文件历史

提交图

485 次代码提交

作者 SHA1 备注 提交日期
nv-dlasalle 17d604b5c7 [Feature] Allow using NCCL for communication in dgl.NodeEmbedding and dgl.SparseOptimizer (#2824)
* Split from NCCL PR

* Fix type in comment

* Expand documentation for sparse_all_to_all_push

* Restore previous behavior in example

* Re-work optimizer to use NCCL based on gradient location

* Allow for running with embedding on CPU but using NCCL for gradient exchange

* Optimize single partition case

* Fix pylint errors

* Add missing include

* fix gradient indexing

* Fix line continuation

* Migrate 'first_step'

* Skip tests without enough GPUs to run NCCL

* Improve empty tensor handling for pytorch 1.5

* Fix indentation

* Allow multiple NCCL communicator to coexist

* Improve handling of empty message

* Update python/dgl/nn/pytorch/sparse_emb.py

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* Update python/dgl/nn/pytorch/sparse_emb.py

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* Keepy empty tensor dimensionaless

* th.empty -> th.tensor

* Preserve shape for empty non-zero dimension tensors

* Use shared state, when embedding is shared

* Add support for gathering an embedding

* Fix typo

* Fix more typos

* Fix backend call

* Use NodeDataLoader to take advantage of ddp

* Update training script to share memory

* Only squeeze last dimension

* Better handle empty message

* Keep embedding on the target device GPU if dgl_sparse if false in RGCN example

* Fix typo in comment

* Add asserts

* Improve documentation in example

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
2021-06-10 21:19:00 -07:00
nv-dlasalle 9497a9be85 [Bugfix][Examples] Fix graphsage multigpu training example training set size (#3002)
* Make multigpu graphsage use whole datset

* Specify queeze dimension

* Remove squeeze dimension

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
2021-06-10 16:35:08 -07:00
Theheavens 6c59fee99b [Model] HetGNN/GTN/HAN/NSHE/MAGNN examples (#2993)
* commit hetgnn

* Update README.md

* Delete examples/pytorch/hetgnn directory

* Update README.md

* Update README.md

* Update README.md

* Revert "Update README.md"

This reverts commit 14cdb3da76c58665ff879eae17ecf9eb28b66cce.

* Update README.md

* Add files via upload

* Update README.md

* Update README.md
2021-06-08 08:54:27 +08:00
Tong He 972a9f1323 [Doc] Re-organize the code for dgl.geometry, and expose it in the doc (#2982)
* reorg and expose dgl.geometry

* fix lint

* fix test

* fix
2021-06-07 11:19:39 +08:00
Alex P 6e9d16459e [Fix] Fixed AttributeError with new version of torchtext (0.9+). (#2985) 2021-06-05 02:01:20 +08:00
KounianhuaDu 60426278bf [Example] TAHIN (#2864)
* tahin

* readme

* readme

* readme

* readme

* readme

* readme

* main

* main

* new_line

* update

Co-authored-by: zhjwy9343 <6593865@qq.com>
2021-06-03 16:03:55 +08:00
Moritz Blum 22d0df8b6a [Doc] Update link_predict.py docstring (#2960)
corrected docstring, the model uses two R-GCN layers

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-06-02 12:08:28 +08:00
Da Zheng 18dbaebebc [Distributed] Specify the graph format for distributed training (#2948)
* explicitly set the graph format.

* fix.

* fix.

* fix launch script.

* fix readme.

Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal>
2021-05-26 18:09:30 +08:00
yifeim c018436588 [Example] add latent dirichlet allocation (#2883)
* add lda model

* tweak latent dirichlet allocation

* Update README.md

* Update README.md

* update example index

* update header

* minor tweak

* add example test

* update doc

* Update README.md

* Update README.md

* add partial_fit for free

* Update examples/pytorch/lda/lda_model.py

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* Update examples/pytorch/lda/example_20newsgroups.py

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* Update lda_model.py

* bugfix torch Gamma uses rate parameter

Co-authored-by: Yifei Ma <yifeim@amazon.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
2021-05-17 20:25:36 +08:00
Quan (Andy) Gan 7c7113f660 add use_ddp to dataloaders (#2911) 2021-05-17 15:46:02 +08:00
Quan (Andy) Gan caa6d6072c [Feature] Replacing thread_wrapped_func with minimal mp.Process wrapper (#2905)
* standardizing thread_wrapped_func

* lints

* Update __init__.py
2021-05-14 11:34:49 +08:00
xnouhz 85231dc93b [Example] Label Propagation and Correct&Smooth (#2852)
* [example] label propagation and correct&smooth

* update

* update

* update

* update

* [docs] add speed for c&s

* update

* [fix] remove gat&consistent with the author's code

* [feat] multi-type adj norm supported

* update

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-05-12 18:45:46 +08:00
lt610 d70ca6eb7c [Example] graphsaint (#2792)
* graphsaint

* graphsaint

* graphsaint

* graphsaint

* fixed the model

* fixed some bugs

* fixed the computing of normalization and updated the results

* fixed some bugs and updated the results

* Update utils.py

* Update train_sampling.py

* Update train_sampling.py

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
2021-05-11 16:25:56 +08:00
Quan (Andy) Gan 70695ff8f8 [Model] Training GraphSAGE with PyTorch Lightning (#2878)
* pytorch lightning initial examples

* revert most changes in dataloader to favor #2886.

