文件历史

2070 次代码提交

作者 SHA1 备注 提交日期
VoVAllen dd65ee211e [CI] Change tests for flexibility
* change ci image

* fix

* force bash

* fix

* fix python version

* fix

* fix

* fix

* update gpu

* cuda

* jenkins

* fix build sh

* fix

* Revert "fix"

This reverts commit 6b091914b3ef6b4300fa662ee375aa4b27944f5c.

* try fix

* fix

* Revert "fix"

This reverts commit e42c3035fa4974c6b197aaba0748f7b45113ddaa.

* try fix

* fix

* fix

* fix

* fix

* fix

* fix

* fix tests

* try fix

* fix

* fix

* fix

* fix

* fix

* fix

* fix ctx problem

* fix many tests

* fix typo

* add backend

* move to pytorch folder

* fix?

* fix ci

* try skip

* try false

* try?

* try?

* Revert to 7d9a52f

* fix various

* fix lint

* Revert Jenkinsfile

* revert env

* revert env

* address comment

* remove file
2019-12-16 14:54:37 +08:00
Da Zheng adea4ba1d0 fix doc. (#1100) 2019-12-13 05:24:37 -08:00
Mufei Li b599f6ed96 Update (#1090) 2019-12-11 13:39:18 +08:00
Zihao Ye 870857cfba udp (#1083) 2019-12-09 14:52:20 +08:00
VoVAllen a5a052b5bf [Fix] Fix #1078, #1077 and add nightly build to readme 2019-12-09 00:03:35 +08:00
Zihao Ye fa0ee46a01 [hotfix] node id validity check (#1073)
* fix

* improve

* fix lint

* upd

* fix

* upd
2019-12-06 01:36:41 +08:00
VoVAllen 35653ddd0a [Fix] Fix karate due to networkx version change 2019-12-04 22:02:10 +08:00
Quan (Andy) Gan 49b406c981 memory leak fix in PyTorch (#1060) 2019-11-29 14:37:33 +08:00
Quan (Andy) Gan 365d361725 [Bug] Fix #1036 (#1037)
* fix

* unit test
2019-11-29 11:53:29 +08:00
Zhang Zhi 4f6063124b [Graph]To(device) should return updated object (#1057)
* To(device) should return updated object

* Add test case and doc

* Add another doc

* Add descriptions  and a test

* Pass test
2019-11-29 00:15:22 +08:00
Mufei Li ead64de98e [Hetero] Batching/Unbatching DGLHeteroGraph (#1017)
* Update

* Update

* Update

* Fix

* CI style fix

* CI fix style

* Fix

* Try CI

* Fix test

* Update

* Update

* Update

* Update
2019-11-26 14:40:50 +08:00
Mufei Li 6694f7b945 [Bug] Fix DGLHeteroGraph.edge_type_subgraph (#1040)
* Update

* Try CI
2019-11-25 03:35:25 +08:00
Jacob Stevens 45aa158408 Fix example code in saving graphs (#1034) 2019-11-22 13:38:58 +08:00
Mufei Li f1542b9dfa Fix (#1019) 2019-11-20 15:14:40 +08:00
Chao Ma a0193fd539 Small change for kvstore api (#981)
* Small change for kvstore api

* fix ci

* fix ci
2019-11-08 16:25:12 +08:00
Chao Ma 7897fa3b9c add init api on kvserver (#975) 2019-11-05 16:21:35 +08:00
Chao Ma cccde032f4 [kvstore] Performance improvement for distributed kvstore (#972)
* Performance improvment for distributed kvstore

* update

* update
2019-11-04 18:27:00 +08:00
Zihao Ye fdd0fe651d hotfix (#971) 2019-11-04 12:11:53 +08:00
Zihao Ye 9a0511c8e9 [NN] nn modules & examples update (#890)
* upd

* damn it

* fuck

* fuck pylint

* fudge

* remove some comments about MXNet

* upd

* upd

* damn it

* damn it

* fuck

* fuck

* upd

* upd

* pylint bastard

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd
2019-11-03 17:29:42 -05:00
Quan (Andy) Gan a6d5a0cbdd [BUG] Fix #717 (#946)
* [BUG] Fix #717

* fix mxnet test
2019-10-28 09:29:07 +08:00
Mufei Li 52c7ef49fc [Model Zoo] AttentiveFP (#955)
* Update

* Fix style

* Update

* Update

* Fix

* Update

* Update
2019-10-26 01:57:34 +08:00
Mufei Li 4eba1ce2a4 [Chemistry] Hot fix (#953)
* Hot fix

