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3215 次代码提交

作者 SHA1 备注 提交日期
VoVAllen 5f2f100b80 [Feature] convert np.ndarray to backend tensor when setting ndata/edata(#850) 2019-09-11 14:37:45 +08:00
Mufei Li 9df8cd3242 [Model Zoo] Fix JTNN (#843)
* Update

* Update

* Update

* Update

* Update
2019-09-10 16:14:37 +08:00
VoVAllen 4e0e66971b [Fix on Mac] Data format (#848)
* Add serialization

* add serialization

* add serialization

* lalalalalalalala

* lalalalalalalala

* serialize

* serialize

* nnn

* WIP: import tvm runtime node system

* WIP: object system

* containers

* tested basic container composition

* tested custom object

* tmp

* fix setattr bug

* tested object container return

* fix lint

* some comments about get/set state

* fix lint

* fix lint

* update cython

* fix cython

* ffi doc

* fix doc

* WIP: using object system for graph

* c++ side refactoring done; compiled

* remove stale apis

* fix bug in DGLGraphCreate; passed test_graph.py

* fix bug in python modify; passed utest for pytorch/cpu

* fix lint

* Add serialization

* Add serialization

* fix

* fix typo

* serialize with new ffi

* commit

* commit

* commit

* save

* save

* save

* save

* commit

* clean

* Delete tt2.py

* fix lint

* Add serialization

* fix lint 2

* fix lint

* fix lint

* fix lint

* fix lint

* Fix Lint

* Add serialization

* Change to Macro

* fix

* fix

* fix bugs

* refactor

* refactor

* updating dmlc-core to include force flag

* trying tempfile

* delete leaked pointer

* Fix assert

* fix assert

* add comment and test case

* add graph labels

* add load labels

* lint

* lint

* add graph labels

* lint

*  fix windows

* fix

* update dmlc-core to latest

* fix

* fix camel naming

* fix

* poke ci
2019-09-10 15:51:27 +08:00
VoVAllen 0fb13f7b9d [Feature] Data format (#728)
* Add serialization

* add serialization

* add serialization

* lalalalalalalala

* lalalalalalalala

* serialize

* serialize

* nnn

* WIP: import tvm runtime node system

* WIP: object system

* containers

* tested basic container composition

* tested custom object

* tmp

* fix setattr bug

* tested object container return

* fix lint

* some comments about get/set state

* fix lint

* fix lint

* update cython

* fix cython

* ffi doc

* fix doc

* WIP: using object system for graph

* c++ side refactoring done; compiled

* remove stale apis

* fix bug in DGLGraphCreate; passed test_graph.py

* fix bug in python modify; passed utest for pytorch/cpu

* fix lint

* Add serialization

* Add serialization

* fix

* fix typo

* serialize with new ffi

* commit

* commit

* commit

* save

* save

* save

* save

* commit

* clean

* Delete tt2.py

* fix lint

* Add serialization

* fix lint 2

* fix lint

* fix lint

* fix lint

* fix lint

* Fix Lint

* Add serialization

* Change to Macro

* fix

* fix

* fix bugs

* refactor

* refactor

* updating dmlc-core to include force flag

* trying tempfile

* delete leaked pointer

* Fix assert

* fix assert

* add comment and test case

* add graph labels

* add load labels

* lint

* lint

* add graph labels

* lint

*  fix windows

* fix

* update dmlc-core to latest

* fix

* fix camel naming
2019-09-09 20:57:51 +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
xiang song(charlie.song) bcd33e0ac0 [Kernel][Perf] Message builtin with broadcasting performance optimization (#815)
* 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

* Test performance of udf

* trigger

* Fix doc

* Add nn.TGConv and example

* Update test code

* 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 for mxnet TAGCov

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix

* Minor opt for URRevel

* Delete test code

* Update code style and notes.

* Fix func name
2019-09-09 01:11:37 +08:00
Mufei Li 189c2c0907 [Model Zoo] Refactor Model Zoo for Chemistry (#839)
* Update

* Update

* Update

* Update fix

* Update

* Update

* Refactor

* Update

* Update

* Update

* Update

* Update

* Update

* Fix style
2019-09-07 20:01:09 +08:00
Zihao Ye 5b417683f6 [docfix] Update the README of metapath2vec (#832)
* upd

* fig edgebatch edges

* add test

* trigger

* upd
2019-09-05 16:43:12 +08:00
Zihao Ye aa0a53d7a6 [Doc] Add cite section in README (#827)
* upd

* upd
2019-09-04 21:04:02 +08:00
VoVAllen 3386f466ac [Fix test backend] Fix softmax in mxnet backend (#828) 2019-09-04 17:36:20 +08:00
VoVAllen 8731050394 [Example] Fix GIN Example (#826)
* Add serialization

* fix gin

* Add serialization

* fix gin

* fix
2019-09-03 17:55:27 +08:00
ziqiaomeng ddeb86f91c [Example] metapath2vec (#764)
* Prepare for metapath sampler

This file is just for reviewing metapath sampling algorithm (Python version).

