Commits · f103bbf9ee76bb1cbca9f8876986318680e95053 · OpenDAS / dgl

08 Feb, 2020 2 commits

[Data format] Serialization for UnitGraph (#1242) · f103bbf9

Jinjing Zhou authored Feb 08, 2020



* graph format

* fix lint

* lint

* fix

* unit test

* lint

* add magic num

* move serialize out of struct

* lint
Co-authored-by: zhoujinjing09 <zhoujinjing09@users.noreply.github.com>

f103bbf9

[DGL-LifeSci] Fix broken links (#1248) · 3f0c1005
Mufei Li authored Feb 08, 2020
```
* Fix

* Update
```
3f0c1005

07 Feb, 2020 1 commit

[Example] Fix Rgcn hetero nonedetermistic in graph and model initialization (#1244) · 77ae4d53

xiang song(charlie.song) authored Feb 07, 2020

* Fix model save and load problem.

Add offline inference example

* Fix test

* Fix randomness problem between test runs

* Make rdf loader deterministic

77ae4d53

04 Feb, 2020 1 commit

[Feature] Preference to COO for "hypersparse" unit graphs & graph compaction (#1238) · eeeb52f4

Quan (Andy) Gan authored Feb 04, 2020

* unit graph that prefers coo queries

* auto detect coo preference

* forgot some functions

* disable lint on detect_prefer_coo

* reorg

* change comment

* lint

* fix

* move array_utils.h to src

* compact graph impl

* fix redundant copying in idhashmap

* docstring

* moving preference detection to C

* lint

* fix unit test & address comments

* hypersparse autorestrict

* docstring & fix

* revert copyto and asnumbits

* fix stupid bug

* lint

* leave a TODO for sorted COO

* fixing same node type mapping to different id in different graphs

* addresses comments

* made induced nodes a feautre column

* lint?

eeeb52f4

03 Feb, 2020 2 commits

[DGL-LifeSci] Migration and Refactor (#1226) · 828a5e5b

Mufei Li authored Feb 04, 2020

* 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

828a5e5b

fix regression in #1237 (#1239) · e4948c5c
Quan (Andy) Gan authored Feb 03, 2020

e4948c5c

31 Jan, 2020 2 commits

[Doc] Fix the doc of NeighborSampler. (#1236) · c167373e
Da Zheng authored Jan 31, 2020
```
* fix.

* fix.
```
c167373e

[Feature] Random Walk for 0.5 (#1209) · a9dabcc7

Quan (Andy) Gan authored Jan 31, 2020

* trying to refactor IndexSelect

* partial implementation

* add index select and assign for floats as well

* move to random choice source

* more updates

* fixes

* fixes

* more fixes

* adding python impl

* fixes

* unit test

* lint

* lint x2

* lint x3

* update metapath2vec

* debugging performance

* still debugging for performance

* tuning

* switching to succvec

* redo

* revert non-uniform sampler to use vector

* still not fast

* why does this crash with OpenMP???

* because there was a data race!!!

* add documentations and remove assign op

* lint

* lint x2

* lol what have i done

* lint x3

* fix and disable gpu testing

* bugfix

* generic random walk

* reorg the random walk source code

* Update randomwalks.h

* Update randomwalks_cpu.cc

* rename file

* move internal function to anonymous ns

* reorg & docstrings

* constant restart probability

* docstring fix

* more commit

* random walk with restart, tested

* some fixes

* switch to using NDArray for choice

* massive fix & docstring

* lint x?

* lint x??

* fix

* export symbols

* skip gpu test

* addresses comments

* replaces another VecToIdArray

* add randomwalks.h to include

* replace void * with template

a9dabcc7

26 Jan, 2020 1 commit
- [Doc] Re-organize API docs and tutorials (#1222) · 5967d817
  Minjie Wang authored Jan 26, 2020
```
* reorg tutorials and api docs

* fix
```
  5967d817
20 Jan, 2020 1 commit
- [Feature] Add environment variable to switch on/off MXNet set_np_shape (#1207) · f1a8f926
  Tong He authored Jan 20, 2020
```
* add env var

* Trigger CI

* simplification

* add doc
```
  f1a8f926
19 Jan, 2020 1 commit

[Tensorflow] Several nn & example (#1191) · a00636a0

VoVAllen authored Jan 19, 2020

* 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

a00636a0

18 Jan, 2020 1 commit

[Bug Fix] Add boundary check for heterograph build with card as input (#1192) · 31a7d509

xiang song(charlie.song) authored Jan 18, 2020

* Add boundary check for heterograph build with card as input

* Fix when u or v is empty

* fix test_kernel.py error print

* Revert "fix test_kernel.py error print"

This reverts commit a71c20292549c0ac62a5326c30669ca4bde8febc.

