提交

687 次代码提交

作者 SHA1 备注 提交日期
Quan Gan 263656f893 bump to 0.4.1 0.4.1 2019-11-04 11:06:05 +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
xiang song(charlie.song) 7f65199a86 [NN]Supporting TransR in app/kg score_func (#945)
* Add TransR for kge

* Now Pytorch TransR can run

* Add MXNet TransR

* Now mxnet can work with small dim size

* Add test

* Pass simple test_score

* Update test with transR score func

* Update RESCAL MXNet

* Add missing funcs

* Update init func for transR score

* Revert "Update init func for transR score"

This reverts commit 0798bb886095e7581f6675da5343376844ce45b9.

* Update score func of TransR MXNet

Make it more memory friendly and faster,
thourgh it is still very slow and memory consuming

* Update best config

* Fix ramdom seed for test

* Init score-func specific var

* Update Readme
2019-11-01 10:50:44 -07:00
John Andrilla a85382b0ff [doc] simple readability and style changes (#965) 2019-11-01 17:28:18 +08:00
xiang song(charlie.song) 82499e602b [Bug Fix] Fix package reliability bug of networkx (#949)
* 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 for mxnet TAGCov

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix

* reproduce the bug

* Fix concurrency bug reported at #755.
Also make test_shared_mem_store.py more deterministic.

* Update test_shared_mem_store.py

* Update dmlc/core

* networkx >= 2.4 will break our examples

* Update tutorials/requirements

* fix selfloop edges

* upd version
2019-10-29 23:34:31 -04:00
Jacob Stevens 98c1448bfc [Cleanup] Change Byte to Bool for training masks (#954)
* Change Byte to Bool for training masks

* Check if module has Bool, otherwise use Byte
2019-10-29 17:14:08 -04:00
Mufei Li 86cf154be9 [Misc] Update README(s) (#962)
* Update

* Update
2019-10-29 15:37:25 +08:00
Quan (Andy) Gan a6d5a0cbdd [BUG] Fix #717 (#946)
* [BUG] Fix #717

* fix mxnet test
2019-10-28 09:29:07 +08:00
Mufei Li 421b05e7b8 [Model] Clean up for Cluster GCN (#940)
* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Fix
2019-10-26 21:02:47 +08:00
Mufei Li 52c7ef49fc [Model Zoo] AttentiveFP (#955)
* Update

* Fix style

* Update

* Update

* Fix

* Update

* Update
2019-10-26 01:57:34 +08:00
Quan (Andy) Gan 43028f702f Update README.md (#916)
* Update README.md

* Update README.md
2019-10-25 22:18:41 +08:00
Mufei Li 4eba1ce2a4 [Chemistry] Hot fix (#953)
* Hot fix

* CI
2019-10-25 15:05:21 +08:00
Mufei Li 577cf2e63b [Model Zoo] Refactor and Add Utils for Chemistry (#928)
* Refactor

* Add note

* Update

* CI
2019-10-22 00:47:45 +08:00
Da Zheng 0bf3b6ddb3 add KG statistics. (#931)
* add KG statistics.

* add Freebase.

* fix link.
2019-10-21 22:49:46 +08:00
Chao Ma 70ee4b5e28 Add more test to kvstore (#944) 2019-10-21 17:46:43 +08:00
Chao Ma ff9f67ee0d Send any shape of tensor rather than matrix (#942) 2019-10-21 17:27:03 +08:00
Mufei Li ae3102d3a2 [Dataset] Migration for Chemistry Datasets (#926)
* Update

* Update
2019-10-21 16:38:28 +08:00
Xiagkun Hu c37076dfe6 [Model] Gated Graph Neural Network for bAbI tasks (#880)
* rrn model and sudoku

* add README

* refine the code, add doc strings

* add sudoku solver

* add example for sudoku_solver

* ggnn example

* Rewrite README file

* fix typos
2019-10-21 16:07:32 +08:00
John Andrilla 8d84865548 Voice and tone updates for readability (#938)
Simple editorial updates
2019-10-21 09:06:56 +08:00
Aaron Markham 9c095a725a [Doc] minor spelling updates (#935)
* minor spelling updates

