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peizhou001 9699b93136 [API Deprecation]Change DGLHeteroGraph to DGLGraph in DOC (#4840)
* 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

Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>

* [Cleanup] Remove duplicate entries of CUB submodule   (issue# 4395) (#4499)

* remove third_part/cub

* remove from third_party

Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>

* [Bug] Enable turn on/off libxsmm at runtime (#4455)

* enable turn on/off libxsmm at runtime by adding a global config and related API


Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>

* [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

Co-authored-by: xiny <xiny@nvidia.com>

* [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* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information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

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [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

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* 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

Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Clarify the message name, which is 'm'. (#4462)

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Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>

* [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

Co-authored-by: Quan Gan <coin2028@hotmail.com>

* [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>

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [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

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Misc] Try use official pylint workflow. (#4568)

* polish update_version

* update pylint workflow.

* add

* revert.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [CI] refine stage logic (#4565)

* [CI] refine stage logic

* refine

* refine

* remove (#4570)

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* 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>
Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>
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* [Deprecation] Dataset Attributes (#4546)

* Update

* CI

* CI

* Update

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* [Example] Bug Fix (#4665)

* Update

* CI

* CI

* Update

* Update

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* Update

* Update (#4724)

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* change DGLHeteroGraph to DGLGraph in DOC

* revert c change

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2022-11-10 08:38:47 +08:00

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.. _guide_ko-minibatch-edge-classification-sampler:
6.2 이웃 샘플링을 사용한 에지 분류 GNN 모델 학습하기
-----------------------------------------
:ref:`(English Version) <guide-minibatch-edge-classification-sampler>`
에지 분류/리그레션 모델을 학습하는 것은 몇 가지 눈에 띄는 차이점이 있지만 노드 분류/리그레션과 어느정도 비슷하다.
이웃 샘플러 및 데이터 로더 정의하기
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:ref:`노드 분류에서 사용한 것과 같은 이웃 샘플러<guide_ko-minibatch-node-classification-sampler>` 를 사용할 수 있다.
.. code:: python
sampler = dgl.dataloading.MultiLayerFullNeighborSampler(2)
에지 분류에 DGL이 제공하는 이웃 샘플러를 사용하려면, 미니-배치의 에지들의 집합을 iterate 하는 :class:`~dgl.dataloading.pytorch.EdgeDataLoader` 와 함께 사용해야한다. 이것은 아래 모듈에서 사용될 에지 미니-배치로부터 만들어질 서브 그래프와 *message flow graph* (MFG)들을 리턴한다.
