dmlc--dgl
9699b93136
* Update from master (#4584)
* [Example][Refactor] Refactor graphsage multigpu and full-graph example (#4430)
* Add refactors for multi-gpu and full-graph example
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* [Feature] Added exclude_self and output_batch to knn graph construction (Issues #4323 #4316) (#4389)
* * Added "exclude_self" and "output_batch" options to knn_graph and segmented_knn_graph
* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information
* * Changed defaults on new knn_graph and segmented_knn_graph function parameters, for compatibility; pytorch/test_geometry.py was failing
* * Added test to ensure dgl.remove_self_loop function correctly updates batch information
* * Added new knn_graph and segmented_knn_graph parameters to dgl.nn.KNNGraph and dgl.nn.SegmentedKNNGraph
* * Formatting
* * Oops, I missed the one in segmented_knn_graph when I fixed the similar thing in knn_graph
* * Fixed edge case handling when invalid k specified, since it still needs to be handled consistently for tests to pass
* Fixed context of batch info, since it must match the context of the input position data for remove_self_loop to succeed
* * Fixed batch info resulting from knn_graph when output_batch is true, for case of 3D input tensor, representing multiple segments
* * Added testing of new exclude_self and output_batch parameters on knn_graph and segmented_knn_graph, and their wrappers, KNNGraph and SegmentedKNNGraph, into the test_knn_cuda test
* * Added doc comments for new parameters
* * Added correct handling for uncommon case of k or more coincident points when excluding self edges in knn_graph and segmented_knn_graph
* Added test cases for more than k coincident points
* * Updated doc comments for output_batch parameters for clarity
* * Linter formatting fixes
* * Extracted out common function for test_knn_cpu and test_knn_cuda, to add the new test cases to test_knn_cpu
* * Rewording in doc comments
* * Removed output_batch parameter from knn_graph and segmented_knn_graph, in favour of always setting the batch information, except in knn_graph if x is a 2D tensor
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* add comments
* [Readability] Auto fix setup.py and update-version.py (#4446)
* Auto fix update-version
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* [Doc] Change random.py to random_partition.py in guide on distributed partition pipeline (#4438)
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* [Doc] fix print issue in tutorial (#4459)
* [Example][Refactor] Refactor RGCN example (#4327)
* Refactor full graph entity classification
* Refactor rgcn with sampling
* README update
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* Update
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* [Example] SEAL for OGBL (#4291)
* [Example] SEAL for OGBL
* update index
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* efficiency test
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* [BugFix] fix crash due to incorrect dtype in dgl.to_block() (#4487)
* [BugFix] fix crash due to incorrect dtype in dgl.to_block()
* fix test failure in TF
* [Feature] Make TensorAdapter Stream Aware (#4472)
* Allocate tensors in DGL's current stream
* make tensoradaptor stream-aware
* replace TAemtpy with cpu allocator
* fix typo
* try fix cpu allocation
* clean header
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* reformat
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* Move mock version of dgl_sparse library to DGL main repo (#4524)
* init
* Add api doc for sparse library
* support op btwn matrices with differnt sparsity
* Fixed docstring
* addresses comments
* lint check
* change keyword format to fmt
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* [DistPart] expose timeout config for process group (#4532)
* [DistPart] expose timeout config for process group
* refine code
* Update tools/distpartitioning/data_proc_pipeline.py
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* [Feature] Import PyTorch's CUDA stream management (#4503)
* add set_stream
* add .record_stream for NDArray and HeteroGraph
* refactor dgl stream Python APIs
* test record_stream
* add unit test for record stream
* use pytorch's stream
* fix lint
* fix cpu build
* address comments
* address comments
* add record stream tests for dgl.graph
* record frames and update dataloder
* add docstring
* update frame
* add backend check for record_stream
* remove CUDAThreadEntry::stream
* record stream for newly created formats
* fix bug
* fix cpp test
* fix None c_void_p to c_handle
* [examples]educe memory consumption (#4558)
* [examples]educe memory consumption
* reffine help message
* refine
* [Feature][REVIEW] Enable DGL cugaph nightly CI (#4525)
* Added cugraph nightly scripts
* Removed nvcr.io//nvidia/pytorch:22.04-py3 reference
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* Revert "[Feature][REVIEW] Enable DGL cugaph nightly CI (#4525)" (#4563)
This reverts commit ec171c648a.
