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184 Commits

Author SHA1 Message Date
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
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
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
Quan (Andy) Gan
d41d07d0f6 [Doc and bugfix] Add docs and user guide and update tutorial for sampling pipeline (#3774) 
* 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
Mufei Li
3bd5a9b6d1 [Doc] Fix Doc (#3777) 
* Update

* Update

* Update

* Update
 2022-02-25 17:21:06 +08:00
Mufei Li
6d9433b04f [Transform] [Doc] Rename transform to transforms and update doc (#3765) 
* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Fix
 2022-02-24 21:28:15 +08:00
Rhett Ying
2f4146a4c2 [Dataset] add train_idx/val_idx/test_idx as dataset attributes (#3769) 
* add train_idx/val_idx/test_idx as dataset attributes

* refine docstring
 2022-02-24 15:17:40 +08:00
Rhett Ying
4b182b9063 toctree typo for dataset adapters (#3764) 
* toctree typo for dataset adapters

* Update docs/source/api/python/dgl.data.rst
 2022-02-23 18:46:19 +08:00
Minjie Wang
0227ddfb66 [NN] Rework RelGraphConv and HGTConv (#3742) 
* WIP: TypedLinear and new RelGraphConv

* wip

* further simplify RGCN

* a bunch of tweak for performance; add basic cpu support

* update on segmm

* wip: segment.cu

* new backward kernel works

* fix a bunch of bugs in kernel; leave idx_a for future

* add nn test for typed_linear

* rgcn nn test

* bugfix in corner case; update RGCN README

* doc

* fix cpp lint

* fix lint

* fix ut

* wip: hgtconv; presorted flag for rgcn

* hgt code and ut; WIP: some fix on reorder graph

* better typed linear init

* fix ut

* fix lint; add docstring
 2022-02-23 12:10:20 +08:00
dddg617
9e358dfe66 [NN] HeteroLinear and HeteroEmbedding (#3678) 
* modify hetero

* modify rst document

* update hetero

* update hetero

* update hetero

* update hetero

* Update

* Update

* Update

* Update

* 20220216

* Update

* Update

* Fix

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: ShelkerX <925089962@qq.com>
 2022-02-17 16:16:51 +08:00
RhettYing
6106a99d0a refine 2022-02-17 02:00:10 +00:00
RhettYing
e0f054fb27 [Doc] add doc for DGLCSVDataset 2022-02-17 00:52:16 +00:00
Israt Nisa
b3d3a2c4b0 [Feature] Gather mm (#3641) 
* init

* init

* working cublasGemm

* benchmark high-mem/low-mem, err gather_mm output

* cuda kernel for bmm like kernel

* removed cpu copy for E_per_Rel

* benchmark code from Minjie

* fixed cublas results in gathermm sorted

* use GPU shared mem in unsorted gather mm

* minor

* Added an optimal version of gather_mm_unsorted

* lint

* init gather_mm_scatter

* cublas transpose added

* fixed h_offset for multiple rel

* backward unittest

* cublas support to transpose W

* adding missed file

* forgot to add header file

* lint

* lint

* cleanup

* lint

* docstring

* lint

* added unittest

* lint

* lint

* unittest

* changed err type

* skip cpu test

* skip CPU code

* move in-len loop inside

* lint

* added check different dim length for B

* w_per_len is optional now

* moved gather_mm to pytorch/backend with backward support

* removed a_/b_trans support

* transpose op inside GEMM call

* removed out alloc from API, changed W 2D to 3D

* Added se_gather_mm, Separate API for sortedE

* Fixed gather_mm (unsorted) user interface

* unsorted gmm backward + separate CAPI for un/sorted A

* typecast to float to support atomicAdd

* lint typecast

* lint

* added gather_mm_scatter

* minor

* const

* design changes

* Added idx_a, idx_b support gmm_scatter

* dgl doc

* lint

* adding gather_mm in ops

* lint

* lint

* minor

* removed benchmark files

* minor

* empty commit

Co-authored-by: Israt Nisa <nisisrat@amazon.com>
 2022-02-14 22:27:23 -05:00
Jinjing Zhou
dc78e11c3f [Dataset] Adapter to convert a dataset for link prediction task (#3699) 
* add ut

* add doc link

* install dep

* add

* Revert "install dep"

This reverts commit e574a83771.

