56ffb650fe
[API Deprecation]Deprecate contrib module ( #5114 )
2023-01-06 20:16:01 +08:00
edf2d52666
[Dist][Optim] Fixed race conditions in distributed SparseAdam and SparseAdagrad ( #3971 )
...
* * Fixed race condition bug in distributed/optim/pytorch/sparse_optim.py's SparseAdam::update, corresponding with the bug fixed in the non-distributed version in https://github.com/dmlc/dgl/pull/3013 , though using the newer Event-based approach from that corresponding function. The race condition would often result in NaNs, like the previously fixed bug. https://github.com/dmlc/dgl/issues/2760
* * Fixed race condition bug in SparseAdagrad::update corresponding with the one fixed in SparseAdam::update in the previous commit. Same info applies.
* * Fixed typo in all copies of a repeatedly-copied comment near bug fixed 3 commits ago, checking all implementations nearby for a corresponding bug. (All of them appear to have been fixed as of 2 commits ago.)
* * Removed trailing whitespace
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com >
2022-05-09 09:05:31 -07:00
6d9433b04f
[Transform] [Doc] Rename transform to transforms and update doc ( #3765 )
...
* Update
* Update
* Update
* Fix
* Update
* Update
* Update
* Fix
2022-02-24 21:28:15 +08:00
36c7b77167
[LifeSci] Move to Independent Repo ( #1592 )
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* Move LifeSci
* Remove doc
2020-06-05 21:28:24 +08:00
b8dffcd57f
[DGL-LifeSci] Handle Same Labels for ROC AUC ( #1581 )
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* Handle corner case for ROC AUC
* Update
* Update doct
2020-06-03 01:21:08 +08:00
38b9c0f82f
[DGL-LifeSci] Allow Generating Vocabulary from a New Dataset ( #1577 )
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* Generate vocabulary from a new dataset
* CI"
2020-06-02 14:21:48 +08:00
165c67ccda
[DGL-LifeSci] Pre-trained GIN ( #1558 )
...
* Update
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
2020-05-25 00:02:12 +08:00
039fefc2fb
[DGL-LifeSci] WLN for Reaction Prediction ( #1530 )
...
* Update
* Update
* Update
* Update
* Update
* Fix bug
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* UPdate
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Udpate
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Finalize
2020-05-16 10:16:02 +08:00
ad222fb939
Update ( #1447 )
2020-04-16 03:17:57 +08:00
011656fd96
[DGL-LifeSci] Weave for Molecular Property Prediction ( #1441 )
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* featurize for weave model
* weave module for molecular graphs
* Update
* completed weave model
* update the whole weave model
* Update
* update atom (node) features
'
* "featurizer"
* Add files via upload
add edge featurizer
* Add files via upload
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
Co-authored-by: mufeili <mufeili1996@gmail.com >
2020-04-15 03:09:31 +08:00
e317f715e0
deprecate DGL-KE. ( #1432 )
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* deprecate DGL-KE.
* Update README.md
* remove from CI.
* remove tests.
Co-authored-by: Zheng <dzzhen@3c22fb0ed81b.ant.amazon.com >
2020-04-09 01:08:33 -07:00
d3560b7155
[DGL-LifeSci] Documentation ( #1414 )
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* Update
* Update
* Update
2020-04-02 21:19:07 +08:00
0ee9f56e72
[DGL-LifeSci] Final release preparation for 0.2.1
2020-04-02 15:02:50 +08:00
b76ac11c90
[DGL-LifeSci] Release Preparation (CI, Docker, Conda build) ( #1399 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* add docs
* Fix style
* Fix lint
* Bug fix
* Fix test
* Update
* Update
* Update
* Update
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-04-01 15:45:03 +08:00
1b9bc16b1a
[KG]Update README and config ( #1375 )
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* Update README and config
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-60-78.ec2.internal >
2020-03-19 17:06:02 +08:00
635dfb4a59
[DGL-KE] Add license to every file header ( #1368 )
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* update metis
* update
* update dataloader
* update dataloader
* new script
* update
* update
* update
* update
* update
* update
* update
* update dataloader
* update
* update
* update
* update
* update
* update
* update
* Add license to every filer header
2020-03-17 17:46:18 +08:00
f8ae6350b1
[DGL-KE] Add METIS preprocessing pipeline ( #1365 )
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* update metis
* update
* update dataloader
* update dataloader
* new script
* update
* update
* update
* update
* update
* update
* update
* update dataloader
* update
* update
* update
* update
* update
2020-03-17 17:15:04 +08:00
2ce0e21b6b
Update ( #1366 )
2020-03-16 22:00:19 +08:00
f9ad1c80da
fix. ( #1358 )
...
