Commits · 8f0df39ee106efb665af90c61dddfdfbf4899991 · OpenDAS / dgl

02 Nov, 2022 1 commit

[NN] Add DegreeEncoder for graph transformer (#4742) · 9d9280cb

ZhenyuLU_Heliodore authored Nov 02, 2022



* Add files via upload

This file will contain several utility modules for Graph Transformer. DegreeEncoder has been implemented in this file now.

* Update graph_transformer.py

* Update nn-pytorch.rst

Add graph_transformer.DegreeEncoder in Utility Modules

* Update test_nn.py

* Update __init__.py

* Update graph_transformer.py

* Update test_nn.py

* Update graph_transformer.py

fix unused import

* Update graph_transformer.py

add module doc-string

* Update graph_transformer.py

* Update graph_transformer.py
Co-authored-by: rudongyu <ru_dongyu@outlook.com>

9d9280cb

01 Nov, 2022 1 commit

[Dist] Enable save and load for Distributed Optimizer (#4752) · 2caa6bd0

peizhou001 authored Nov 01, 2022



* add save/load for distributed  optimizer
Co-authored-by: Ubuntu <ubuntu@ip-172-31-16-19.ap-northeast-1.compute.internal>

2caa6bd0

31 Oct, 2022 1 commit

[NN] Add a learned laplacian positional encoder (#4750) · ed66a209

Zhiteng Li authored Oct 31, 2022



* add a learned laplacian positional encoder

* leverage black to beautify the python code

* refine according to dongyu's comments
Co-authored-by: rudongyu <ru_dongyu@outlook.com>

ed66a209

27 Oct, 2022 1 commit

[Model] Heterogeneous graph support for GNNExplainer (#4401) · 4b1fb681

Infinity_X authored Oct 27, 2022



* [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>

4b1fb681

12 Oct, 2022 1 commit

Add Metapath2vec module (#4660) · f846d902

LuckyLiuM authored Oct 13, 2022



* 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>

f846d902

10 Oct, 2022 1 commit

[Transform] Double Radius Node Labeling (#4513) · 303b150f

rudongyu authored Oct 10, 2022

* add double radius node labeling

* add doc

* add test

* fix lint issue

* update

* update

* update

* update

* fix lint

303b150f

30 Sep, 2022 1 commit

[Sparse] Improve API docs (#4663) · 09ec5fd5

Israt Nisa authored Sep 30, 2022



* replace with pow

* autosummary for attributes

* revert accidental push

* revert accidental push

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

09ec5fd5

29 Sep, 2022 1 commit

Add Deepwalk module (#4562) · eb729c54

LuckyLiuM authored Sep 29, 2022



* 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>

eb729c54

28 Sep, 2022 1 commit

Add `sddmm` operator in mock_sparse library (#4579) · fa05ccb9

Israt Nisa authored Sep 28, 2022



* 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>

fa05ccb9

27 Sep, 2022 1 commit

[Sparse] Migration of Unary, Softmax, Matmul Ops (#4616) · 977b1ba4

Mufei Li authored Sep 27, 2022



* 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>

977b1ba4

26 Sep, 2022 1 commit

[Sparse] Add reduction operators (#4600) · 544a2cd1

czkkkkkk authored Sep 26, 2022

* [Sparse] Add reduction operators

* Fix linting problem

* Fix linting problem

* Fix linting problem

* Fix docstring

* Fix test cases

* Fix linting problem

* Skip reduction unittests

544a2cd1

23 Sep, 2022 1 commit

[Sparse] Add Transposition for SparseMatrix and DiagMatrix (#4597) · db64cc37

czkkkkkk authored Sep 23, 2022



* [Sparse] Add Transposition

* Fix docstring

* Fix linting problem

* Minor fix

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

db64cc37

20 Sep, 2022 1 commit

[Sparse] Migrate DiagMatrix class (#4567) · 73b9f3a1

Mufei Li authored Sep 20, 2022



* 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>

73b9f3a1

14 Sep, 2022 1 commit

Move mock version of dgl_sparse library to DGL main repo (#4524) · cf035927

Israt Nisa authored Sep 14, 2022



* 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>

cf035927

05 Sep, 2022 1 commit

[Bug] Enable turn on/off libxsmm at runtime (#4455) · 62af41c2

peizhou001 authored Sep 05, 2022



* 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>

62af41c2

17 Aug, 2022 1 commit

[Doc] Update distributed chapter according to new pipeline (#4275) · 3bcb268a

Minjie Wang authored Aug 17, 2022

* 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

3bcb268a

16 Aug, 2022 1 commit

[Feature] enable graph partition book support canonical etypes (#4343) · 39987bc5