* [Misc] Add flake8 lint workflow. (#4566)
* Add pyproject.toml for autopep8.
* Add pyproject.toml for autopep8.
* Add flake8 annotation in workflow.
* remove
* add
* clean up
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* [Misc] Try use official pylint workflow. (#4568)
* polish update_version
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* add
* revert.
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* [CI] refine stage logic (#4565)
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* Update pylint. (#4574)
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* Update pylint.yml
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* Add pyproject.toml for autopep8.
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* [Feature] Bump DLPack to v0.7 and decouple DLPack from the core library (#4454)
* rename `DLContext` to `DGLContext`
* rename `kDLGPU` to `kDLCUDA`
* replace DLTensor with DGLArray
* fix linting
* Unify DGLType and DLDataType to DGLDataType
* Fix FFI
* rename DLDeviceType to DGLDeviceType
* decouple dlpack from the core library
* fix bug
* fix lint
* fix merge
* fix build
* address comments
* rename dl_converter to dlpack_convert
* remove redundant comments
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.. _guide_cn-minibatch-link-classification-sampler:
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6.3 针对链接预测任务的邻居采样训练方法
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--------------------------------------------------------------------
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:ref:`(English Version) <guide-minibatch-link-classification-sampler>`
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结合负采样来定义邻居采样器和数据加载器
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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用户仍然可以使用与节点/边分类中相同的邻居采样器。
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.. code:: python
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sampler = dgl.dataloading.MultiLayerFullNeighborSampler(2)
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DGL中的
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:class:`~dgl.dataloading.pytorch.EdgeDataLoader`
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还支持生成用于链接预测的负样本。为此,用户需要定义负采样函数。例如,
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:class:`~dgl.dataloading.negative_sampler.Uniform`
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函数是基于均匀分布的采样函数,它对于每个边的源节点,采样 ``k`` 个负样本的目标节点。
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以下数据加载器将为每个边的源节点均匀采样5个负样本的目标节点。
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.. code:: python
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dataloader = dgl.dataloading.EdgeDataLoader(
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g, train_seeds, sampler,
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negative_sampler=dgl.dataloading.negative_sampler.Uniform(5),
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batch_size=args.batch_size,
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shuffle=True,
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drop_last=False,
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pin_memory=True,
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num_workers=args.num_workers)
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关于内置的负采样方法,用户可以参考 :ref:`api-dataloading-negative-sampling`。
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用户还可以自定义负采样函数,它应当以原图 ``g`` 和小批量的边ID数组 ``eid`` 作为入参,
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并返回源节点ID数组和目标节点ID数组。
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下面给出了一个自定义的负采样方法的示例,该采样方法根据与节点的度的幂成正比的概率分布对负样本目标节点进行采样。
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.. code:: python
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class NegativeSampler(object):
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def __init__(self, g, k):
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# 缓存概率分布
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self.weights = g.in_degrees().float() ** 0.75
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self.k = k
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def __call__(self, g, eids):
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src, _ = g.find_edges(eids)
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src = src.repeat_interleave(self.k)
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dst = self.weights.multinomial(len(src), replacement=True)
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return src, dst
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dataloader = dgl.dataloading.EdgeDataLoader(
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g, train_seeds, sampler,
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negative_sampler=NegativeSampler(g, 5),
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batch_size=args.batch_size,
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shuffle=True,
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drop_last=False,
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pin_memory=True,
