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作者 SHA1 备注 提交日期
Mohammad Amin Khashkhashi Moghaddam 0285021235 Fix bug in GIN Dataset degree OHE logic (#1498) 
In the previous code, the same vector was being assigned to all the nodes in each graph.
`:` was used incorrectly assuming that only one row will be selected for each column but all rows were selected for each column.
 2020-05-09 15:11:41 +08:00
Jinjing Zhou 30b8074af4 [Fix] Fix stream creation and empty dict in tensor serialization (#1489) 
* add functions

* fix litn

* add unit test

* fix

* fix

* fix

* fix

* support empty dict

* simplify logic

* Update tensor_serialize.py
 2020-05-02 14:24:03 +08:00
Mohammad Amin Khashkhashi Moghaddam f1e4f3786d Fix bug in using degree_as_nlabel for GIN dataset (#1451) 
In order to make the `label2idx` dictionary, tensor values should be used and not the tensor itself.

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2020-04-29 17:42:45 +08:00
Jinjing Zhou 1506560e1e [Data] Add utils to save dict of tensors (#1481) 
* add functions

* fix litn

* add unit test

* fix

* fix
 2020-04-27 12:26:41 -07:00
Jinjing Zhou aa17d78af7 Fix (#1478) 2020-04-27 20:02:34 +08:00
Minjie Wang 3efb5d8ecf [NN] Add HeteroGraphConv module for cleaner module definition (#1385) 
* Add HeteroGraphConv

* add custom aggregator; some docstring

* debugging

* rm print

* fix some acc bugs

* fix initialization problem in weight basis

* passed tests

* lint

* fix graphconv flag; add error message

* add mxnet heteroconv

* more fix for mx

* lint

* fix torch cuda test

* fix mx test_nn

* add exhaust test for graphconv

* add tf heteroconv

* fix comment
 2020-03-27 18:47:06 +08:00
Da Zheng a0721405cf [BUGFIX] don’t import dgl in the package. (#1382) 
* fix dgl data.

* remove more.

* fix.

* fix.

Co-authored-by: Ubuntu <ubuntu@ip-172-31-16-150.us-west-2.compute.internal>
 2020-03-22 01:29:16 -07:00
Zihao Ye 09ade2f265 upd (#1321) 2020-03-06 14:17:48 +08:00
Zihao Ye 93ac29ce34 [Refactor] Unify DGLGraph, BatchedDGLGraph and DGLSubGraph (#1216) 
* upd

* upd

* upd

* lint

* fix

* fix test

* fix

* fix

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd tutorial

* upd

* upd

* fix kg

* upd doc organization

* refresh test

* upd

* refactor doc

* fix lint

Co-authored-by: Minjie Wang <minjie.wang@nyu.edu>
 2020-03-05 18:03:57 +08:00
Quan (Andy) Gan 1c4bfb62bb [Performance] Replace np.array with np.asarray (#1301) 
* replace np.array with np.asarray

* fix

Co-authored-by: Minjie Wang <minjie.wang@nyu.edu>
 2020-03-03 20:45:41 +08:00
Minjie Wang 537d37c26c [Misc] add requests as the package dependency (#1268) 2020-02-17 23:45:17 +08:00
xiang song(charlie.song) 77ae4d5321 [Example] Fix Rgcn hetero nonedetermistic in graph and model initialization (#1244) 
* Fix model save and load problem.

Add offline inference example

* Fix test

* Fix randomness problem between test runs

* Make rdf loader deterministic
 2020-02-07 11:07:09 +08:00
Mufei Li 828a5e5bc6 [DGL-LifeSci] Migration and Refactor (#1226) 
* First commit

* Update

* Update splitters

* Update

* Update

* Update

* Update

* Update

* Update

* Migrate ACNN

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Finish classification

* Update

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Update

* Update

* trigger CI

* Fix CI

* Update

* Update

* Update

* Add default values

* Rename

* Update deprecation message
 2020-02-04 01:38:09 +08:00
VoVAllen 319118341d [Dataset] Change download repo link to https://data.dgl.ai (CDN) (#1175) 
* change download link to cdn

* Update env_var.rst
 2020-01-07 17:16:45 +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
VoVAllen a5a052b5bf [Fix] Fix #1078, #1077 and add nightly build to readme 2019-12-09 00:03:35 +08:00
VoVAllen 35653ddd0a [Fix] Fix karate due to networkx version change 2019-12-04 22:02:10 +08:00
Jacob Stevens 45aa158408 Fix example code in saving graphs (#1034) 2019-11-22 13:38:58 +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
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
Mufei Li ae3102d3a2 [Dataset] Migration for Chemistry Datasets (#926) 
* Update