* Update docs/source/features/builtin.rst
2019-10-19 00:47:07 +08:00
Chao Ma 02fb05817b [KG] Add RESCAL model to DGL-KGE (#923)
* Add RESCAL model

* update

* update

* match acc

* update

* add README.md

* fix
2019-10-11 23:45:25 -07:00
xiang song(charlie.song) 20439e1c27 Fix bug of KG train.py script. (#922)
It cannot work when only mxnet backend is installed.
2019-10-11 10:13:09 -07:00
xiang song(charlie.song) 93e3c49ddc [KG] Update CI to cover Knowledge Graph (#913)
* 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 for mxnet TAGCov

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix

* reproduce the bug

* Fix concurrency bug reported at #755.
Also make test_shared_mem_store.py more deterministic.

* Update test_shared_mem_store.py

* Update dmlc/core

* Update Knowledge Graph CI with new Docker image

* Remove unused line_profierx

* Poke Jenkins

* Update test with exit code check and simplify docker

* Update Jenkinsfile to make app test a standalone stage

* Update kg_test

* Update Jenkinsfile

* Make some KG test parallel

* Update

* KG MXNet does not support ComplEx

* Update Jenkinsfile

* Update Jenkins file

* Change torch-1.2 to torch-1.2-cu92

* ci

* Update ubuntu_install_mxnet_cpu.sh

* Update ubuntu_install_mxnet_gpu.sh

* We only need to test train and eval script.
Delete some test code
2019-10-11 01:32:34 -07:00
xiang song(charlie.song) bde75256be [KG] ComplEx score func for MXNet (#918)
* 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 for mxnet TAGCov

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix

* reproduce the bug

* Fix concurrency bug reported at #755.
Also make test_shared_mem_store.py more deterministic.

* Update test_shared_mem_store.py

* Update dmlc/core

* Add complEx for mxnet

* ComplEx is ready for MXNet
2019-10-10 23:01:11 -07:00
Da Zheng c26b1bae89 [KG] a little update on readme. (#914)
* update readme.

* Update README.md
2019-10-09 13:44:06 -07:00
Chao Ma fc1aa1940d update the web link of d2l (#915) 2019-10-09 12:30:01 +09:00
Minjie Wang 5eae8e0543 [Fix] Fix typo in KGE readme 2019-10-08 12:14:47 -04:00
Quan (Andy) Gan 9d64927c57 [Doc] Fix hetero tutorial directory (#912) 2019-10-08 22:21:22 +08:00
Quan (Andy) Gan a1cdc7a536 minor docstring fix (#910) 2019-10-08 16:49:01 +08:00
Quan (Andy) Gan 3ee7e11268 [Hetero][Tutorial] Heterograph tutorials (#878)
* heterograph tutorial skeleton

* [WIP][Tutorial] Heterogeneous graph tutorial

* fix

* update
2019-10-08 15:33:54 +08:00
xiang song(charlie.song) fd1b14747a [Bug fix] Fix concurrency bug reported at issue#755 (#823)
* 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 for mxnet TAGCov

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix

* reproduce the bug

* Fix concurrency bug reported at #755.
Also make test_shared_mem_store.py more deterministic.

* Update test_shared_mem_store.py

* Update dmlc/core
2019-10-07 23:00:46 -07:00
Quan (Andy) Gan 5e17ef5d93 [Release] Fix Conda CMake flags (#907)
* [Release] Fix CMake flags

* more fix
v0.4.0
2019-10-07 17:26:57 +08:00
Quan (Andy) Gan 8c20c6668a [Release] Bump conda version (#906) 2019-10-07 08:42:39 +08:00
Quan (Andy) Gan 8c6cead225 [Windows] Working around a mysterious VS2015 error (#905) 2019-10-07 00:35:05 +08:00
Mufei Li e2b7f745ca [Hetero] Doc (#892)
* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* style fixes & undefined name fix

* transpose=False in test
2019-10-06 20:17:40 +08:00
Quan (Andy) Gan b3d596b5bd extend warning to other adjacency_matrix() calls (#904) 2019-10-06 15:44:03 +08:00
Da Zheng bce51cbd65 [BUGFIX] check the number of columns in subgraph.copy_from_parent (#903)
* check the number of columns.