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num_workers=args.num_workers)
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调整模型以进行小批次训练
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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如 :ref:`guide_cn-training-link-prediction` 中所介绍的,
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用户可以通过比较边(正样本)与不存在的边(负样本)的得分来训练链路模型。用户可以重用在边分类/回归中的节点表示模型,
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来计算边的分数。
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.. code:: python
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class StochasticTwoLayerGCN(nn.Module):
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def __init__(self, in_features, hidden_features, out_features):
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super().__init__()
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self.conv1 = dgl.nn.GraphConv(in_features, hidden_features)
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self.conv2 = dgl.nn.GraphConv(hidden_features, out_features)
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def forward(self, blocks, x):
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x = F.relu(self.conv1(blocks[0], x))
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x = F.relu(self.conv2(blocks[1], x))
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return x
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对于得分的预测,只需要预测每个边的标量分数而不是类别的概率分布,
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因此本示例说明了如何使用边的两个端点的向量的点积来计算分数。
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.. code:: python
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class ScorePredictor(nn.Module):
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def forward(self, edge_subgraph, x):
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with edge_subgraph.local_scope():
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edge_subgraph.ndata['x'] = x
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edge_subgraph.apply_edges(dgl.function.u_dot_v('x', 'x', 'score'))
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return edge_subgraph.edata['score']
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使用负采样方法后,DGL的数据加载器将为每个小批次生成三项:
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- 一个正样本图,其中包含采样得到的小批次内所有的边。
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- 一个负样本图,其中包含由负采样方法生成的所有不存在的边。
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- 邻居采样方法生成的块的列表。
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因此,可以如下定义链接预测模型,该模型的输入包括上述三项以及输入的特征。
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.. code:: python
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class Model(nn.Module):
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def __init__(self, in_features, hidden_features, out_features):
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super().__init__()
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self.gcn = StochasticTwoLayerGCN(
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in_features, hidden_features, out_features)
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def forward(self, positive_graph, negative_graph, blocks, x):
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x = self.gcn(blocks, x)
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pos_score = self.predictor(positive_graph, x)
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neg_score = self.predictor(negative_graph, x)
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return pos_score, neg_score
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模型的训练
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~~~~~~~~~~~~~
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训练循环通过数据加载器去遍历数据,将得到的图和输入特征传入上述模型。
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.. code:: python
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model = Model(in_features, hidden_features, out_features)
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model = model.cuda()
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opt = torch.optim.Adam(model.parameters())
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for input_nodes, positive_graph, negative_graph, blocks in dataloader:
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blocks = [b.to(torch.device('cuda')) for b in blocks]
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positive_graph = positive_graph.to(torch.device('cuda'))
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negative_graph = negative_graph.to(torch.device('cuda'))
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input_features = blocks[0].srcdata['features']
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pos_score, neg_score = model(positive_graph, negative_graph, blocks, input_features)
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loss = compute_loss(pos_score, neg_score)
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opt.zero_grad()
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loss.backward()
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opt.step()
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DGL提供了在同构图上做链路预测的一个示例:
