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Infinity_X 4b1fb6816a [Model] Heterogeneous graph support for GNNExplainer (#4401) 
* [Model] Heterogeneous graph support for GNNExplainer (#1)

* add HeteroGNNExplainer

* GNNExplainer for heterogeenous graph

* fix typo

* variable name cleanup

* added HeteroGNNExplainer test

* added doc indexing for HeteroGNNExplainer

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py

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

* Update gnnexplainer.py

Change DGLHeteroGraph to DGLGraph, and specified parameter inputs

* Added ntype parameter to the explainer_node call

* responding to @mufeili's comment regarding restoring empty lines at appriopiate places to be consistent with existing practices

* responding to @mufeili's comment regarding restoring empty lines at appriopiate places that were missed in the last commit

* docstring comments added based on @mufeili suggestions

* indorporated @mufeili requested changes related to docstring model declaration.

* example model and test_nn.py added for explain_graphs

* explain_nodes fixed and fixed the way hetero num nodes and edges are handled

* white spaces removed

* lint issues fixed

* explain_graph model updated

* explain nodes model updated

* minor fixes related to gpu compatability

* cuda support added

* simplify WIP

* _init_masks for ennexplainer updated to match heterographs

* Update

* model simplified and docstring comments updated

* nits: docstring udpated

* lint check issues updated

* lint check updated

* soem formatting updated

* disabling int32 testing for GNNExplainer

* Update

Co-authored-by: Kangkook Jee <kangkook.jee@gmail.com>
Co-authored-by: ahadjawaid <94938815+ahadjawaid@users.noreply.github.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: kxm180046 <kxm180046@utdallas.edu>
Co-authored-by: Kunal Mukherjee <kunmukh@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>
 2022-10-27 21:01:36 +08:00
LuckyLiuM f846d902cf Add Metapath2vec module (#4660) 
* metapath2vec package

* fix bugs --metapath2vec package

* add unittest and fix bugs

* fix pyling messages

* del init.py

* fix bugs

* modify metapath2vec and add deepwalk

* metapath2vec module

* Update

* Update

* rollback to initial metapath2vec

* Update

* Update

* Update

* Update

Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
 2022-10-13 01:01:07 +08:00
rudongyu 303b150f8c [Transform] Double Radius Node Labeling (#4513) 
* 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
Rhett Ying a49b96ee16 [doc] add doc for saving original node/edge IDs in dist part pipeline (#4655) 
* [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
Israt Nisa 09ec5fd5e3 [Sparse] Improve API docs (#4663) 
* 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
LuckyLiuM eb729c5401 Add Deepwalk module (#4562) 
* 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
Israt Nisa fa05ccb961 Add sddmm operator in mock_sparse library (#4579) 
* 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
Mufei Li 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
czkkkkkk 544a2cd192 [Sparse] Add reduction operators (#4600) 
* [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
czkkkkkk db64cc3760 [Sparse] Add Transposition for SparseMatrix and DiagMatrix (#4597) 
* [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
Mufei Li 73b9f3a1da [Sparse] Migrate DiagMatrix class (#4567) 
* 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
Israt Nisa cf03592743 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>
 2022-09-14 12:08:20 -04:00
peizhou001 62af41c245 [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>
 2022-09-05 17:38:34 +08:00
Quan (Andy) Gan 2dd06b2152 [Build][Doc] Specify the sphinx version (#4465) 
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2022-09-01 13:52:08 +08:00
Rhett Ying bd311aa68d [doc] fix invalid link in user guide (#4468) 2022-08-25 23:16:44 +08:00
Mufei Li 7a41c126f6 [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>
 2022-08-22 18:12:55 +08:00
Mufei Li bc2fef9c32 [Doc] Misc Fix for User Guide 7.1 Data Preprocessing (#4433) 
* 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
Minjie Wang 3bcb268a36 [Doc] Update distributed chapter according to new pipeline (#4275) 
* 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
Rhett Ying 39987bc599 [Feature] enable graph partition book support canonical etypes (#4343) 
* [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
Xin Yao 86c81b4e92 [Feature] Add CUDA Weighted Neighborhood Sampling (#4064) 
* 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
Dewvin 7e6a6b4ac0 [Feature] Add CUDA Weighted Randomwalk Sampling (#4243) 
* [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
Mufei Li 05d9d4969b Update (#4277) 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-53-142.us-west-2.compute.internal>
 2022-07-21 13:27:42 +08:00
Hongyi ZHANG 5c76e47f78 [Docs] fix ffi docs (#4248) 
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2022-07-14 13:20:42 +08:00
Vibhu Jawa 9ae117d3cd [Feature] Add to_cugraph and from_cugraph to DGL (#4166) 
* 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
Xin Yao 32f12ee19e [Doc] Unify the minimal versions required for PyTorch/TensorFlow/MXNet (#4180) 2022-06-29 18:37:19 +08:00
PotatoChipsNinja 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
Rhett Ying 69226588a5 [Dist] defer to load node/edge feats (#4143) 
* [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
ndickson-nvidia 5f04fc2b31 [Doc] Updated transform ops list in dgl.rst (Issue #4087) (#4123) 
* * 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
RecLusIve-F defa292bc0 [Dataset] Add Flickr and Yelp dataset (#4099) 
* 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
Xin Zhang 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
RecLusIve-F 89655cfda2 [Dataset] Add WikiCS Dataset (#4035) 
* 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
Mufei Li d9c25521bc [Data] AsGraphPredDataset (#4073) 
* Update

