文件历史

110 次代码提交

作者 SHA1 备注 提交日期
Mufei Li fb9d213848 Fix SAGEConv (#1792) 2020-07-12 13:32:14 +08:00
xiang song(charlie.song) d6b4e286b6 RGCN minibatch using homogeneous graph. (#1745)
* minibatch rgcn

* minibatch based rgcn

* remove ogb

* lint

* Add sparse emb

* Fix

* Fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-87-240.ec2.internal>
2020-07-07 00:26:10 +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
Axel Nilsson b6c4deb4e9 [NN] ChebConv update (#1460)
* New version for the convolutional layer

* Minor changes

* Minor changes

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

Co-authored-by: Zihao Ye <zihaoye.cs@gmail.com>

* Resolved variable miss-naming, import simplifying and raising warning

* Added dg_warnings instead of warnings.warn

* add doc

* upd

* upd

Co-authored-by: Zihao Ye <zihaoye.cs@gmail.com>
Co-authored-by: yzh119 <expye@outlook.com>
2020-06-24 15:59:44 +08:00
xiang song(charlie.song) 61f007c43b [NN] Add low memory support for nn.RelGraphConv (#1631)
* Add low memory support for relgraphconv
y

* lint

* Add tf support

* Fix lint

* Fix mxnet

* Fix mxnet

* Fix

* minor fix

* Fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
2020-06-15 13:49:11 +08:00
zhjwy9343 02dd6d9021 [Feature] Add dot product attention (#1604)
* Add dotproduct attention

* [Feature] Add dotproduct attention

* [Feature] Add dotproduct attention

* [Feature] Add dotproduct attention

* [New] Update landing page

* [New] Update landing page

* [New] Update landing page

* [Doc] Update landing page

* [Doc] Update landing page

* [Doc] Update landing page

* [Doc] Update landing page

* [Doc] Update landing page

* [Doc] Update landing page

* [Doc] Update landing page

* [Doc] Update landing page

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
2020-06-12 09:29:39 +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
Minjie Wang f25bc176d0 [Hetero] Improve speed of several Hetero APIs (#1486)
* add clone function to frame

* add utest

* replace all local_var with local_scope

* fix utest

* avoid creating canonical types in __getitem__

* lint

* try another utest  appraoch for mx

* utest
2020-05-01 15:21:33 +08:00
Adam J. Stewart aefc080e30 [Doc] Fix GraphConv math notation (#1430) 2020-04-09 11:31:31 +08:00
Jinjing Zhou 7e0893e697 [Docs] Fix doc build doesn't work for nn.tensorflow and nn.mxnet (#1413)
* fix

* lint

* fix
2020-04-02 20:31:07 +08:00
Zihao Ye af61e2fbb4 [Feature] Support nn modules for bipartite graphs. (#1392)
* init gat

* fix

* gin

* 7 nn modules

* rename & lint

* upd

* upd

* fix lint

* upd test

* upd

* lint

* shape check

* upd

* lint

* address comments

* update tensorflow

Co-authored-by: Quan Gan <coin2028@hotmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2020-03-29 16:48:38 +08:00
Minjie Wang 3efb5d8ecf [NN] Add HeteroGraphConv module for cleaner module definition (#1385)
* Add HeteroGraphConv

* add custom aggregator; some docstring

* debugging

* rm print

* fix some acc bugs

* fix initialization problem in weight basis

* passed tests

* lint

* fix graphconv flag; add error message

* add mxnet heteroconv

* more fix for mx

* lint

* fix torch cuda test

* fix mx test_nn

* add exhaust test for graphconv

* add tf heteroconv

* fix comment
2020-03-27 18:47:06 +08:00
Quan (Andy) Gan 4af02022b2 [Bug] Multiple fixes (#1374)
* multiple fixes

* lint

* lint x2
2020-03-19 11:19:44 +08:00
Zihao Ye 988c8b20a4 [DOC] Improve the docstring of GATConv and new APIs (#1339)
* upd

* upd

* upd

* upd

* upd
2020-03-11 01:14:22 +08:00
Quan (Andy) Gan a9520f71ce [Model][Sampler] GraphSAGE model, bipartite graph conversion & remove edges API (#1297)
* remove edge and to bipartite and graphsage with sampling

