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1382 次代码提交

作者 SHA1 备注 提交日期
xiang song(charlie.song) 41f8a162f4 [Feature Improvement]Edge Sampler w and w/o replacement (#1116)
* Add weight based edge sampler

* Can run, edge weight work.
TODO: test node weight

* Fix node weight sample

* Fix y

* Update doc

* Fix syntex

* Fix

* Fix GPU test for sampler

* Fix test

* Fix

* Refactor EdgeSampler to act as class object not function that it
can record its own private states.

* clean

* Fix

* Fix

* Fix run bug on kg app

* update

* update test

* test

* Simply python API and fix some C code

* Fix

* Fix

* Fix syntex

* Fix

* Update API description

* add replacement for edge sampler

* Now edge sampler support replacement and no-replacement

* Fix

* Fix

* change kg/app to use edge sampler with replacement config

* Update replacement algo

* Fix syntax

* Update

* Update

Co-authored-by: Da Zheng <zhengda1936@gmail.com>
2019-12-24 16:25:40 +08:00
Da Zheng e890a899fc Partition a graph with HALO nodes (#1076)
* get subgraph with halo.

* add partition function.

* add comment.

* parallel partition.

* fix a compilation error.

* fix lint error.

* address comments.

* add comments.

* fix for TF.
2019-12-23 08:46:53 -08:00
VoVAllen d30a69bf27 [Backend] TF backend (#978)
* tf

* add builtin support

* fiix

* pytest

* fix

* fix

* fix some bugs

* fix selecting

* fix todo

* fix test

* fix test fail in tf

* fix

* fix

* fix gather row

* fix gather row

* log backend

* fix gather row

* fix gather row

* fix for pytorch

* fix

* fix

* fix

* fix

* fix

* fix tests

* fix

* fix

* fix

* fix

* fix

* fix

* fix convert

* fix

* fix

* fix

* fix inplace

* add alignment setting

* add debug option

* Revert "add alignment setting"

This reverts commit ec63fb3506ea84fff7d447a1fbdfd1d5d1fb6110.

* tf ci

* fix lint

* fix lint

* add tfdlpack

* fix type

* add env

* fix backend

* fix

* fix tests

* remove one_hot

* remove comment

* remove comment

* fix

* use pip to install all

* fix test

* fix base

* fix

* fix

* add skip

* upgrade cmake

* change version

* change ci

* fix

* fix

* fix

* fix

* fix seg fault

* fix

* fix python version

* fix

* try fix

* fix

* fix

* tf takes longer time in ci

* change py version

* fix

* fix

* fix oom

* change kg env

* change kg env

* 啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊

* 我再也不搞各种乱七八糟环境了……

* use pytest

* Chang image
2019-12-20 15:56:51 +08:00
Mufei Li cf9ba90fd4 [Chem] ACNN and various utilities (#1117)
* Add several splitting methods

* Update

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Finally

* CI
2019-12-19 11:54:40 +08:00
Zihao Ye 6beef85b07 upd (#1113) 2019-12-17 15:24:04 +08:00
xiang song(charlie.song) 632a9af8f9 [Feature] No-Uniform Edge Sampler (#1087)
* Add weight based edge sampler

* Can run, edge weight work.
TODO: test node weight

* Fix node weight sample

* Fix y

* Update doc

* Fix syntex

* Fix

* Fix GPU test for sampler

* Fix test

* Fix

* Refactor EdgeSampler to act as class object not function that it
can record its own private states.

* clean

* Fix

* Fix

* Fix run bug on kg app

* update

* update test

* test

* Simply python API and fix some C code

* Fix

* Fix

* Fix syntex

* Fix

* Update API description
2019-12-16 11:26:34 -08:00
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