303b150f8c
[Transform] Double Radius Node Labeling ( #4513 )
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* add double radius node labeling
* add doc
* add test
* fix lint issue
* update
* update
* update
* update
* fix lint
2022-10-10 14:15:08 +08:00
a49b96ee16
[doc] add doc for saving original node/edge IDs in dist part pipeline ( #4655 )
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* [doc] add doc for saving original node/edge IDs in dist part pipeline
* move added docs into advanced topic
* fix ypo
* refine
2022-10-08 17:36:58 +08:00
09ec5fd5e3
[Sparse] Improve API docs ( #4663 )
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* replace with pow
* autosummary for attributes
* revert accidental push
* revert accidental push
* added example
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
2022-09-30 12:34:42 +08:00
eb729c5401
Add Deepwalk module ( #4562 )
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* metapath2vec package
* fix bugs --metapath2vec package
* add unittest and fix bugs
* fix pyling messages
* del init.py
* fix bugs
* modify metapath2vec and add deepwalk
* deepwalk module
* del metapath2vec files
* Update
* Update
* Update
* Update
* Update
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-09-29 09:30:56 +08:00
fa05ccb961
Add sddmm operator in mock_sparse library ( #4579 )
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* sddmm init
* SDDMM with N-D nonzero values
* drop support for vector shaped non zero elements
* address comments
* skip cpu test
* skip GPU test too
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2022-09-28 11:50:30 -04:00
977b1ba448
[Sparse] Migration of Unary, Softmax, Matmul Ops ( #4616 )
...
* Update
* lint
* Fix
* Update
* Update
* Update
* update
* Fix
* Update
* Fix
* Fix
* Fix
* CI
* Update
* Update
* Update
* update test
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal >
2022-09-27 19:34:46 +08:00
544a2cd192
[Sparse] Add reduction operators ( #4600 )
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* [Sparse] Add reduction operators
* Fix linting problem
* Fix linting problem
* Fix linting problem
* Fix docstring
* Fix test cases
* Fix linting problem
* Skip reduction unittests
2022-09-26 16:06:05 +08:00
db64cc3760
[Sparse] Add Transposition for SparseMatrix and DiagMatrix ( #4597 )
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* [Sparse] Add Transposition
* Fix docstring
* Fix linting problem
* Minor fix
* Minor fix
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2022-09-23 15:17:55 +08:00
73b9f3a1da
[Sparse] Migrate DiagMatrix class ( #4567 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal >
2022-09-20 17:17:43 +08:00
cf03592743
Move mock version of dgl_sparse library to DGL main repo ( #4524 )
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* 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 >
2022-09-14 12:08:20 -04:00
62af41c245
[Bug] Enable turn on/off libxsmm at runtime ( #4455 )
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* 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 >
2022-09-05 17:38:34 +08:00
bd311aa68d
[doc] fix invalid link in user guide ( #4468 )
2022-08-25 23:16:44 +08:00
7a41c126f6
[Doc] Change random.py to random_partition.py in guide on distributed partition pipeline ( #4438 )
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* Update distributed-preprocessing.rst
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal >
2022-08-22 18:12:55 +08:00
bc2fef9c32
[Doc] Misc Fix for User Guide 7.1 Data Preprocessing ( #4433 )
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* Update
* rollback for partition_algo/random.py
Co-authored-by: Ubuntu <ubuntu@ip-172-31-20-21.us-west-2.compute.internal >
2022-08-18 20:27:40 +08:00
3bcb268a36
[Doc] Update distributed chapter according to new pipeline ( #4275 )
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* dist index chapter
* preproc chapter
* rst
* tools page
* partition chapter
* rst
* hetero chapter
* 7.1 step1
* add parmetis back
* changed based on feedback
* address comments
2022-08-17 13:30:04 +08:00
39987bc599
[Feature] enable graph partition book support canonical etypes ( #4343 )
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* [Feature] enable graph partition book support canonical etypes
* fix lint
* fix lint
* add todo
* refine according to review comments
* fix lint
* refine naming
* revert PartitionPolicy __init__
* refine docstring
* fix doc string
2022-08-16 11:52:02 +08:00
86c81b4e92
[Feature] Add CUDA Weighted Neighborhood Sampling ( #4064 )
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* add weighted sampling without replacement (A-Chao)
* improve Algorithm A-Chao with block-wise prefix sum
* correctly fill out_idxs
* implement weighted sampling with replacement
* small fix
* merge host-side code of weighted/uniform sampling
* enable unit tests for cuda weighted sampling
* move thrust/cub wrapper to the cmake file
* update docs accordingly
* fix linting
* fix linting
* fix unit test
* Bump external CUB/Thrust versions
* Fix code style and update description of algorithm design
* [Feature] GPU support weighted graph neighbor sampling
commit by pengqirong(OPPO)
* merge pengqirong's implementation
* revert the change to cub and thrust
* fix linting
* use DeviceSegmentedSort for better performance
* add more comments
* add necessary notes
* add necessary notes
* resolve some comments
* define THRUST_CUB_WRAPPED_NAMESPACE
* fix doc
Co-authored-by: 彭齐荣 <657017034@qq.com >
2022-07-29 11:08:48 +08:00
7e6a6b4ac0
[Feature] Add CUDA Weighted Randomwalk Sampling ( #4243 )
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* [Feature] Add CUDA Weighted Randomwalk Sampling
* [Feature] Add CUDA Weighted Randomwalk Sampling
* [Feature] Add CUDA Weighted Randomwalk Sampling
* [Feature] Add CUDA Weighted Randomwalk Sampling
* fix empty prob array && enable non-uniform for restart && enable unit tests
* update doc and guide for randomwalk and pinsage
* update comments
Co-authored-by: zhenliangqiu <ubuntu@ip-172-31-24-245.ap-southeast-1.compute.internal >
Co-authored-by: xiny <xiny@nvidia.com >
2022-07-26 13:42:39 +08:00
05d9d4969b
Update ( #4277 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-53-142.us-west-2.compute.internal >
2022-07-21 13:27:42 +08:00
5c76e47f78
[Docs] fix ffi docs ( #4248 )
...