* fixes

* fixes

* fixes

* reenable multigpu training

* fixes

* compatibility in DGLGraph

* rename to compact_as_bipartite

* bugfix

* lint

* add offline inference

* skip GPU tests

* fix

* addresses comments

* fix

* fix

* fix

* more tests

* more docs and unit tests

* workaround for empty slice on empty data
2020-03-08 02:38:29 +08:00
Jinjing Zhou 978ac41097 [NN] Fix RelGraphConv num_bases error message (#1309)
* Fix RelGraphConv when num_bases is None

* Improve error message in when num_bases is wrong

* Fix integer modulo by zero exception when num_bases is 0

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
2020-03-06 01:00:48 +08:00
Jinjing Zhou e2db791312 [Feature] Import subpackge based on backend of dgl.nn (#1305)
* automatically select nn backend

* rename load_backend to private

* switch to backend_name

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
2020-03-05 19:59:45 +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
Mufei Li 828a5e5bc6 [DGL-LifeSci] Migration and Refactor (#1226)
* First commit

* Update

* Update splitters

* Update

* Update

* Update

* Update

* Update

* Update

* Migrate ACNN

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Finish classification

* Update

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Update

* Update

* trigger CI

* Fix CI

* Update

* Update

* Update

* Add default values

* Rename

* Update deprecation message
2020-02-04 01:38:09 +08:00
Quan (Andy) Gan e4948c5cbc fix regression in #1237 (#1239) 2020-02-03 11:50:06 +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
Quan (Andy) Gan 86fe58ebb8 [Bug] Another fix on PyTorch memory leakage issue (#1139)
* another fix

* another try

* fix

* rewriting with kernel functions

* revert mxnet softmax changes

* lint fix

Co-authored-by: Zihao Ye <zihaoye.cs@gmail.com>
2020-01-14 22:54:19 +08:00
Zihao Ye aa06e4579f [Doc] Improve the docstring of several nn modules. (#1187)
* upd

* upd

* upd

* upd

* lint

* upd

* upd

* upd

* upd

* upd

Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com>
2020-01-09 21:14:33 +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
Zihao Ye 870857cfba udp (#1083) 2019-12-09 14:52:20 +08:00
Zihao Ye fdd0fe651d hotfix (#971) 2019-11-04 12:11:53 +08:00
Zihao Ye 9a0511c8e9 [NN] nn modules & examples update (#890)
* upd

* damn it

* fuck

* fuck pylint

* fudge

* remove some comments about MXNet

* upd

* upd

* damn it

* damn it

* fuck

* fuck

* upd

* upd

* pylint bastard

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd
2019-11-03 17:29:42 -05:00
VoVAllen ddb5d804f9 [Refactor] Break NN modules into files (#859)
* break nn modules into files

* break mxnet nn modules

* fix lint

* fix lint
2019-09-16 14:44:15 +08:00
Zihao Ye 6a4b5ae98a [Feature] Edge softmax on a subset of edges in the graph. (#842)
* upd

* add test

* fix

* upd

* merge

* hotfix

* upd

* fix
2019-09-09 13:44:56 +08:00
MilkshakeForReal 98954c5641 [docs]update conv.py (#822)
* Update conv.py

* Update conv.py

change `oto` to `to
2019-09-02 09:05:57 +08:00
VoVAllen 36ec71a268 [Doc] Quick Fix doc (#820)
* fix doc

* poke ci

* poke ci

* upd

* fix doc

* upd

* add title for all nn

* upd

* fix warning

* fix
2019-09-01 22:30:50 +08:00
MilkshakeForReal c4989b40aa Update conv.py (#818) 2019-09-01 13:31:35 +08:00
xiang song(charlie.song) e17add5602 [NN] Add MXNet impl for TAGCN module. (#799)
* upd

* fig edgebatch edges

* add test

* trigger

* Update README.md for pytorch PinSage example.

Add noting that the PinSage model example under
example/pytorch/recommendation only work with Python 3.6+
as its dataset loader depends on stanfordnlp package
which work only with Python 3.6+.

* Provid a frame agnostic API to test nn modules on both CPU and CUDA side.

