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f46080a4d1ebffb2aede1df0bf03a24276036b71
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146 Commits

Author SHA1 Message Date
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
Tong He
789b03f433 [Doc] Add KNN Benchmark Results (#3055) 
* add knn benchmark result

* update
 2021-06-28 16:13:56 +08:00
Kay Liu
9706eaa895 [Feature] add permission information and fix import problems (#3036) 
* [Feature] add positive negative statistics

* [Feature] add permission information and fix import problem

* fix backend incompatible problem

* modify random split to remove sklearn usage

* modify file read to remove pandas usage

* add datasets into doc

* add random seed in data splitting

* add dataset unit test

* usage permission information update

Co-authored-by: zhjwy9343 <6593865@qq.com>
 2021-06-21 11:55:15 +08:00
zhjwy9343
55e7796ac5 Revert "[Feature] add permission information and fix import problems (#2998)" (#3029) 
This reverts commit cba5b188b5.

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-06-17 13:58:38 +08:00
Kay Liu
cba5b188b5 [Feature] add permission information and fix import problems (#2998) 
* [Feature] add positive negative statistics

* [Feature] add permission information and fix import problem

* fix backend incompatible problem

* modify random split to remove sklearn usage

* modify file read to remove pandas usage

* add datasets into doc

Co-authored-by: zhjwy9343 <6593865@qq.com>
 2021-06-16 18:24:17 +08:00
Mufei Li
5be937a7fb [Kernel] Slicing Batched Graphs (#2965) 
* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Update

* Update

* Add files via upload

* Add files via upload

* Update

* Lint

* Add files via upload

* Lint

* Update

* Update

* Update

* Update

* Update

* Lint Fix

* Lint

Co-authored-by: Ubuntu <ubuntu@ip-172-31-12-161.us-west-2.compute.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2021-06-10 12:07:44 +08:00
Tong He
972a9f1323 [Doc] Re-organize the code for dgl.geometry, and expose it in the doc (#2982) 
* reorg and expose dgl.geometry

* fix lint

* fix test

* fix
 2021-06-07 11:19:39 +08:00
Da Zheng
6e7f19f27b [Distributed] add distributed in-degree and out-degree. (#2918) 
* add distributed in-degree and out-degree.

* update comments.

* fix a bug.

* add tests.

* add tests.

* fix a bug.

* fix docstring.

* update doc.

* fix

* fix.

Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2021-05-18 19:46:09 +08:00
Quan (Andy) Gan
657c220de7 [Feature] Python interface for adjacency matrix summation and multiplication (#2893) 
* test commit

* fixes

* oops

* add docs

* lint

* why does it say I have a trailing whitespace

* oh ok

* fixes

* why there's an invalid argument error

* address comments

* fix

* address comments
 2021-05-17 19:47:02 +08:00
kyawlinoo
b03077b60d [NN] GCNII model added <https://arxiv.org/pdf/2007.02133.pdf> (#2874) 
* Auto stash before rebase of "origin/pytorch-nn-working"

GCNII model added

* linting

* linting

* lint

* Frequency Adaptive gcn init comit

* Revert "Frequency Adaptive gcn init comit"

This reverts commit 86a80586ac.

* Update python/dgl/nn/pytorch/conv/gcn2conv.py

modified docstring

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

* added beta formula and changed param name

* fix docstring

* lint

* white space lint

* update docstring

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

* docstring formula update

* added gcn2

* added GCN2Conv

* Update nn.pytorch.rst

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2021-05-17 10:25:59 +08:00
Quan (Andy) Gan
caa6d6072c [Feature] Replacing thread_wrapped_func with minimal mp.Process wrapper (#2905) 
* standardizing thread_wrapped_func

* lints

* Update __init__.py
 2021-05-14 11:34:49 +08:00
YYY
c18f957d0e [Model] add implementation of twirls (#2770) 
* add implementation of twirls

* format the code

* fix some format error, and ignore others

* fix format errors

* fix format errors

* expose unfolding & attention

* Update nn.pytorch.rst

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2021-05-11 09:58:48 +08:00
xiang song(charlie.song)
975eb8fc5d [Distributed] Distributed node embedding and sparse optimizer (#2733) 
* Draft for sparse emb

