文件历史

136 次代码提交

作者 SHA1 备注 提交日期
xiang song(charlie.song) e17add5602 [NN] Add MXNet impl for TAGCN module. (#799)
* upd

* fig edgebatch edges

* add test

* trigger

* Update README.md for pytorch PinSage example.

Add noting that the PinSage model example under
example/pytorch/recommendation only work with Python 3.6+
as its dataset loader depends on stanfordnlp package
which work only with Python 3.6+.

* Provid a frame agnostic API to test nn modules on both CPU and CUDA side.

1. make dgl.nn.xxx frame agnostic
2. make test.backend include dgl.nn modules
3. modify test_edge_softmax of test/mxnet/test_nn.py and
    test/pytorch/test_nn.py work on both CPU and GPU

* Fix style

* Delete unused code

* Make agnostic test only related to tests/backend

1. clear all agnostic related code in dgl.nn
2. make test_graph_conv agnostic to cpu/gpu

* Fix code style

* fix

* doc

* Make all test code under tests.mxnet/pytorch.test_nn.py
work on both CPU and GPU.

* Fix syntex

* Remove rand

* Add TAGCN nn.module and example

* Now tagcn can run on CPU.

* Add unitest for TGConv

* Fix style

* For pubmed dataset, using --lr=0.005 can achieve better acc

* Fix style

* Fix some descriptions

* trigger

* Fix doc

* Add nn.TGConv and example

* Fix bug

* Update data in mxnet.tagcn test acc.

* Fix some comments and code

* delete useless code

* Fix namming

* Fix bug

* Fix bug

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix
2019-08-28 13:19:17 +08:00
Quan (Andy) Gan 14bffe9728 [NN] Renaming NearestNeighborGraph to KNNGraph (#802)
* initial commit

* second commit

* another commit

* change docstring

* migrating to dgl.nn

* fixes

* docs

* lint

* multiple fixes

* doc

* renaming nearest neighbor graph
2019-08-28 12:20:35 +08:00
Quan (Andy) Gan dc19cd5687 [Example] Dynamic Graph CNN on Point Cloud (#789)
* initial commit

* second commit

* another commit

* change docstring

* migrating to dgl.nn

* fixes

* docs

* lint

* multiple fixes

* doc
2019-08-28 09:21:57 +08:00
Mufei Li e590feeb62 [Model Zoo] GAT on Tox21 (#793)
* GAT

* Fix mistake

* Fix

* hotfix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Update

* Update

* Fix style

* Hotfix

* Hotfix

* Hotfix

* Fix

* Fix

* Update

* CI trial

* Update

* Update

* Update
2019-08-28 04:47:16 +08:00
VoVAllen 3192beb42d [Model zoo] JTNN model zoo (#790)
* jtnn model zoo

* poke ci

* fix line sep

* fix

* Fix import order

* fix render

* fix render

* revert

* fix

* Resolve conflict

* dix

* remove create_var

* refactor

* fix

* refactor

* readme

* format

* fix lint

* fix lint

* pylint

* lint

* fix lint

* fix lint

* add hint

* fix

* Remove vocab

* Add explanation for warning

* add directory

* Load model to cpu by default

* Update
2019-08-28 04:04:54 +08:00
Mufei Li 331337fe5f [Model Zoo] Clean up for Alchemy dataset (#800)
* Make dataset framework agnostic

* Update

* Update

* Fix

* Remove unused import
2019-08-28 00:08:59 +08:00
Zihao Ye 9314aabd1f [Refactor] Interface of nn modules (#798)
* refactor

* upd mpnn
2019-08-27 22:29:25 +08:00
Zihao Ye 650f6ee1e0 [NN] Add commonly used GNN models from examples to dgl.nn modules. (#748)
* gat

* upd

* upd sage

* upd

* upd

* upd

* upd

* upd

* add gmmconv

* upd ggnn

* upd

* upd

* upd

* upd

* add citation examples

* add README

* fix cheb

* improve doc

* formula

* upd

* trigger

* lint

* lint

* upd

* add test for transform

* add test

* check

* upd

* improve doc

* shape check

* upd

* densechebconv, currently not correct (?)

