Commits · f8ae6350b1af26951f10026b80abbddde664cd9c · OpenDAS / dgl

17 Mar, 2020 1 commit

[DGL-KE] Add METIS preprocessing pipeline (#1365) · f8ae6350

Chao Ma authored Mar 17, 2020

* update metis

* update

* update dataloader

* update dataloader

* new script

* update

* update

* update

* update

* update

* update

* update

* update dataloader

* update

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* update

* update

f8ae6350

16 Mar, 2020 3 commits

Update (#1366) · 2ce0e21b
Mufei Li authored Mar 16, 2020

2ce0e21b
Update instructions for building from source (#1363) · 16627575
Mufei Li authored Mar 16, 2020
```
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
```
16627575

[Model] RGCN mini-batch training; Better bipartite graph support (#1337) · 6111ea46

Minjie Wang authored Mar 16, 2020

* change the model to use node embedding only

* minibatch training

* add readme

* small fix

* backward-compatible

* backward compatible

* modify to_block; rgcn changed

* fix

* fix transform

* fix bug in unittest script

* docstring

* fix lint

* add tests

* address comments; fix offline eval

* gitignore

6111ea46

15 Mar, 2020 4 commits
- Update README.md · 9120ee60
  Minjie Wang authored Mar 15, 2020
  
  9120ee60
- [Model][Perf] Improve sage sampling performance (#1364) · d876680a
  Minjie Wang authored Mar 15, 2020
```
* improve speed

* fix bugs

* upd reg test
```
  d876680a
- fix. (#1358) · f9ad1c80
  Da Zheng authored Mar 14, 2020
```
Co-authored-by: Chao Ma <mctt90@gmail.com>
```
  f9ad1c80
- [KG] partition a KG. (#1351) · eb71c804
  Da Zheng authored Mar 14, 2020
```
* partition a KG.

* get tid.

* support builtin

* fix a minor bug.
Co-authored-by: Chao Ma <mctt90@gmail.com>
```
  eb71c804
14 Mar, 2020 1 commit

[DGL-LifeSci] WLN for Reaction Center Prediction (#1360) · 545cc065

Mufei Li authored Mar 14, 2020

* Update

* Update

* Update

* Update

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* Update

* Update

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* Update

545cc065

13 Mar, 2020 3 commits

[Optimization] Optimize performance of COOSort (#1349) · 5a1ef70f

xiang song(charlie.song) authored Mar 13, 2020



* Fix coo_sort

* Add COOSort test

* Fix

* omp

* coo2csr can benefit from sorted coo

* Add more test code

* Add LIBCXX_ENABLE_PARALLEL_ALGORITHMS to Makefile

* upd

* Turn off LIBCXX_ENABLE_PARALLEL_ALGORITHMS by default
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

5a1ef70f

Update (#1359) · f3b866f4
Mufei Li authored Mar 13, 2020

f3b866f4

[Feature] Filtered MRR metrics for R-GCN example (#1298) · 6c7c4039

hgalioulline authored Mar 13, 2020



* Add filtered metrics for R-GCN example

* Add new line to end of file

* Add evaluation protocol argument option for R-GCN example

* Update README
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

6c7c4039

12 Mar, 2020 2 commits
- Fix for dataloader (#1353) · 87842db4
  xiang song(charlie.song) authored Mar 12, 2020
  
  87842db4
- [BUGFIX] metis partition should generate a subgraph to the original graph. (#1352) · 3938b399
  Da Zheng authored Mar 11, 2020
```
* fix a partition.

* add comments.
```
  3938b399
11 Mar, 2020 2 commits

[Feature] Improve the speed of to_bidirected (#1327) · 1a584ced

Da Zheng authored Mar 10, 2020

* make graph symmetric

* call gklib routine.

* use gklib version except in windows.

* minor errors.

* fix test.

* update doc.

* fix a compile error.

* fix.

* add comments for the new C API.

* fix a bug.

* address comments.

* fix compile error.

* fix comment.

1a584ced

fix sampler. (#1350) · 9432cd63
Da Zheng authored Mar 10, 2020

9432cd63

10 Mar, 2020 4 commits
- [DOC] Improve the docstring of GATConv and new APIs (#1339) · 988c8b20
  Zihao Ye authored Mar 11, 2020
```
* upd

* upd

* upd

* upd

* upd
```
  988c8b20
- [KG] make batch size compatible with neg sample size (#1343) · e6584043
  Da Zheng authored Mar 10, 2020
```
* adjust batch size.

* fix for eval.py

* adjust parameters in distributed training.

* move code.
```
  e6584043
- [Optimization] Optimize CompactGraph (#1328) · 7b3a7b14
  xiang song(charlie.song) authored Mar 10, 2020
```
* compact

* prealloc memory for hashtable

* Fix

* upd

* Reduce memory

* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
```
  7b3a7b14
- rewrite to use dataloader (#1333) · 20e1bb45
  Quan (Andy) Gan authored Mar 10, 2020
```
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
```
  20e1bb45
09 Mar, 2020 6 commits