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`无监督学习GraphSAGE <https://github.com/dmlc/dgl/blob/master/examples/pytorch/graphsage/train_sampling_unsupervised.py>`__。
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异构图上的随机批次训练
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~~~~~~~~~~~~~~~~~~~~~~~~
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计算异构图上的节点表示的模型也可以用于计算边分类/回归中的边两端节点的表示。
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.. code:: python
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class StochasticTwoLayerRGCN(nn.Module):
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def __init__(self, in_feat, hidden_feat, out_feat, rel_names):
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super().__init__()
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self.conv1 = dglnn.HeteroGraphConv({
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rel : dglnn.GraphConv(in_feat, hidden_feat, norm='right')
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for rel in rel_names
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})
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self.conv2 = dglnn.HeteroGraphConv({
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rel : dglnn.GraphConv(hidden_feat, out_feat, norm='right')
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for rel in rel_names
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})
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def forward(self, blocks, x):
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x = self.conv1(blocks[0], x)
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x = self.conv2(blocks[1], x)
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return x
|
|
|
|
对于得分的预测,同构图和异构图之间唯一的实现差异是后者需要用
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|
:meth:`dgl.DGLGraph.apply_edges`
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|
来遍历所有的边类型。
|
|
|
|
.. code:: python
|
|
|
|
class ScorePredictor(nn.Module):
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|
def forward(self, edge_subgraph, x):
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with edge_subgraph.local_scope():
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|
edge_subgraph.ndata['x'] = x
|
|
for etype in edge_subgraph.canonical_etypes:
|
|
edge_subgraph.apply_edges(
|
|
dgl.function.u_dot_v('x', 'x', 'score'), etype=etype)
|
|
return edge_subgraph.edata['score']
|
|
|
|
class Model(nn.Module):
|
|
def __init__(self, in_features, hidden_features, out_features, num_classes,
|
|
etypes):
|
|
super().__init__()
|
|
self.rgcn = StochasticTwoLayerRGCN(
|
|
in_features, hidden_features, out_features, etypes)
|
|
self.pred = ScorePredictor()
|
|
|
|
def forward(self, positive_graph, negative_graph, blocks, x):
|
|
x = self.rgcn(blocks, x)
|
|
pos_score = self.pred(positive_graph, x)
|
|
neg_score = self.pred(negative_graph, x)
|
|
return pos_score, neg_score
|
|
|
|
数据加载器的定义也与边分类/回归里的定义非常相似。唯一的区别是用户需要提供负采样方法,
|
|
并且提供边类型和边ID张量的字典,而不是节点类型和节点ID张量的字典。
|
|
|
|
.. code:: python
|
|
|
|
sampler = dgl.dataloading.MultiLayerFullNeighborSampler(2)
|
|
dataloader = dgl.dataloading.EdgeDataLoader(
|
|
g, train_eid_dict, sampler,
|
|
negative_sampler=dgl.dataloading.negative_sampler.Uniform(5),
|
|
batch_size=1024,
|
|
shuffle=True,
|
|
drop_last=False,
|
|
num_workers=4)
|
|
|
|
如果用户想自定义负采样函数,那么该函数应以初始图以及由边类型和边ID张量构成的字典作为输入。
|
|
它返回以边类型为键、源节点-目标节点数组对为值的字典。示例如下所示:
|
|
|
|
.. code:: python
|
|
|
|
class NegativeSampler(object):
|
|
def __init__(self, g, k):
|
|
# 缓存概率分布
|
|
self.weights = {
|
|
etype: g.in_degrees(etype=etype).float() ** 0.75
|
|
for _, etype, _ in g.canonical_etypes
|
|
}
|
|
self.k = k
|
|
|
|
def __call__(self, g, eids_dict):
|
|
result_dict = {}
|
|
for etype, eids in eids_dict.items():
|
|
src, _ = g.find_edges(eids, etype=etype)
|
|
src = src.repeat_interleave(self.k)
|
|
dst = self.weights[etype].multinomial(len(src), replacement=True)
|
|
result_dict[etype] = (src, dst)
|
|
return result_dict
|
|
|
|
随后,需要向数据载入器提供边类型和对应边ID的字典,以及负采样器。示例如下所示:
|
|
|
|
.. code:: python
|
|
|
|
train_eid_dict = {
|
|
g.edges(etype=etype, form='eid')
|
|
for etype in g.etypes}
|
|
|
|
dataloader = dgl.dataloading.EdgeDataLoader(
|
|
g, train_eid_dict, sampler,
|
|
negative_sampler=NegativeSampler(g, 5),
|
|
batch_size=1024,
|
|
shuffle=True,
|
|
drop_last=False,
|
|
num_workers=4)
|
|
|
|
异构图上的随机批次模型训练与同构图中的训练几乎相同,不同之处在于,
|
|
``compute_loss`` 是以边类型字典和预测结果字典作为输入。
|
|
|
|
.. code:: python
|
|
|
|
model = Model(in_features, hidden_features, out_features, num_classes, etypes)
|
|
model = model.cuda()
|
|
opt = torch.optim.Adam(model.parameters())
|
|
|
|
for input_nodes, positive_graph, negative_graph, blocks in dataloader:
|
|
blocks = [b.to(torch.device('cuda')) for b in blocks]
|
|
positive_graph = positive_graph.to(torch.device('cuda'))
|
|
negative_graph = negative_graph.to(torch.device('cuda'))
|
|
input_features = blocks[0].srcdata['features']
|
|
pos_score, neg_score = model(positive_graph, negative_graph, blocks, input_features)
|
|
loss = compute_loss(pos_score, neg_score)
|
|
opt.zero_grad()
|
|
loss.backward()
|
|
opt.step()
|
|
|
|
|
|
|