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
* Fix format
* Update
* Update
* Update
* [Cleanup] Remove async_transferer (#4505)
* Remove async_transferer
* remove test
* Remove AsyncTransferer
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* remove third_part/cub
* remove from third_party
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* [Bug] Enable turn on/off libxsmm at runtime (#4455)
* enable turn on/off libxsmm at runtime by adding a global config and related API
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* [Feature] Unify the cuda stream used in core library (#4480)
* Use an internal cuda stream for CopyDataFromTo
* small fix white space
* Fix to compile
* Make stream optional in copydata for compile
* fix lint issue
* Update cub functions to use internal stream
* Lint check
* Update CopyTo/CopyFrom/CopyFromTo to use internal stream
* Address comments
* Fix backward CUDA stream
* Avoid overloading CopyFromTo()
* Minor comment update
* Overload copydatafromto in cuda device api
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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* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information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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* [CI] only known devs are authorized to trigger CI (#4518)
* [CI] only known devs are authorized to trigger CI
* fix if author is null
* add comments
* [Readability] Auto fix setup.py and update-version.py (#4446)
* Auto fix update-version
* Auto fix setup.py
* Auto fix update-version
* Auto fix setup.py
* [Doc] Change random.py to random_partition.py in guide on distributed partition pipeline (#4438)
* Update distributed-preprocessing.rst
* Update
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* fix unpinning when tensoradaptor is not available (#4450)
* [Doc] fix print issue in tutorial (#4459)
* [Example][Refactor] Refactor RGCN example (#4327)
* Refactor full graph entity classification
* Refactor rgcn with sampling
* README update
* Update
* Results update
* Respect default setting of self_loop=false in entity.py
* Update
* Update README
* Update for multi-gpu
* Update
* [doc] fix invalid link in user guide (#4468)
* [Example] directional_GSN for ogbg-molpcba (#4405)
* version-1
* version-2
* version-3
* update examples/README
* Update .gitignore
* update performance in README, delete scripts
* 1st approving review
* 2nd approving review
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* Clarify the message name, which is 'm'. (#4462)
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* [Refactor] Auto fix view.py. (#4461)
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* [Example] SEAL for OGBL (#4291)
* [Example] SEAL for OGBL
* update index
* update
* fix readme typo
* add seal sampler
* modify set ops
* prefetch
* efficiency test
* update
* optimize
* fix ScatterAdd dtype issue
* update sampler style
* update
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* [CI] use https instead of http (#4488)
* [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
* redirect AllocDataSpace as well
* resolve comments
* [Build][Doc] Specify the sphinx version (#4465)
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* reformat
* reformat
* Auto fix update-version
* Auto fix setup.py
* reformat
* 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
Co-authored-by: Israt Nisa <nisisrat@amazon.com>
* [DistPart] expose timeout config for process group (#4532)
* [DistPart] expose timeout config for process group
* refine code
* Update tools/distpartitioning/data_proc_pipeline.py
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
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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
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
* 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
* update pylint workflow.
* add
* revert.
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* [CI] refine stage logic (#4565)
* [CI] refine stage logic
* refine
* refine
* remove (#4570)
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* Add Pylint workflow for flake8. (#4571)
* remove
* Add pylint.
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* [Misc] Update the python version in Pylint workflow for flake8. (#4572)
* remove
* Add pylint.
* Change the python version for pylint.
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* Update pylint. (#4574)
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* [Misc] Use another workflow. (#4575)
* Update pylint.
* Use another workflow.
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* Update pylint. (#4576)
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* Update pylint.yml
* Update pylint.yml
* Delete pylint.yml
* [Misc]Add pyproject.toml for autopep8 & black. (#4543)
* Add pyproject.toml for autopep8.