* address comments
2021-05-11 11:28:13 +08:00
xiang song(charlie.song) 975eb8fc5d [Distributed] Distributed node embedding and sparse optimizer (#2733)
* Draft for sparse emb

* add some notes

* Fix

* Add sparse optim for dist pytorch

* Update test

* Fix

* upd

* upd

* Fix

* Fix

* Fix bug

* add transductive exmpale

* Fix example

* Some fix

* Upd

* Fix lint

* lint

* lint

* lint

* upd

* Fix lint

* lint

* upd

* remove dead import

* update

* lint

* update unitest

* update example

* Add adam optimizer

* Add unitest and update data

* upd

* upd

* upd

* Fix docstring and fix some bug in example code

* Update rgcn readme

Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-25.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-24-210.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal>
2021-05-03 08:37:40 +08:00
Hengrui Zhang b2b531e041 [Example] add implementation of grace (#2828)
* [Example] add implementation of grace

* [Doc] add grace in the index file

* fix

* fix typos

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-04-27 12:43:03 +08:00
Mufei Li 2ae891a78c Update main.py (#2872) 2021-04-26 17:12:19 +08:00
xnouhz 756fdd8e90 [Example] DeeperGCN (#2831)
* [example] deepergcn

* update

* update

* update

* update

* update

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-04-25 18:37:41 +08:00
Chen Sirui 3c387988d7 [Example] DCRNN and GaAN (#2858)
* Ready for PR

* refractor code

Co-authored-by: Ubuntu <ubuntu@ip-172-31-45-47.ap-northeast-1.compute.internal>
Co-authored-by: Tianjun Xiao <xiaotj1990327@gmail.com>
2021-04-23 22:33:39 +08:00
Chen Sirui ebc6a85a80 [Bugfix] TGN model bugfix and improvement (#2860)
* Add DCRNN Example

* Bugfix DCRNN

* Bugfix DCRNN

* Bugfix Train/eval have different flow

* Performance Matched

* modified tgn for research

* kind of fixed 2hop issue

* remove data

* bugfix and improve the performance

* Refractor Code

Co-authored-by: Ubuntu <ubuntu@ip-172-31-45-47.ap-northeast-1.compute.internal>
Co-authored-by: Tianjun Xiao <xiaotj1990327@gmail.com>
2021-04-23 15:44:22 +08:00
Tingzhang Zhao 4579bbf7b7 Update README.md (#2853)
Change the format of  README.md
2021-04-21 13:05:25 +08:00
Quan (Andy) Gan 6232ee8d44 Update README.md (#2820)
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
2021-04-20 13:17:30 +08:00
Tingzhang Zhao e58eeebfb6 [Model] Add RECT example (#2813)
* Update README.md

Add description of RECT

* [Example] Add implementation of RECT

[Example] Add implementation of RECT

* Update classify.py

Modify the class names and the function names mentioned above

* Update main.py

Modify the function names mentioned above

* Update label_utils.py

Adjust the comments

* Update README.md

Add the github information

Co-authored-by: Tianjun Xiao <xiaotj1990327@gmail.com>
2021-04-19 21:48:38 +08:00
nv-dlasalle e70138bbe4 [Performance][GPU] Enable GPU uniform edge sampling (#2716)
* Start on uniform GPU sampling

* Save more work

* Get cu file compiling

* Update sampling

* More changes

* Get GPU sampling for uniform probabilities solved

* Fix batch tensor migration

* Fix

* update kernels

* expand blocking

* Undo testing change

* Cut down on sampling overhead

* Fix replacement

* Update unit tests

* Add option to gpu sample in graphsage

* Copy only csc to gpu

* Add ogbn support

* Fix linting

* Remove nvtx from sample

* Improve documentation and error checking

* Expand documentation

* Update assert checking

* delete extra space

* Use standard dataloader when dataset is a dictionary

* ogb -> ogbn

* Fix edge selection determinism

* Fix typos

* Remove nvtx

* Add comment for self.fanout_arrays and assert

* Fix linting

* Migrate to scalarbatcher

* Fix indentation

* Fix batcher

* Fix indexing

* Only use databatcher for GPU

* Convert to DGL NDArray to PyTorch Tensor

* Add optimization for PyTorch's F.tensor() for list of GPU tensors

Co-authored-by: Da Zheng <zhengda1936@gmail.com>
2021-04-14 18:55:09 -07:00
maqy 195f99362d [example] multi gpus training for mag240m (#2835)
* multi gpus training for mag240m