* add some notes

* Fix

* Add sparse optim for dist pytorch

* Update test

* Fix

* upd

* upd

* Fix

* Fix

* Fix bug

* add transductive exmpale

* Fix example

* Some fix

* Upd

* Fix lint

* lint

* lint

* lint

* upd

* Fix lint

* lint

* upd

* remove dead import

* update

* lint

* update unitest

* update example

* Add adam optimizer

* Add unitest and update data

* upd

* upd

* upd

* Fix docstring and fix some bug in example code

* Update rgcn readme

Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-25.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-24-210.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal>
 2021-05-03 08:37:40 +08:00
Hengrui Zhang
a1f59c3b68 [Feature] QM9Edge Dataset Support (#2704) 
* [Feature] Support QM9Edge Datset

* Update qm9_edge.py

* disable tqdm

* Update qm9_edge.py

* Update qm9_edge.py

* Update qm9_edge.py

* Update qm9_edge.py

* Update qm9_edge.py

* Update qm9_edge.py

* Update qm9_edge.py

* remove preprocessing part

* add comparisons in qm9.py

* [docs] add qm9edge dataset

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
 2021-03-09 14:51:21 +08:00
Quan (Andy) Gan
99751d4960 [Doc] Rename block to message flow graph (#2702) 
* rename block to mfg

* revert

* rename
 2021-02-25 18:26:19 +08:00
Minjie Wang
8a07ab7737 [Doc] Tutorials re-organization (#2683) 
* reorg

* change titles

* rm some stale API doc; minor fix

* fix docs

* add warning

* rm new-tutorial run in ci

* lint
 2021-02-20 17:42:45 +08:00
Da Zheng
0fc649523b [Doc] Distributed heterogeneous graph training (#2654) 
* update DistGraph docstrings.

* add user guide.

* add doc string.

* fix.

* fix.

* fix.

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-02-19 10:48:05 -08:00
xiang song(charlie.song)
453d358d2c [Doc] Fix docs for sparse optimizer (#2680) 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-02-19 14:07:35 +08:00
Quan (Andy) Gan
3a19bbc508 fix doc (#2604) 2021-02-02 11:04:43 +08:00
Minjie Wang
4ca706e1b4 [Doc] Update doc of dgl.function (#2585) 
* update doc of dgl.function

* small fix
 2021-01-28 16:32:18 +08:00
Zihao Ye
7bab1365e2 [feature] Supporting half precision floating data type (fp16). (#2552) 
* add tvm as submodule

* compilation is ok but calling fails

* can call now

* pack multiple modules, change names

* upd

* upd

* upd

* fix cmake

* upd

* upd

* upd

* upd

* fix

* relative path

* upd

* upd

* upd

* singleton

* upd

* trigger

* fix

* upd

* count reducible

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* only keep related files

* upd

* upd

* upd

* upd

* lint

* lint

* lint

* lint

* pylint

* upd

* upd

* compilation

* fix

* upd

* upd

* upd

* upd

* upd

* upd

* upd doc

* refactor

* fix

* upd number

Co-authored-by: Zhi Lin <linzhilynn@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-42-78.us-east-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-21-156.us-east-2.compute.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-01-28 11:21:58 +08:00
xiang song(charlie.song)
a7e941c379 [Feature] Add support for sparse embedding (#2451) 
* Add sparse embedding for dgl and update rgcn example

* upd

* Fix

* Revert "Fix"

This reverts commit 4da87cdfb8.

* Fix

* upd

* upd

* Fix

* Add unitest and update impl

* fix

* Clean up rgcn example code

* upd

* upd

* update

* Fix

* update score

* sparse for sage

* remove model sparse

* upd

* upd

* remove global norm

* revert delete model_sparse.py

* update according to comments

* Fix doc

* upd

* Fix test

* upd

* lint

* lint

* lint

* upd

* upd

* clean up

Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal>
 2021-01-28 00:26:49 +08:00
Tong He
0855d25501 [NN] Support scalar edge weight for GraphConv, SAGEConv and GINConv (#2557) 
* add edge weight in forward

* fix lint

* fix

* fix

* address comments

* add utils

* add util to normalize in gcn way

* fix lint

* add unittest

* fix lint

* fix docstring

* fix docstring

* address comments

* improve notation consistence

* use preferred fn
 2021-01-26 23:34:12 +08:00
Quan (Andy) Gan
6c23fba8fa [Doc][Org] move edge_softmax to functional (#2442) 
* move edge_softmax to functional