* 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
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>
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* [Deprecation] Dataset Attributes (#4546)
* Update
* CI
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* Update
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* [Example] Bug Fix (#4665)
* Update
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* Update
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* change DGLHeteroGraph to DGLGraph in DOC
* revert c change
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.. _guide_cn-minibatch-edge-classification-sampler:
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6.2 针对边分类任务的邻居采样训练方法
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----------------------------------------------------------------------
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:ref:`(English Version) <guide-minibatch-edge-classification-sampler>`
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边分类/回归的训练与节点分类/回归的训练类似,但还是有一些明显的区别。
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定义邻居采样器和数据加载器
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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用户可以使用
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:ref:`和节点分类一样的邻居采样器 <guide_cn-minibatch-node-classification-sampler>`。
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.. code:: python
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sampler = dgl.dataloading.MultiLayerFullNeighborSampler(2)
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想要用DGL提供的邻居采样器做边分类,需要将其与
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:class:`~dgl.dataloading.pytorch.EdgeDataLoader` 结合使用。
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:class:`~dgl.dataloading.pytorch.EdgeDataLoader` 以小批次的形式对一组边进行迭代,
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从而产生包含边小批次的子图以及供下文中模块使用的 ``块``。
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例如,以下代码创建了一个PyTorch数据加载器,该PyTorch数据加载器以批的形式迭代训练边ID的数组
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``train_eids``,并将生成的块列表放到GPU上。
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.. code:: python
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dataloader = dgl.dataloading.EdgeDataLoader(
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g, train_eid_dict, sampler,
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batch_size=1024,
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shuffle=True,
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drop_last=False,
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num_workers=4)
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有关DGL的内置采样器的完整列表,用户可以参考
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:ref:`neighborhood sampler API reference <api-dataloading-neighbor-sampling>`。
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如果用户希望开发自己的邻居采样器,或者想要对块的概念有更详细的了解,请参考
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:ref:`guide_cn-minibatch-customizing-neighborhood-sampler`。
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小批次邻居采样训练时删边
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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用户在训练边分类模型时,有时希望从计算依赖中删除出现在训练数据中的边,就好像这些边根本不存在一样。
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否则,模型将 "知道" 两个节点之间存在边的联系,并有可能利用这点 "作弊" 。
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因此,在基于邻居采样的边分类中,用户有时会希望从采样得到的小批次图中删去部分边及其对应的反向边。
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用户可以在实例化
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:class:`~dgl.dataloading.pytorch.EdgeDataLoader`
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时设置 ``exclude='reverse_id'``,同时将边ID映射到其反向边ID。
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通常这样做会导致采样过程变慢很多,这是因为DGL要定位并删除包含在小批次中的反向边。
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.. code:: python
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n_edges = g.number_of_edges()
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dataloader = dgl.dataloading.EdgeDataLoader(
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g, train_eid_dict, sampler,
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# 下面的两个参数专门用于在邻居采样时删除小批次的一些边和它们的反向边
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exclude='reverse_id',
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reverse_eids=torch.cat([
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torch.arange(n_edges // 2, n_edges), torch.arange(0, n_edges // 2)]),
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batch_size=1024,
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shuffle=True,
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drop_last=False,
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num_workers=4)
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调整模型以适用小批次训练
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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边分类模型通常由两部分组成:
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- 获取边两端节点的表示。
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- 用边两端节点表示为每个类别打分。
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第一部分与
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:ref:`随机批次训练节点分类 <guide_cn-minibatch-node-classification-model>`
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完全相同,用户可以简单地复用它。输入仍然是DGL的数据加载器生成的块列表和输入特征。
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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 = dglnn.GraphConv(in_features, hidden_features)
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self.conv2 = dglnn.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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第二部分的输入通常是前一部分的输出,以及由小批次边导出的原始图的子图。
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子图是从相同的数据加载器产生的。用户可以调用 :meth:`dgl.DGLGraph.apply_edges` 计算边子图中边的得分。
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以下代码片段实现了通过合并边两端节点的特征并将其映射到全连接层来预测边的得分。
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.. code:: python
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class ScorePredictor(nn.Module):
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def __init__(self, num_classes, in_features):
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super().__init__()
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self.W = nn.Linear(2 * in_features, num_classes)
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def apply_edges(self, edges):
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data = torch.cat([edges.src['x'], edges.dst['x']])
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return {'score': self.W(data)}
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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(self.apply_edges)
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return edge_subgraph.edata['score']
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模型接受数据加载器生成的块列表、边子图以及输入节点特征进行前向传播,如下所示:
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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, num_classes):
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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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self.predictor = ScorePredictor(num_classes, out_features)
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def forward(self, edge_subgraph, blocks, x):
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x = self.gcn(blocks, x)
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return self.predictor(edge_subgraph, x)