[DGL-KE] Clean up argument for DGL-KE (#1325) · d98c71ef

Chao Ma authored Mar 09, 2020

* update

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* clean up args

* change args for eval

* update

* update

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* update num_worker=8

* add num_proc=1

* update

* update

* add eval percent

* update

* update

* update

* save emb

* update

* update

* update

* update

* update

* remove neg_chunk_size

* update

* update

* update

* remove

* update

* remove

* change num_thread

d98c71ef

[Error Message] Improve the error message (#1342) · 53b39f06
Jinjing Zhou authored Mar 09, 2020
```
* patch

* fix+1

* add readme

* fix error message
```
53b39f06
[Test] Instruction for write regression test (#1341) · a0139923
Jinjing Zhou authored Mar 09, 2020
```
* patch

* fix+1

* add readme
```
a0139923
[Test] asv conf fix (#1338) · 9abe0413
Jinjing Zhou authored Mar 09, 2020
```
* patch

* fix+1
```
9abe0413

[KGE] Kg loader (#1300) · f9ba3cdc

xiang song(charlie.song) authored Mar 09, 2020



* Now dataset accepts user define datasets

* UPdate README

* Fix eval

* Fix

* Fix Freebase

* Fix

* Fix

* upd

* upd

* Update README

* Update some docstrings.

* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-8-26.us-east-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-78.us-east-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-60-78.ec2.internal>

f9ba3cdc

[KG] save config when saving the model (#1336) · 614acf2c
Da Zheng authored Mar 08, 2020
```
* save config.

* save more.
```
614acf2c

08 Mar, 2020 3 commits

Fix submodule has submodules (#1332) · 7ee77f72
xiang song(charlie.song) authored Mar 09, 2020
```
Co-authored-by: Ubuntu <ubuntu@ip-172-31-60-78.ec2.internal>
```
7ee77f72
[Fix] asv patch (#1330) · 081e5e0f
Jinjing Zhou authored Mar 08, 2020

081e5e0f

[Feature] add metis partitioning to DGL (#1308) · 0e153c4b

Da Zheng authored Mar 07, 2020



* add metis.

* add test.

* construct partition id.

* link to METIS github repo.

* update metis.

* add a tool for partitioning a graph.

* update metis.

* update.

* update.

* fix metis.

* fix lint

* fix indent.

* another way of building metis.

* disable metis in windows.

* test windows

* fix.

* disable metis for windows properly.

* fix for tensorflow.

* skip test for gpu.

* make graph symmetric

* address comments.

* more comments.

* fix compile

* fix a bug.

* add test.

* change the default #hops of HALO nodes.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-26-167.us-east-2.compute.internal>

0e153c4b

07 Mar, 2020 3 commits

[Model][Sampler] GraphSAGE model, bipartite graph conversion & remove edges API (#1297) · a9520f71

Quan (Andy) Gan authored Mar 08, 2020

* 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

a9520f71

[Bugfix] Allows node types with no inbound/outbound edges (#1323) · ce6e19f2

Quan (Andy) Gan authored Mar 08, 2020

* add num nodes in ctors

* fix

* lint

* addresses comments

* replace with constexpr

* remove function with rvalue reference

* address comments

ce6e19f2

fix csrtocoo (#1324) · ac74233c
Quan (Andy) Gan authored Mar 07, 2020

ac74233c

06 Mar, 2020 2 commits

[Feature] More serialization support (#1295) · 9caff617

Jinjing Zhou authored Mar 06, 2020



* fix script

* t

* fix weird bugs

* fix

* fix

* upload

* fix

* fix

* lint

* fix

* tmp

* fix serialization

* fix

* fix lint

* fix message

* fix

* lint

* address comment

* fix

* lint

* fix

* fix

* fix

* Remove duplicate serialization for meta graph
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

9caff617

upd (#1321) · 09ade2f2
Zihao Ye authored Mar 06, 2020

09ade2f2

05 Mar, 2020 6 commits

[README] Update README.md (#1317) · 19797bb6

Jinjing Zhou authored Mar 06, 2020



* Update README.md

* Update README.md

* Update README.md
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

19797bb6

[NN] Fix RelGraphConv num_bases error message (#1309) · 978ac410

Jinjing Zhou authored Mar 06, 2020



* 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>

978ac410

Update (#1319) · 4ec8f204
Mufei Li authored Mar 05, 2020

4ec8f204
[Fix] Fix build on macos(clang) (#1318) · 066d290f
Jinjing Zhou authored Mar 05, 2020
```
* fix

* data type

* fix

* fix

* fix
```
066d290f

[Feature] Import subpackge based on backend of dgl.nn (#1305) · e2db7913

Jinjing Zhou authored Mar 05, 2020



* automatically select nn backend

* rename load_backend to private

* switch to backend_name
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

e2db7913

[Refactor] Unify DGLGraph, BatchedDGLGraph and DGLSubGraph (#1216) · 93ac29ce

Zihao Ye authored Mar 05, 2020



* 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>

93ac29ce