* remove unused function

* small changes

* more fix

* use multi gpus to eval and more fix

Co-authored-by: Quan Gan <coin2028@hotmail.com>
2021-04-13 20:29:43 +08:00
Chen Sirui afc83aa216 Graphsim (#2794)
* Add hgat example

* Add experiment

* Clean code

* clear the code

* Add index in README

* Add index in README

* Add index in README

* Add index in README

* Add index in README

* Add index in README

* Change the code title and folder name

* Ready to merge

* Prepare for rebase and change message passing function

* use git ignore to handle empty file

* change file permission to resolve empty file

* Change permission

* change file mode

* Finish Coding

* working code cpu

* pyg compare

* Accelerate with batching

* FastMode Enabled

* update readme

* Update README.md

* refractor code

* add graphsim code

* modified code

* few fix

* Modified graphsim

* Simple Model Added

* Clean up code

* Refractor the code for Merge

* Bugfix enable gradient when train

* update readme and format

Co-authored-by: Chen <chesirui@3c22fbe5458c.ant.amazon.com>
Co-authored-by: Tianjun Xiao <xiaotj1990327@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-4-63.ap-northeast-1.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-45-47.ap-northeast-1.compute.internal>
2021-04-12 19:02:36 +08:00
TianleZhang d70eade4f2 bug fix type mismatch (#2830)
int has no attribute of item

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
2021-04-11 20:33:03 +08:00
Da Zheng bfbbefa793 [Distributed] Fix a bug in multiprocessing sampling. (#2826)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-73-81.ec2.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
2021-04-08 01:29:33 -07:00
xnouhz 2afa3598ba [Example] JKNet (#2795)
* [example] jknet

* update

* update

* update

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-04-07 14:29:33 +08:00
Ruoyun Huang 2980137719 [Doc] Typo in command example. (#2816)
* Typo in command example. 

process_nowplaying_rs.py is the right name under this folder.

* Update README.md

* Update README.md

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
2021-04-07 09:43:37 +08:00
Sergey Ivanov 672e322719 [Model] Add BGNN example (#2740)
* Add BGNN example

* Update bgnn example

* Remove uncessary files

* update model index

* style fix

* Add Readme for BGNN example

* Update documentation; remove preprocessing

Co-authored-by: s.ivanov <s.ivanov@mesos-slave080-am6.central.criteo.prod>
Co-authored-by: s.ivanov <s.ivanov@mesos-slave150-am6.central.criteo.prod>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
Co-authored-by: s.ivanov <s.ivanov@mesos-slave148-am6.central.criteo.prod>
Co-authored-by: s.ivanov <s.ivanov@mesos-slave078-am6.central.criteo.prod>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-04-07 00:16:09 +08:00
KounianhuaDu e61138be19 [Example] CompGCN (#2768)
* compgcn

* readme

* readme

* update

* readme

Co-authored-by: zhjwy9343 <6593865@qq.com>
2021-04-05 20:45:38 +08:00
Quan (Andy) Gan cfe6e70b7a RGAT baseline for OGB-LSC node classification challenge (#2810)
* RGAT baseline

* update links (data.dgl.ai hasn't refreshed yet)

* nvm still use dgl.ai domain

* descriptions

* actually it took less

* address comments

* stop worrying about cache

* update links

* oops
2021-04-05 18:21:18 +08:00
Yu Sun cba5af22eb [bugfix] Fix bugs in vgae (#2727)
* [Example]Variational Graph Auto-Encoders

* change dgl dataset to single directional graph

* clean code

* refresh

* fix bug

* fix bug

* fix bug

* add gpu

Co-authored-by: Tianjun Xiao <xiaotj1990327@gmail.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-04-03 20:02:04 +08:00
Da Zheng e36c5db614 [Distributed] Simplify distributed API (#2775)
* remove num_workers.

* remove num_workers.

* remove num_workers.

* remove num-servers.

* update error message.

* update docstring.

* fix docs.

* fix tests.

* fix test.

* fix.

* print messages in test.

* fix.

* fix test.

* fix.

