dmlc--dgl
Mufei Li
698 行
24 KiB
Python
698 行
24 KiB
Python
"""Classes and functions for batching multiple graphs together."""
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from __future__ import absolute_import
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import numpy as np
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from collections import Iterable
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from .base import ALL, is_all
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from .frame import FrameRef, Frame
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from .graph import DGLGraph
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from . import graph_index as gi
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from . import backend as F
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from . import utils
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__all__ = ['BatchedDGLGraph', 'batch', 'unbatch', 'split',
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'sum_nodes', 'sum_edges', 'mean_nodes', 'mean_edges']
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class BatchedDGLGraph(DGLGraph):
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"""Class for batched DGL graphs.
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A :class:`BatchedDGLGraph` basically merges a list of small graphs into a giant
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graph so that one can perform message passing and readout over a batch of graphs
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simultaneously.
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The nodes and edges are re-indexed with a new id in the batched graph with the
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rule below:
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====== ========== ======================== === ==========================
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item Graph 1 Graph 2 ... Graph k
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====== ========== ======================== === ==========================
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raw id 0, ..., N1 0, ..., N2 ... ..., Nk
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new id 0, ..., N1 N1 + 1, ..., N1 + N2 + 1 ... ..., N1 + ... + Nk + k - 1
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====== ========== ======================== === ==========================
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The batched graph is read-only, i.e. one cannot further add nodes and edges.
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A ``RuntimeError`` will be raised if one attempts.
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To modify the features in :class:`BatchedDGLGraph` has no effect on the original
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graphs. See the examples below about how to work around.
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Parameters
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----------
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graph_list : iterable
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A collection of :class:`~dgl.DGLGraph` objects to be batched.
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node_attrs : None, str or iterable, optional
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The node attributes to be batched. If ``None``, the :class:`BatchedDGLGraph` object
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will not have any node attributes. By default, all node attributes will be batched.
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An error will be raised if graphs having nodes have different attributes. If ``str``
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or ``iterable``, this should specify exactly what node attributes to be batched.
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edge_attrs : None, str or iterable, optional
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Same as for the case of :attr:`node_attrs`
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Examples
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--------
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Create two :class:`~dgl.DGLGraph` objects.
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**Instantiation:**
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>>> import dgl
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>>> import torch as th
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>>> g1 = dgl.DGLGraph()
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>>> g1.add_nodes(2) # Add 2 nodes
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>>> g1.add_edge(0, 1) # Add edge 0 -> 1
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>>> g1.ndata['hv'] = th.tensor([[0.], [1.]]) # Initialize node features
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>>> g1.edata['he'] = th.tensor([[0.]]) # Initialize edge features
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>>> g2 = dgl.DGLGraph()
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>>> g2.add_nodes(3) # Add 3 nodes
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>>> g2.add_edges([0, 2], [1, 1]) # Add edges 0 -> 1, 2 -> 1
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>>> g2.ndata['hv'] = th.tensor([[2.], [3.], [4.]]) # Initialize node features
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>>> g2.edata['he'] = th.tensor([[1.], [2.]]) # Initialize edge features
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Merge two :class:`~dgl.DGLGraph` objects into one :class:`BatchedDGLGraph` object.
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When merging a list of graphs, we can choose to include only a subset of the attributes.
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>>> bg = dgl.batch([g1, g2], edge_attrs=None)
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>>> bg.edata
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{}
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Below one can see that the nodes are re-indexed. The edges are re-indexed in
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the same way.
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>>> bg.nodes()
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tensor([0, 1, 2, 3, 4])
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>>> bg.ndata['hv']
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tensor([[0.],
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[1.],
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[2.],
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[3.],
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[4.]])
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**Property:**
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We can still get a brief summary of the graphs that constitute the batched graph.
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>>> bg.batch_size
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2
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>>> bg.batch_num_nodes
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[2, 3]
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>>> bg.batch_num_edges
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[1, 2]
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**Readout:**
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Another common demand for graph neural networks is graph readout, which is a
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function that takes in the node attributes and/or edge attributes for a graph
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and outputs a vector summarizing the information in the graph.
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:class:`BatchedDGLGraph` also supports performing readout for a batch of graphs at once.
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Below we take the built-in readout function :func:`sum_nodes` as an example, which
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sums over a particular kind of node attribute for each graph.
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>>> dgl.sum_nodes(bg, 'hv') # Sum the node attribute 'hv' for each graph.