1. make dgl.nn.xxx frame agnostic
2. make test.backend include dgl.nn modules
3. modify test_edge_softmax of test/mxnet/test_nn.py and
    test/pytorch/test_nn.py work on both CPU and GPU

* Fix style

* Delete unused code

* Make agnostic test only related to tests/backend

1. clear all agnostic related code in dgl.nn
2. make test_graph_conv agnostic to cpu/gpu

* Fix code style

* fix

* doc

* Make all test code under tests.mxnet/pytorch.test_nn.py
work on both CPU and GPU.

* Fix syntex

* Remove rand

* Add TAGCN nn.module and example

* Now tagcn can run on CPU.

* Add unitest for TGConv

* Fix style

* For pubmed dataset, using --lr=0.005 can achieve better acc

* Fix style

* Fix some descriptions

* trigger

* Fix doc

* Add nn.TGConv and example

* Fix bug

* Update data in mxnet.tagcn test acc.

* Fix some comments and code

* delete useless code

* Fix namming

* Fix bug

* Fix bug

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix
2019-08-28 13:19:17 +08:00
Quan (Andy) Gan 14bffe9728 [NN] Renaming NearestNeighborGraph to KNNGraph (#802)
* initial commit

* second commit

* another commit

* change docstring

* migrating to dgl.nn

* fixes

* docs

* lint

* multiple fixes

* doc

* renaming nearest neighbor graph
2019-08-28 12:20:35 +08:00
Quan (Andy) Gan dc19cd5687 [Example] Dynamic Graph CNN on Point Cloud (#789)
* initial commit

* second commit

* another commit

* change docstring

* migrating to dgl.nn

* fixes

* docs

* lint

* multiple fixes

* doc
2019-08-28 09:21:57 +08:00
Mufei Li e590feeb62 [Model Zoo] GAT on Tox21 (#793)
* GAT

* Fix mistake

* Fix

* hotfix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Update

* Update

* Fix style

* Hotfix

* Hotfix

* Hotfix

* Fix

* Fix

* Update

* CI trial

* Update

* Update

* Update
2019-08-28 04:47:16 +08:00
Zihao Ye 9314aabd1f [Refactor] Interface of nn modules (#798)
* refactor

* upd mpnn
2019-08-27 22:29:25 +08:00
Zihao Ye 650f6ee1e0 [NN] Add commonly used GNN models from examples to dgl.nn modules. (#748)
* gat

* upd

* upd sage

* upd

* upd

* upd

* upd

* upd

* add gmmconv

* upd ggnn

* upd

* upd

* upd

* upd

* add citation examples

* add README

* fix cheb

* improve doc

* formula

* upd

* trigger

* lint

* lint

* upd

* add test for transform

* add test

* check

* upd

* improve doc

* shape check

* upd

* densechebconv, currently not correct (?)

* fix cheb

* fix

* upd

* upd sgc-reddit

* upd

* trigger
2019-08-27 18:21:19 +08:00
xiang song(charlie.song) 11fb217a76 [NN] Add TAGCN nn.module and example (#788)
* upd

* fig edgebatch edges

* add test

* trigger

* Update README.md for pytorch PinSage example.

Add noting that the PinSage model example under
example/pytorch/recommendation only work with Python 3.6+
as its dataset loader depends on stanfordnlp package
which work only with Python 3.6+.

* Provid a frame agnostic API to test nn modules on both CPU and CUDA side.

1. make dgl.nn.xxx frame agnostic
2. make test.backend include dgl.nn modules
3. modify test_edge_softmax of test/mxnet/test_nn.py and
    test/pytorch/test_nn.py work on both CPU and GPU

* Fix style

* Delete unused code

* Make agnostic test only related to tests/backend

1. clear all agnostic related code in dgl.nn
2. make test_graph_conv agnostic to cpu/gpu

* Fix code style

* fix

* doc

* Make all test code under tests.mxnet/pytorch.test_nn.py
work on both CPU and GPU.

* Fix syntex

* Remove rand

* Add TAGCN nn.module and example

* Now tagcn can run on CPU.