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2022-07-14 13:20:42 +08:00
9ae117d3cd
[Feature] Add to_cugraph and from_cugraph to DGL ( #4166 )
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* Added to_cugraph and from_cugraph functionality
* fix from_cugraph example
* Addressed Reviews
* Fix linting
* Apply suggestions to docstrings from code review
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
* Add API docs and remove `from_cugraph` alias
* move cugraph tests to tests/cugraph/test_basics.py
* remove ununsed imports from test_basics.py
* remove pytest.importorskip as no longer needed
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2022-07-07 11:52:17 +08:00
32f12ee19e
[Doc] Unify the minimal versions required for PyTorch/TensorFlow/MXNet ( #4180 )
2022-06-29 18:37:19 +08:00
d1f6f3a848
[Doc] fix a bug in guide_cn ( #4149 )
...
Co-authored-by: Xin Yao <xiny@nvidia.com >
2022-06-24 13:08:07 +08:00
69226588a5
[Dist] defer to load node/edge feats ( #4143 )
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* [Dist] defer to load node/edge feats
* fix lint
* Update python/dgl/distributed/partition.py
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
* Update python/dgl/distributed/partition.py
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
* fix lint
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
2022-06-20 19:44:37 +08:00
5f04fc2b31
[Doc] Updated transform ops list in dgl.rst (Issue #4087 ) ( #4123 )
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* * Added functions from dgl.transforms.functional that were missing from the list for documentation in dgl.rst
* * Sorted transform ops list in dgl.rst in alphabetical order
Co-authored-by: Xin Yao <xiny@nvidia.com >
2022-06-15 14:52:37 +08:00
defa292bc0
[Dataset] Add Flickr and Yelp dataset ( #4099 )
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* Add Flickr and Yelp dataset
* Update flickr.py
* update
* Update yelp.py
* Update yelp.py
* update
* Update yelp.py
* Update test_data.py
* Update yelp.py
* update
* Update test_data.py
* Update yelp.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-06-14 16:14:12 +08:00
92063d88f0
fix indent in minibatch-custom-sampler.rst ( #4063 )
...
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-06-03 01:00:31 +08:00
89655cfda2
[Dataset] Add WikiCS Dataset ( #4035 )
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* Fix bugs & Update dataset
* Update
* Update wikics.py
* Update wikics.py
* Update test_data.py
* Update wikics.py
* Update wikics.py
* Update wikics.py
* update
* Update module.py
* Update dgl.data.rst
* Update wikics.py
* Update wikics.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-06-02 23:03:17 +08:00
d9c25521bc
[Data] AsGraphPredDataset ( #4073 )
...
* Update
* CI
* Update
* Update
* Fix
* Fix
2022-06-02 16:18:48 +08:00
bef993076e
[Bugfix] Fix PinSAGE Benchmark ( #4058 )
...