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tensor([[1.], # 0 + 1
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[9.]]) # 2 + 3 + 4
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**Message passing:**
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For message passing and related operations, :class:`BatchedDGLGraph` acts exactly
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the same as :class:`~dgl.DGLGraph`.
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**Update Attributes:**
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Updating the attributes of the batched graph has no effect on the original graphs.
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>>> bg.edata['he'] = th.zeros(3, 2)
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>>> g2.edata['he']
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tensor([[1.],
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[2.]])}
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Instead, we can decompose the batched graph back into a list of graphs and use them
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to replace the original graphs.
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>>> g1, g2 = dgl.unbatch(bg) # returns a list of DGLGraph objects
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>>> g2.edata['he']
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tensor([[0., 0.],
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[0., 0.]])}
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"""
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def __init__(self, graph_list, node_attrs, edge_attrs):
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def _get_num_item_and_attr_types(g, mode):
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if mode == 'node':
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num_items = g.number_of_nodes()
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attr_types = set(g.node_attr_schemes().keys())
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elif mode == 'edge':
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num_items = g.number_of_edges()
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attr_types = set(g.edge_attr_schemes().keys())
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return num_items, attr_types
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def _init_attrs(attrs, mode):
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if attrs is None:
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return []
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elif is_all(attrs):
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attrs = set()
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# Check if at least a graph has mode items and associated features.
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for i in range(len(graph_list)):
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g = graph_list[i]
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g_num_items, g_attrs = _get_num_item_and_attr_types(g, mode)
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if g_num_items > 0 and len(g_attrs) > 0:
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attrs = g_attrs
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ref_g_index = i
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break
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# Check if all the graphs with mode items have the same associated features.
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if len(attrs) > 0:
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for i in range(len(graph_list)):
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g = graph_list[i]
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g_num_items, g_attrs = _get_num_item_and_attr_types(g, mode)
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if g_attrs != attrs and g_num_items > 0:
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raise ValueError('Expect graph {} and {} to have the same {} '
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'attributes when {}_attrs=ALL, got {} and '
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'{}'.format(ref_g_index, i, mode, mode, attrs, g_attrs))
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return attrs
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elif isinstance(attrs, str):
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return [attrs]
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elif isinstance(attrs, Iterable):
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return attrs
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else:
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raise ValueError('Expected {} attrs to be of type None str or Iterable, '
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'got type {}'.format(mode, type(attrs)))
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node_attrs = _init_attrs(node_attrs, 'node')
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edge_attrs = _init_attrs(edge_attrs, 'edge')
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# create batched graph index
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batched_index = gi.disjoint_union([g._graph for g in graph_list])
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# create batched node and edge frames
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if len(node_attrs) == 0:
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batched_node_frame = FrameRef(Frame(num_rows=batched_index.number_of_nodes()))
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else:
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# NOTE: following code will materialize the columns of the input graphs.
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cols = {key: F.cat([gr._node_frame[key] for gr in graph_list
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if gr.number_of_nodes() > 0], dim=0)
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for key in node_attrs}
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batched_node_frame = FrameRef(Frame(cols))
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if len(edge_attrs) == 0:
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batched_edge_frame = FrameRef(Frame(num_rows=batched_index.number_of_edges()))
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else:
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cols = {key: F.cat([gr._edge_frame[key] for gr in graph_list
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if gr.number_of_edges() > 0], dim=0)
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for key in edge_attrs}
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batched_edge_frame = FrameRef(Frame(cols))
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super(BatchedDGLGraph, self).__init__(
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graph_data=batched_index,
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node_frame=batched_node_frame,
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edge_frame=batched_edge_frame)
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# extra members
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self._batch_size = 0
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self._batch_num_nodes = []
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self._batch_num_edges = []
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for gr in graph_list:
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if isinstance(gr, BatchedDGLGraph):
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# handle the input is again a batched graph.
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self._batch_size += gr._batch_size
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self._batch_num_nodes += gr._batch_num_nodes
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self._batch_num_edges += gr._batch_num_edges
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else:
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self._batch_size += 1
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self._batch_num_nodes.append(gr.number_of_nodes())
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self._batch_num_edges.append(gr.number_of_edges())
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@property
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def batch_size(self):
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"""Number of graphs in this batch.
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Returns
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-------
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int
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Number of graphs in this batch."""
