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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

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

* 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

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* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information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

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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>
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* [Deprecation] Dataset Attributes (#4546)

* Update

* CI

* CI

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

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.. _guide_ko-training-edge-classification:
5.2 에지 분류 및 리그레션(Regression)
--------------------------------
:ref:`(English Version) <guide-training-edge-classification>`
때론 그래프의 에지들의 속성을 예측을 원하는 경우가 있다. 이를 위해서 *에지 분류/리그레션* 모델을 만들고자 한다.
우선, 예제로 사용할 에지 예측을 위한 임의의 그래프를 만든다.
.. code:: python
src = np.random.randint(0, 100, 500)
dst = np.random.randint(0, 100, 500)
# make it symmetric
edge_pred_graph = dgl.graph((np.concatenate([src, dst]), np.concatenate([dst, src])))
# synthetic node and edge features, as well as edge labels
edge_pred_graph.ndata['feature'] = torch.randn(100, 10)
edge_pred_graph.edata['feature'] = torch.randn(1000, 10)
edge_pred_graph.edata['label'] = torch.randn(1000)
# synthetic train-validation-test splits
edge_pred_graph.edata['train_mask'] = torch.zeros(1000, dtype=torch.bool).bernoulli(0.6)
개요
~~~~~~~~~
앞 절에서 우리는 멀티 레이어 GNN을 사용해서 노드 분류하는 방법을 알아봤다. 임의의 노드에 대한 hidden representation을 계산하기 위해서 같은 기법을 적용한다. 그러면 에지들에 대한 예측은 그것들의 부속 노드들의 representation들로 부터 도출할 수 있다.
에지에 대한 예측을 계산하는 가장 일반적인 방법은 그 에지의 부속 노드들의 representation들과 부수적으로 그 에지에 대한 피쳐들의 parameterized 함수로 표현하는 것이다.
노드 분류 모델과 구현상의 차이점
~~~~~~~~~~~~~~~~~~~~~~~~
이전 절에서 만든 모델을 사용해서 노드 representation을 계산한다고 가정하면, :meth:`~dgl.DGLGraph.apply_edges` 메소드로 에지 예측을 계산하는 컴포넌트만 작성하면 된다.
예를 들어, 에지 리그레션을 위해서 각 에지에 대한 점수를 계산하고자 한다면, 아래 코드와 같이 각 에지에 대한 부속 노드의 representation들의 dot product를 계산하면 된다.
.. code:: python
import dgl.function as fn
class DotProductPredictor(nn.Module):
def forward(self, graph, h):
# h contains the node representations computed from the GNN defined
# in the node classification section (Section 5.1).
with graph.local_scope():
graph.ndata['h'] = h
graph.apply_edges(fn.u_dot_v('h', 'h', 'score'))
return graph.edata['score']
또한 MLP를 사용해서 각 에지에 대한 벡터 값을 예측하는 예측하는 함수를 작성할 수도 있다. 이 벡터 값은 미래의 다운스트림 테스크들에 사용될 수 있다. 즉, 범주형 분류의 logit으로 사용.
.. code:: python
class MLPPredictor(nn.Module):
def __init__(self, in_features, out_classes):
super().__init__()
self.W = nn.Linear(in_features * 2, out_classes)
def apply_edges(self, edges):
h_u = edges.src['h']
h_v = edges.dst['h']
score = self.W(torch.cat([h_u, h_v], 1))
return {'score': score}
def forward(self, graph, h):
# h contains the node representations computed from the GNN defined
# in the node classification section (Section 5.1).
with graph.local_scope():
graph.ndata['h'] = h
graph.apply_edges(self.apply_edges)
return graph.edata['score']
학습 룹(loop)
~~~~~~~~~~~
노드 representation 계산 모델과 에지 예측 모델을 만들었다면, 모든 에지들에 대한 예측값을 계산하는 전체 그래프를 이용한 학습 룹을 작성할 수 있다.
