86cf154be9
[Misc] Update README(s) ( #962 )
...
* Update
* Update
2019-10-29 15:37:25 +08:00
421b05e7b8
[Model] Clean up for Cluster GCN ( #940 )
...
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Fix
2019-10-26 21:02:47 +08:00
52c7ef49fc
[Model Zoo] AttentiveFP ( #955 )
...
* Update
* Fix style
* Update
* Update
* Fix
* Update
* Update
2019-10-26 01:57:34 +08:00
577cf2e63b
[Model Zoo] Refactor and Add Utils for Chemistry ( #928 )
...
* Refactor
* Add note
* Update
* CI
2019-10-22 00:47:45 +08:00
ff9f67ee0d
Send any shape of tensor rather than matrix ( #942 )
2019-10-21 17:27:03 +08:00
ae3102d3a2
[Dataset] Migration for Chemistry Datasets ( #926 )
...
* Update
* Update
2019-10-21 16:38:28 +08:00
c37076dfe6
[Model] Gated Graph Neural Network for bAbI tasks ( #880 )
...
* rrn model and sudoku
* add README
* refine the code, add doc strings
* add sudoku solver
* add example for sudoku_solver
* ggnn example
* Rewrite README file
* fix typos
2019-10-21 16:07:32 +08:00
9c790b1143
[Dataset] Add CoraFull, Amazon, KarateClub, Coauthor Dataset ( #855 )
...
* convert np.ndarray to backend tensor
* add datasets
* add qm7
* add dataset
* add dataset
* fix
* change ppi
* tu dataset
* add datasets
* fix
* fix
* fix
* fix
* add docstring
* docs
* doc
2019-10-01 01:19:59 +08:00
1c91f460d3
[Hetero][Model] RGCN for heterogeneous input ( #885 )
...
* new hetero RGCN
* bgs running
* fix gpu
* am dataset
* fix bug in label preparation
* Fix AM training; add result
* rm sym link
* new embed layer; mutag
* mutag matched; other fix
* minor fix
* dataset refactor
* new data loading
* rm old files
* refactor
* docstring
* include literal nodes in AIFB dataset
* address comments
* docstring
2019-09-29 00:21:17 -04:00
51a73504fe
[Model] Add Pytorch example for Cluster GCN ( #877 )
...
* initial commit of cluster GCN
* update readme
* fix small bugs running ppi
* nearly sota ppi training script&update readme
* rm unused imports&add shebang line to scripts
* minor comments&readme appended
* add rnd seed control&update readme
2019-09-28 10:10:42 +08:00
c03046a08f
[Model][Hetero] HAN ( #868 )
...
* Add HAN
* Fix
* WIP; load raw ACM dataset
* DGL's own preprocessing with metapath coalescer
* various fixes
* comparison against simple logistic regression
* rename
* fix test
2019-09-27 12:53:16 +08:00
9737b2700f
[Model][Hetero] GCMC using new hetero APIs ( #860 )
...
* init
* rm data
* README
* fix rating values that are not decimal
* rm stale codes
* small fix
* upd
* rewrite decoder
* fix many
* many fix; performance matched
* upd; handle sparse input
* upd
* address comments
* more docstring; download data automatically
* shared param mode
2019-09-26 17:50:38 -04:00
e3921d5dec
[Sampler] Metapath sampler for metapath2vec ( #861 )
...
* metapath sampler
* lint & fixes
* lint x2
* lint x3
* fix windows
* remove max_cycle argument
* add todo note
2019-09-26 16:42:33 -04:00
7782276962
[KVStore] Distributed kvstore ( #851 )
...
* update
* speedup
* add some comments
2019-09-11 14:54:50 +08:00
9df8cd3242
[Model Zoo] Fix JTNN ( #843 )
...
* Update
* Update
* Update
* Update
* Update
2019-09-10 16:14:37 +08:00
6a4b5ae98a
[Feature] Edge softmax on a subset of edges in the graph. ( #842 )
...
* upd
* add test
* fix
* upd
* merge
* hotfix
* upd
* fix
2019-09-09 13:44:56 +08:00
189c2c0907
[Model Zoo] Refactor Model Zoo for Chemistry ( #839 )
...
* Update
* Update
* Update
* Update fix
* Update
* Update
* Refactor
* Update
* Update
* Update
* Update
* Update
* Update
* Fix style
2019-09-07 20:01:09 +08:00
5b417683f6
[docfix] Update the README of metapath2vec ( #832 )
...