* fix cheb

* fix

* upd

* upd sgc-reddit

* upd

* trigger
2019-08-27 18:21:19 +08:00
Mufei Li 8079d98617 Misc update (#796) 2019-08-27 16:08:36 +08:00
lunar 3bc73931f8 [Model Zoo] Molecule Regression (#779)
* [Model] MPNN

* [Model] MPNN 🔨 reorganize the mpnn/sch/mgcn model & alchemy dataset

* [Model] MPNN alchemy dataloader refactoring

* [Model] Chem model zoo minor change

* [Model] Chem Model Zoo 🔥 remove old samples

* [Model Zoo] molecule regression minor change

* Fix dataset import

* Fix dataset import

* [Model Zoo] molecule regression test set

* [Model Zoo] molecule prediction MPNN model hyperparameter tuning

* [Model Zoo] molecule prediction ✏️ mpnn performance update
2019-08-26 17:42:33 +08:00
Mufei Li 73b2668fe2 [Model Zoo] DGMG for molecule generation (#783)
* DGMG for molecule generation

* Fix CI check

* Fix for CI

* Trial for CI due to shared memory

* Update

* Better interface for dataset configuration

* Update

* Handle corner cases

* Update README

* Fix

* Fix

* Fix

* Fix

* Fix

* Refactor

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix

* Fix

* Fix

* Fix

* Fix

* Finallly
2019-08-26 03:39:20 +08:00
xiang song(charlie.song) 11fb217a76 [NN] Add TAGCN nn.module and example (#788)
* upd

* fig edgebatch edges

* add test

* trigger

* Update README.md for pytorch PinSage example.

Add noting that the PinSage model example under
example/pytorch/recommendation only work with Python 3.6+
as its dataset loader depends on stanfordnlp package
which work only with Python 3.6+.

* Provid a frame agnostic API to test nn modules on both CPU and CUDA side.

1. make dgl.nn.xxx frame agnostic
2. make test.backend include dgl.nn modules
3. modify test_edge_softmax of test/mxnet/test_nn.py and
    test/pytorch/test_nn.py work on both CPU and GPU

* Fix style

* Delete unused code

* Make agnostic test only related to tests/backend

1. clear all agnostic related code in dgl.nn
2. make test_graph_conv agnostic to cpu/gpu

* Fix code style

* fix

* doc

* Make all test code under tests.mxnet/pytorch.test_nn.py
work on both CPU and GPU.

* Fix syntex

* Remove rand

* Add TAGCN nn.module and example

* Now tagcn can run on CPU.

* Add unitest for TGConv

* Fix style

* For pubmed dataset, using --lr=0.005 can achieve better acc

* Fix style

* Fix some descriptions

* trigger

* Fix doc
2019-08-25 22:17:46 +08:00
Minjie Wang 708765f0a1 [NN] RGCN modules (#744)
* rgcn module

* support id input

* WIP: model codes

* use faster index select

* dropout

* self loop

* WIP: link prediction

* fix lint

* WIP: docs

* docstring

* docstring

* merge two child classes

* mxnet rgcn module

* fix lint

* fix lint

* fix rename bug

* add uniform edge sampler

* fix fn name

* docstring

* fix mxnet rgcn module

* fix mx rgcn

* enable test on cuda
2019-08-23 16:38:48 -04:00
VoVAllen 0f12763725 [Model] Early stop GAT (#750)
* Add early stop

* add mxnet version

* Poke ci
2019-08-21 14:58:56 +08:00
Sahand 77c58289a7 [Bugfix][Model] Fixing RGCN evaluation bug (#778) 2019-08-20 15:54:03 -04:00
Mufei Li 35bed2a9d0 Rename early stop (#773) 2019-08-18 13:46:44 +08:00
xiang song(charlie.song) 165d453806 [Doc] Update README.md for pytorch PinSage example. (#770)
Add noting that the PinSage model example under
example/pytorch/recommendation only work with Python 3.6+
as its dataset loader depends on stanfordnlp package
which work only with Python 3.6+.
2019-08-16 02:23:05 -03:00
Mufei Li cd9fb7baa0 [Model Zoo] Refactor GCN on Tox21 (#766)
* [Model zoo] Model zoo (#765)

* tox21

* fix ci

* fix ci

* fix urls to url

* add doc

* remove binary

* model zoo

* test

* markdown

* fix typo

* fix typo

* fix typo

* raise error

* fix lint

* remove unnecessary

* fix doc

* fix

* fix

* fix

* fix

* fix

* fix

* Update

* CI

* Fix

* Fix

* Fix

* Fix

* Fix

* CI
2019-08-16 02:49:25 +08:00
Xiagkun Hu b2f7f0ee7c [Model] Recurrent Relational Network (RRN) on sudoku (#733)
* rrn model and sudoku

* add README

* refine the code, add doc strings

* add sudoku solver
2019-08-10 02:00:11 +08:00
lunar e1f08644fb [Model] Schnet & MGCN (#726)
* [Model] SchNet

