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e2e524df41cb84b99d3ff7fc9508e14634fdb044
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107 Commits

Author SHA1 Message Date
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
Jinjing Zhou
0afacfb873 Fix create_format_ to create_formats (#2184) 
* Update dgl.DGLGraph.rst

* Update gcn.py
 2020-09-12 14:44:30 +08:00
Zihao Ye
5bc029b99f upd (#2097) 2020-08-23 21:25:31 +08:00
Minjie Wang
163398c036 Update dgl.DGLGraph.rst 2020-08-23 10:53:33 +08:00
Tianjun Xiao
7ead28c315 [Doc] [NN] Fix message and nn user guide link (#2090) 
* fix user guide link

* some fix on tensorflow
 2020-08-22 00:18:22 +08:00
Xiangkun Hu
6f26cfcaec [Doc] Fix links and references in dataset user guide (#2085) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960.

* data pipeline user guide

* remove chapter numbers

* Update data.rst

* image in dataset userguide

* update links using ref

* modify the link of save_graphs and load_graphs in dataset user guide

* move image to s3 server.

* fix links and ref
 2020-08-21 21:09:26 +08:00
Minjie Wang
f13b9b6212 [Doc] Scan the API docs and make many changes (#2080) 
* WIP: api

* dgl.sampling, dgl.data

* dgl.sampling; dgl.dataloading

* sampling packages

* convert

* subgraph

* deprecate

* subgraph APIs

* All docstrings for convert/subgraph/transform

* almost all funcs under dgl namespace

* WIP: DGLGraph

* done graph query

* message passing functions

* lint

* fix merge error

* fix test

* lint

* fix

Co-authored-by: Quan Gan <coin2028@hotmail.com>
 2020-08-20 23:26:49 +08:00
Da Zheng
9da1629c9d [Distributed] Some small fixes on doc (#2049) 
* quick fix.

* update sparse optimizer.

* fix.

* fix
 2020-08-18 21:13:19 -07:00
Da Zheng
75ffc31f76 [Doc] Update the docstring of distributed APIs. (#2025) 
* add doc.

* update DistGraph.

* add DistTensor.

* update DistEmbedding.

* add partition.py

* add sampling.

* fix.

* add graph partition book and create a base class.

* fix test.

* add rst.

* update doc rst.

* update.

* fix.

* fix docs

* update distributed tensor and embeddings.

* add checks.

* update DistGraph.

* update initialization.

* fix graph partition book.

* update graph partition book.

* update partition.

* update partition.

* fix.

* add example code.

* update DistGraph

* Update python/dgl/distributed/dist_context.py

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

* Update python/dgl/distributed/dist_context.py

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

* Update python/dgl/distributed/dist_dataloader.py

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

* Update python/dgl/distributed/dist_dataloader.py

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

* Update python/dgl/distributed/dist_dataloader.py

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

* update initialize.

* update dataloader.

* update distgraph.

* update DistGraph.

* update DistTensor.

* update.

* more updates.

* fix lint.

* add num_nodes and num_edges

Co-authored-by: Chao Ma <mctt90@gmail.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-18 11:53:45 -07:00
Tianjun Xiao
65866989c0 [NN] [Doc] Fix nn api doc (#2047) 
* fix mxnet nn doc and no note on chebconv

* change notes to note to highlight
 2020-08-18 23:47:16 +08:00
Mufei Li
be444e52d9 [Doc/Feature] Refactor, doc update and behavior fix for graphs (#1983) 
* Update graph

* Fix for dgl.graph

* from_scipy

* Replace canonical_etypes with relations

* from_networkx

* Update for hetero_from_relations

* Roll back the change of canonical_etypes to relations

* heterograph

* bipartite

* Update doc

* Fix lint

* Fix lint

* Fix test cases

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix test

* Fix

* Update

* Use DGLError

* Update

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* rewrite sanity checks

* delete unnecessary checks

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Fix

* Update

* Fix

* Update

* Fix

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
 2020-08-18 04:26:29 +08:00
Jinjing Zhou
0afc3cf8e1 [NN] Add ChebConv for Tensorflow (#2038) 
* add chebconv

* fix

* lint

* fix lint

* docs
 2020-08-17 22:12:27 +08:00
Quan (Andy) Gan
4f1da61b58 [Doc] fix inconsistencies in minibatch user guide (#2032) 2020-08-17 12:43:43 +08:00
Quan (Andy) Gan
1f7b219594 [Doc] User guide section 5 and 6 (#2029) 
* [Doc] User guide section 5 and 6

* oops

* fix
 2020-08-17 09:47:01 +08:00
Xiangkun Hu
62e69b67aa [Doc] Modify the link of save_graphs and load_graphs in dataset user guide (#2027) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960.