* Turn op validation check on graph and bipartite by default

* upd

* udp

* upd

* update test

31a7d509

17 Jan, 2020 1 commit

[Test] Fix the random seed in test_kernel.py and fix the _print_error (#1194) · c49582c9

xiang song(charlie.song) authored Jan 17, 2020



* Fix the random seed and fix the _print_error

* Fix check_positive_edge_sampler sample weight.
Co-authored-by: Zihao Ye <zihaoye.cs@gmail.com>
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com>

c49582c9

16 Jan, 2020 1 commit

[Bug?] Fix non-determinism when setting the same seed across different runs... · 64f6f3c1

Quan (Andy) Gan authored Jan 16, 2020

[Bug?] Fix non-determinism when setting the same seed across different runs with single thread (#1205)

* fix multithread random seed value

* more fix

* typo

* what did i wrote

64f6f3c1

14 Jan, 2020 1 commit

[Bug] Another fix on PyTorch memory leakage issue (#1139) · 86fe58eb

Quan (Andy) Gan authored Jan 14, 2020



* another fix

* another try

* fix

* rewriting with kernel functions

* revert mxnet softmax changes

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

86fe58eb

11 Jan, 2020 1 commit
- Fix (#1195) · a199b58a
  Mufei Li authored Jan 12, 2020
  
  a199b58a
10 Jan, 2020 1 commit
- [KG][Optimization] Remove copy from parent in minibatch generation (#1193) · cd9599ab
  xiang song(charlie.song) authored Jan 11, 2020
```
* remote copy from parent

* upd

* make test_sampler easier to pass
```
  cd9599ab
09 Jan, 2020 6 commits
- [BUG] Fix empty heterograph creation with list & tuple (#1188) · 28a24414
  Quan (Andy) Gan authored Jan 09, 2020
```
* [BUG] Fix empty heterograph creation with list & tuple

* more fix
```
  28a24414
- [Doc] Improve the docstring of several nn modules. (#1187) · aa06e457
  Zihao Ye authored Jan 09, 2020
```
* upd

* upd

* upd

* upd

* lint

* upd

* upd

* upd

* upd

* upd
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com>
```
  aa06e457
- [Feature] Pickle support for heterograph (#1177) · 3ef757db
  Quan (Andy) Gan authored Jan 09, 2020
```
* [Feature] Pickle support for heterograph

* fix lint
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com>
```
  3ef757db
- [Feature] Add dgl.nn.*.Sequential for usability (#1166) · ca302a13
  Zihao Ye authored Jan 09, 2020
```
* upd

* upd

* upd

* upd

* lint

* upd

* upd

* upd

* upd
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com>
```
  ca302a13
- Update README.md (#1184) · 3d664628
  Quan (Andy) Gan authored Jan 09, 2020
  
  3d664628
- [BUG] Fix MovieLens feature assignment (#1183) · bfc2d303
  Quan (Andy) Gan authored Jan 09, 2020
```
Fixes #1182 .

This is embarrassing.
```
  bfc2d303
08 Jan, 2020 1 commit

[Feature][KG] Multi-GPU training support for DGL KGE (#1178) · bb6a6476

xiang song(charlie.song) authored Jan 08, 2020

* multi-gpu

* Pytorch can run but test has acc problem

* pytorch train/eval can run in multi-gpu

* Fix eval

* Fix

* Fix mxnet

* trigger

* triger

* Fix mxnet score_func

* Fix

* check

* FIx default arg

* Fix train_mxnet mix_cpu_gpu

* Make relation mix_cpu_gpu

* delete some dead code

* some opt for update

* Fix cpu grad update

bb6a6476

07 Jan, 2020 2 commits
- [Refactor] Renaming class methods of sampler utilities to improve readability (#1180) · f1420d19
  Zihao Ye authored Jan 07, 2020
```
* upd

* upd
```
  f1420d19
- [Dataset] Change download repo link to https://data.dgl.ai (CDN) (#1175) · 31911834
  VoVAllen authored Jan 07, 2020
```
* change download link to cdn

* Update env_var.rst
```
  31911834
06 Jan, 2020 2 commits