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return self._batch_size
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@property
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def batch_num_nodes(self):
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"""Number of nodes of each graph in this batch.
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Returns
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-------
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list
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Number of nodes of each graph in this batch."""
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return self._batch_num_nodes
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@property
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def batch_num_edges(self):
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"""Number of edges of each graph in this batch.
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Returns
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-------
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list
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Number of edges of each graph in this batch."""
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return self._batch_num_edges
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# override APIs
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def add_nodes(self, num, reprs=None):
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"""Add nodes. Disabled because BatchedDGLGraph is read-only."""
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raise RuntimeError('Readonly graph. Mutation is not allowed.')
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def add_edge(self, u, v, reprs=None):
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"""Add one edge. Disabled because BatchedDGLGraph is read-only."""
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raise RuntimeError('Readonly graph. Mutation is not allowed.')
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def add_edges(self, u, v, reprs=None):
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"""Add many edges. Disabled because BatchedDGLGraph is read-only."""
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raise RuntimeError('Readonly graph. Mutation is not allowed.')
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# new APIs
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def __getitem__(self, idx):
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"""Slice the batch and return the batch of graphs specified by the idx."""
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# TODO
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pass
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def __setitem__(self, idx, val):
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"""Set the value of the slice. The graph size cannot be changed."""
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# TODO
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pass
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def split(graph_batch, num_or_size_splits):
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"""Split the batch."""
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# TODO(minjie): could follow torch.split syntax
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pass
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def unbatch(graph):
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"""Return the list of graphs in this batch.
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Parameters
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----------
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graph : BatchedDGLGraph
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The batched graph.
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Returns
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-------
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list
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A list of :class:`~dgl.DGLGraph` objects whose attributes are obtained
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by partitioning the attributes of the :attr:`graph`. The length of the
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list is the same as the batch size of :attr:`graph`.
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Notes
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-----
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Unbatching will break each field tensor of the batched graph into smaller
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partitions.
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For simpler tasks such as node/edge state aggregation, try to use
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readout functions.
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See Also
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--------
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batch
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"""
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assert isinstance(graph, BatchedDGLGraph)
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bsize = graph.batch_size
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bn = graph.batch_num_nodes
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be = graph.batch_num_edges
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pttns = gi.disjoint_partition(graph._graph, utils.toindex(bn))
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# split the frames
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node_frames = [FrameRef(Frame(num_rows=n)) for n in bn]
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edge_frames = [FrameRef(Frame(num_rows=n)) for n in be]
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for attr, col in graph._node_frame.items():
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col_splits = F.split(col, bn, dim=0)
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for i in range(bsize):
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node_frames[i][attr] = col_splits[i]
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for attr, col in graph._edge_frame.items():
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col_splits = F.split(col, be, dim=0)
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for i in range(bsize):
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edge_frames[i][attr] = col_splits[i]
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return [DGLGraph(graph_data=pttns[i],
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node_frame=node_frames[i],
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edge_frame=edge_frames[i]) for i in range(bsize)]
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def batch(graph_list, node_attrs=ALL, edge_attrs=ALL):
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"""Batch a collection of :class:`~dgl.DGLGraph` and return a
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:class:`BatchedDGLGraph` object that is independent of the :attr:`graph_list`.
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Parameters
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----------
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graph_list : iterable
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A collection of :class:`~dgl.DGLGraph` to be batched.
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node_attrs : None, str or iterable
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The node attributes to be batched. If ``None``, the :class:`BatchedDGLGraph`
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object will not have any node attributes. By default, all node attributes will
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be batched. If ``str`` or iterable, this should specify exactly what node
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attributes to be batched.
