文件历史

提交图

705 次代码提交

作者 SHA1 备注 提交日期
Hengrui Zhang 0d1dcdcd2e [bugfix] fix a bug found in v0.7 bug bash in the 'grace' model (#3109)
* Update aug.py

* Update aug.py

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-07-07 14:50:02 +08:00
Tianjun Xiao 22e8c120be [Example ] fix faiss issue on k 3 for hilander model (#3105)
* fix faiss issue on k 3

* Add Hilander paper link

Co-authored-by: Tong He <hetong007@gmail.com>
2021-07-06 13:22:56 +08:00
Tong He 9c41c22d7b [Model] Official implementation for HiLANDER model. (#3087)
* add hilander model implementation draft

* use focal loss

* fix

* change data root

* add necessary scripts

* update download links

* update

* update example table

* fix

* update readme with numbers

* add empty folder

* only eval at the end

* set up hilander

* inform results may fluctuate

* address comments

Co-authored-by: sneakerkg <xiaotj1990327@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-212.us-east-2.compute.internal>
2021-07-04 20:08:58 +08:00
Da Zheng 0884d02465 [Distributed] Fix bugs in partitioning on heterogeneous graphs. (#3085)
* fix bugs in partitioning on heterogeneous graphs.

* fix.

* fix.

* fix example.

* fix.

* fix test.

* fix.

* fix.

* fix.

* fix tests.

Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal>
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com>
2021-07-02 21:16:14 +08:00
nv-dlasalle 02e5d47d2a [Example][Bugfix] Fix RGCN example datasplitting (#3037)
* Fix example datasplitting

* Remove left-over split parameter

* Remove unused parameter

* Set epoch when using multiple GPUs

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
2021-06-29 10:16:28 +08:00
Tomohiro Endo 7f4086da7a cuda() to to(device) (#3064)
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
2021-06-28 11:56:24 +08:00
WangYQ 2f43cdb3c8 deal with situation where num_layers equals 1 (#3066) 2021-06-28 10:17:16 +08:00
Quan (Andy) Gan 427a5a96e0 [Doc] Update NodeDataLoader and EdgeDataLoader for GPU-based neighbor sampling (#3046)
* update docstrings and tidy code

* add docs

* address comments

* Update __init__.py

* address comments
2021-06-25 10:46:21 +08:00
Quan (Andy) Gan acd21a6d60 [Feature] Support direct creation from CSR and CSC (#3045)
* csr and csc creation

* fix

* fix

* fixes to adj transpose

* fine

* raise error if indptr did not match number of nodes

* fix

* huh?

* oh

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-06-25 10:05:47 +08:00
maqy 31f4483af7 add HAN sampling demo (#3005)
Co-authored-by: maqy1995 <maqingyun0718>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
2021-06-23 20:27:18 +08:00
Tomohiro Endo cb2327d4a9 [Example] Fix error in gcn train due to missing argument (#3040)
* Fix example

* Remove register_data_args and revert  to dataset

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-06-23 15:50:07 +08:00
Quan (Andy) Gan e667545da5 [Feature] Node2vec (#2992)
* add seal example

* 1. add paper infomation in examples/README
2. adjust codes
3. option test

* use latest `to_simple` to replace coalesce graph function

* remove outdated codes

* remove useless comment

* Node2vec
1.implement node2vec random walk c++ op
2.implement node2vec model
3.implement node2vec example

* add CMakeLists file modify

* refine c++ codes

* refine c++ codes

* add missing whitespace

* refine python codes

* add codes

* add node2vec_impl.h

* fix codes

* fix code style problem

* fixes

* remove

* lots of changes

* add benchmark

* fixes

Co-authored-by: smilexuhc <smile.xuhc@gmail.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-06-23 14:47:56 +08:00
Mufei Li ff519f98c3 [API] Standardize Subgraph APIs (#2929)
* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Update

* Fix subgraph tests

* Capture stdout for distributed test

* Capture stdout for distributed test

* Update

* Update

* Update

* Update subgraph.cc

Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-17.us-west-2.compute.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
2021-06-21 19:53:37 +08:00
Da Zheng aaec3d8a0b [Distributed] Support hierarchical partitioning (#3000)
* add.

* fix.

* fix.

* fix.

* fix.

* add tests.

* support node split and edge split.

* support 1 partition.

* add tests.

* fix.

* fix test.

* use hierarchical partition.

* add check.

Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-22-57.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal>
2021-06-16 16:58:23 +08:00
Hengrui Zhang 18eaad17cc fix bugs (#3008)
Co-authored-by: zhjwy9343 <6593865@qq.com>
2021-06-16 15:27:47 +08:00
Hengrui Zhang 36c6c64957 Replace QM9_v2 with built-in QM9Edge Dataset (#3026)
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-06-16 14:35:40 +08:00
espylapiza 305d5c16df [Example] update ogbn-arxiv and ogbn-proteins results (#3018)
* [Example] GCN on ogbn-arxiv dataset

* Add README.md

* Update GCN implementation on ogbn-arxiv

* Update GCN on ogbn-arxiv

* Fix typo

* Use evaluator to get results

* Fix duplicated

* Fix duplicated

* Update GCN on ogbn-arxiv

* Add GAT for ogbn-arxiv

* Update README.md

* Update GAT on ogbn-arxiv

* Update README.md

* Update README

* Update README.md

* Update README.md

* Add GAT implementation for ogbn-proteins

* Add GAT implementation for ogbn-proteins

* Add GAT implementation for ogbn-proteins

* Add GAT implementation for ogbn-proteins

* Add GAT implementation for ogbn-proteins

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Update examples for ogbn-arxiv

* Add examples for ogbn-products.

* Update examples for ogbn-proteins.

* Update examples for ogbn-proteins.

* Update examples for ogbn-proteins.

* Update examples for ogbn-proteins.

* Update examples for ogbn-proteins.

* Update examples for ogbn-proteins.

* Update examples for ogbn-proteins.

* Update examples for ogbn-proteins.

* Update examples for ogbn-proteins.

* Update examples for ogbn-products.

* Update examples for ogbn-products.

* Update examples for ogbn-arxiv.

* Update examples for ogbn-arxiv.

* Update examples for ogbn-arxiv.

* Update examples for ogbn-proteins.

* Update examples for ogbn-products.

* Update examples for ogbn-proteins.

* Update examples for ogbn-arxiv.

* Update examples for ogbn-proteins.

* Update README.md

* [Example] ogbn-arxiv & ogbn-proteins

* [Example] ogbn-arxiv & ogbn-proteins

* [Example] ogbn-arxiv & ogbn-proteins

* [Example] ogbn-arxiv & ogbn-proteins

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Zihao Ye <expye@outlook.com>
2021-06-16 12:33:43 +08:00
Hengrui Zhang b4ad59d77f [Model] reformat and update performance of grace (#3009)
* reformat and update performance

* Update README.md

* Fix typos

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2021-06-15 17:02:37 +08:00
nv-dlasalle 8b64ae59b8 [Performance] Perform to_block on the GPU when the dataloader is created with a GPU device. (#3016)
* add output device for dataloading

* Update dataloader

* Get sampler device from dataloader

* Fix line length

* Update examples

* Fix to_block GPU for empty relation types

* Handle the case where the DistGraph has None for the underlying graph

Co-authored-by: Da Zheng <zhengda1936@gmail.com>
2021-06-13 18:51:00 +08:00
nv-dlasalle 79b057f0cf Fix example to test_acc is always computed at last epoch (#3014) 2021-06-12 18:02:00 -07:00
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