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Xiangkun Hu 73b9c6f18c [Dataset] GDELTDataset (#1911) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.

* gdelt dataset

* Update gdelt.py

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-03 17:43:50 +08:00
Xiangkun Hu 06ea03d0f8 [Dataset] ICEWS18Dataset (#1913) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.

* ICEWS18Dataset

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-03 17:07:02 +08:00
Tong He b5be4f4bbf [Dataset] Update dataset hash with deterministic function (#1919) 
* update hash with deterministic function

* update docstring

* add test on determination
 2020-08-03 16:17:00 +08:00
Tong He 39ed096630 [Dataset] Builtin LegacyTUDataset and TUDataset (#1891) 
* add LegacyTUDataset and TUDataset

* update docstrings and url

* update docstrings

* add hash to fix save/load

* update docstring and use hash

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-03 14:40:36 +08:00
Xiangkun Hu 22485e58d3 [Dataset] BitcoinOTCDataset (#1910) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.

* bitcoinotc dataset

* Update bitcoinotc.py
 2020-08-03 12:15:04 +08:00
Xiangkun Hu d22f96feb4 [Dataset] QM7bDataset (#1915) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.

* QM7bDataset

* Update qm7b.py

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-03 11:58:31 +08:00
Xiangkun Hu 9bcce7bead [Dataset] PPIDataset (#1906) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.

* Revert "Revert "PPIDataset""

This reverts commit 6938a4cbe3ac6e38d3e0188b5699e5c952a6102e.

* update doc string

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-03 00:30:01 +08:00
Xiangkun Hu 743c38401c [Dataset] KarateClubDataset (#1897) 
* karateclub dataset

* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.

* Update karate.py

* doc string

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-08-02 22:39:11 +08:00
xiang song(charlie.song) cb2c4ec17b Fix (#1909) 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
 2020-08-02 14:53:21 +08:00
xiang song(charlie.song) 303e42367d Hot Fix docstring (#1907) 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
 2020-08-01 23:24:24 +08:00
xiang song(charlie.song) b347590a37 [Dataset] Citation graph (#1902) 
* citation graph

* GCN example use new citatoin dataset

* mxnet gat

* triger

* Fix

* Fix gat

* fix

* Fix tensorflow dgi

* Fix appnp, graphsage for mxnet

* fix monet and sgc for mxnet

* Fix tagcn

* update sgc, appnp

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
 2020-08-01 19:25:50 +08:00
Tong He 18c960a1b5 [Dataset] Builtin MiniGCDataset (#1890) 
* add minigc

* fix

* update docstrings

* update docstring

* add hash to fix save/load

* update hash
 2020-07-31 17:40:02 +08:00
Tong He f05bd4971c [Dataset] Builtin GINDataset (#1889) 
* update GINDataset

* update

* update docstring

* update

* update docstrings

* add hash to fix save/load

* fix some stupid bugs

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-07-31 17:12:14 +08:00
Tong He fb02aa2d85 [Dataset] Add hash function to distinguish instances from the same dataset class (#1894) 
* add hash function in base data classes

* update doc
 2020-07-31 15:53:32 +08:00
xiang song(charlie.song) dbb028acc8 [Dataset] Builtin knowledge graph dataset (#1881) 
* buildin knowledge graph dataset

* upd

* docstring

* Fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Tong He <hetong007@gmail.com>
 2020-07-30 23:37:33 +08:00
Minjie Wang 444becf00a [Misc] Move many deprecated codes to the deprecate folder (#1893) 
* some file movements

* move some codes to deprecated

* more deprecation

* lint

* remove useless test
 2020-07-30 18:17:33 +08:00
xiang song(charlie.song) faa1dc56fc hot fix (#1888) 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
 2020-07-30 12:02:49 +08:00
xiang song(charlie.song) aee1067941 [Dataset] RDF dataset with DGL-Dataset template (#1869) 
* update rdf builtin dataset

* Fix

* use new dataset

* fix

* rdf dataset using new framework

* tf work

* Fix mxnet

* Fix tensorflow

* Fix mxnet

* Update

* upd

* update some docstring

* clean some dead code

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
 2020-07-30 09:12:00 +08:00
Minjie Wang 44089c8b4d [Refactor][Graph] Merge DGLGraph and DGLHeteroGraph (#1862) 
* Merge

* [Graph][CUDA] Graph on GPU and many refactoring (#1791)