* Delete metapath_sampler

* Prepare for metapath sampler

This file is just for reviewing metapath sampling algorithm (Python code).

* Add files via upload

* Create metapath2vec.md

* Add files via upload

* Delete data_handler.py

* Delete word2vec.py

* Delete word_train.py

* Add files via upload

Metapath2vec implementations. Metapath2vec++ needs negative sampler optimization.

* Delete shuffle_training.py

* Delete test.py

* Add files via upload

* Delete sampler.py

* Delete metapath_sampler.md

* Add files via upload

* Update and rename shuffle_training.py to metapath2vec.py

* Update reading_data.py

* Update metapath2vec.md

* Update metapath2vec.md

* Update metapath2vec.md

* Update metapath2vec.md

* Update metapath2vec.md

* Create label 2

* Delete label 2

* Create testing.md

* Add files via upload

* Create sample.md

* Add files via upload

* Delete sampler.py

* Add files via upload

* Delete googlescholar.8area.author.label.txt

* Delete googlescholar.8area.venue.label.txt

* Delete testing.md

* Delete id_author.txt

* Delete id_conf.txt

* Delete paper.txt

* Delete paper_author.txt

* Delete paper_conf.txt

* Delete sample.md

* Delete sampler.py

* Add files via upload

* Add files via upload

* Add files via upload

* Delete reading_data.py

* Add files via upload

* Add files via upload

* Delete metapath2vec.py

* Add files via upload

* Rename shuffle_training.py to metapath2vec.py

* Update metapath2vec.md

* Delete reading_data.py

* add comments and remov e commented codes
2019-09-02 00:03:21 -07:00
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
Mufei Li a9a0592c3e Hot fix (#816) 2019-09-01 02:11:03 +08:00
VoVAllen 1e2abc9ae9 [Docs] Adjust doc (#808)
* fix doc

* poke ci

* poke ci

* upd

* fix doc

* upd

* add title for all nn

* upd
2019-08-31 00:17:49 +08:00
Zihao Ye 8844246aea [bugfix] Disable shared memory test that may fails CI. (#810)
* upd

* up

* upd

* upd
2019-08-30 15:42:05 +08:00
Quan (Andy) Gan f212cde471 Update README.md (#811) 2019-08-30 10:01:59 +08:00
Da Zheng 6ab593ec01 throw an error when using with mxnet < 1.5. (#767) 2019-08-28 14:26:21 -07:00
Da Zheng 1c9c033919 [Doc] add figures for explanation (#807)
* fix.

* update
2019-08-29 04:05:22 +08:00
Mufei Li 1b5820a5d6 Fix (#806) 2019-08-29 01:18:04 +08:00
Quan (Andy) Gan 98b825e3a1 [Doc][Conda] Fixing pytorch.nn.factory docs and Conda license (#805)
* [Conda] Update license

* doc fixes
2019-08-28 16:56:31 +08:00
Quan (Andy) Gan a5b661a23e [Doc] Fixing pytorch nn factory docs (#804) 2019-08-28 16:23:06 +08:00
Quan (Andy) Gan 828e269cf4 [Doc] Fixing KNNGraph docs (#803) 2019-08-28 14:52:22 +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 ad15947f0e [bugfix] Fix several issues in test_kernel (#801)
* upd

* stable
2019-08-28 04:24:00 +08:00
VoVAllen 3192beb42d [Model zoo] JTNN model zoo (#790)
* jtnn model zoo

* poke ci

* fix line sep

* fix

* Fix import order

* fix render

* fix render

* revert

* fix

* Resolve conflict

* dix

* remove create_var

* refactor

* fix

* refactor

* readme

* format

* fix lint

* fix lint

* pylint

* lint

* fix lint

* fix lint

* add hint

* fix

* Remove vocab

* Add explanation for warning

* add directory

* Load model to cpu by default

* Update
2019-08-28 04:04:54 +08:00
Da Zheng 30c4625171 fix. (#794) 2019-08-27 09:56:38 -07:00
Mufei Li 331337fe5f [Model Zoo] Clean up for Alchemy dataset (#800)
* Make dataset framework agnostic