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DGL保证边子图中的节点与生成的块列表中最后一个块的输出节点相同。
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模型的训练
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~~~~~~~~~~~~~
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模型的训练与节点分类的随机批次训练的情况非常相似。用户可以遍历数据加载器以获得由小批次边组成的子图,
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以及计算其两端节点表示所需的块列表。
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.. code:: python
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model = Model(in_features, hidden_features, out_features, num_classes)
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model = model.cuda()
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opt = torch.optim.Adam(model.parameters())
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for input_nodes, edge_subgraph, blocks in dataloader:
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blocks = [b.to(torch.device('cuda')) for b in blocks]
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edge_subgraph = edge_subgraph.to(torch.device('cuda'))
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input_features = blocks[0].srcdata['features']
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edge_labels = edge_subgraph.edata['labels']
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edge_predictions = model(edge_subgraph, blocks, input_features)
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loss = compute_loss(edge_labels, edge_predictions)
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opt.zero_grad()
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loss.backward()
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opt.step()
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异构图上的模型训练
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~~~~~~~~~~~~~~~~~~~~~~~~
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在异构图上,计算节点表示的模型也可以用于计算边分类/回归所需的两端节点的表示。
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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
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在同构图和异构图上做评分预测时,代码实现的唯一不同在于调用
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:meth:`~dgl.DGLGraph.apply_edges`
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时需要在特定类型的边上进行迭代。
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.. code:: python
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class ScorePredictor(nn.Module):
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def __init__(self, num_classes, in_features):
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super().__init__()
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self.W = nn.Linear(2 * in_features, num_classes)
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def apply_edges(self, edges):
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data = torch.cat([edges.src['x'], edges.dst['x']])
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return {'score': self.W(data)}
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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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for etype in edge_subgraph.canonical_etypes:
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edge_subgraph.apply_edges(self.apply_edges, etype=etype)
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return edge_subgraph.edata['score']
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class Model(nn.Module):
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def __init__(self, in_features, hidden_features, out_features, num_classes,
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etypes):
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super().__init__()
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self.rgcn = StochasticTwoLayerRGCN(
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in_features, hidden_features, out_features, etypes)
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self.pred = ScorePredictor(num_classes, out_features)
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def forward(self, edge_subgraph, blocks, x):
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x = self.rgcn(blocks, x)
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return self.pred(edge_subgraph, x)
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数据加载器的定义也与节点分类的非常相似。唯一的区别是用户需要使用
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:class:`~dgl.dataloading.pytorch.EdgeDataLoader`
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而不是
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:class:`~dgl.dataloading.pytorch.NodeDataLoader`,
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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。
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.. code:: python
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sampler = dgl.dataloading.MultiLayerFullNeighborSampler(2)
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dataloader = dgl.dataloading.EdgeDataLoader(
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g, train_eid_dict, sampler,
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batch_size=1024,
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shuffle=True,
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drop_last=False,
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num_workers=4)
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如果用户希望删除异构图中的反向边,情况会有所不同。在异构图上,
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反向边通常具有与正向边本身不同的边类型,以便区分 ``向前`` 和 ``向后`` 关系。
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例如,``关注`` 和 ``被关注`` 是一对相反的关系, ``购买`` 和 ``被买下`` 也是一对相反的关系。
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如果一个类型中的每个边都有一个与之对应的ID相同、属于另一类型的反向边,
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则用户可以指定边类型及其反向边类型之间的映射。删除小批次中的边及其反向边的方法如下。
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|
|
|
.. code:: python
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|
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|
dataloader = dgl.dataloading.EdgeDataLoader(
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|
g, train_eid_dict, sampler,
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# 下面的两个参数专门用于在邻居采样时删除小批次的一些边和它们的反向边
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|
exclude='reverse_types',
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|
reverse_etypes={'follow': 'followed by', 'followed by': 'follow',
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|
'purchase': 'purchased by', 'purchased by': 'purchase'}
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|
|
|
batch_size=1024,
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|
shuffle=True,
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|
drop_last=False,
|
|
num_workers=4)
|
|
|
|
除了 ``compute_loss`` 的代码实现有所不同,异构图的训练循环与同构图中的训练循环几乎相同,
|
|
计算损失函数接受节点类型和预测的两个字典。
|
|
|
|
.. 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, edge_subgraph, blocks in dataloader:
|
|
blocks = [b.to(torch.device('cuda')) for b in blocks]
|
|
edge_subgraph = edge_subgraph.to(torch.device('cuda'))
|
|
input_features = blocks[0].srcdata['features']
|
|
edge_labels = edge_subgraph.edata['labels']
|
|
edge_predictions = model(edge_subgraph, blocks, input_features)
|
|
loss = compute_loss(edge_labels, edge_predictions)
|
|
opt.zero_grad()
|
|
loss.backward()
|
|
opt.step()
|
|
|
|
`GCMC <https://github.com/dmlc/dgl/tree/master/examples/pytorch/gcmc>`__
|
|
是一个在二分图上做边分类的代码示例。
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|