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edge_attrs : None, str or iterable, optional
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Same as for the case of :attr:`node_attrs`
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Returns
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-------
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BatchedDGLGraph
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one single batched graph
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See Also
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--------
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BatchedDGLGraph
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unbatch
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"""
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return BatchedDGLGraph(graph_list, node_attrs, edge_attrs)
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_readout_on_attrs = {
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'nodes': ('ndata', 'batch_num_nodes', 'number_of_nodes'),
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'edges': ('edata', 'batch_num_edges', 'number_of_edges'),
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}
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def _sum_on(graph, on, input, weight):
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data_attr, batch_num_objs_attr, num_objs_attr = _readout_on_attrs[on]
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data = getattr(graph, data_attr)
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input = data[input]
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if weight is not None:
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weight = data[weight]
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weight = F.reshape(weight, (-1,) + (1,) * (F.ndim(input) - 1))
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input = weight * input
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if isinstance(graph, BatchedDGLGraph):
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n_graphs = graph.batch_size
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batch_num_objs = getattr(graph, batch_num_objs_attr)
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n_objs = getattr(graph, num_objs_attr)()
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seg_id = F.zerocopy_from_numpy(
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np.arange(n_graphs, dtype='int64').repeat(batch_num_objs))
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seg_id = F.copy_to(seg_id, F.context(input))
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y = F.unsorted_1d_segment_sum(input, seg_id, n_graphs, 0)
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return y
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else:
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return F.sum(input, 0)
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def sum_nodes(graph, input, weight=None):
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"""Sums all the values of node field :attr:`input` in :attr:`graph`, optionally
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multiplies the field by a scalar node field :attr:`weight`.
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Parameters
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----------
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graph : DGLGraph or BatchedDGLGraph
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The graph
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input : str
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The input field
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weight : str, optional
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The weight field. If None, no weighting will be performed,
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otherwise, weight each node feature with field :attr:`input`.
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for summation. The weight feature associated in the :attr:`graph`
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should be a tensor of shape ``[graph.number_of_nodes(), 1]``.
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Returns
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-------
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tensor
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The summed tensor.
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Notes
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-----
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If graph is a :class:`BatchedDGLGraph` object, a stacked tensor is
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returned instead, i.e. having an extra first dimension.
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Each row of the stacked tensor contains the readout result of the
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corresponding example in the batch. If an example has no nodes,
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a zero tensor with the same shape is returned at the corresponding row.
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Examples
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--------
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>>> import dgl
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>>> import torch as th
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Create two :class:`~dgl.DGLGraph` objects and initialize their
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node features.
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>>> g1 = dgl.DGLGraph() # Graph 1
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>>> g1.add_nodes(2)
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>>> g1.ndata['h'] = th.tensor([[1.], [2.]])
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>>> g1.ndata['w'] = th.tensor([[3.], [6.]])
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>>> g2 = dgl.DGLGraph() # Graph 2
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>>> g2.add_nodes(3)
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>>> g2.ndata['h'] = th.tensor([[1.], [2.], [3.]])
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Sum over node attribute :attr:`h` without weighting for each graph in a
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batched graph.
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>>> bg = dgl.batch([g1, g2], node_attrs='h')
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>>> dgl.sum_nodes(bg, 'h')
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tensor([[3.], # 1 + 2
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[6.]]) # 1 + 2 + 3
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Sum node attribute :attr:`h` with weight from node attribute :attr:`w`
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for a single graph.
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>>> dgl.sum_nodes(g1, 'h', 'w')
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tensor([15.]) # 1 * 3 + 2 * 6
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See Also
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--------
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mean_nodes
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sum_edges
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mean_edges
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"""
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return _sum_on(graph, 'nodes', input, weight)
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def sum_edges(graph, input, weight=None):
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"""Sums all the values of edge field :attr:`input` in :attr:`graph`,
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optionally multiplies the field by a scalar edge field :attr:`weight`.
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Parameters
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----------
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graph : DGLGraph or BatchedDGLGraph
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The graph
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input : str
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The input field
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weight : str, optional
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The weight field. If None, no weighting will be performed,
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otherwise, weight each edge feature with field :attr:`input`.
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for summation. The weight feature associated in the :attr:`graph`
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should be a tensor of shape ``[graph.number_of_edges(), 1]``.
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Returns
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-------
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tensor
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The summed tensor.
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Notes
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-----
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If graph is a :class:`BatchedDGLGraph` object, a stacked tensor is
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returned instead, i.e. having an extra first dimension.
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Each row of the stacked tensor contains the readout result of the
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corresponding example in the batch. If an example has no edges,
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a zero tensor with the same shape is returned at the corresponding row.
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Examples
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--------
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>>> import dgl
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>>> import torch as th
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Create two :class:`~dgl.DGLGraph` objects and initialize their
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edge features.
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>>> g1 = dgl.DGLGraph() # Graph 1
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>>> g1.add_nodes(2)
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>>> g1.add_edges([0, 1], [1, 0])
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>>> g1.edata['h'] = th.tensor([[1.], [2.]])
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>>> g1.edata['w'] = th.tensor([[3.], [6.]])
