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.. _guide-training-graph-classification:
5.4 Graph Classification
----------------------------------
:ref:`(中文版) <guide_cn-training-graph-classification>`
Instead of a big single graph, sometimes one might have the data in the
form of multiple graphs, for example a list of different types of
communities of people. By characterizing the friendship among people in
the same community by a graph, one can get a list of graphs to classify. In
this scenario, a graph classification model could help identify the type
of the community, i.e. to classify each graph based on the structure and
overall information.
Overview
~~~~~~~~
The major difference between graph classification and node
classification or link prediction is that the prediction result
characterizes the property of the entire input graph. One can perform the
message passing over nodes/edges just like the previous tasks, but also
needs to retrieve a graph-level representation.
The graph classification pipeline proceeds as follows:
.. figure:: https://data.dgl.ai/tutorial/batch/graph_classifier.png
:alt: Graph Classification Process
Graph Classification Process
From left to right, the common practice is:
- Prepare a batch of graphs
- Perform message passing on the batched graphs to update node/edge features
- Aggregate node/edge features into graph-level representations
- Classify graphs based on graph-level representations
Batch of Graphs
^^^^^^^^^^^^^^^
Usually a graph classification task trains on a lot of graphs, and it
will be very inefficient to use only one graph at a time when
training the model. Borrowing the idea of mini-batch training from
common deep learning practice, one can build a batch of multiple graphs
and send them together for one training iteration.
In DGL, one can build a single batched graph from a list of graphs. This
batched graph can be simply used as a single large graph, with connected
components corresponding to the original small graphs.
.. figure:: https://data.dgl.ai/tutorial/batch/batch.png
:alt: Batched Graph
Batched Graph
The following example calls :func:`dgl.batch` on a list of graphs.
A batched graph is a single graph, while it also carries information
about the list.
.. code:: python
import dgl
import torch as th
g1 = dgl.graph((th.tensor([0, 1, 2]), th.tensor([1, 2, 3])))
g2 = dgl.graph((th.tensor([0, 0, 0, 1]), th.tensor([0, 1, 2, 0])))
bg = dgl.batch([g1, g2])
bg
# Graph(num_nodes=7, num_edges=7,
# ndata_schemes={}
# edata_schemes={})
bg.batch_size
# 2
bg.batch_num_nodes()
# tensor([4, 3])
bg.batch_num_edges()
# tensor([3, 4])
bg.edges()
# (tensor([0, 1, 2, 4, 4, 4, 5], tensor([1, 2, 3, 4, 5, 6, 4]))
Please note that most dgl transformation functions will discard the batch information.
In order to maintain such information, please use :func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph.
Graph Readout
^^^^^^^^^^^^^
Every graph in the data may have its unique structure, as well as its
node and edge features. In order to make a single prediction, one usually
aggregates and summarizes over the possibly abundant information. This
type of operation is named *readout*. Common readout operations include
summation, average, maximum or minimum over all node or edge features.
Given a graph :math:`g`, one can define the average node feature readout as
.. math:: h_g = \frac{1}{|\mathcal{V}|}\sum_{v\in \mathcal{V}}h_v
where :math:`h_g` is the representation of :math:`g`, :math:`\mathcal{V}` is
the set of nodes in :math:`g`, :math:`h_v` is the feature of node :math:`v`.
DGL provides built-in support for common readout operations. For example,
:func:`dgl.mean_nodes` implements the above readout operation.
Once :math:`h_g` is available, one can pass it through an MLP layer for
classification output.
Writing Neural Network Model
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The input to the model is the batched graph with node and edge features.
Computation on a Batched Graph
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
First, different graphs in a batch are entirely separated, i.e. no edges
between any two graphs. With this nice property, all message passing
functions still have the same results.
Second, the readout function on a batched graph will be conducted over
each graph separately. Assuming the batch size is :math:`B` and the
feature to be aggregated has dimension :math:`D`, the shape of the
readout result will be :math:`(B, D)`.
.. code:: python
import dgl
import torch
g1 = dgl.graph(([0, 1], [1, 0]))
g1.ndata['h'] = torch.tensor([1., 2.])
g2 = dgl.graph(([0, 1], [1, 2]))
g2.ndata['h'] = torch.tensor([1., 2., 3.])
dgl.readout_nodes(g1, 'h')
# tensor([3.]) # 1 + 2
bg = dgl.batch([g1, g2])
dgl.readout_nodes(bg, 'h')
# tensor([3., 6.]) # [1 + 2, 1 + 2 + 3]
Finally, each node/edge feature in a batched graph is obtained by
concatenating the corresponding features from all graphs in order.
.. code:: python
bg.ndata['h']
# tensor([1., 2., 1., 2., 3.])
Model Definition
^^^^^^^^^^^^^^^^
Being aware of the above computation rules, one can define a model as follows.
