提交

605 次代码提交

作者 SHA1 备注 提交日期
Quan Gan d601aaa23d update version 0.3.1 v0.3.1 2019-08-28 05:45:36 +00:00
Quan Gan bac662c392 Merge branch 'master' into 0.3.x 2019-08-28 05:39:07 +00:00
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
Zihao Ye ad15947f0e [bugfix] Fix several issues in test_kernel (#801)
* upd

* stable
2019-08-28 04:24:00 +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
Da Zheng 30c4625171 fix. (#794) 2019-08-27 09:56:38 -07:00
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
Zihao Ye 2c234118c3 [Feature] Add builtin mean reducer (#787)
* upd

* upd

* upd

* upd

* upd

* passed test

* add note

* upd

* trigger

* slight change

* upd

* upd

* trigger

* fix

* simplify

* upd

* upd

* fudge

* upd

* trigger

* test partial

* upd

* trigger
2019-08-25 16:30:51 -04:00
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
Quan (Andy) Gan 52d4535b61 [Hetero][RFC] Heterogeneous graph Python interfaces & Message Passing (#752)
* moving heterograph index to another file

* node view

* python interfaces

* heterograph init

* bug fixes

* docstring for readonly

* more docstring

* unit tests & lint

* oops

* oops x2

* removed node/edge addition

* addressed comments

* lint

* rw on frames with one node/edge type

* homograph with underlying heterograph demo

* view is not necessary

* bugfix

* replace

* scheduler, builtins not working yet

* moving bipartite.h to header

* moving back bipartite to bipartite.h

* oops

* asbits and copyto for bipartite

* tested update_all and send_and_recv

* lightweight node & edge type retrieval

* oops

* sorry

* removing obsolete code

* oops

* lint

* various bug fixes & more tests

* UDF tests

* multiple type number_of_nodes and number_of_edges

* docstring fixes

* more tests

* going for dict in initialization

* lint

* updated api as per discussions

* lint

* bug

* bugfix

* moving back bipartite impl to cc

* note on views

* fix
2019-08-23 15:45:37 -04:00
Da Zheng 66971c1aa4 [Feature] Add edge sampling for link prediction (#780)
* add edge sampler.

* add test and run.

* add negative sampling.

* remap the edge subgraph vid.

* negative graph excludes edges of positive edgs.

* remove print.

* avoid sampling NodeFlow when expand_factor or num_hops is 0.

* fix a bug when excluding nodes in negative graph.

* support multigraph.

* exclude positive edges.

* fix memory leak.

* return subgraph object directly.

* fix many problems.

* add comments.

* address comments
2019-08-21 23:05:24 -07:00
xiang song(charlie.song) 2bff8339dd [Test] Provid a frame agnostic API to test nn modules on both CPU and CUDA side. (#775)
* 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
2019-08-21 16:40:41 +08:00
Da Zheng be936da849 use FFI for subgraph. (#781) 2019-08-21 01:04:11 -07:00
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
Quan (Andy) Gan 788420dff3 [Refactor] Decoupling ImmutableGraph from Kernels (#749)
* csr interface

* csr wrapper for immutable graph

* lint

* silly fix

* docstring
2019-08-18 20:15:56 +08:00
Mufei Li 35bed2a9d0 Rename early stop (#773) 2019-08-18 13:46:44 +08:00
Mufei Li 02029dce9b Sync initializers (#772) 2019-08-17 20:25:54 +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
Quan (Andy) Gan fd3d54ba98 bump up version for prerelease (#768) 2019-08-16 10:32:54 +08:00
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
Quan (Andy) Gan bdcba9c85c setup for prerelease builds (#763) 2019-08-14 23:13:37 +08:00
VoVAllen 2ee3c78c7c [Dataset] Tox21 (#760)
* tox21

* fix ci

* fix ci

* fix urls to url

* add doc

* remove binary
2019-08-14 16:55:01 +08:00
Zihao Ye 17b60e1af0 [Bugfix] EdgeBatch.edges call attempts tuple item assignment (#747)
* upd

* fig edgebatch edges

* add test

* trigger
2019-08-11 04:07:41 +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
Chao Ma 747a8beea5 [Fix] Hold NDArray reference during send() (#740)
* fix NDArray reference

* fix lint

* capture NDArray in the closure
2019-08-07 13:28:41 +08:00
Quan (Andy) Gan 16061925d5 [NodeFlow] Non-uniform neighbor sampling (#711)
* nonuniform sampler

* unit test

* test on out neighbors

* error checks

* lint

* fix

* clarification

* use macro switcher

* use empty array for uniform sampling

* oops

* Revert "oops"

This reverts commit a11f9ae707aaeb67fb5921c887a17d3711d5b04a.

* Revert "use empty array for uniform sampling"

This reverts commit 8526ce4cade89f2c1b09a08aca8830375ebafb31.