* CI
2019-10-25 15:05:21 +08:00
Mufei Li 577cf2e63b [Model Zoo] Refactor and Add Utils for Chemistry (#928)
* Refactor

* Add note

* Update

* CI
2019-10-22 00:47:45 +08:00
Chao Ma ff9f67ee0d Send any shape of tensor rather than matrix (#942) 2019-10-21 17:27:03 +08:00
Mufei Li ae3102d3a2 [Dataset] Migration for Chemistry Datasets (#926)
* Update

* Update
2019-10-21 16:38:28 +08:00
Quan (Andy) Gan a1cdc7a536 minor docstring fix (#910) 2019-10-08 16:49:01 +08:00
Mufei Li e2b7f745ca [Hetero] Doc (#892)
* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* style fixes & undefined name fix

* transpose=False in test
2019-10-06 20:17:40 +08:00
Quan (Andy) Gan b3d596b5bd extend warning to other adjacency_matrix() calls (#904) 2019-10-06 15:44:03 +08:00
Da Zheng bce51cbd65 [BUGFIX] check the number of columns in subgraph.copy_from_parent (#903)
* check the number of columns.

* add test.
2019-10-05 18:35:56 -07:00
Da Zheng 15b951d4c4 [KG][Model] Knowledge graph embeddings (#888)
* 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 for mxnet TAGCov

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix

* init version.

* change default value of regularization.

* avoid specifying adversarial_temperature

* use default eval_interval.

* remove original model.

* remove optimizer.

* set default value of num_proc

* set default value of log_interval.

* don't need to set neg_sample_size_valid.

* remove unused code.

* use uni_weight by default.

* unify model.

* rename model.

* remove unnecessary data sampler.

* remove the code for checkpoint.

* fix eval.

* raise exception in invalid arguments.

* remove RowAdagrad.

* remove unsupported score function for now.

* Fix bugs of kg
Update README

* Update Readme for mxnet distmult

* Update README.md

* Update README.md

* revert changes on dmlc

* add tests.

* update CI.

* add tests script.

* reorder tests in CI.

* measure performance.

* add results on wn18

* remove some code.

* rename the training script.

* new results on TransE.

* remove --train.

* add format.

* fix.

* use EdgeSubgraph.

* create PBGNegEdgeSubgraph to simplify the code.

* fix test

* fix CI.

* run nose for unit tests.

* remove unused code in dataset.

* change argument to save embeddings.

* test training and eval scripts in CI.

* check Pytorch version.

* fix a minor problem in config.

* fix a minor bug.

* fix readme.

* Update README.md

* Update README.md

* Update README.md
2019-10-02 12:57:29 -07:00
Da Zheng 3e454476b6 edge sampler return head nodes and tail nodes. (#889)
* edge sampler return head nodes and tail nodes.

* edge subgraph.

* use VecToIdArray

* example.

* fix compile error.
2019-09-30 21:25:16 -07:00
VoVAllen 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
Quan (Andy) Gan 33b8700b7d [Bugfix][Hetero] Fix typo (#891)
Don't know why it passed the merging test...
2019-09-30 17:05:58 +08:00
Quan (Andy) Gan 0ca52bfc88 [Hetero] Create heterograph from dictionary of edge lists (#882)
* [Hetero] Create heterograph from dictionary of edge lists

* rename

* address comments
2019-09-30 15:41:41 +08:00
Minjie Wang 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
Da Zheng 65e1ba4f60 Sort csr (#886)
* sort

* sort in parallel.

* fix a bug in sorting adj

* rename.

* add more comments.

* accelerate GetData

* fix tests.

* avoid sorting multiple times.

* add test.

* change back.

* sort.

* add sort_csr.

* Fix a bug.

* fix.

* revert modifcation.

* rename

* speed up EdgeIds.
2019-09-28 10:52:12 -07:00
VoVAllen 54e1ef2e06 [Fix] Fix serialize NDArray when shape is 0 (#884)
* fix

* fix bugs
2019-09-28 19:21:38 +08:00
Mufei Li 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
VoVAllen e16667bfb9 [Fix] Fix Transform (#876)
* add transform

* lint

* lint

* fix

* fixmx

* fix

* add test

* fix typo

* fix default num_classes

* change to non-inplace operation

* fix lint

* fix

* fix

* fix lint

* fixlint
2019-09-26 21:21:53 -04:00
Quan (Andy) Gan 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
Da Zheng 1db697ec65 Improve edge sampler (#881)
* optimizer for sampling all negative edges.

* allow to disable checking false negative.

* fix lint.

* fix docstring.

* fix for comment.