Co-authored-by: Chao Ma <mctt90@gmail.com >
2020-03-15 12:23:32 +08:00
eb71c804e8
[KG] partition a KG. ( #1351 )
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* partition a KG.
* get tid.
* support builtin
* fix a minor bug.
Co-authored-by: Chao Ma <mctt90@gmail.com >
2020-03-15 11:53:44 +08:00
545cc065c0
[DGL-LifeSci] WLN for Reaction Center Prediction ( #1360 )
...
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
2020-03-14 13:13:38 +08:00
f3b866f4eb
Update ( #1359 )
2020-03-13 17:38:57 +08:00
87842db48e
Fix for dataloader ( #1353 )
2020-03-12 19:09:46 +08:00
9432cd63ca
fix sampler. ( #1350 )
2020-03-11 11:01:03 +08:00
e65840434b
[KG] make batch size compatible with neg sample size ( #1343 )
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* adjust batch size.
* fix for eval.py
* adjust parameters in distributed training.
* move code.
2020-03-10 01:14:33 -07:00
d98c71ef90
[DGL-KE] Clean up argument for DGL-KE ( #1325 )
...
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* clean up args
* change args for eval
* update
* update
* update
* 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
2020-03-09 23:11:56 +08:00
f9ba3cdc81
[KGE] Kg loader ( #1300 )
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* 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 >
2020-03-08 23:57:40 -07:00
614acf2c28
[KG] save config when saving the model ( #1336 )
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* save config.
* save more.
2020-03-08 18:00:18 -07:00
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
c23a61bd5c
fix s3 link ( #1310 )
2020-03-04 21:01:29 +08:00
00ba409440
[DGL-KE] Distributed training of DGL-KE ( #1290 )
...
* update
* change name
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* change worker number
* update
* update
* update
* update
* update
* update
* test
* update
* update
* update
* remove barrier
* max_step
* update
* add complex
* update
* chmod +x
* update
* update
* random partition
* random partition
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* change num_test_proc
* update num_thread
* update
2020-03-02 14:17:54 +08:00
97e792654f
Update setup.py ( #1270 )
2020-02-18 17:35:45 +08:00
49fe5b3c83
[KG][Optimization] Soft relation partition ( #1252 )
...
* Several optimizations on DGL-KG:
1. Sorted positive edges for sampling which can reduce random
memory access during positive sampling
2. Asynchronous node embedding update
3. Balanced Relation Partition that gives balanced number of
edges in each partition. When there is no cross partition
relation, relation embedding can be pin into GPU memory
4. tunable neg_sample_size instead of fixed neg_sample_size
* Fix test
* Fix test and eval.py
* Now TransR is OK
* Fix single GPU with mix_cpu_gpu
* Add app tests
* Fix test script
* fix mxnet
* Fix sample
* Add docstrings
* Fix
* Default value for num_workers
* Add soft relation part
* Upd
* Some fix
* upd
* Now work
* Fix TransR
* Fix eval and add some doc string
* triger
* upd
* Add some training scripts for freebase multi-gpu
* upd
* upd
* upd
2020-02-15 23:59:02 -08:00
ffe5898317
[Optimization][KG] Several optimizations on DGL-KG ( #1233 )
...
* Several optimizations on DGL-KG:
1. Sorted positive edges for sampling which can reduce random
memory access during positive sampling
2. Asynchronous node embedding update
3. Balanced Relation Partition that gives balanced number of
edges in each partition. When there is no cross partition
relation, relation embedding can be pin into GPU memory
4. tunable neg_sample_size instead of fixed neg_sample_size
* Fix test
* Fix test and eval.py
* Now TransR is OK
* Fix single GPU with mix_cpu_gpu
* Add app tests
* Fix test script
* fix mxnet
* Fix sample
* Add docstrings
* Fix
* Default value for num_workers
* Upd
* upd
2020-02-09 13:01:00 -08:00
3f0c10058a
[DGL-LifeSci] Fix broken links ( #1248 )
...