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>>> g2 = dgl.DGLGraph() # Graph 2
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>>> g2.add_nodes(3)
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>>> g2.add_edges([0, 1, 2], [1, 2, 0])
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>>> g2.edata['h'] = th.tensor([[1.], [2.], [3.]])
|
|
|
|
Sum over edge attribute :attr:`h` without weighting for each graph in a
|
|
batched graph.
|
|
|
|
>>> bg = dgl.batch([g1, g2], edge_attrs='h')
|
|
>>> dgl.sum_edges(bg, 'h')
|
|
tensor([[3.], # 1 + 2
|
|
[6.]]) # 1 + 2 + 3
|
|
|
|
Sum edge attribute :attr:`h` with weight from edge attribute :attr:`w`
|
|
for a single graph.
|
|
|
|
>>> dgl.sum_edges(g1, 'h', 'w')
|
|
tensor([15.]) # 1 * 3 + 2 * 6
|
|
|
|
See Also
|
|
--------
|
|
sum_nodes
|
|
mean_nodes
|
|
mean_edges
|
|
"""
|
|
return _sum_on(graph, 'edges', input, weight)
|
|
|
|
|
|
def _mean_on(graph, on, input, weight):
|
|
data_attr, batch_num_objs_attr, num_objs_attr = _readout_on_attrs[on]
|
|
data = getattr(graph, data_attr)
|
|
input = data[input]
|
|
|
|
if weight is not None:
|
|
weight = data[weight]
|
|
weight = F.reshape(weight, (-1,) + (1,) * (F.ndim(input) - 1))
|
|
input = weight * input
|
|
|
|
if isinstance(graph, BatchedDGLGraph):
|
|
n_graphs = graph.batch_size
|
|
batch_num_objs = getattr(graph, batch_num_objs_attr)
|
|
n_objs = getattr(graph, num_objs_attr)()
|
|
|
|
seg_id = F.zerocopy_from_numpy(
|
|
np.arange(n_graphs, dtype='int64').repeat(batch_num_objs))
|
|
seg_id = F.copy_to(seg_id, F.context(input))
|
|
if weight is not None:
|
|
w = F.unsorted_1d_segment_sum(weight, seg_id, n_graphs, 0)
|
|
y = F.unsorted_1d_segment_sum(input, seg_id, n_graphs, 0)
|
|
y = y / w
|
|
else:
|
|
y = F.unsorted_1d_segment_mean(input, seg_id, n_graphs, 0)
|
|
return y
|
|
else:
|
|
if weight is None:
|
|
return F.mean(input, 0)
|
|
else:
|
|
y = F.sum(input, 0) / F.sum(weight, 0)
|
|
return y
|
|
|
|
def mean_nodes(graph, input, weight=None):
|
|
"""Averages all the values of node field :attr:`input` in :attr:`graph`,
|
|
optionally multiplies the field by a scalar node field :attr:`weight`.
|
|
|
|
Parameters
|
|
----------
|
|
graph : DGLGraph or BatchedDGLGraph
|
|
The graph
|
|
input : str
|
|
The input field
|
|
weight : str, optional
|
|
The weight field. If None, no weighting will be performed,
|
|
otherwise, weight each node feature with field :attr:`input`.
|
|
for calculating mean. The weight feature associated in the :attr:`graph`
|
|
should be a tensor of shape ``[graph.number_of_nodes(), 1]``.
|
|
|
|
Returns
|
|
-------
|
|
tensor
|
|
The averaged tensor.
|
|
|
|
Notes
|
|
-----
|
|
If graph is a :class:`BatchedDGLGraph` object, a stacked tensor is
|
|
returned instead, i.e. having an extra first dimension.
|
|
Each row of the stacked tensor contains the readout result of
|
|
corresponding example in the batch. If an example has no nodes,
|
|
a zero tensor with the same shape is returned at the corresponding row.
|
|
|
|
Examples
|
|
--------
|
|
|
|
>>> import dgl
|
|
>>> import torch as th
|
|
|
|
Create two :class:`~dgl.DGLGraph` objects and initialize their
|
|
node features.
|
|
|
|
>>> g1 = dgl.DGLGraph() # Graph 1
|
|
>>> g1.add_nodes(2)
|
|
>>> g1.ndata['h'] = th.tensor([[1.], [2.]])
|
|
>>> g1.ndata['w'] = th.tensor([[3.], [6.]])