* change examples

* fixes

* revert

* fix

* fix

* remove

* fix

* test

* add init

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-01-26 12:46:37 +08:00
Quan (Andy) Gan
2288098ba6 [Feature] Converting a block to a graph and allow block construction (#2555) 
* first commit

* more commit

* fix and docstring

* add to api reference

* address comments

* Update convert.py
 2021-01-24 12:44:54 +08:00
xnouhz
2c6d071617 [Feature] QM9 Dataset Support (#2521) 
* [Model] MixHop for Node Classification task

* [docs] update

* [docs] update

* [fix] remove seed option

* [fix] update readme

* [feature] support qm9 dataset

* [style] update

* [docs] fix the details

* [fix] indexing only support int

* [style] update

* [fix] multiple backends support

* [docs] add qm9

* [fix] Z type: float32 -> int32

* [fix] Z type: int32 -> long

* [docs] add ref

* [docs] fix

* [docs] update

* [docs] update

* [fix] test eval

* [docs] fix example

Co-authored-by: xnuohz@126.com <ubuntu@ip-172-31-44-184.us-east-2.compute.internal>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-01-21 01:33:30 +08:00
Da Zheng
1db7588739 fix. (#2534) 
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-01-14 14:23:36 +08:00
Quan (Andy) Gan
e018939729 [Tutorial] New tutorials for small graphs (#2482) 
* new tutorials for small graphs

* address changes and use GraphDataLoader

* fix and add data

* fix load_data

* style fixes

* Update 5_graph_classification.py
 2021-01-10 22:24:21 +08:00
Tong He
e2e524df41 [Feature] Add GraphDataLoader implementation (#2496) 
* add graph dataloader

* add to doc

* fix

* fix

* fix docstring

* update according to torch default_collate

* add unittest

* fix

* fix lint

* fix
 2021-01-07 13:38:21 +08:00
Zihao Ye
fa5f4d6aa7 [Doc] Hotfix on docstring of set_batch_num_edges (#2498) 2021-01-06 21:45:04 +08:00
Zihao Ye
f960468f50 [feature] APIs for manually set batch_num_nodes and batch_num_edges (#2430) 
* wip

* udp

* upd

* fix typo

* lint

* lint

* upd

* upd

* lint

* lint

* upd

* upd

* tftest

* fix

* fallback numpy

* fix tf

* docstring

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
 2021-01-04 23:43:58 +08:00
Zihao Ye
baace710cf [documentation] Improve the docstring of global pooling layer (#2437) 
* upd

* fix-link

* lint
 2020-12-21 10:12:54 +08:00
Zihao Ye
6b02babbad [doc] Add docstring for segment reduce. (#2375) 2020-11-27 18:04:13 +08:00
Mufei Li
45e3e9af2c [WIP] Misc Fix (#2359) 
* Update

* Update

* Update
 2020-11-19 23:54:55 +08:00
nv-dlasalle
6eda605ccd [BugFix][Dataloading] Disable AsyncTransferer copying to anywhere but the GPU (#2323) 
* Disable copying for anywhere but the GPU

* Remove unused import and remove references to transferring from the GPU from the docs

* Skip gpu test in cpu mode

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2020-11-07 21:34:54 +08:00
nv-dlasalle
d453d72dd1 [Doc][Dataloading] Expand documentation of AsyncTransferer (#2313) 
* Update docs

* Make non-default streams non-blocking
 2020-11-02 12:28:30 -08:00
nv-dlasalle
f673fc2553 [Dataloading] Add class for copying tensors to/from the GPU on a non-default stream (#2284) 
* Add async transferer class

* Add async ndarray copy interface

* Add python bindings

* Fix comment

* Add python class

* Fix linting issues

* Add python unit test

* Update python interface

* move async_transferer to cuda only directory

* Fix linting issue

* Move out of contrib

* Add doc strings

* Move test compute from backend

* Update comment

* Fix test naming

* Fix argument usage

* Wrap/unwrap backend parameters

* Move to dataloading

* Move to 'dataloading'

* Make GPU/CPU compatible

* Fix unit tests

* Add docs

* Use only backend interface for datamovement in unit test
 2020-10-30 07:29:06 -07:00
Mufei Li
7a6d66682f Update dgl.data.rst (#2217) 2020-09-21 10:15:24 +08:00
Mufei Li
877101a96b [Doc] Update Doc for UDFs (#2131) 
* Update Doc for UDFs

* add degree bucketing explanation

* Update udf.rst

* Update

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2020-09-13 04:57:06 +08:00