* Fix
* Update
2020-02-08 18:42:51 +08:00
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
cd9599ab04
[KG][Optimization] Remove copy from parent in minibatch generation ( #1193 )
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* remote copy from parent
* upd
* make test_sampler easier to pass
2020-01-10 15:59:09 -08:00
bb6a64763e
[Feature][KG] Multi-GPU training support for DGL KGE ( #1178 )
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* 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
2020-01-08 18:07:04 +08:00
1022d5d64d
[KG] PBG's way of constructing negative edges ( #1159 )
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* 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.
2020-01-04 19:25:06 -08:00
1de192f445
[KG] More fixes on eval ( #1168 )
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* remove parallel sampling for multiprocessing.
* avoid memory copy in eval.
* remove print.
2020-01-04 13:33:13 -08:00
346bc23556
[KG] Disable filter in evaluation ( #1162 )
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* add no_eval_filter
* fix eval.
2020-01-03 13:02:34 +08:00
7451bb2a01
merge eval results in all processes. ( #1160 )
2020-01-01 21:40:31 -08:00
162dc19a5d
Accelerate edge sampling ( #1151 )
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* 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 >
2019-12-31 01:40:20 -08:00
f81841532f
[KG] reduce memory consumption. ( #902 )
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* reduce memory consumption.
* fix a bug.
* fix a bug.
* fix.
2019-12-28 21:55:50 -08:00
41f8a162f4
[Feature Improvement]Edge Sampler w and w/o replacement ( #1116 )
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* Add weight based edge sampler
* Can run, edge weight work.
TODO: test node weight
* Fix node weight sample
* Fix y
* Update doc
* Fix syntex
* Fix
* Fix GPU test for sampler
* Fix test
* Fix
* Refactor EdgeSampler to act as class object not function that it
can record its own private states.
* clean
* Fix
* Fix
* Fix run bug on kg app
* update
* update test
* test
* Simply python API and fix some C code
* Fix
* Fix
* Fix syntex
* Fix
* Update API description
* add replacement for edge sampler
* Now edge sampler support replacement and no-replacement
* Fix
* Fix
* change kg/app to use edge sampler with replacement config
* Update replacement algo
* Fix syntax
* Update
* Update
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2019-12-24 16:25:40 +08:00
d30a69bf27
[Backend] TF backend ( #978 )
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* tf
* add builtin support
* fiix
* pytest
* fix
* fix
* fix some bugs
* fix selecting
* fix todo
* fix test
* fix test fail in tf
* fix
* fix
* fix gather row
* fix gather row
* log backend
* fix gather row
* fix gather row
* fix for pytorch
* fix
* fix
* fix
* fix
* fix
* fix tests
* fix
* fix
* fix
* fix
* fix
* fix
* fix convert
* fix
* fix
* fix
* fix inplace
* add alignment setting
* add debug option
* Revert "add alignment setting"
This reverts commit ec63fb3506ea84fff7d447a1fbdfd1d5d1fb6110.
* tf ci
* fix lint
* fix lint
* add tfdlpack
* fix type
* add env
* fix backend
* fix
* fix tests
* remove one_hot
* remove comment
* remove comment
* fix
* use pip to install all
* fix test
* fix base
* fix
* fix
* add skip
* upgrade cmake
* change version
* change ci
* fix
* fix
* fix
* fix
* fix seg fault
* fix
* fix python version
* fix
* try fix
* fix
* fix
* tf takes longer time in ci
* change py version
* fix
* fix
* fix oom
* change kg env
* change kg env
* 啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊
* 我再也不搞各种乱七八糟环境了……
* use pytest
* Chang image
2019-12-20 15:56:51 +08:00
1552090a24
set default backend. ( #1104 )
2019-12-13 08:30:14 -08:00
ae743dcc02
remove tqdm. ( #1051 )
2019-12-01 14:41:45 -08:00
dca0e376e0
[KG][Score Func] Update TransE with L2 distance support. ( #1059 )
...
* Add L2 distance score for TransE
* Update README.md
* Use linalg.gemm to speedup mx l2 dist
* Fix
2019-12-01 14:03:36 -08:00
8b17a5c1d5
[Model] add RotatE to dgl-kg ( #964 )
...
Add RotatE support for KGE (apps/kg)
Performance Result:
Dataset FB15k:
Result from Paper:
MR: 40
MRR: 0.797
HIT@1: 74.6
HIT@3: 83.0
HIT@10: 88.4
Our Impl:
MR: 39.6
MRR: 0.725
HIT@1: 62.8
HIT@3: 80.2
HIT@10: 87.5
2019-11-14 10:39:05 +08:00
peizhou001