* CI

* Update

* Update

* Fix

* Fix
 2022-06-02 16:18:48 +08:00
Mufei Li bef993076e [Bugfix] Fix PinSAGE Benchmark (#4058) 
* Update

* Update

* Update dgl.data.rst

* CI
 2022-05-28 00:31:57 +08:00
rudongyu 3fe5eea791 [NN] Label Propagation & Directional Graph Networks (#4017) 
* 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
Mufei Li 65b0b9e8c3 [Dataset & Transform] Synthetic Datasets for Explainability and SIGNDiffusion Transform (#3982) 
* 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
RecLusIve-F b2ec5a2ea6 [Transform] Add FeatMask and RowFeatNormalizer transforms (#3968) 
* [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
Mufei Li 248bece633 [NN] GINEConv (#3934) 
* Update

* Update

* Update

* Update

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2022-04-25 14:41:05 +08:00
Quan (Andy) Gan 4375c2d7e4 [Doc] Fix documentation in dgl.multiprocessing namespace (#3929) 
* fix docs

* remove

* oh

* fix
 2022-04-16 00:35:06 +08:00
Quan (Andy) Gan e06e63d5d5 [Feature] Enable UVA sampling with CPU indices (#3892) 
* 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
rudongyu dc5035b1f3 [NN] Add EGNN & PNA (#3901) 
* 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
Krzysztof Sadowski 4c7bd314b4 [Feature] Radius Graph (#3829) 
* 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
rudongyu 290b7c25c2 [Transform] Random Walk Positional Encoding & Laplacian Positional Encoding (#3869) 
* [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
Mufei Li 9fee20b91d [Sampler] [Example] SAINTSampler and Simplify GraphSAINT Example (#3879) 
* 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
Minjie Wang ae3316c846 [Doc] Update doc of dataloading package. (#3886) 
* wip: dataloading doc

* update dataloading package doc and many others

* lint
 2022-03-26 21:59:02 +08:00
István Ketykó e963256882 [Doc] Update message-api.rst (#3844) 
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
Quan (Andy) Gan 7d4160869c [Bug] Fix multiple issues in distributed multi-GPU GraphSAGE example (#3870) 
* 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
Rhett Ying 16409ff852 [Doc] fix display issue of node/edge_split (#3858) 
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2022-03-25 09:18:08 +08:00
Mufei Li 8005978e1e [NN] Grouped reversible residual connections for GNNs (#3842) 
* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update
 2022-03-23 16:58:39 +08:00
Xin Yao 8425c936c2 update doc for gpu&uva sampling (#3787) 
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2022-02-28 21:17:32 +08:00
Mufei Li ec64581c96 [Doc] Misc fix for doc (#3782) 
* Update nn-pytorch.rst

* Update dgl.data.rst

* Update dgl.rst
 2022-02-28 16:03:32 +08:00