[KVStore] Fix memory leak bug. (#1174) · 38d292e5

Chao Ma authored Jan 06, 2020

* API change of kvstore

* add demo for kvstore

* update

* remove duplicated log

* change queue size

* update

* update

* update

* update

* update

* update

* update

* update

* update

* fix lint

* change name

* update

* fix lint

* update

* update

* update

* update

* change message queue size to a python argument

* change default queue size to 2GB

* OMP_NUM_THREADS=1

* add multiple NICs support for kvstore

* test

* fix lint

* update

* update

* update

* update

* update

* update

* update

* fix lint

* fix lint

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* fix lint

* update

* fix lint

* delete msg

* clear kv msg

* update

* update

* update

* update

* update

* update

* is not None

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

38d292e5

some comments (#1132) · e705118b
Quan (Andy) Gan authored Jan 06, 2020

e705118b

05 Jan, 2020 2 commits

[Fix issue] Fix issue 1170 (#1171) · 6d0a9c42

Chao Ma authored Jan 05, 2020

* API change of kvstore

* add demo for kvstore

* update

* remove duplicated log

* change queue size

* update

* update

* update

* update

* update

* update

* update

* update

* update

* fix lint

* change name

* update

* fix lint

* update

* update

* update

* update

* change message queue size to a python argument

* change default queue size to 2GB

* OMP_NUM_THREADS=1

* add multiple NICs support for kvstore

* test

* fix lint

* update

* update

* update

* update

* update

* update

* update

* fix lint

* fix lint

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* fix lint

* update

* fix lint

6d0a9c42

[KG] PBG's way of constructing negative edges (#1159) · 1022d5d6

Da Zheng authored Jan 04, 2020

* attach positive.

* add neg_deg_sample.

* add comment.

* add neg_deg_sample for eval.

* change the edge sampler.

* rename edge sampler in KG.

* allow specifying chunk size and negative sample size separately.

* fix bugs in KG.

* add check in sampler.

* add more checks.

* fix

* add comment.

* add comments.

1022d5d6

04 Jan, 2020 1 commit

[KG] More fixes on eval (#1168) · 1de192f4

Da Zheng authored Jan 04, 2020

* remove parallel sampling for multiprocessing.

* avoid memory copy in eval.

* remove print.

1de192f4

03 Jan, 2020 1 commit
- [KG] Disable filter in evaluation (#1162) · 346bc235
  Da Zheng authored Jan 02, 2020
```
* add no_eval_filter

* fix eval.
```
  346bc235
02 Jan, 2020 1 commit
- merge eval results in all processes. (#1160) · 7451bb2a
  Da Zheng authored Jan 01, 2020
  
  7451bb2a
01 Jan, 2020 1 commit

[Feature] Bag of samplers for efficient categorical sampling w/ and w/o replacement (#1142) · dfb10db8

Zihao Ye authored Jan 01, 2020

* upd

* upd

* lint

* upd

* upd

* lint

* upd

* refactor

* lint

* upd

* upd

* upd

* lint

* fix

* fix

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* complete test

* upd

* upd

* fix

* vir

* upd

* fix

* fuck

* fix numerical

dfb10db8

31 Dec, 2019 2 commits

Accelerate edge sampling (#1151) · 162dc19a

Da Zheng authored Dec 31, 2019



* accel edge sampling.

* measure sampling time.

* attach positive.

* add neg_deg_sample.

* fix a minor bug.

* remove unnecessary code.

* Revert "add neg_deg_sample."

This reverts commit 45f3c08c87e33589563ca7e6a3ec91cb1239910e.

* Revert "attach positive."

This reverts commit 503d7821555b69b7ccfed55ce8b87ee24fff852d.
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

162dc19a

[Bug Fix]edge sample hotfix (#1152) · 61b78e6e

xiang song(charlie.song) authored Dec 31, 2019

* hot fix

* Fix docs

* Fix ArrayHeap float overflow bug

* Fix

* Clean some dead code

* Fix

* FIx

* Add some comments

* run test

61b78e6e

30 Dec, 2019 2 commits

[KVStore] Reduce memory cost of kvstore (#1156) · 6731ea3a

Chao Ma authored Dec 30, 2019

* API change of kvstore

* add demo for kvstore

* update

* remove duplicated log

* change queue size

* update

* update

* update

* update

* update

* update

* update

* update

* update

* fix lint

* change name

* update

* fix lint

* update

* update

* update

* update

* change message queue size to a python argument

* change default queue size to 2GB

* OMP_NUM_THREADS=1

* add multiple NICs support for kvstore

* test

* fix lint

* update

* update

* update

* update

* update

* update

* update

* fix lint

* fix lint

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* fix lint

6731ea3a

[KVStore] Made kvstore can support multiple NICs (#1150) · 4f02bb75

Chao Ma authored Dec 30, 2019

* API change of kvstore

* add demo for kvstore

* update

* remove duplicated log

* change queue size

* update

* update

* update

* update

* update

* update

* update

* update

* update

* fix lint

* change name

* update

* fix lint

* update

* update

* update

* update

* change message queue size to a python argument

* change default queue size to 2GB

* OMP_NUM_THREADS=1

* add multiple NICs support for kvstore

* test

* fix lint

* update

* update

* update

* update

* update

* update

* update

* fix lint

* fix lint

* update

* update

* update

* update

4f02bb75

29 Dec, 2019 1 commit
- [KG] reduce memory consumption. (#902) · f8184153
  Da Zheng authored Dec 28, 2019
```
* reduce memory consumption.

* fix a bug.

* fix a bug.

* fix.
```
  f8184153
28 Dec, 2019 1 commit
- fix deprecation warning (#1147) · 655d7568
  Quan (Andy) Gan authored Dec 28, 2019
  
  655d7568