* Update
* Update
* Update dgl.data.rst
* CI
2022-05-28 00:31:57 +08:00
3fe5eea791
[NN] Label Propagation & Directional Graph Networks ( #4017 )
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* add label propagation module
* fix prev bug in example
* add dgn
* fix linting and doc issues
* update label propagation & dgn
* update label propagation & dgn
* update example
* fix unit test
* fix agg heritage issue
* fix agg issue
* fix lint
* fix idx
* fix lp gpu issue
* Update
* Update
Co-authored-by: mufeili <mufeili1996@gmail.com >
2022-05-20 15:23:19 +08:00
65b0b9e8c3
[Dataset & Transform] Synthetic Datasets for Explainability and SIGNDiffusion Transform ( #3982 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Update
* Update
* Update
2022-05-16 22:32:09 +08:00
b2ec5a2ea6
[Transform] Add FeatMask and RowFeatNormalizer transforms ( #3968 )
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* [Model]P-GNN
* updata
* [Example]P-GNN
* Update README.md
* Add NodeFeatureMasking and NormalizeFeatures
* Update
* Update transforms.rst
* Update
* Update
* Update
* Update test_transform.py
* Update
* Update
* Update test_transform.py
* Update module.py
* Update module.py
* Update module.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-05-07 11:59:39 +08:00
248bece633
[NN] GINEConv ( #3934 )
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* Update
* Update
* Update
* Update
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2022-04-25 14:41:05 +08:00
4375c2d7e4
[Doc] Fix documentation in dgl.multiprocessing namespace ( #3929 )
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* fix docs
* remove
* oh
* fix
2022-04-16 00:35:06 +08:00
e06e63d5d5
[Feature] Enable UVA sampling with CPU indices ( #3892 )
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* enable UVA sampling with CPU indices
* add docs
* add more docs
* lint
* fix
* fix
* better error message
* use mp.Barrier instead of queues
* revert
* revert
* oops
* revert dgl.multiprocessing.spawn
* Update pytorch.py
2022-04-12 20:56:51 +08:00
dc5035b1f3
[NN] Add EGNN & PNA ( #3901 )
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* add EGNN & PNA
* fix egnn issues
* fix pna issues
* update pna conv
* add doc strings
* update pnaconv
* fix unused args issue
* fix moment aggregation issue
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-04-07 17:44:57 +08:00
4c7bd314b4
[Feature] Radius Graph ( #3829 )
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* radius graph
* remove trailing whitespaces from docs
* disable invalid name for transform func
* disable radius graph module invalid name
* move pylint disable before init
* fix missing nodes from point set
* update docs indexing
* add compute mode as optional param
* radius graph test
* remove trailing whitespaces
* fix precision when comparing tensors
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-03-30 17:23:29 +08:00
290b7c25c2
[Transform] Random Walk Positional Encoding & Laplacian Positional Encoding ( #3869 )
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* [Transform] Random Walk Positional Encoding & Laplacian Positional Encoding
* Update python/dgl/transforms/module.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py & python/dgl/transforms/module.py
* update python/dgl/transforms/functional.py
* update doc indexing
* update unit test
* support weighted graphs for random_walk_pe
* change reference
* fix linter errors
* fix datatype compatibility with MXNet & TF
* fix device errors
* fix result precision errors
* change tensorflow abs api
* reboost CI
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-03-30 15:59:28 +08:00
9fee20b91d
[Sampler] [Example] SAINTSampler and Simplify GraphSAINT Example ( #3879 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2022-03-30 13:51:37 +08:00
ae3316c846
[Doc] Update doc of dataloading package. ( #3886 )
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* wip: dataloading doc
* update dataloading package doc and many others
* lint
2022-03-26 21:59:02 +08:00
e963256882
[Doc] Update message-api.rst ( #3844 )
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fix #3812
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2022-03-25 23:22:20 +08:00
7d4160869c
[Bug] Fix multiple issues in distributed multi-GPU GraphSAGE example ( #3870 )
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* fix distributed multi-GPU example device
* try Join
* update version requirement in README
* use model.join
* fix docs
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2022-03-25 22:04:02 +08:00
16409ff852
[Doc] fix display issue of node/edge_split ( #3858 )
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Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2022-03-25 09:18:08 +08:00
8005978e1e
[NN] Grouped reversible residual connections for GNNs ( #3842 )
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* Update
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
2022-03-23 16:58:39 +08:00
8425c936c2
update doc for gpu&uva sampling ( #3787 )
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Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2022-02-28 21:17:32 +08:00
ec64581c96
[Doc] Misc fix for doc ( #3782 )
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* Update nn-pytorch.rst
* Update dgl.data.rst
* Update dgl.rst
2022-02-28 16:03:32 +08:00
d41d07d0f6
[Doc and bugfix] Add docs and user guide and update tutorial for sampling pipeline ( #3774 )
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* huuuuge update
* remove
* lint
* lint
* fix
* what happened to nccl
* update multi-gpu unsupervised graphsage example
* replace most of the dgl.mp.process with torch.mp.spawn
* update if condition for use_uva case
* update user guide
* address comments
* incorporating suggestions from @jermainewang
* oops
* fix tutorial to pass CI
* oops
* fix again
Co-authored-by: Xin Yao <xiny@nvidia.com >
2022-02-28 02:21:51 +08:00
3bd5a9b6d1
[Doc] Fix Doc ( #3777 )
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* Update
* Update
* Update
* Update
2022-02-25 17:21:06 +08:00
6d9433b04f
[Transform] [Doc] Rename transform to transforms and update doc ( #3765 )
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* Update
* Update
* Update
* Fix
* Update
* Update
* Update
* Fix
2022-02-24 21:28:15 +08:00
rudongyu