_nodes, sgi.induced_edges, sgi)
def subgraphs(self, nodes):
"""Return a list of subgraphs, each induced in the corresponding given
nodes in the list.
Equivalent to
``[self.subgraph(nodes_list) for nodes_list in nodes]``
Parameters
----------
nodes : a list of lists or iterable
A list of node ID arrays to construct corresponding subgraphs.
All nodes in all the list items must exist in the graph.
Returns
-------
G : A list of DGLSubGraph
The subgraphs.
See Also
--------
DGLSubGraph
subgraph
"""
from . import subgraph
induced_nodes = [utils.toindex(n) for n in nodes]
sgis = self._graph.node_subgraphs(induced_nodes)
return [subgraph.DGLSubGraph(self, sgi.induced_nodes, sgi.induced_edges, sgi)
for sgi in sgis]
def edge_subgraph(self, edges):
"""Return the subgraph induced on given edges.
Parameters
----------
edges : list, or iterable
An edge ID array to construct subgraph.
All edges must exist in the subgraph.
Returns
-------
G : DGLSubGraph
The subgraph.
The edges are relabeled so that edge `i` in the subgraph is mapped
to edge `edges[i]` in the original graph.
The nodes are also relabeled.
One can retrieve the mapping from subgraph node/edge ID to parent
node/edge ID via `parent_nid` and `parent_eid` properties of the
subgraph.
Examples
--------
The following example uses PyTorch backend.
>>> G = dgl.DGLGraph()
>>> G.add_nodes(5)
>>> G.add_edges([0, 1, 2, 3, 4], [1, 2, 3, 4, 0]) # 5-node cycle
>>> SG = G.edge_subgraph([0, 4])
>>> SG.nodes()
tensor([0, 1, 2])
>>> SG.edges()
(tensor([0, 2]), tensor([1, 0]))
>>> SG.parent_nid
tensor([0, 1, 4])
>>> SG.parent_eid
tensor([0, 4])
See Also
--------
DGLSubGraph
subgraph
"""
from . import subgraph
induced_edges = utils.toindex(edges)
sgi = self._graph.edge_subgraph(induced_edges)
return subgraph.DGLSubGraph(self, sgi.induced_nodes, sgi.induced_edges, sgi)
def adjacency_matrix(self, transpose=False, ctx=F.cpu()):
"""Return the adjacency matrix representation of this graph.
By default, a row of returned adjacency matrix represents the
destination of an edge and the column represents the source.
When transpose is True, a row represents the source and a column
represents a destination.
Parameters
----------
transpose : bool, optional (default=False)
A flag to transpose the returned adjacency matrix.
ctx : context, optional (default=cpu)
The context of returned adjacency matrix.
Returns
-------
SparseTensor
The adjacency matrix.
"""
return self._graph.adjacency_matrix(transpose, ctx)[0]
def incidence_matrix(self, typestr, ctx=F.cpu()):
"""Return the incidence matrix representation of this graph.
An incidence matrix is an n x m sparse matrix, where n is
the number of nodes and m is the number of edges. Each nnz
value indicating whether the edge is incident to the node
or not.
There are three types of an incidence matrix :math:`I`:
* ``in``:
- :math:`I[v, e] = 1` if :math:`e` is the in-edge of :math:`v`
(or :math:`v` is the dst node of :math:`e`);
- :math:`I[v, e] = 0` otherwise.
* ``out``:
- :math:`I[v, e] = 1` if :math:`e` is the out-edge of :math:`v`
(or :math:`v` is the src node of :math:`e`);
- :math:`I[v, e] = 0` otherwise.
* ``both``:
- :math:`I[v, e] = 1` if :math:`e` is the in-edge of :math:`v`;
- :math:`I[v, e] = -1` if :math:`e` is the out-edge of :math:`v`;
- :math:`I[v, e] = 0` otherwise (including self-loop).
Parameters
----------
typestr : str
Can be either ``in``, ``out`` or ``both``
ctx : context, optional (default=cpu)
The context of returned incidence matrix.
Returns
-------
SparseTensor
The incidence matrix.
"""
return self._graph.incidence_matrix(typestr, ctx)[0]
def line_graph(self, backtracking=True, shared=False):
"""Return the line graph of this graph.
See :func:`~dgl.transform.line_graph`.
"""
return dgl.line_graph(self, backtracking, shared)
def reverse(self, share_ndata=False, share_edata=False):
"""Return the reverse of this graph.
See :func:`~dgl.transform.reverse`.
"""
return dgl.reverse(self, share_ndata, share_edata)
def filter_nodes(self, predicate, nodes=ALL):
"""Return a tensor of node IDs that satisfy the given predicate.