다음 코드 예제는 PyTorch DataLoader를 만든다. 이는 베치들에 있는 학습 에지 ID 배열 :math:`train_eids` 들을 iterate 하고, 생성된 MFG들의 리스트를 GPU로 옮겨놓는다.
.. code:: python
dataloader = dgl.dataloading.EdgeDataLoader(
g, train_eid_dict, sampler,
batch_size=1024,
shuffle=True,
drop_last=False,
num_workers=4)
.. note::
Message flow graph의 개념은 :doc:`Stochastic Training Tutorial <tutorials/large/L0_neighbor_sampling_overview>` 를 참고하자.
빌트인으로 지원되는 샘플러들에 대한 전체 목록은 :ref:`neighborhood sampler API reference <api-dataloading-neighbor-sampling>` 에 있다.
:ref:`guide_ko-minibatch-customizing-neighborhood-sampler` 에는 여러분만의 이웃 샘플러 만드는 방법과 MFG 개념에 대한 보다 상세한 설명을 담고 있다.
이웃 샘플링을 위해서 원본 그래프에서 미니 배치의 에지들 제거하기
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
에지 분류 모델을 학습할 때, 때로는 computation dependency에서 학습 데이터에 있는 에지들을 존재하지 않았던 것처럼 만들기 위해 제거하는 것이 필요하다. 그렇지 않으면, 모델은 두 노드들 사이에 에지가 존재한다는 사실을 *인지* 할 것이고, 이 정보를 학습에 잠재적으로 이용할 수 있기 때문이다.
따라서, 에지 분류의 경우 때로는 이웃 샘플링은 미니-배치안에 샘플된 에지들 및 undirected 그래프인 경우 샘플된 에지의 역방향 에지들도 원본 그래프에서 삭제하기도 한다. :class:`~dgl.dataloading.pytorch.EdgeDataLoader` 객체를 만들 때, ``exclude='reverse_id'`` 를 에지 ID와 그와 연관된 reverse 에지 ID들의 매핑 정보와 함께 지정할 수 있다.
.. code:: python
n_edges = g.number_of_edges()
dataloader = dgl.dataloading.EdgeDataLoader(
g, train_eid_dict, sampler,
# The following two arguments are specifically for excluding the minibatch
# edges and their reverse edges from the original graph for neighborhood
# sampling.
exclude='reverse_id',
reverse_eids=torch.cat([
torch.arange(n_edges // 2, n_edges), torch.arange(0, n_edges // 2)]),
batch_size=1024,
shuffle=True,
drop_last=False,
num_workers=4)
모델을 미니-배치 학습에 맞게 만들기
~~~~~~~~~~~~~~~~~~~~~~~~~~~
에지 분류 모델은 보통은 다음과 같이 두 부분으로 구성된다:
- 첫번째는 부속 노드(incident node)들의 representation을 얻는 부분
- 두번째는 부속 노드의 representation들로부터 에지 점수를 계산하는 부분
첫번째 부분은 :ref:`노드 분류<guide_ko-minibatch-node-classification-model>` 와 완전히 동일하기에, 단순하게 이를 재사용할 수 있다. 입력 DGL에서 제공하는 데이터 로더가 만들어 낸 MFG들의 리스트와 입력 피쳐들이 된다.
.. code:: python
class StochasticTwoLayerGCN(nn.Module):
def __init__(self, in_features, hidden_features, out_features):
super().__init__()
self.conv1 = dglnn.GraphConv(in_features, hidden_features)
self.conv2 = dglnn.GraphConv(hidden_features, out_features)
def forward(self, blocks, x):
x = F.relu(self.conv1(blocks[0], x))
x = F.relu(self.conv2(blocks[1], x))
return x
두번째 부분에 대한 입력은 보통은 이전 부분의 출력과 미니배치의 에지들에 의해서 유도된 원본 그래프의 서브 그래프가 된다. 서브 그래프는 같은 데이터 로더에서 리턴된다. :meth:`dgl.DGLGraph.apply_edges` 를 사용해서 에지 서브 그래프를 사용해서 에지들의 점수를 계산한다.
다음 코드는 부속 노드 피처들을 연결하고, 이를 dense 레이어에 입력해서 얻은 결과로 에지들의 점수를 예측하는 예를 보여준다.
.. code:: python
class ScorePredictor(nn.Module):
def __init__(self, num_classes, in_features):
super().__init__()
self.W = nn.Linear(2 * in_features, num_classes)
def apply_edges(self, edges):
data = torch.cat([edges.src['x'], edges.dst['x']])
return {'score': self.W(data)}
def forward(self, edge_subgraph, x):
with edge_subgraph.local_scope():
edge_subgraph.ndata['x'] = x
edge_subgraph.apply_edges(self.apply_edges)
return edge_subgraph.edata['score']
전체 모델은 아래와 같이 데이터 로더로부터 얻은 MFG들의 리스트와 에지 서브 그래프, 그리고 입력 노드 피쳐들을 사용한다.
.. code:: python
class Model(nn.Module):
def __init__(self, in_features, hidden_features, out_features, num_classes):
super().__init__()
self.gcn = StochasticTwoLayerGCN(
in_features, hidden_features, out_features)
self.predictor = ScorePredictor(num_classes, out_features)