노드 representation 계산 모델로 ``SAGE`` 를, 에지 예측 모델로 ``DotPredictor`` 을 사용한다.
.. code:: python
class Model(nn.Module):
def __init__(self, in_features, hidden_features, out_features):
super().__init__()
self.sage = SAGE(in_features, hidden_features, out_features)
self.pred = DotProductPredictor()
def forward(self, g, x):
h = self.sage(g, x)
return self.pred(g, h)
이 예제에서 학습/검증/테스트 에지 셋이 에지의 이진 마스크로 구분된다고 가정한다. 또한 early stopping이나 모델 저장은 포함하지 않는다.
.. code:: python
node_features = edge_pred_graph.ndata['feature']
edge_label = edge_pred_graph.edata['label']
train_mask = edge_pred_graph.edata['train_mask']
model = Model(10, 20, 5)
opt = torch.optim.Adam(model.parameters())
for epoch in range(10):
pred = model(edge_pred_graph, node_features)
loss = ((pred[train_mask] - edge_label[train_mask]) ** 2).mean()
opt.zero_grad()
loss.backward()
opt.step()
print(loss.item())
.. _guide_ko-training-edge-classification-heterogeneous-graph:
Heterogeneous 그래프
~~~~~~~~~~~~~~~~~~
Heterogeneous 그래프들에 대한 에지 분류는 homogeneous 그래프와 크게 다르지 않다. 하나의 에지 타입에 대해서 에지 분류를 수행하자 한다면, 모든 노드 티압에 대한 노드 representation을 구하고, :meth:`~dgl.DGLGraph.apply_edges` 메소드를 사용해서 에지 타입을 예측하면 된다.
예를 들면, heterogeneous 그래프의 하나의 에지 타입에 대한 동작하는 ``DotProductPredictor`` 를 작성하고자 한다면, ``apply_edges`` 메소드에 해당 에지 타입을 명시하기만 하면 된다.
.. code:: python
class HeteroDotProductPredictor(nn.Module):
def forward(self, graph, h, etype):
# h contains the node representations for each edge type computed from
# the GNN for heterogeneous graphs defined in the node classification
# section (Section 5.1).
with graph.local_scope():
graph.ndata['h'] = h # assigns 'h' of all node types in one shot
graph.apply_edges(fn.u_dot_v('h', 'h', 'score'), etype=etype)
return graph.edges[etype].data['score']
비슷하게 ``HeteroMLPPredictor`` 를 작성할 수 있다.
.. code:: python
class HeteroMLPPredictor(nn.Module):
def __init__(self, in_features, out_classes):
super().__init__()
self.W = nn.Linear(in_features * 2, out_classes)
def apply_edges(self, edges):
h_u = edges.src['h']
h_v = edges.dst['h']
score = self.W(torch.cat([h_u, h_v], 1))
return {'score': score}
def forward(self, graph, h, etype):
# h contains the node representations for each edge type computed from
# the GNN for heterogeneous graphs defined in the node classification
# section (Section 5.1).
with graph.local_scope():
graph.ndata['h'] = h # assigns 'h' of all node types in one shot
graph.apply_edges(self.apply_edges, etype=etype)
return graph.edges[etype].data['score']
특정 타입의 에지에 대해서, 각 에지의 점수를 예측하는 end-to-end 모델을 다음과 같다:
.. code:: python
class Model(nn.Module):
def __init__(self, in_features, hidden_features, out_features, rel_names):
super().__init__()
self.sage = RGCN(in_features, hidden_features, out_features, rel_names)
self.pred = HeteroDotProductPredictor()
def forward(self, g, x, etype):
h = self.sage(g, x)
return self.pred(g, h, etype)
모델을 사용하는 방법은 노드 타입과 피쳐들에 대한 사전을 모델에 간단하게 입력하면 된다.
.. code:: python
model = Model(10, 20, 5, hetero_graph.etypes)
user_feats = hetero_graph.nodes['user'].data['feature']
item_feats = hetero_graph.nodes['item'].data['feature']
label = hetero_graph.edges['click'].data['label']
train_mask = hetero_graph.edges['click'].data['train_mask']
node_features = {'user': user_feats, 'item': item_feats}
학습 룹은 homogeneous 그래프의 것과 거의 유사하다. 예를 들어, 에지 타입 ``click`` 에 대한 에지 레이블을 예측하는 것은 다음과 같이 간단히 구현된다.