|
|
|
|
>>> g2 = dgl.DGLGraph() # Graph 2
|
|
>>> g2.add_nodes(3)
|
|
>>> g2.ndata['h'] = th.tensor([[1.], [2.], [3.]])
|
|
|
|
Average over node attribute :attr:`h` without weighting for each graph in a
|
|
batched graph.
|
|
|
|
>>> bg = dgl.batch([g1, g2], node_attrs='h')
|
|
>>> dgl.mean_nodes(bg, 'h')
|
|
tensor([[1.5000], # (1 + 2) / 2
|
|
[2.0000]]) # (1 + 2 + 3) / 3
|
|
|
|
Sum node attribute :attr:`h` with normalized weight from node attribute :attr:`w`
|
|
for a single graph.
|
|
|
|
>>> dgl.mean_nodes(g1, 'h', 'w') # h1 * (w1 / (w1 + w2)) + h2 * (w2 / (w1 + w2))
|
|
tensor([1.6667]) # 1 * (3 / (3 + 6)) + 2 * (6 / (3 + 6))
|
|
|
|
See Also
|
|
--------
|
|
sum_nodes
|
|
sum_edges
|
|
mean_edges
|
|
"""
|
|
return _mean_on(graph, 'nodes', input, weight)
|
|
|
|
def mean_edges(graph, input, weight=None):
|
|
"""Averages all the values of edge field :attr:`input` in :attr:`graph`,
|
|
optionally multiplies the field by a scalar edge field :attr:`weight`.
|
|
|
|
Parameters
|
|
----------
|
|
graph : DGLGraph or BatchedDGLGraph
|
|
The graph
|
|
input : str
|
|
The input field
|
|
weight : optional, str
|
|
The weight field. If None, no weighting will be performed,
|
|
otherwise, weight each edge feature with field :attr:`input`.
|
|
for calculating mean. The weight feature associated in the :attr:`graph`
|
|
should be a tensor of shape ``[graph.number_of_edges(), 1]``.
|
|
|
|
Returns
|
|
-------
|
|
tensor
|
|
The averaged tensor.
|
|
|
|
Notes
|
|
-----
|
|
If graph is a :class:`BatchedDGLGraph` object, a stacked tensor is
|
|
returned instead, i.e. having an extra first dimension.
|
|
Each row of the stacked tensor contains the readout result of
|
|
corresponding example in the batch. If an example has no edges,
|
|
a zero tensor with the same shape is returned at the corresponding row.
|
|
|
|
Examples
|
|
--------
|
|
|
|
>>> import dgl
|
|
>>> import torch as th
|
|
|
|
Create two :class:`~dgl.DGLGraph` objects and initialize their
|
|
edge features.
|
|
|
|
>>> g1 = dgl.DGLGraph() # Graph 1
|
|
>>> g1.add_nodes(2)
|
|
>>> g1.add_edges([0, 1], [1, 0])
|
|
>>> g1.edata['h'] = th.tensor([[1.], [2.]])
|
|
>>> g1.edata['w'] = th.tensor([[3.], [6.]])
|
|
|
|
>>> g2 = dgl.DGLGraph() # Graph 2
|
|
>>> g2.add_nodes(3)
|
|
>>> g2.add_edges([0, 1, 2], [1, 2, 0])
|
|
>>> g2.edata['h'] = th.tensor([[1.], [2.], [3.]])
|
|
|
|
Average over edge attribute :attr:`h` without weighting for each graph in a
|
|
batched graph.
|
|
|
|
>>> bg = dgl.batch([g1, g2], edge_attrs='h')
|
|
>>> dgl.mean_edges(bg, 'h')
|
|
tensor([[1.5000], # (1 + 2) / 2
|
|
[2.0000]]) # (1 + 2 + 3) / 3
|
|
|
|
Sum edge attribute :attr:`h` with normalized weight from edge attribute :attr:`w`
|
|
for a single graph.
|
|
|
|
>>> dgl.mean_edges(g1, 'h', 'w') # h1 * (w1 / (w1 + w2)) + h2 * (w2 / (w1 + w2))
|
|
tensor([1.6667]) # 1 * (3 / (3 + 6)) + 2 * (6 / (3 + 6))
|
|
|
|
See Also
|
|
--------
|
|
sum_nodes
|
|
mean_nodes
|
|
sum_edges
|
|
"""
|
|
return _mean_on(graph, 'edges', input, weight)
|