* re-reverting

* use a method
2019-08-07 09:42:08 +08:00
Zihao Ye 742d79a792 upd (#741) 2019-08-06 18:39:05 +08:00
Zihao Ye 5d3f470b72 [Feature] DGL Pooling modules (#669)
* removal doc

* glob

* upd

* rm knn

* add softmax

* upd

* upd

* add broadcast and s2s

* optimize max_on

* forsaken changes to heterograph

* upd

* upd

* upd

* upd

* upd

* bugfix

* upd

* upd

* upd

* upd

* format upd

* upd format

* upd doc

* upd

* import order

* upd

* rm warnings

* fix

* upd test

* upd

* upd

* fix device

* upd

* upd

* upd

* upd

* remove 1.1

* upd

* trigger

* trigger

* add more tests

* fix device

* upd

* upd

* refactor

* fix?

* fix

* upd docstring

* refactor

* upd

* fix

* upd

* upd

* upd

* fix

* upd docs

* add shape

* refactor & upd doc

* upd doc

* upd
2019-08-06 01:43:25 +08:00
Chao Ma c3516f1a8e [Network] Refactoring Communicator (#679)
* Refactoring Communicator

* fix lint

* change non-const reference

* add header file

* use MemoryBuffer

* update PR

* fix bug on csr shape

* zero-copy msg_queue

* fix lint

* fix lint

* fix lint

* add header file

* fix windows build error

* fix windows build error

* update

* fix lint

* update

* fix lint

* fix lint

* add more test

* fix windows test

* update windows test

* update windows test

* update windows test

* update

* fix lint

* fix lint

* update

* update

* update

* update

* use STATUS code

* update test

* remove mem_cpy

* fix lint

* update

* finish

* ConstructNFTensor

* add test for deallocator

* update

* fix lint
2019-08-05 10:49:25 +08:00
Minjie Wang fc9d30fae4 [Graph] add local scope function (#735)
* add local scope function

* fix lint

* fix docstring

* change local_scope to local_var; add context manager

* address comments
2019-08-02 00:11:48 -04:00
Quan (Andy) Gan e9e587b6cb [Refactor] C random number generator (#729)
* rng refactor

* fix bugs

* unit test

* remove setsize

* lint

* fix test

* use explicit instantiation instead of inlining

* stricter test

* use tvm solution

* moved python interface to dgl.random

* lint

* address comments

* make getthreadid an inline function
2019-07-31 17:54:30 +08:00
Da Zheng 34ac2ab47b [Fix] Fix MXNet install doc (#732) 2019-07-30 09:25:41 +08:00
Quan (Andy) Gan 86f28d6553 [Misc] Provide a "return 1s instead of edge IDs" option in scipy adjacency matrix (#730)
* return 1 option in scipy adjacency matrix

* lint

* use dgl warning

* i'm an idiot

* lint x2

* rename
2019-07-29 21:40:09 +08:00
Minjie Wang 7ad663c3a9 [Hetero] Heterograph C++ implementation; Bipartite and Python wrapper (#725)
* finish bipartite graph implementation; compiled

* finished heterograph implementation; compiled

* WIP: apis

* C API codes

* compiled

* WIP: python

* HeteroGraphIndex

* WIP: test

* add DGLContext support in ffi

* fix bug in has edge

* unittests except edge subgraph

* edge subgraph

* fix lint

* address comments

* poke ci

* try fix

* fix msvc
2019-07-27 15:22:56 -04:00
Minjie Wang 6c77f26438 [Doc] Update README.md (#724) 2019-07-23 15:59:03 -04:00
Minjie Wang 67dc11971f [Refactor] Use object system for all CAPIs (#716)
* WIP: using object system for graph

* c++ side refactoring done; compiled

* remove stale apis

* fix bug in DGLGraphCreate; passed test_graph.py

* fix bug in python modify; passed utest for pytorch/cpu

* fix lint

* address comments
2019-07-23 12:47:05 -04:00
Minjie Wang b0d9e7aa43 [Refactor] Separating graph and sparse matrix operations (#699)
* WIP: array refactoring

* WIP: implementation

* wip

* most csr part

* WIP: on coo

* WIP: coo

* finish refactoring immutable graph

* compiled

* fix undefined ndarray copy bug; add COOToCSR when coo has no data array

* fix bug in COOToCSR

* fix bug in CSR constructor

* fix bug in in_edges(vid)

* fix OutEdges bug

* pass test_graph

* pass test_graph

* fix bug in CSR constructor

* fix bug in CSR constructor

* fix bug in CSR constructor

* fix stupid bug

* pass gpu test

* remove debug printout

* fix lint

* rm biparate grpah

* fix lint

* address comments

* fix bug in Clone

* cpp utests
2019-07-17 17:49:38 -04:00
Da Zheng f79188da4c fix. (#712) 2019-07-15 16:25:29 -07:00
Quan (Andy) Gan 6d42005052 [WIP][CI] Build Windows packages within virtualenv (#709)
* try venv for win64

* update

* update

* trying another

* update

* update

* update

* trigger ci

* update

* update
2019-07-12 16:50:54 -07:00