* Update
 2019-10-21 16:38:28 +08:00
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
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
VoVAllen 54e1ef2e06 [Fix] Fix serialize NDArray when shape is 0 (#884) 
* fix

* fix bugs
 2019-09-28 19:21:38 +08:00
VoVAllen 0fb13f7b9d [Feature] Data format (#728) 
* Add serialization

* add serialization

* add serialization

* lalalalalalalala

* lalalalalalalala

* serialize

* serialize

* nnn

* WIP: import tvm runtime node system

* WIP: object system

* containers

* tested basic container composition

* tested custom object

* tmp

* fix setattr bug

* tested object container return

* fix lint

* some comments about get/set state

* fix lint

* fix lint

* update cython

* fix cython

* ffi doc

* fix doc

* 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

* Add serialization

* Add serialization

* fix

* fix typo

* serialize with new ffi

* commit

* commit

* commit

* save

* save

* save

* save

* commit

* clean

* Delete tt2.py

* fix lint

* Add serialization

* fix lint 2

* fix lint

* fix lint

* fix lint

* fix lint

* Fix Lint

* Add serialization

* Change to Macro

* fix

* fix

* fix bugs

* refactor

* refactor

* updating dmlc-core to include force flag

* trying tempfile

* delete leaked pointer

* Fix assert

* fix assert

* add comment and test case

* add graph labels

* add load labels

* lint

* lint

* add graph labels

* lint

*  fix windows

* fix

* update dmlc-core to latest

* fix

* fix camel naming
 2019-09-09 20:57:51 +08:00
Mufei Li 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
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
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
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
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
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
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
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
Mufei Li 306bb3f9ad [Bugfix] Fix minigc (#585) 2019-05-29 21:59:03 -04:00
Da Zheng 8c79885d8b [BUGFIX] fix the error message in the data loader. (#509) 
* fix.

* Change to required=True

* Update description

* Change back
 2019-04-26 09:52:45 +09:00
Zhengwei ad9da36add [Model] Add DGI Model (#501) 2019-04-22 11:37:06 +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
VoVAllen c69dbbb736 [Bug Fix] Fix TUDataset Processing bug (#489) 
* add graph classification dataset

* add node label

* add TUDataset

* Modify to consistent with Qi Huang's implementation

* add docs

* Add docs

* Fix change of environment variable

* Update tu.py

* Update tu.py

* Fix error when add node with np.int64

* Fix processing bug
 2019-04-11 19:30:50 +08:00
VoVAllen 00fc680aae [Dataset] Add TUDataset (#473) 
* add graph classification dataset

* add node label

* add TUDataset

* Modify to consistent with Qi Huang's implementation

* add docs

* Add docs

* Fix change of environment variable

* Update tu.py

* Update tu.py

* Fix error when add node with np.int64
 2019-04-10 09:37:53 -04:00
Quan (Andy) Gan c07ae34a99 [Bugfix] removing non-determinism in data loading (#413) 
[Bugfix] Removing non-determinism in data loading
 2019-02-26 01:24:48 -05:00
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
Ziyue Huang 51293a3273 [Data] reddit data loader (#372) 
* reddit data loader

* upload to S3

* update

* add self loop

* address comments

* fi
 2019-02-08 10:53:39 -08:00
Mufei Li 3cbfc25a32 [Tutorial] Batched Graph Classification (#360) 
* batched_graph_classification

* Fix

* Fix

* update tutorial with new dataset

* Final

* Fix doc for dataset

* small fix
 2019-01-25 15:13:52 -05:00
Minjie Wang abf12fc757 [Data] Synthetic dataset for graph classificaiton (#364) 
* minigc dataset

* more comments

* sphinx
 2019-01-25 10:47:47 -05:00
Gan Quan 37feb479fd [Release] 0.1.2 updates (#276) 
* 0.1.2 release

* oops

* more fixes on windows

* [Bugfix] fix download dir (#275)

* fix download dir

* add doc for the env var
 2018-12-07 01:54:13 -05:00
Da Zheng 1bbc885b40 move batcher to examples. (#269) 
* move pytorch code to examples.

* fix.

* fix tutorial
 2018-12-06 06:45:27 -08:00