GitLab

* [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>

* 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>

* add double radius node labeling

* add doc

* add test

* fix lint issue

* update

* update

* update

* update

* fix lint

* [doc] add doc for saving original node/edge IDs in dist part pipeline

* move added docs into advanced topic

* fix ypo

* refine

* replace with pow

* autosummary for attributes

* revert accidental push

* revert accidental push

* added example
Co-authored-by: Israt Nisa <nisisrat@amazon.com>

* 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>

* 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>

* 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>

* [Sparse] Add reduction operators

* Fix linting problem

* Fix linting problem

* Fix linting problem

* Fix docstring

* Fix test cases

* Fix linting problem

* Skip reduction unittests

* [Sparse] Add Transposition

* Fix docstring

* Fix linting problem

* Minor fix

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

* 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>

* 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>

* 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>

* Update distributed-preprocessing.rst

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

* Update

* rollback for partition_algo/random.py
Co-authored-by: Ubuntu <ubuntu@ip-172-31-20-21.us-west-2.compute.internal>

* 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

* [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

* 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>

* [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>

Co-authored-by: Ubuntu <ubuntu@ip-172-31-53-142.us-west-2.compute.internal>

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

* 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>

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

* [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>

* * 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>

* 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>

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

* 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>

* Update

* CI

* Update

* Update

* Fix

* Fix

* Update

* Update

* Update dgl.data.rst

* CI

* 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>

* 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

* [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>

* Update

* Update

* Update

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

* fix docs

* remove

* oh

* fix

* 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

* 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>

* 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>