* data pipeline user guide

* remove chapter numbers

* Update data.rst

* image in dataset userguide

* update links using ref

* modify the link of save_graphs and load_graphs in dataset user guide
 2020-08-15 09:21:08 +08:00
Jinjing Zhou
de2e608bb3 Update dgl.rst (#2020) 2020-08-14 18:18:45 +08:00
Xiangkun Hu
f4f78803cf [Doc] Update links by :ref in dataset user guide (#2024) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960.

* data pipeline user guide

* remove chapter numbers

* Update data.rst

* image in dataset userguide

* update links using ref
 2020-08-14 17:28:54 +08:00
Quan (Andy) Gan
cd48435206 [Transform] Docstring and subframes (#1962) 
* update knn graph docs

* more docs

* [Doc] transform module docstrings

* remove copy_ndata and copy_edata

* fix

* lint

* fix

* fix

* fix

* clean up docstrings

* fix docstring

* dtype specifications

* addresses comments

* fix

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-13 10:41:43 +08:00
Tianjun Xiao
69f5869f3b [Doc] NN doc refactor Conv Layers (#1672) 
* go through gcn, relgcn

* fix tagconv formula

* fix doc in sageconv

* fix sgconv doc

* replace hat with tilde

* more comments on gmmconv

* fix agnnconv chebconv doc

* modify nnconv doc

* remove &

* add nn conv examples

* Rebase master

* More merge conflicts

* check homo

* add back self loop for some convs, check homo in tranform

* add example for denseconv

* add example and doc for dotgat and cfconv

* check in-degree for graphconv

* add language fix

* gconv address all comments

* another round of change based on api template

* change agnn

* go through agnn, appnp, atomic, cf, cheb, dense, gat, sage modules

* finish pytorch part of nn conv

* mxnet graphconv done

* tensorflow graphconv works

* add new modules into doc

* add comments to not split code

* refine doc

* resr

* more comments

* more fix

* finish conv and dense conv part api

* pylint fix

* fix pylink

* fix pylint

* more fix

* fix

* fix test fail because zere in degree

* fix test fail

* sage is not update for mxnet tf

Co-authored-by: Ubuntu <ubuntu@ip-172-31-0-81.us-east-2.compute.internal>
 2020-08-12 18:47:19 +08:00
Quan (Andy) Gan
f5eb80d221 [Feature] Edge DataLoader for edge classification & link prediction (#1828) 
* clean commit

* oops forgot the most important files

* use einsum

* copy feature from frontier to block

* Revert "copy feature from frontier to block"

This reverts commit 5224ec963e.

* temp fix

* unit test

* fix

* revert jtnn

* lint

* fix win64

* docstring fixes and doc indexing

* revert einsum in sparse bidecoder

* fix some examples

* lint

* fix due to some tediousness in remove_edges

* addresses comments

* fix

* more jtnn fixes

* fix
 2020-08-11 18:00:58 +08:00
Minjie Wang
c2cd6eb22e [Doc] Reorg doc (#1989) 2020-08-10 23:19:03 +08:00
Zihao Ye
18bfec24cf [hotfix] Refactor edge softmax module (#1967) 
* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd
 2020-08-07 23:50:12 +08:00
Xiangkun Hu
3d8377062c [Doc] Dataset api doc add save_info(), load_info() (#1954) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960.

* update doc

* Update data.rst

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-06 22:25:45 +08:00
Tong He
967ecb8064 [Dataset] Fix the docstring format for dgl.data section (#1941) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960.

* update data rst

* update data doc and docstring

* API doc rst for dataset

* docstring

* update api doc

* add url format

* update docstring

* update citation graph

* update knowledge graph

* update gc datasets

* fix index

* Rst fix (#3)

* Fix syntax

* syntax

* update docstring

* update doc (#4)

* final update

* fix rdflib

* fix rdf

Co-authored-by: HuXiangkun <huxk_hit@qq.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-06 14:47:49 +08:00
Zihao Ye
05a4337901 [Doc] Introduce the relation of message passing APIs and operators in docstring. (#1878) 
* upd

* fix typo

* upd
 2020-07-29 00:41:47 +08:00
Zihao Ye
2fa2b4534e [Feature] Support higher order derivative for message passing. (#1877) 
* upd