* add

* merge fix

* rm files

* fix

* fix

* fix

* fix

* fix typo

* fix tf

* fix

* fix

* fix

* fix

* fix

* fix dependency

* fix test

* fix

* fix

* add doc

* fix

* fix

* fix test

* fix test

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2022-02-11 16:59:14 +08:00
Quan (Andy) Gan
701b4fccc2 [Sampling] New sampling pipeline plus asynchronous prefetching (#3665) 
* initial update

* more

* more

* multi-gpu example

* cluster gcn, finalize homogeneous

* more explanation

* fix

* bunch of fixes

* fix

* RGAT example and more fixes

* shadow-gnn sampler and some changes in unit test

* fix

* wth

* more fixes

* remove shadow+node/edge dataloader tests for possible ux changes

* lints

* add legacy dataloading import just in case

* fix

* update pylint for f-strings

* fix

* lint

* lint

* lint again

* cherry-picking commit fa9f494

* oops

* fix

* add sample_neighbors in dist_graph

* fix

* lint

* fix

* fix

* fix

* fix tutorial

* fix

* fix

* fix

* fix warning

* remove debug

* add get_foo_storage apis

* lint
 2022-01-30 16:13:00 +08:00
Minjie Wang
5152a87982 [Data] Utility function and class for converting a dataset for node prediction (#3695) 
* add ut

* add doc link

* install dep

* fix  ci

* fix ut; more comments

* remove deprecated attributes in rdf datasets; fix label feature name

* address comments

* fix ut for other frameworks
 2022-01-30 14:31:37 +08:00
Mufei Li
2b98e764e8 [Transform] Modules for Augmentation (#3668) 
* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix lint

* lint

* Update

* Update

* lint fix

* Fix CI

* Fix

* Fix CI

* Update

* Fix

* Update

* Update

* Augmentation (#10)

* Update

* PPR

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* CI

* lint

* lint

* Update

* Update

* Fix AddEdge

* try import

* Update

* Fix

* CI

Co-authored-by: Ubuntu <ubuntu@ip-172-31-31-136.us-west-2.compute.internal>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2022-01-25 20:29:46 +08:00
Jeremy Goh
8f5baa15e4 [Doc] Fix spelling, references and update info on building docs (#3682) 
* Fix ref to message-passing guide

* Fix pygments and spacing

* Update build documentation steps in README.md

* Use links

* Adjust parameters in SAGEConv docstring in same order as init

* Fix spelling error

* Change doc link
 2022-01-25 17:22:18 +08:00
Xin Yao
40b44a43a9 [Feature] Pin dgl.graph to the page-locked memory (#3616) 
* implement pin_memory/unpin_memory/is_pinned for dgl.graph

* update python docstring

* update c++ docstring

* add test

* fix the broken UnifiedTensor

* eliminate extra context parameter for pin/unpin

* fix linting

* fix typo

* disable new format materialization for pinned graphs

* update python doc for pin_memory_

* fix unit test

* update doc

* change unitgraph and heterograph's PinMemory to in-place

* update comments for NDArray's PinMemory_ and PinData

* update doc

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2022-01-21 16:13:12 +08:00
Mufei Li
48cbea720e [Transform] Module Interface for Transform (#3636) 
* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix lint

* lint

* Update

* Update

* lint fix

* Fix CI

* Fix

* Fix CI

* Update

* Fix

* Update

* Update

* resolve conflict

* Fix CI

Co-authored-by: Ubuntu <ubuntu@ip-172-31-31-136.us-west-2.compute.internal>
 2022-01-17 17:45:07 +08:00
Quan (Andy) Gan
90f10b31cb [Feature] Negative sampling (#3599) 
* first commit

* a bunch of fixes

* add unique

* lint

* lint

* lint

* address comments

* Update negative_sampler.py

* fix

* description

* address comments and fix

* fix

* replace unique with replace

* test pylint

* Update negative_sampler.py
 2022-01-07 18:26:14 +08:00
Mufei Li
d6eecf90a1 [NN] TransE and TransR (#3530) 
* Update

* Update

* Update

* Update

* Update

* CI

* CI

* CI

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-12-07 10:13:13 +08:00
Mufei Li
d2ef24335c [NN] EdgePredictor (#3518) 
* Update

* Update

* Fix

* Update

* Update

* update

* Fix test

* CI

* CI
 2021-12-02 14:25:31 +08:00
Mufei Li
9e7fbf9567 [NN] JumpingKnowledge (#3512) 
* Update

* Fix
 2021-11-19 16:37:25 +08:00
Quan (Andy) Gan
b8ce0f41a3 [Sampling] Cluster-GCN and ShaDow-GNN DataLoader (#3487) 
* first commit