def forward(self, edge_subgraph, blocks, x):
x = self.gcn(blocks, x)
return self.predictor(edge_subgraph, x)
DGL에서는 에지 서브 그래프의 노드들이 MFG들의 리스트에서 마지막 MFG의 출력 노드들과 동일하도록 확인한다.
학습 룹
~~~~~
학습 룹은 노드 분류의 학습 룹과 비슷하다. 데이터 로더를 iterate해서, 미니배치의 에지들에 의해서 유도된 서브 그래프와 에지들의 부속 노드(incident node)들의 representation들을 계산하기 위한 MFG들의 목록을 얻는다.
.. code:: python
model = Model(in_features, hidden_features, out_features, num_classes)
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()
Heterogeneous 그래프의 경우
~~~~~~~~~~~~~~~~~~~~~~~~
Heterogeneous 그래프들의 노드 representation들을 계산하는 모델은 에지 분류/리그레션을 위한 부속 노드 representation들을 구하는데 사용될 수 있다.
.. code:: python
class StochasticTwoLayerRGCN(nn.Module):
def __init__(self, in_feat, hidden_feat, out_feat, rel_names):
super().__init__()
self.conv1 = dglnn.HeteroGraphConv({
rel : dglnn.GraphConv(in_feat, hidden_feat, norm='right')
for rel in rel_names
})
self.conv2 = dglnn.HeteroGraphConv({
rel : dglnn.GraphConv(hidden_feat, out_feat, norm='right')
for rel in rel_names
})
def forward(self, blocks, x):
x = self.conv1(blocks[0], x)
x = self.conv2(blocks[1], x)
return x
점수를 예측하기 위한 homogeneous 그래프와 heterogeneous 그래프간의 유일한 구현상의 차이점은 :meth:`~dgl.DGLGraph.apply_edges` 를 호출할 때 에지 타입들을 사용한다는 점이다.
.. code:: python
class ScorePredictor(nn.Module):
def __init__(self, num_classes, in_features):
super().__init__()
self.W = nn.Linear(2 * in_features, num_classes)
def apply_edges(self, edges):
data = torch.cat([edges.src['x'], edges.dst['x']])
return {'score': self.W(data)}
def forward(self, edge_subgraph, x):
with edge_subgraph.local_scope():
edge_subgraph.ndata['x'] = x
for etype in edge_subgraph.canonical_etypes:
edge_subgraph.apply_edges(self.apply_edges, 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(num_classes, out_features)
def forward(self, edge_subgraph, blocks, x):
x = self.rgcn(blocks, x)
return self.pred(edge_subgraph, x)
데이터 로더 구현도 노드 분류을 위한 것과 아주 비슷하다. 유일한 차이점은 :class:`~dgl.dataloading.pytorch.NodeDataLoader` 대신에 :class:`~dgl.dataloading.pytorch.EdgeDataLoader` 를 사용하고, 노드 타입과 노드 ID 텐서들의 사전 대신에 에지 타입과 에지 ID 텐서들의 사전을 사용한다는 것이다.
.. code:: python
sampler = dgl.dataloading.MultiLayerFullNeighborSampler(2)
dataloader = dgl.dataloading.EdgeDataLoader(
g, train_eid_dict, sampler,
batch_size=1024,
shuffle=True,
drop_last=False,
num_workers=4)
만약 heterogeneous 그래프에서 역방향의 에지를 배제하고자 한다면 약간 달라진다. Heterogeneous 그래프에서 역방향 에지들은 에지와는 다른 에지 타입을 갖는 것이 보통이다. 이는 “forward”와 “backward” 관계들을 구분직기 위해서이다. (즉, ``follow````followed by`` 는 서로 역 관계이고, ``purchase````purchased by`` 는 서로 역 관계인 것 처럼)
만약 어떤 타입의 에지들이 다른 타입의 같은 ID를 갖는 역방향 에지를 갖는다면, 에지 타입들과
그것들의 반대 타입간의 매핑을 명시할 수 있다. 미니배치에서 에지들과 그것들의 역방향 에지를 배제하는 것은
다음과 같다.
.. code:: python
dataloader = dgl.dataloading.EdgeDataLoader(
g, train_eid_dict, sampler,
# The following two arguments are specifically for excluding the minibatch
# edges and their reverse edges from the original graph for neighborhood
# sampling.
exclude='reverse_types',
reverse_etypes={'follow': 'followed by', 'followed by': 'follow',
'purchase': 'purchased by', 'purchased by': 'purchase'}
batch_size=1024,
shuffle=True,
drop_last=False,
num_workers=4)
학습 룹은 ``compute_loss`` 의 구현이 노드 타입들과 예측 값에 대한 두 사전들을 인자로 받는다는 점을 제외하면,
homogeneous 그래프의 학습 룹 구현과 거의 같다.
.. 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>`__ 은 이분 그래프(bipartite graph)에 대한 에지 분류 예제이다.