* fix typo
 2020-07-28 23:11:06 +08:00
Zihao Ye
2b8eb5be6f [refactor] Move spmm and sddmm operators to operator module (#1873) 
* upd

* upd

* upd

* upd
 2020-07-28 18:39:12 +08:00
Zihao Ye
bc209bff94 [bugfix] Fix the deterministic of kernel test and add documentation. (#1799) 
* upd

* upd

* upd

* relax

* relax too

* upd
 2020-07-14 04:22:31 +08:00
Quan (Andy) Gan
168a88e570 [Sampling] NodeDataLoader for node classification (#1635) 
* neighbor sampler data loader first commit

* more commit

* nodedataloader

* fix

* update RGCN example

* update OGB

* fixes

* fix minibatch RGCN crashing with self loop

* reverting gatconv test code

* fix

* change to new solution that doesn't require tf dataloader

* fix

* lint

* fix

* fixes

* change doc

* fix docstring

* docstring fixes

* return seeds and input nodes from data loader

* fixes

* fix test

* fix windows build problem

* add pytorch wrapper

* fixes

* add pytorch wrapper

* add unit test

* add -1 support to sample_neighbors & fix docstrings

* docstring fix

* lint

* add minibatch rgcn evaluations

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Tong He <hetong007@gmail.com>
 2020-07-02 16:31:05 +08:00
Mufei Li
36c7b77167 [LifeSci] Move to Independent Repo (#1592) 
* Move LifeSci

* Remove doc
 2020-06-05 21:28:24 +08:00
Mufei Li
90d2118da5 [Dataset] Change Cora Split (#1583) 
* Use new version of Cora

* Fix import
 2020-06-03 15:45:38 +08:00
Quan (Andy) Gan
7ba9cbc63e [Docs] Fix docstrings and documentations (#1420) 
* fix docs of to_block

* fix

* oops

* more fixes
 2020-05-19 13:04:55 +08:00
Zihao Ye
c2e61ce10b [Refactor] Restrict sparse format for DGLHeteroGraph (#1474) 
* upd

* simplify

* further simplify

* lint

* doc

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* lint

* rename format

* upd

* lint

* upd

* upd

* upd

* udp

* debug

* upd

* upd

* upd

* upd

* upd

* 无可厚非吧

* 中三边肥

* 你一定要喊吗

* lint

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* Update unit_graph.h

Co-authored-by: Zihao Ye <yzh119@192.168.0.110>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2020-05-14 22:11:12 +08:00
Zihao Ye
93ac29ce34 [Refactor] Unify DGLGraph, BatchedDGLGraph and DGLSubGraph (#1216) 
* upd

* upd

* upd

* lint

* fix

* fix test

* fix

* fix

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd tutorial

* upd

* upd

* fix kg

* upd doc organization

* refresh test

* upd

* refactor doc

* fix lint

Co-authored-by: Minjie Wang <minjie.wang@nyu.edu>
 2020-03-05 18:03:57 +08:00
Minjie Wang
5967d81782 [Doc] Re-organize API docs and tutorials (#1222) 
* reorg tutorials and api docs

* fix
 2020-01-26 21:26:34 +08:00
VoVAllen
a00636a02b [Tensorflow] Several nn & example (#1191) 
* several nn example

* appnp

* fix lint

* lint

* add dgi

* fix

* fix

* fix

* fff

* docs

* 111

* fix

* change init

* change result

* tiaocan+1

* fix

* fix lint

* fix

* fix
 2020-01-19 22:48:40 +08:00
Zihao Ye
ca302a13ac [Feature] Add dgl.nn.*.Sequential for usability (#1166) 
* upd

* upd

* upd

* upd

* lint

* upd

* upd

* upd

* upd

Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com>
 2020-01-09 12:39:22 +08:00
Mufei Li
cf9ba90fd4 [Chem] ACNN and various utilities (#1117) 
* Add several splitting methods

* Update

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Finally

* CI
 2019-12-19 11:54:40 +08:00
Da Zheng
869093e890 fix doc of EdgeSampler. (#1093) 2019-12-12 19:15:06 -08:00
Mufei Li
ead64de98e [Hetero] Batching/Unbatching DGLHeteroGraph (#1017) 
* Update

* Update

* Update

* Fix

* CI style fix

* CI fix style

* Fix

* Try CI

* Fix test

* Update

* Update

* Update

* Update
 2019-11-26 14:40:50 +08:00