.. code:: python
import dgl.nn.pytorch as dglnn
import torch.nn as nn
class Classifier(nn.Module):
def __init__(self, in_dim, hidden_dim, n_classes):
super(Classifier, self).__init__()
self.conv1 = dglnn.GraphConv(in_dim, hidden_dim)
self.conv2 = dglnn.GraphConv(hidden_dim, hidden_dim)
self.classify = nn.Linear(hidden_dim, n_classes)
def forward(self, g, h):
# Apply graph convolution and activation.
h = F.relu(self.conv1(g, h))
h = F.relu(self.conv2(g, h))
with g.local_scope():
g.ndata['h'] = h
# Calculate graph representation by average readout.
hg = dgl.mean_nodes(g, 'h')
return self.classify(hg)
Training Loop
~~~~~~~~~~~~~
Data Loading
^^^^^^^^^^^^
Once the model is defined, one can start training. Since graph
classification deals with lots of relatively small graphs instead of a big
single one, one can train efficiently on stochastic mini-batches
of graphs, without the need to design sophisticated graph sampling
algorithms.
Assuming that one have a graph classification dataset as introduced in
:ref:`guide-data-pipeline`.
.. code:: python
import dgl.data
dataset = dgl.data.GINDataset('MUTAG', False)
Each item in the graph classification dataset is a pair of a graph and
its label. One can speed up the data loading process by taking advantage
of the GraphDataLoader to iterate over the dataset of
graphs in mini-batches.
.. code:: python
from dgl.dataloading import GraphDataLoader
dataloader = GraphDataLoader(
dataset,
batch_size=1024,
drop_last=False,
shuffle=True)
Training loop then simply involves iterating over the dataloader and
updating the model.
.. code:: python
import torch.nn.functional as F
# Only an example, 7 is the input feature size
model = Classifier(7, 20, 5)
opt = torch.optim.Adam(model.parameters())
for epoch in range(20):
for batched_graph, labels in dataloader:
feats = batched_graph.ndata['attr']
logits = model(batched_graph, feats)
loss = F.cross_entropy(logits, labels)
opt.zero_grad()
loss.backward()
opt.step()
For an end-to-end example of graph classification, see
`DGL's GIN example <https://github.com/dmlc/dgl/tree/master/examples/pytorch/gin>`__.
The training loop is inside the
function ``train`` in
`main.py <https://github.com/dmlc/dgl/blob/master/examples/pytorch/gin/main.py>`__.
The model implementation is inside
`gin.py <https://github.com/dmlc/dgl/blob/master/examples/pytorch/gin/gin.py>`__
with more components such as using
:class:`dgl.nn.pytorch.GINConv` (also available in MXNet and Tensorflow)
as the graph convolution layer, batch normalization, etc.
Heterogeneous graph
~~~~~~~~~~~~~~~~~~~
Graph classification with heterogeneous graphs is a little different
from that with homogeneous graphs. In addition to graph convolution modules
compatible with heterogeneous graphs, one also needs to aggregate over the nodes of
different types in the readout function.
The following shows an example of summing up the average of node
representations for each node type.
.. code:: python
class RGCN(nn.Module):
def __init__(self, in_feats, hid_feats, out_feats, rel_names):
super().__init__()
self.conv1 = dglnn.HeteroGraphConv({
rel: dglnn.GraphConv(in_feats, hid_feats)
for rel in rel_names}, aggregate='sum')
self.conv2 = dglnn.HeteroGraphConv({
rel: dglnn.GraphConv(hid_feats, out_feats)
for rel in rel_names}, aggregate='sum')
def forward(self, graph, inputs):
# inputs is features of nodes
h = self.conv1(graph, inputs)
h = {k: F.relu(v) for k, v in h.items()}
h = self.conv2(graph, h)
return h
class HeteroClassifier(nn.Module):
def __init__(self, in_dim, hidden_dim, n_classes, rel_names):
super().__init__()
self.rgcn = RGCN(in_dim, hidden_dim, hidden_dim, rel_names)
self.classify = nn.Linear(hidden_dim, n_classes)
def forward(self, g):
h = g.ndata['feat']
h = self.rgcn(g, h)
with g.local_scope():
g.ndata['h'] = h
# Calculate graph representation by average readout.
hg = 0
for ntype in g.ntypes:
hg = hg + dgl.mean_nodes(g, 'h', ntype=ntype)
return self.classify(hg)
The rest of the code is not different from that for homogeneous graphs.
.. code:: python
# etypes is the list of edge types as strings.
model = HeteroClassifier(10, 20, 5, etypes)
opt = torch.optim.Adam(model.parameters())
for epoch in range(20):
for batched_graph, labels in dataloader:
logits = model(batched_graph)
loss = F.cross_entropy(logits, labels)
opt.zero_grad()
loss.backward()
opt.step()