Parameters
----------
predicate : callable
A function of signature ``func(nodes) -> tensor``.
``nodes`` are :class:`NodeBatch` objects as in :mod:`~dgl.udf`.
The ``tensor`` returned should be a 1-D boolean tensor with
each element indicating whether the corresponding node in
the batch satisfies the predicate.
nodes : int, iterable or tensor of ints
The nodes to filter on. Default value is all the nodes.
Returns
-------
tensor
The filtered nodes.
Examples
--------
Construct a graph object for demo.
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(3)
>>> g.ndata['x'] = th.tensor([[1.], [-1.], [1.]])
Define a function for filtering nodes with feature :math:`1`.
>>> def has_feature_one(nodes): return (nodes.data['x'] == 1).squeeze(1)
Filter the nodes with feature :math:`1`.
>>> g.filter_nodes(has_feature_one)
tensor([0, 2])
See Also
--------
filter_edges
"""
if is_all(nodes):
v = utils.toindex(slice(0, self.number_of_nodes()))
else:
v = utils.toindex(nodes)
n_repr = self.get_n_repr(v)
nbatch = NodeBatch(self, v, n_repr)
n_mask = predicate(nbatch)
if is_all(nodes):
return F.nonzero_1d(n_mask)
else:
nodes = F.tensor(nodes)
return F.boolean_mask(nodes, n_mask)
def filter_edges(self, predicate, edges=ALL):
"""Return a tensor of edge IDs that satisfy the given predicate.
Parameters
----------
predicate : callable
A function of signature ``func(edges) -> tensor``.
``edges`` are :class:`EdgeBatch` objects as in :mod:`~dgl.udf`.
The ``tensor`` returned should be a 1-D boolean tensor with
each element indicating whether the corresponding edge in
the batch satisfies the predicate.
edges : valid edges type
Edges on which to apply ``func``. See :func:`send` for valid
edges type. Default value is all the edges.
Returns
-------
tensor
The filtered edges represented by their ids.
Examples
--------
Construct a graph object for demo.
.. note:: Here we use pytorch syntax for demo. The general idea applies
to other frameworks with minor syntax change (e.g. replace
``torch.tensor`` with ``mxnet.ndarray``).
>>> import torch as th
>>> g = dgl.DGLGraph()
>>> g.add_nodes(3)
>>> g.ndata['x'] = th.tensor([[1.], [-1.], [1.]])
>>> g.add_edges([0, 1, 2], [2, 2, 1])
Define a function for filtering edges whose destinations have
node feature :math:`1`.
>>> def has_dst_one(edges): return (edges.dst['x'] == 1).squeeze(1)
Filter the edges whose destination nodes have feature :math:`1`.
>>> g.filter_edges(has_dst_one)
tensor([0, 1])
See Also
--------
filter_nodes
"""
if is_all(edges):
eid = ALL
u, v, _ = self._graph.edges()
elif isinstance(edges, tuple):
u, v = edges
u = utils.toindex(u)
v = utils.toindex(v)
# Rewrite u, v to handle edge broadcasting and multigraph.
u, v, eid = self._graph.edge_ids(u, v)
else:
eid = utils.toindex(edges)
u, v, _ = self._graph.find_edges(eid)
src_data = self.get_n_repr(u)
edge_data = self.get_e_repr(eid)
dst_data = self.get_n_repr(v)
ebatch = EdgeBatch(self, (u, v, eid), src_data, edge_data, dst_data)
e_mask = predicate(ebatch)
if is_all(edges):
return F.nonzero_1d(e_mask)
else:
edges = F.tensor(edges)
return F.boolean_mask(edges, e_mask)
def readonly(self, readonly_state=True):
"""Set this graph's readonly state in-place.
Parameters
----------
readonly_state : bool, optional
New readonly state of the graph, defaults to True.
Examples
--------
>>> G = dgl.DGLGraph()
>>> G.add_nodes(3)
>>> G.add_edge(0, 1)
>>> G.readonly()
>>> try:
>>> G.add_nodes(5)
>>> fail = False
>>> except:
>>> fail = True
>>>
>>> fail
True
>>> G.readonly(False)
>>> G.add_nodes(5)
>>> G.number_of_nodes()
8
"""
if readonly_state != self.is_readonly:
self._graph.readonly(readonly_state)
def __repr__(self):
ret = ('DGLGraph(num_nodes={node}, num_edges={edge},\n'
' ndata_schemes={ndata}\n'
' edata_schemes={edata})')
return ret.format(node=self.number_of_nodes(), edge=self.number_of_edges(),
ndata=str(self.node_attr_schemes()),
edata=str(self.edge_attr_schemes()))
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