* Update

* Update

* Fix

* Remove unused import
2019-08-28 00:08:59 +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
Mufei Li 8079d98617 Misc update (#796) 2019-08-27 16:08:36 +08:00
lunar 3bc73931f8 [Model Zoo] Molecule Regression (#779)
* [Model] MPNN

* [Model] MPNN 🔨 reorganize the mpnn/sch/mgcn model & alchemy dataset

* [Model] MPNN alchemy dataloader refactoring

* [Model] Chem model zoo minor change

* [Model] Chem Model Zoo 🔥 remove old samples

* [Model Zoo] molecule regression minor change

* Fix dataset import

* Fix dataset import

* [Model Zoo] molecule regression test set

* [Model Zoo] molecule prediction MPNN model hyperparameter tuning

* [Model Zoo] molecule prediction ✏️ mpnn performance update
2019-08-26 17:42:33 +08:00
Zihao Ye 2c234118c3 [Feature] Add builtin mean reducer (#787)
* upd

* upd

* upd

* upd

* upd

* passed test

* add note

* upd

* trigger

* slight change

* upd

* upd

* trigger

* fix

* simplify

* upd

* upd

* fudge

* upd

* trigger

* test partial

* upd

* trigger
2019-08-25 16:30:51 -04:00
Mufei Li 73b2668fe2 [Model Zoo] DGMG for molecule generation (#783)
* DGMG for molecule generation

* Fix CI check

* Fix for CI

* Trial for CI due to shared memory

* Update

* Better interface for dataset configuration

* Update

* Handle corner cases

* Update README

* Fix

* Fix

* Fix

* Fix

* Fix

* Refactor

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix

* Fix

* Fix

* Fix

* Fix

* Finallly
2019-08-26 03:39:20 +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
Quan (Andy) Gan 52d4535b61 [Hetero][RFC] Heterogeneous graph Python interfaces & Message Passing (#752)
* moving heterograph index to another file

* node view

* python interfaces

* heterograph init

* bug fixes

* docstring for readonly

* more docstring

* unit tests & lint

* oops

* oops x2

* removed node/edge addition

* addressed comments

* lint

* rw on frames with one node/edge type

* homograph with underlying heterograph demo

* view is not necessary

* bugfix

* replace

* scheduler, builtins not working yet

* moving bipartite.h to header

* moving back bipartite to bipartite.h

* oops

* asbits and copyto for bipartite

* tested update_all and send_and_recv

* lightweight node & edge type retrieval

* oops

* sorry

* removing obsolete code

* oops

* lint

* various bug fixes & more tests

* UDF tests

* multiple type number_of_nodes and number_of_edges

* docstring fixes

* more tests

* going for dict in initialization

* lint

* updated api as per discussions

* lint

* bug

* bugfix

* moving back bipartite impl to cc

* note on views

* fix
2019-08-23 15:45:37 -04:00
Da Zheng 66971c1aa4 [Feature] Add edge sampling for link prediction (#780)
* add edge sampler.

* add test and run.

* add negative sampling.

* remap the edge subgraph vid.

* negative graph excludes edges of positive edgs.

* remove print.

* avoid sampling NodeFlow when expand_factor or num_hops is 0.

* fix a bug when excluding nodes in negative graph.

* support multigraph.

* exclude positive edges.

* fix memory leak.

* return subgraph object directly.

* fix many problems.

* add comments.

* address comments
2019-08-21 23:05:24 -07:00
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
Da Zheng be936da849 use FFI for subgraph. (#781) 2019-08-21 01:04:11 -07:00
VoVAllen 0f12763725 [Model] Early stop GAT (#750)
* Add early stop

* add mxnet version

* Poke ci
2019-08-21 14:58:56 +08:00
Sahand 77c58289a7 [Bugfix][Model] Fixing RGCN evaluation bug (#778) 2019-08-20 15:54:03 -04:00
Quan (Andy) Gan 788420dff3 [Refactor] Decoupling ImmutableGraph from Kernels (#749)
* csr interface

* csr wrapper for immutable graph

* lint

* silly fix

* docstring
2019-08-18 20:15:56 +08:00
Mufei Li 35bed2a9d0 Rename early stop (#773) 2019-08-18 13:46:44 +08:00
Mufei Li 02029dce9b Sync initializers (#772) 2019-08-17 20:25:54 +08:00