* next commit

* third commit

* add ShaDow-GNN sampler and unit tests

* fixes

* lint

* cr*p

* lint

* fix lint

* fixes and more unit tests

* more tests

* fix docs

* lint

* fix

* fix

* fix

* fixes

* fix doc
 2021-11-16 13:16:25 +08:00
Mufei Li
dfa32ae092 [NN] GNNExplainer (#3490) 
* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* lint fix

* lint fix

* Fix lint

* Update

* Fix CI

* Fix CI

* Fix

* CI

* Fix

* Update

* Fix

* Fix

* Fix CI

* Fix CI
 2021-11-11 02:22:22 +08:00
Mufei Li
f46080a4d1 [Feature] k-hop Subgraph Extraction (#3458) 
* Update

* Fix

* Fix

* Update

* Update

* Update

* Fix CI

* Fix

* Fix

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Fix for TF
 2021-11-04 15:47:35 +08:00
Shaked Brody
e2f33fd5cc [NN][Model] GATv2 (#3473) 
* [Model][Core] GATv2

* lint

* gatv2conv.py

* lint

* lint

* style and docs

* lint

* gatv2conv fix

Co-authored-by: Shaked Brody shakedbr@campus.technion.ac.il <shakedbr@tangerine.cslcs.technion.ac.il>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
 2021-11-03 21:55:56 +08:00
Kamil Kamiński
51c6509704 [NN] Add EGATConv nn.module (#3425) 
* added nn pytorch egatconv

* aligned with test build

* aligned with test build

* fixed wihite spaces

* fixed wihite spaces

* fixed wihite spaces

* added missing egatconv in imports

* added indentation in forward

* GATConv based implementation

* removed **kw_args

* added dgl relative imports

* PR corrections

* added DGL Error to EGATConv imports

* Update test_nn.py

Co-authored-by: Argusmocny <k.kaminski@cent.uw.edu.pl>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
 2021-10-28 00:38:08 +08:00
David Min
b78acd67ce [Doc] Add an official documentation of UnifiedTensor (#3194) 
* Add pytorch-direct version

* remove

* add documentation for UnifiedTensor

* Revert "add documentation for UnifiedTensor"

This reverts commit 63ba42644d.

* add UnifiedTensor documentation

* Update python/dgl/contrib/unified_tensor.py

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

Co-authored-by: shhssdm <shhssdm@gmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2021-08-02 22:40:51 +08:00
Jinjing Zhou
2583ec5934 [Doc] Fix WeightBasis documentation (#3189) 
* fix

* fix type

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-07-28 18:56:10 +08:00
xiang song(charlie.song)
d7390763f0 [Distributed] Deprecate old DistEmbedding impl, use synchronized embedding impl (#3111) 
* fix.

* fix.

* fix.

* fix.

* Fix test

* Deprecate old DistEmbedding impl, use synchronized embedding impl

* update doc

Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal>
Co-authored-by: Da Zheng <zhengda1936@gmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-07-14 00:15:53 +08:00
Rhett-Ying
175f53decf [Feature] enable edge reorder in dgl.reorder_graph() (#3113) 
* [Feature] enable edge reorder in dgl.reorder_graph()

* refine doc string

* refine doc string for dgl.reorder_graph

* refine doc string further
 2021-07-12 14:11:46 +08:00
Quan (Andy) Gan
751685a979 [Doc] Add documentation for DGLGraph.adj_sparse (#3096) 
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-07-07 11:24:47 +08:00
Zihao Ye
c372f0aed6 [doc] Expose dgl.partition APIs (#3103) 2021-07-06 12:17:56 +08:00
Minjie Wang
d3e4460b98 [Doc] Add docstring for missing APIs (#3088) 
* add docstring for missing API; fix some docstring

* rename apis; address comments
 2021-07-05 18:40:07 +08:00
Rhett-Ying
4307fe8895 [Feature] Add dgl.reorder() to re-order graph according to specified … (#3063) 
* [Feature] Add dgl.reorder() to re-order graph according to specified strategy

* fix unit test failure for metis reorder

* fix unit test failure on mxnet_cpu

* refine unit test for dgl.reorder

* fix unit test failure on mxnet

* fix array_equal error for mxnet unit test

* fix unit test failure for mxnet

* convert metis output to numpy array explicitly

Co-authored-by: Tong He <hetong007@gmail.com>
 2021-06-30 13:29:08 +08:00
Quan (Andy) Gan
61fba9da0f [Doc] Add Node2Vec docstrings to documentation server (#3068) 
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-06-29 22:29:10 +08:00