* upd
* fig edgebatch edges
* add test
* trigger
* upd
2019-09-05 16:43:12 +08:00
8731050394
[Example] Fix GIN Example ( #826 )
...
* Add serialization
* fix gin
* Add serialization
* fix gin
* fix
2019-09-03 17:55:27 +08:00
ddeb86f91c
[Example] metapath2vec ( #764 )
...
* Prepare for metapath sampler
This file is just for reviewing metapath sampling algorithm (Python version).
* Delete metapath_sampler
* Prepare for metapath sampler
This file is just for reviewing metapath sampling algorithm (Python code).
* Add files via upload
* Create metapath2vec.md
* Add files via upload
* Delete data_handler.py
* Delete word2vec.py
* Delete word_train.py
* Add files via upload
Metapath2vec implementations. Metapath2vec++ needs negative sampler optimization.
* Delete shuffle_training.py
* Delete test.py
* Add files via upload
* Delete sampler.py
* Delete metapath_sampler.md
* Add files via upload
* Update and rename shuffle_training.py to metapath2vec.py
* Update reading_data.py
* Update metapath2vec.md
* Update metapath2vec.md
* Update metapath2vec.md
* Update metapath2vec.md
* Update metapath2vec.md
* Create label 2
* Delete label 2
* Create testing.md
* Add files via upload
* Create sample.md
* Add files via upload
* Delete sampler.py
* Add files via upload
* Delete googlescholar.8area.author.label.txt
* Delete googlescholar.8area.venue.label.txt
* Delete testing.md
* Delete id_author.txt
* Delete id_conf.txt
* Delete paper.txt
* Delete paper_author.txt
* Delete paper_conf.txt
* Delete sample.md
* Delete sampler.py
* Add files via upload
* Add files via upload
* Add files via upload
* Delete reading_data.py
* Add files via upload
* Add files via upload
* Delete metapath2vec.py
* Add files via upload
* Rename shuffle_training.py to metapath2vec.py
* Update metapath2vec.md
* Delete reading_data.py
* add comments and remov e commented codes
2019-09-02 00:03:21 -07:00
a9a0592c3e
Hot fix ( #816 )
2019-09-01 02:11:03 +08:00
1b5820a5d6
Fix ( #806 )
2019-08-29 01:18:04 +08:00
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
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
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
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
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
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
9314aabd1f
[Refactor] Interface of nn modules ( #798 )
...
* refactor
* upd mpnn
2019-08-27 22:29:25 +08:00
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
8079d98617
Misc update ( #796 )
2019-08-27 16:08:36 +08:00
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
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
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
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
0f12763725
[Model] Early stop GAT ( #750 )
...
* Add early stop
* add mxnet version
* Poke ci
2019-08-21 14:58:56 +08:00
77c58289a7
[Bugfix][Model] Fixing RGCN evaluation bug ( #778 )
2019-08-20 15:54:03 -04:00
35bed2a9d0
Rename early stop ( #773 )
2019-08-18 13:46:44 +08:00
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
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
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
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
bf3994eea6
[Model][Hotfix] DiffPool formatting fix ( #696 )
...
* formatting
* formatting
2019-07-02 15:19:57 +08:00
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
714f2e1ced
fix node id dtype ( #674 )
2019-06-20 10:53:26 +08:00
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
f3d3fdf8cd
add reddit example. ( #658 )
2019-06-14 22:53:59 +08:00
94ecb8eb96
[BUGFIX] copy graph index to shared memory. ( #634 )
...
* copy graph index to shared memory.
* fix.
* fix.
* fix.
* use a diff name for in-csr and out-csr.
* fix lint.
* remove print.
* add test.
* add comments.
2019-06-12 01:32:25 -07:00
411bcd7e6c
[BUGFIX] extand DGLGraph graph_data. ( #632 )
...
* enable tutorial test in CI.
* extand DGLGraph graph_data.
* update doc.
* Revert "enable tutorial test in CI."
This reverts commit cd774067180922bb6ae979bde4aecbffc61c8147.
* accept DGLGraph in graph store.
2019-06-09 17:22:04 -07:00
fc7775a20f
Define node/edge Ids in NodeFlow more clearly ( #628 )
...
* add tests.
* distinguish layer-local nid and nodeflow nid.
* use numpy assert_array_equal and assert_allclose
* fix map_from_parent_nid
* fix test
* fix test.
* renmae remap.
* update doc.
* update doc.
* update doc.
* fix test.
* fix test.
2019-06-09 12:10:07 -07:00
Mufei Li