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal>
2021-03-29 19:19:23 -07:00
Quan (Andy) Gan 66f7fe8bce Update model.py (#2796) 2021-03-29 16:30:32 +08:00
Mufei Li a655123b4e [Example] Baselines for OGB-LSC-PCQM4M (#2778)
* Update

* Add files via upload

* Add files via upload

* Add files via upload
2021-03-29 14:07:07 +08:00
colten a1b5b42af4 remove unused and undefined function (#2791)
Co-authored-by: messi-k <messi.k@kakaocorp.com>
2021-03-28 00:17:11 +08:00
Chen Sirui d04d59eef9 [Example] Temporal Graph Neural Network (#2636)
* Add hgat example

* Add experiment

* Clean code

* clear the code

* Add index in README

* Add index in README

* Add index in README

* Add index in README

* Add index in README

* Add index in README

* Change the code title and folder name

* Ready to merge

* Prepare for rebase and change message passing function

* use git ignore to handle empty file

* change file permission to resolve empty file

* Change permission

* change file mode

* Finish Coding

* working code cpu

* pyg compare

* Accelerate with batching

* FastMode Enabled

* update readme

* Update README.md

* refractor code

* Fix Bug

* add a simple temporal sampling method

* test results

* add train speed result

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* fix bug

* Fixed Grammar and Format Issue

Co-authored-by: Chen <chesirui@3c22fbe5458c.ant.amazon.com>
Co-authored-by: Tianjun Xiao <xiaotj1990327@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-4-63.ap-northeast-1.compute.internal>
Co-authored-by: WangXuhongCN <wangxuhongcn@163.com>
Co-authored-by: WangXuhongCN <34096632+WangXuhongCN@users.noreply.github.com>
2021-03-23 08:57:21 +08:00
Hengrui Zhang bcffdb82c9 [Example] Add implementation of mvgrl (#2739)
* [Example ]add mvgrl

* [Doc] add mvgrl to readme

* add more comments

* fix typos

* replace tab with space

* [doc] replace tab with space

* [Doc] fix a typo

* fix minor typos

* fix typos

* fix typos

* fix typos

* fix typos

* fix

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-03-22 21:20:21 +08:00
Kaiqiang Xu e6f6c2eb31 [Bugfix] Update deprecated method name in load_graph.py (#2769)
Method `dataset.num_labels` has been deprecated and replaced by `dataset.num_classes`.  
Updating the method name to avoid runtime warning.

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-03-22 20:07:32 +08:00
KounianhuaDu 9aac93ff21 Gnnexplainer (#2717)
* gnn-explainer

* gnn-explainer

* gnn-explainer

* gnn-explainer

* fix

* fix

* fix

* readme

* readme

Co-authored-by: zhjwy9343 <6593865@qq.com>
2021-03-22 18:13:08 +08:00
Da Zheng bb54206620 remove pyinstrument. (#2772)
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
2021-03-21 20:27:12 -07:00
Roger Tu 93074dd358 Bug fix for RGCN Link Prediction Example Exceeding Specified Epochs (#2757)
* Address bug where epochs exceed specified limit

* fix spacing
2021-03-17 14:29:45 +08:00
xnouhz 0b47e86803 [Example] Add DimeNet(++) for Molecular Graph Property Prediction (#2706)
* [example] arma

* update

* update

* update

* update

* update

* [example] dimenet

* [docs] update dimenet

* [docs] update tf results

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-03-09 17:08:59 +08:00
Tianqi Zhang (张天启) 91cb347719 [Example][Bug Fix] Improve DiffPool (#2730)
* change DiffPoolBatchedGraphLayer

* fix bug and add benchmark

* upt

* upt

* upt

* upt

Co-authored-by: Tong He <hetong007@gmail.com>
2021-03-09 16:03:00 +08:00
Hengrui Zhang 3317522622 [Example] Add implementation of InfoGraph (#2644)
* Add implementation of unsupervised model

* [Doc] Update Implementor's information

* [doc] add index of infograph

* [Feature] QM9_v2 Dataset Support

* fix a typo

* move qm9dataset from data to examples

* Update qm9_v2.py

* Infograph -> InfoGraph

* add implementation and results of semi-supervised model

* Update README.md

* Update README.md

* fix a typo

* Remove the duplicated links.

* fix some typos

* fix typos

* update model.py

* update collate fn

* remove unused functions

* Update model.py

* add device option

* Update evaluate_embedding.py

* Update evaluate_embedding.py

* Update unsupervised.py

* Fix typos

* fix bugs

* Update README.md

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-03-09 15:26:11 +08:00
Yu Sun f7938649d1 [Example] Variational Graph Auto-Encoders (#2587)
* [Example]Variational Graph Auto-Encoders

* change dgl dataset to single directional graph

* clean code

* refresh

Co-authored-by: Tianjun Xiao <xiaotj1990327@gmail.com>
2021-03-02 10:24:34 +08:00
Da Zheng d0638b1ea9 [Example] Update the example of distributed GNN training of RGCN (#2709)
* support gpu training.

* remove unnecessary arguments.

* update README.

* update time measurement.

* add zero_grad.

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
2021-03-01 12:00:15 -08:00
Da Zheng 28b0a76618 [Example] Provide instructions of setting up passwordless SSH login. (#2707) 2021-02-27 18:34:46 -08:00