* [Model] SchNet model

* [Model] Schnet Model fix device-related bug

* [Model] SchNet fix bugs

* [Model] SchNet fix some bugs

* [Model] Schnet 🎨 code indent format

* [Model] SchNet ✏️ fix some typos
2019-08-07 14:08:31 +08:00
HQ bf3994eea6 [Model][Hotfix] DiffPool formatting fix (#696)
* formatting

* formatting
2019-07-02 15:19:57 +08:00
HQ 684a61ad09 [Model] DiffPool with both DGL and tensorized operatons (#665)
* diffpool original file added

* make diffpool fuse up and running

* minor tweak on tu dataset statistics method

* fix tu

* break

* delete break

* pre_org

* diffpool fuse reorg

* fix random shuffling

* fix bn

* add dgl layers

* early stopping

* add readme

* fix

* add diffpool preprocess script

* tweak tu dataset

* tweak

* tweak

* tweak

* tweak

* tweak

* preprocess dataset

* fix early stopping

* fix

* fix

* fix

* tweak

* readme

* code review

* code review

* dataset code review

* update README

* code review

* tu doc
2019-07-01 20:00:15 +08:00
Quan (Andy) Gan 714f2e1ced fix node id dtype (#674) 2019-06-20 10:53:26 +08:00
Lingfan Yu 82bb9a9b6a [README] Update speed numbers in README (#661)
* update speed numbers in readme

* numbers in examples/pytorch/readme
2019-06-15 14:27:58 -07:00
Tianyi f3d3fdf8cd add reddit example. (#658) 2019-06-14 22:53:59 +08:00
Minjie Wang dec8b49b5d [Examples] Run all the examples (#623)
* all pytorch examples

* scan through mxnet examples

* change reddit data

* tweak numerical range for unittest

* fix ci

* fix ci

* fix

* add seed to workaround
2019-06-09 00:26:13 -04:00
Lingfan Yu 74e13eea61 [Model] Update GAT model code (#622)
* fix gat code to use latest edge softmax module

* avoid transpose

* update README

* use edge_softmax op

* mxnet edge softmax op

* mxnet gat

* update README

* fix unittest

* fix ci

* fix mxnet nn test; relax criteria for prod reducer
2019-06-08 21:41:38 -04:00
Chao Ma e0ce190dfe [Doc] Update README.MD of demo for distributed sampler (#579)
* Update README.md for the demo of distributed sampler

* Update README.MD of demo for distributed sampler
2019-05-30 01:24:13 -04:00
Chao Ma 08d4900fd1 Update README.md for the demo of distributed sampler (#577) 2019-05-28 17:24:33 +08:00
Chao Ma 9aa5ffcab1 [DEMO] Update demo of distributed sampler (#564)
* update

* update

* update demo
2019-05-26 12:10:53 +08:00
Chao Ma 86d60a1ff6 [DEMO] Add Pytorch demo for distributed sampler (#562)
* update

* update

* update

* add sender

* update

* remove duplicate cpde
2019-05-24 11:53:28 +08:00
Chao Ma 49c4a9e4cc [DEMO] Remove duplicate code for sampling (#557)
* update

* update

* re-use single-machine code

* update

* use relative path

* update

* update

* update

* add __init__.py

* add __init__.py

* import sys, os

* fix typo

* update
2019-05-23 16:57:35 +08:00
Chao Ma f99725adbc all demo use python-3 (#555) 2019-05-23 10:38:05 +08:00
Quan (Andy) Gan d8c69d53e2 Fixing typo in JTNN after interface change (#536) 2019-05-16 09:43:03 +08:00
Ziyue Huang e89519150f disable pytorch reddit (#512) 2019-04-28 11:24:14 +08:00
Ziyue Huang 3b96299a45 sampling (#505) 2019-04-23 12:14:38 +08:00
Zhengwei ad9da36add [Model] Add DGI Model (#501) 2019-04-22 11:37:06 +08:00
Aymen Waheb 3f4645918d [Model] Add edge dropout to APPNP (#493)
* [Model] Add edge dropout to APPNP

[Model] Add edge dropout to APPNP

* [Model] Refactor the sampling examples (#498)

* reorganize sampling code.

* speedup gcn_ns.

* speed up gcn_cv

* fix graphsage_cv.

* undo the modification.

* accel training.

* update readme.