* add comments.
2019-09-25 22:56:37 -07:00
Da Zheng 2d489617dd [Feature] find the existence of negative edges. (#875)
* find the existence of negative edges.

* add comment.

* fix test.
2019-09-23 01:59:02 -07:00
Minjie Wang 02fe316d7c [Bugfix][Hetero] fix to_hetero when metagraph is given (#873)
* fix to_hetero when metagraph is given

* minor fix

* add more check
2019-09-22 11:41:49 -04:00
Quan (Andy) Gan f9c0217d27 [Bugfix] Fix number of nodes mismatch in to_homo() conversion (#874) 2019-09-22 19:30:24 +08:00
VoVAllen bf8bb58f60 [Transform] Add to_self_loop, remove_self_loop, onehot_degree transform (#862)
* add transform

* lint

* lint

* fix

* fixmx

* fix

* add test

* fix typo

* fix default num_classes

* change to non-inplace operation

* fix lint

* fix
2019-09-21 00:05:38 +08:00
Minjie Wang 9b4d60799a [Hetero] New syntax (#824)
* WIP. remove graph arg in NodeBatch and EdgeBatch

* refactor: use graph adapter for scheduler

* WIP: recv

* draft impl

* stuck at bipartite

* bipartite->unitgraph; support dsttype == srctype

* pass test_query

* pass test_query

* pass test_view

* test apply

* pass udf message passing tests

* pass quan's test using builtins

* WIP: wildcard slicing

* new construct methods

* broken

* good

* add stack cross reducer

* fix bug; fix mx

* fix bug in csrmm2 when the CSR is not square

* lint

* removed FlattenedHeteroGraph class

* WIP

* prop nodes, prop edges, filter nodes/edges

* add DGLGraph tests to heterograph. Fix several bugs

* finish nx<->hetero graph conversion

* create bipartite from nx

* more spec on hetero/homo conversion

* silly fixes

* check node and edge types

* repr

* to api

* adj APIs

* inc

* fix some lints and bugs

* fix some lints

* hetero/homo conversion

* fix flatten test

* more spec in hetero_from_homo and test

* flatten using concat names

* WIP: creators

* rewrite hetero_from_homo in a more efficient way

* remove useless variables

* fix lint

* subgraphs and typed subgraphs

* lint & removed heterosubgraph class

* lint x2

* disable heterograph mutation test

* docstring update

* add edge id for nx graph test

* fix mx unittests

* fix bug

* try fix

* fix unittest when cross_reducer is stack

* fix ci

* fix nx bipartite bug; docstring

* fix scipy creation bug

* lint

* fix bug when converting heterograph from homograph

* fix bug in hetero_from_homo about ntype order

* trailing white

* docstring fixes for add_foo and data views

* docstring for relation slice

* to_hetero and to_homo with feature support

* lint

* lint

* DGLGraph compatibility

* incidence matrix & docstring fixes

* example string fixes

* feature in hetero_from_relations

* deduplication of edge types in to_hetero

* fix lint

* fix
2019-09-17 15:41:57 -04:00
VoVAllen ddb5d804f9 [Refactor] Break NN modules into files (#859)
* break nn modules into files

* break mxnet nn modules

* fix lint

* fix lint
2019-09-16 14:44:15 +08:00
Chao Ma 4cd5c19e51 use np.unique instead of loop (#858) 2019-09-16 12:01:46 +08:00
xiang song(charlie.song) 0a56d65223 [Feature] x_dot_x builtin kernel support (#831)
* 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

* Start implementing masked-mm kernel.

Add base control flow code.

* Add masked dot declare

* Update func/variable name

* Skeleton compile OK

* Update Implement. Unify BinaryDot with BinaryReduce

* New Impl of x_dot_x, reuse binary reduce template

* Compile OK.

TODO:
1. make sure x_add_x, x_sub_x, x_mul_x, x_div_x work
2. let x_dot_x work
3. make sure backward of x_add_x, x_sub_x, x_mul_x, x_div_x work
4. let x_dot_x backward work

* Fix code style

* Now we can pass the tests/compute/test_kernel.py for add/sub/mul/div forward and backward

* Fix mxnet test code

* Add u_dot_v, u_dot_e, v_dot_e unitest.

* Update doc

* Now also support v_dot_u, e_dot_u, e_dot_v

* Add unroll for some loop

* Add some Opt for cuda backward of dot builtin.

Backward is still slow for dot

* Apply UnravelRavel opt for broadcast backward

* update docstring
2019-09-14 19:27:31 +08:00
Chao Ma 7782276962 [KVStore] Distributed kvstore (#851)
* update

* speedup

* add some comments
2019-09-11 14:54:50 +08:00