* add test.
2019-10-05 18:35:56 -07:00
Da Zheng 3a0bbb3edd [Doc] Update kg readme (#901)
* add Freebase results.

* update.

* explain

* add DistMult.

* reproduce.
2019-10-04 15:05:06 -07:00
Da Zheng df8a7be52d [KG] save embeddings in NumPy (#900)
* fix loading and saving.

* use numpy.
2019-10-04 09:14:16 -07:00
Da Zheng 3bc3109859 use PBG sampler for testing. (#899) 2019-10-02 22:13:09 -07:00
Da Zheng 251a984278 fix (#898) 2019-10-02 18:47:32 -07:00
Da Zheng 190cdbd25f [Doc] Fix KG readme (#897)
* fix.

* update readme.

* shorten format desc.
2019-10-02 17:49:09 -07:00
Da Zheng 15b951d4c4 [KG][Model] Knowledge graph embeddings (#888)
* 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 for mxnet TAGCov

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix

* init version.

* change default value of regularization.

* avoid specifying adversarial_temperature

* use default eval_interval.

* remove original model.

* remove optimizer.

* set default value of num_proc

* set default value of log_interval.

* don't need to set neg_sample_size_valid.

* remove unused code.

* use uni_weight by default.

* unify model.

* rename model.

* remove unnecessary data sampler.

* remove the code for checkpoint.

* fix eval.

* raise exception in invalid arguments.

* remove RowAdagrad.

* remove unsupported score function for now.

* Fix bugs of kg
Update README

* Update Readme for mxnet distmult

* Update README.md

* Update README.md

* revert changes on dmlc

* add tests.

* update CI.

* add tests script.

* reorder tests in CI.

* measure performance.

* add results on wn18

* remove some code.

* rename the training script.

* new results on TransE.

* remove --train.

* add format.

* fix.

* use EdgeSubgraph.

* create PBGNegEdgeSubgraph to simplify the code.

* fix test

* fix CI.

* run nose for unit tests.

* remove unused code in dataset.

* change argument to save embeddings.

* test training and eval scripts in CI.

* check Pytorch version.

* fix a minor problem in config.

* fix a minor bug.

* fix readme.

* Update README.md

* Update README.md

* Update README.md
2019-10-02 12:57:29 -07:00
Da Zheng 1c00f3a85c fix compile error on Mac. (#896) 2019-10-02 00:47:09 -07:00
Da Zheng d0eae92e5a [Test] reduce test. (#895)
* reduce test.

* increase timeout for unittest.
2019-10-02 00:20:39 -07:00
Da Zheng c2b8af452c change the backend to mxnet. (#894) 2019-10-01 23:42:21 -07:00
Da Zheng 3e454476b6 edge sampler return head nodes and tail nodes. (#889)
* edge sampler return head nodes and tail nodes.

* edge subgraph.

* use VecToIdArray

* example.

* fix compile error.
2019-09-30 21:25:16 -07:00
VoVAllen 9c790b1143 [Dataset] Add CoraFull, Amazon, KarateClub, Coauthor Dataset (#855)
* convert np.ndarray to backend tensor

* add datasets

* add qm7

* add dataset

* add dataset

* fix

* change ppi

* tu dataset

* add datasets

* fix

* fix

* fix

* fix

* add docstring

* docs

* doc
2019-10-01 01:19:59 +08:00
Quan (Andy) Gan 33b8700b7d [Bugfix][Hetero] Fix typo (#891)
Don't know why it passed the merging test...
2019-09-30 17:05:58 +08:00
Quan (Andy) Gan 0ca52bfc88 [Hetero] Create heterograph from dictionary of edge lists (#882)
* [Hetero] Create heterograph from dictionary of edge lists

* rename

* address comments
2019-09-30 15:41:41 +08:00