.. code:: python
opt = torch.optim.Adam(model.parameters())
for epoch in range(10):
pred = model(hetero_graph, node_features, 'click')
loss = ((pred[train_mask] - label[train_mask]) ** 2).mean()
opt.zero_grad()
loss.backward()
opt.step()
print(loss.item())
Heterogeneous 그래프의 에지들에 대한 에지 타입 예측하기
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
주어진 에지의 타입을 예측하는 일도 종종 하게된다.
:ref:`heterogeneous 그래프 예제 <guide_ko-training-heterogeneous-graph-example>` 에서는 user와 item을 연결하는 에지가 주어졌을 때, user가 ``click`` 을 선택할지, ``dislike`` 를 선택할지를 예측하고 있다.
이는 추천에서 흔히 쓰이는 평가 예측의 간략한 버전이다.
노드 representation을 얻기 위해서 heterogeneous graph convolution 네트워크를 사용할 수 있다. 이를 위해서 :ref:`이전에 정의한 RGCN <guide_ko-training-rgcn-node-classification>` 를 사용하는 것도 가능하다.
에지 타입을 예측하기 위해서 ``HeteroDotProductPredictor`` 의 용도를 간단히 변경해서 예측할 모든 에지 타입을 “병합“하고 모든 에지들의 각 타입에 대한 점수를 내보내는 하나의 에지 타입만 있는 다른 그래프를 취하게하면 된다.
이 예제에 적용해보면, ``user````item`` 두 노트 타입을 갖으며 ``user````item`` 에 대한 ``click`` 이나 ``dislike`` 같은 모든 에지 타입을 병합하는 단일 에지 타입을 갖는 그래프가 필요하다. 다음 문장으로 간단하게 생성할 수 있다.
.. code:: python
dec_graph = hetero_graph['user', :, 'item']
이 함수는 ``user````item`` 을 노드 타입으로 갖고, 두 노드 타입을 연결하고 있는 모든 에지 타입(예, ``click````dislike`` )을 합친 단일 에지 타입을 갖는 heterogeneous 그래프를 리턴한다.
위 코드는 원래의 에지 타입을 ``dgl.ETYPE`` 이라는 이름의 피처로 리턴하기 때문에, 이를 레이블로 사용할 수 있다.
.. code:: python
edge_label = dec_graph.edata[dgl.ETYPE]
에지 타입 예측 모듈의 입력으로 위 그래프를 사용해서 예측 모델을 다음과 같이 작성한다.
.. code:: python
class HeteroMLPPredictor(nn.Module):
def __init__(self, in_dims, n_classes):
super().__init__()
self.W = nn.Linear(in_dims * 2, n_classes)
def apply_edges(self, edges):
x = torch.cat([edges.src['h'], edges.dst['h']], 1)
y = self.W(x)
return {'score': y}
def forward(self, graph, h):
# h contains the node representations for each edge type computed from
# the GNN for heterogeneous graphs defined in the node classification
# section (Section 5.1).
with graph.local_scope():
graph.ndata['h'] = h # assigns 'h' of all node types in one shot
graph.apply_edges(self.apply_edges)
return graph.edata['score']
노드 representation 모듈과 에지 타입 예측 모듈을 합친 모델은 다음과 같다.
.. code:: python
class Model(nn.Module):
def __init__(self, in_features, hidden_features, out_features, rel_names):
super().__init__()
self.sage = RGCN(in_features, hidden_features, out_features, rel_names)
self.pred = HeteroMLPPredictor(out_features, len(rel_names))
def forward(self, g, x, dec_graph):
h = self.sage(g, x)
return self.pred(dec_graph, h)
학습 룹은 아래와 같이 간단하다.
.. code:: python
model = Model(10, 20, 5, hetero_graph.etypes)
user_feats = hetero_graph.nodes['user'].data['feature']
item_feats = hetero_graph.nodes['item'].data['feature']
node_features = {'user': user_feats, 'item': item_feats}
opt = torch.optim.Adam(model.parameters())
for epoch in range(10):
logits = model(hetero_graph, node_features, dec_graph)
loss = F.cross_entropy(logits, edge_label)
opt.zero_grad()
loss.backward()
opt.step()
print(loss.item())
DGL은 heterogeneous 그래프의 에지들에 대한 타입을 예측하는 문제인 평가 예측 예제로 `Graph Convolutional Matrix Completion <https://github.com/dmlc/dgl/tree/master/examples/pytorch/gcmc>`__ 를 제공한다. `모델 구현 파일 <https://github.com/dmlc/dgl/tree/master/examples/pytorch/gcmc>`__ 에 있는 노드 representation 모듈은 ``GCMCLayer`` 라고 불린다. 이 둘은 여기서 설명하기에는 너무 복잡하니 자세한 설명은 생략한다.