* Add unitest for TGConv

* Fix style

* For pubmed dataset, using --lr=0.005 can achieve better acc

* Fix style

* Fix some descriptions

* trigger

* Fix doc
2019-08-25 22:17:46 +08:00
Minjie Wang 708765f0a1 [NN] RGCN modules (#744)
* rgcn module

* support id input

* WIP: model codes

* use faster index select

* dropout

* self loop

* WIP: link prediction

* fix lint

* WIP: docs

* docstring

* docstring

* merge two child classes

* mxnet rgcn module

* fix lint

* fix lint

* fix rename bug

* add uniform edge sampler

* fix fn name

* docstring

* fix mxnet rgcn module

* fix mx rgcn

* enable test on cuda
2019-08-23 16:38:48 -04:00
xiang song(charlie.song) 2bff8339dd [Test] Provid a frame agnostic API to test nn modules on both CPU and CUDA side. (#775)
* upd

* fig edgebatch edges

* add test

* trigger

* Update README.md for pytorch PinSage example.

Add noting that the PinSage model example under
example/pytorch/recommendation only work with Python 3.6+
as its dataset loader depends on stanfordnlp package
which work only with Python 3.6+.

* Provid a frame agnostic API to test nn modules on both CPU and CUDA side.

1. make dgl.nn.xxx frame agnostic
2. make test.backend include dgl.nn modules
3. modify test_edge_softmax of test/mxnet/test_nn.py and
    test/pytorch/test_nn.py work on both CPU and GPU

* Fix style

* Delete unused code

* Make agnostic test only related to tests/backend

1. clear all agnostic related code in dgl.nn
2. make test_graph_conv agnostic to cpu/gpu

* Fix code style

* fix

* doc

* Make all test code under tests.mxnet/pytorch.test_nn.py
work on both CPU and GPU.

* Fix syntex

* Remove rand
2019-08-21 16:40:41 +08:00
Zihao Ye 742d79a792 upd (#741) 2019-08-06 18:39:05 +08:00
Zihao Ye 5d3f470b72 [Feature] DGL Pooling modules (#669)
* removal doc

* glob

* upd

* rm knn

* add softmax

* upd

* upd

* add broadcast and s2s

* optimize max_on

* forsaken changes to heterograph

* upd

* upd

* upd

* upd

* upd

* bugfix

* upd

* upd

* upd

* upd

* format upd

* upd format

* upd doc

* upd

* import order

* upd

* rm warnings

* fix

* upd test

* upd

* upd

* fix device

* upd

* upd

* upd

* upd

* remove 1.1

* upd

* trigger

* trigger

* add more tests

* fix device

* upd

* upd

* refactor

* fix?

* fix

* upd docstring

* refactor

* upd

* fix

* upd

* upd

* upd

* fix

* upd docs

* add shape

* refactor & upd doc

* upd doc

* upd
2019-08-06 01:43:25 +08:00
Minjie Wang fc9d30fae4 [Graph] add local scope function (#735)
* add local scope function

* fix lint

* fix docstring

* change local_scope to local_var; add context manager

* address comments
2019-08-02 00:11:48 -04:00
VoVAllen fc2e166ba6 [Fix] Fix Memory Leak in Edge Softmax (#692)
* Add serialization

* fix memory leak

* Revert "Add serialization"

This reverts commit e838bb1faa2503d14593d702be00514f936c9027.

* fix
2019-06-28 17:31:54 -04:00
Zihao Ye 8ecedfb369 [Fix] Bugfix in docs and check gradient of edge_softmax in test (#686)
* upd

* Add stronger test

* Update test_nn.py

* Update test_nn.py

* trigger

* trigger

* trigger
2019-06-27 00:43:26 +08:00
Lingfan Yu 5549c70d33 [BugFix] Fix memory leak in DGL edge softmax module (#643)
* fix gat memory increase bug

* work around mxnet memory leak bug

* comments

* poke linter

* lint

* lint
2019-06-10 18:44:23 -04:00
Lingfan Yu 74e13eea61 [Model] Update GAT model code (#622)
* fix gat code to use latest edge softmax module

* avoid transpose

* update README

* use edge_softmax op

* mxnet edge softmax op

* mxnet gat

* update README

* fix unittest

* fix ci

* fix mxnet nn test; relax criteria for prod reducer
2019-06-08 21:41:38 -04:00
Lingfan Yu 8bf97719fa [Bugfix] Fix performance bug in edge softmax operator (#624) 2019-06-07 16:15:29 -07:00