Rhett Ying authored Aug 16, 2022

* [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

39987bc5

07 Jul, 2022 1 commit

[Feature] Add to_cugraph and from_cugraph to DGL (#4166) · 9ae117d3

Vibhu Jawa authored Jul 06, 2022



* 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>

9ae117d3

20 Jun, 2022 1 commit

[Dist] defer to load node/edge feats (#4143) · 69226588

Rhett Ying authored Jun 20, 2022



* [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>

69226588

15 Jun, 2022 1 commit

[Doc] Updated transform ops list in dgl.rst (Issue #4087) (#4123) · 5f04fc2b

ndickson-nvidia authored Jun 15, 2022



* * 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>

5f04fc2b

14 Jun, 2022 1 commit

[Dataset] Add Flickr and Yelp dataset (#4099) · defa292b

RecLusIve-F authored Jun 14, 2022



* 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>

defa292b

02 Jun, 2022 2 commits

[Dataset] Add WikiCS Dataset (#4035) · 89655cfd

RecLusIve-F authored Jun 02, 2022



* 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>

89655cfd

[Data] AsGraphPredDataset (#4073) · d9c25521
Mufei Li authored Jun 02, 2022
```
* Update

* CI

* Update

* Update

* Fix

* Fix
```
d9c25521

27 May, 2022 1 commit
- [Bugfix] Fix PinSAGE Benchmark (#4058) · bef99307
  Mufei Li authored May 28, 2022
```
* Update

* Update

* Update dgl.data.rst

* CI
```
  bef99307
20 May, 2022 1 commit

[NN] Label Propagation & Directional Graph Networks (#4017) · 3fe5eea7

rudongyu authored May 20, 2022



* 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>

3fe5eea7

16 May, 2022 1 commit

[Dataset & Transform] Synthetic Datasets for Explainability and SIGNDiffusion Transform (#3982) · 65b0b9e8

Mufei Li authored May 16, 2022

* 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

65b0b9e8

07 May, 2022 1 commit

[Transform] Add FeatMask and RowFeatNormalizer transforms (#3968) · b2ec5a2e

RecLusIve-F authored May 07, 2022



* [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>

b2ec5a2e

25 Apr, 2022 1 commit

[NN] GINEConv (#3934) · 248bece6

Mufei Li authored Apr 25, 2022



* Update

* Update

* Update

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

248bece6

15 Apr, 2022 1 commit
- [Doc] Fix documentation in dgl.multiprocessing namespace (#3929) · 4375c2d7
  Quan (Andy) Gan authored Apr 16, 2022
```
* fix docs

* remove

* oh

* fix
```
  4375c2d7
12 Apr, 2022 1 commit

[Feature] Enable UVA sampling with CPU indices (#3892) · e06e63d5

Quan (Andy) Gan authored Apr 12, 2022

* 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

e06e63d5

07 Apr, 2022 1 commit

[NN] Add EGNN & PNA (#3901) · dc5035b1

rudongyu authored Apr 07, 2022



* 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>

dc5035b1

30 Mar, 2022 3 commits

[Feature] Radius Graph (#3829) · 4c7bd314

Krzysztof Sadowski authored Mar 30, 2022



* 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>

4c7bd314

[Transform] Random Walk Positional Encoding & Laplacian Positional Encoding (#3869) · 290b7c25

rudongyu authored Mar 30, 2022



* [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>

290b7c25

[Sampler] [Example] SAINTSampler and Simplify GraphSAINT Example (#3879) · 9fee20b9

Mufei Li authored Mar 30, 2022



* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

9fee20b9

26 Mar, 2022 1 commit
- [Doc] Update doc of dataloading package. (#3886) · ae3316c8
  Minjie Wang authored Mar 26, 2022
```
* wip: dataloading doc

* update dataloading package doc and many others

* lint
```
  ae3316c8
25 Mar, 2022 1 commit
- [Doc] fix display issue of node/edge_split (#3858) · 16409ff8
  Rhett Ying authored Mar 25, 2022
```
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
```
  16409ff8
23 Mar, 2022 1 commit
- [NN] Grouped reversible residual connections for GNNs (#3842) · 8005978e
  Mufei Li authored Mar 23, 2022
```
* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update
```
  8005978e
28 Feb, 2022 1 commit
- [Doc] Misc fix for doc (#3782) · ec64581c
  Mufei Li authored Feb 28, 2022
```
* Update nn-pytorch.rst

* Update dgl.data.rst

* Update dgl.rst
```
  ec64581c
27 Feb, 2022 1 commit

[Doc and bugfix] Add docs and user guide and update tutorial for sampling pipeline (#3774) · d41d07d0

Quan (Andy) Gan authored Feb 28, 2022



* 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>

d41d07d0

25 Feb, 2022 1 commit
- [Doc] Fix Doc (#3777) · 3bd5a9b6
  Mufei Li authored Feb 25, 2022
```
* Update

* Update

* Update

* Update
```
  3bd5a9b6