* [Model] Add edge dropout to APPNP

[Model] Add edge dropout to APPNP

update
2019-04-18 20:58:28 +08:00
kitaev-chen a3febc061b [Model] Add GIN Model (#471)
* add gin model

* convert dataset.py to data_ont_the_fly way and put it into dgl.data module

* convert dataset.py to data_ont_the_fly way and put it into dgl.data module
python code checked

* modified document and reference TUDataset; checked python part and bypass cpp part due to error

* change tensor to numpy in dataset and transform in collate@Dataloader

* Change minor format issue

Change minor format issue

* moved logging; adjusted tqdm etc
2019-04-17 14:57:07 +08:00
Quan (Andy) Gan e2e04329a6 [BUG] Update URL for JTNN dataset 2019-04-11 22:23:34 +08:00
Hao Zhang 039a711da1 [Model] fix self-edge bug in GCN and GAT. (#482)
* Update gcn_mp.py

* Update train.py

* Update train.py

* Update train.py

* Update gat_batch.py

* Update gat_batch.py

* Update gcn_mp.py
2019-04-10 09:04:19 -04:00
Aymen Waheb fa887f69f4 [Model] Add APPNP model (#480)
* [Model] Add APPNP model

* update

* Revert "update"

This reverts commit a8e42d19c8b421fb382305a8f04d7426e78ea53c.

* update

* Update appnp.py
2019-04-09 19:54:09 +08:00
Da Zheng 4ea42e3e08 fix gcn. (#469) 2019-04-05 10:56:09 -07:00
Quan (Andy) Gan 6066fee935 [Model][Feature] PinSage & Random Walk with Restart (#453)
* random walk traces generation

* remove outdated comments

* oops put in the wrong place

* explicit inline

* moving rand_r to util

* pinsage-like model on movielens

* the code runs now

* support cuda

* using readonly graph

* moving random walk to public function

* per-thread seed and openmp support

* pinsage-like model on movielens

* the code runs now

* support cuda

* using readonly graph

* using C random walk

* removing profile decorators

* param initialization

* no grad

* leaky relu fixes everything

* train and save

* WIP

* WIP

* WIP

* seems to work

* evaluation output

* swapping order of val/test and train

* debug

* hyperparam tuning

* prior/training dataset split changes

* random walk reorg

* random walk with restart

* signed comparison fix

* migrating random walk to nodeflow

* Revert "migrating random walk to nodeflow"

This reverts commit f2565347cced7c912a58a529b257c033d9f375b7.

* add README and remove dataset

* new endpoint

* lint

* lint x2

* oops forgot test

* including bpr - better for baseline

* addressing fixes

* throwing random walks out from SamplerOp class

* forgot to move RandomWalk; why did this even work?

* removing legacy garbage

* add todo

* address comments

* stupid bug fix

* call ndarrayvector converter to handle traces
2019-03-29 13:01:18 +08:00
Giuseppe Futia 2dff1aba83 [Bugfix] Fix shape of test_relation tensor in RGCN (#464) 2019-03-28 14:34:07 -04:00
Lingfan Yu d3c24cc25b [BugFix] Fix bug in RGCN data processing and use index_select to improve speed (#429)
* use index_select instead of __getitem__

* fix bug in dataset processing

* fix edge_type shape bug

* comments
2019-03-04 10:52:21 -05:00
Minjie Wang 565f0c88fc [WIP] [NN] Refactor NN package (#406)
* refactor graph conv

* docs & tests

* fix lint

* fix lint

* fix lint

* fix lint script

* fix lint

* Update

* Style fix

* Fix style

* Fix style

* Fix gpu case

* Fix for gpu case

* Hotfix edgesoftmax docs

* Handle repeated features

* Add docstring

* Set default arguments

* Remove dropout from nn.conv

* Fix

* add util fn for renaming

* revert gcn_spmv.py

* mx folder

* fix wierd bug

* fix mx

* fix lint
2019-02-25 18:41:21 -05:00
hbsun2113 8c750170e8 [Model][Pytorch] GraphSAGE (#403)
* simple implemention of GraphSAGE

* update the abstract method and `torch.nn` modules are more utilized
2019-02-22 15:48:53 -05:00
Tianyi cdbeb17f2d [Model] Simplifying Graph Convolutional Networks. (#405)
* [Model] Simplifying Graph Convolutional Networks.

* - improve code stype (use nn.Linear)
- use `bias` option
- update hyperparameter and corresponding performance
2019-02-22 15:17:26 +08:00
Hao Zhang 788d8dd4ad [Model]PPI dataloader and inductive learning script. (#395)
* Create ppi.py

* Create train_ppi.py

* Update train_ppi.py

* Update train_ppi.py

* Create gat.py

* Update train.py

* Update train_ppi.py

* Update ppi.py

* Update train_ppi.py

* Update ppi.py

* Update train_ppi.py

* Update train_ppi.py

* Update ppi.py

* Update train_ppi.py

* update docs and readme
2019-02-17 16:41:30 -05:00