* change edge_ids behavior and C++ impl

* fix unittests; remove utils.Index in edge_id

* pass mx and th tests

* pass tf test

* add aten::Scatter_

* Add nonzero; impl CSRGetDataAndIndices/CSRSliceMatrix

* CSRGetData and CSRGetDataAndIndices passed tests

* CSRSliceMatrix basic tests

* fix bug in empty slice

* CUDA CSRHasDuplicate

* has_node; has_edge_between

* predecessors, successors

* deprecate send/recv; fix send_and_recv

* deprecate send/recv; fix send_and_recv

* in_edges; out_edges; all_edges; apply_edges

* in deg/out deg

* subgraph/edge_subgraph

* adj

* in_subgraph/out_subgraph

* sample neighbors

* set/get_n/e_repr

* wip: working on refactoring all idtypes

* pass ndata/edata tests on gpu

* fix

* stash

* workaround nonzero issue

* stash

* nx conversion

* test_hetero_basics except update routines

* test_update_routines

* test_hetero_basics for pytorch

* more fixes

* WIP: flatten graph

* wip: flatten

* test_flatten

* test_to_device

* fix bug in to_homo

* fix bug in CSRSliceMatrix

* pass subgraph test

* fix send_and_recv

* fix filter

* test_heterograph

* passed all pytorch tests

* fix mx unittest

* fix pytorch test_nn

* fix all unittests for PyTorch

* passed all mxnet tests

* lint

* fix tf nn test

* pass all tf tests

* lint

* lint

* change deprecation

* try fix compile

* lint

* update METIDS

* fix utest

* fix

* fix utests

* try debug

* revert

* small fix

* fix utests

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* upd

* trigger

* +1s

* [kernel] Use heterograph index instead of unitgraph index (#1813)

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* upd

* trigger

* +1s

* [Graph] Mutation for Heterograph (#1818)

* mutation add_nodes and add_edges

* Add support for remove_edges, remove_nodes, add_selfloop, remove_selfloop

* Fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* upd

* upd

* upd

* fix

* [Transfom] Mutable transform (#1833)

* add nodesy

* All three

* Fix

* lint

* Add some test case

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* fix

* triger

* Fix

* fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* [Graph] Migrate Batch & Readout module to heterograph (#1836)

* dgl.batch

* unbatch

* fix to device

* reduce readout; segment reduce

* change batch_num_nodes|edges to function

* reduce readout/ softmax

* broadcast

* topk

* fix

* fix tf and mx

* fix some ci

* fix batch but unbatch differently

* new checkk

* upd

* upd

* upd

* idtype behavior; code reorg

* idtype behavior; code reorg

* wip: test_basics

* pass test_basics

* WIP: from nx/ to nx

* missing files

* upd

* pass test_basics:test_nx_conversion

* Fix test

* Fix inplace update

* WIP: fixing tests

* upd

* pass test_transform cpu

* pass gpu test_transform

* pass test_batched_graph

* GPU graph auto cast to int32

* missing file

* stash

* WIP: rgcn-hetero

* Fix two datasety

* upd

* weird

* Fix capsuley

* fuck you

* fuck matthias

* Fix dgmg

* fix bug in block degrees; pass rgcn-hetero

* rgcn

* gat and diffpool fix
also fix ppi and tu dataset

* Tree LSTM

* pointcloud

* rrn; wip: sgc

* resolve conflicts

* upd

* sgc and reddit dataset

* upd

* Fix deepwalk, gindt and gcn

* fix datasets and sign

* optimization

* optimization

* upd

* upd

* Fix GIN

* fix bug in add_nodes add_edges; tagcn

* adaptive sampling and gcmc

* upd

* upd

* fix geometric

* fix

* metapath2vec

* fix agnn

* fix pickling problem of block

* fix utests

* miss file

* linegraph

* upd

* upd

* upd

* graphsage

* stgcn_wave

* fix hgt

* on unittests

* Fix transformer

* Fix HAN

* passed pytorch unittests

* lint

* fix

* Fix cluster gcn

* cluster-gcn is ready

* on fixing block related codes

* 2nd order derivative

* Revert "2nd order derivative"

This reverts commit 523bf6c249bee61b51b1ad1babf42aad4167f206.

* passed torch utests again

* fix all mxnet unittests

* delete some useless tests

* pass all tf cpu tests

* disable

* disable distributed unittest

* fix

* fix

* lint

* fix

* fix

* fix script

* fix tutorial

* fix apply edges bug

* fix 2 basics

* fix tutorial

Co-authored-by: yzh119 <expye@outlook.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-7-42.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-1-5.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal>
 2020-07-28 14:30:41 +08:00
xiang song(charlie.song) 41b905da71 Fix #1826 (#1835) 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
 2020-07-21 16:32:54 +08:00
xiang song(charlie.song) 64557819d9 Basic class for dgl datasetyy (#1809) 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
 2020-07-20 13:12:36 +08:00
xiang song(charlie.song) 8a183e3fcb [BugFix] Fix #1779 (#1781) 
* Fix bug #1779

* Fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
 2020-07-10 17:35:23 +08:00
xiang song(charlie.song) cc73c60cbc [Bug Fix] Fix Heterogenous graph save crash when some edge type names are identical. (#1751) 
* Fix hetero serialize

* Add test case
y

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2020-07-04 21:44:53 +08:00
Jinjing Zhou 18a26fcfb1 [Data] Support HeteroGraph save/load (#1526) 
* 111

* add history version test

* fix

* 111

* save

* ``

* fix1

* 111

* add save heterograph

* lint

* lint

* add tests

* minor fix

* fix

* docs

* add format tets

* use unique_ptr

* fix

* fix interface

* 111

* 111

* fix

* lint

* fix

* add support to s3

* fix

* fix

* fix leak

* fix

* fix docs

* fix

* linlt

* fix

* fix

* fix

* address comment

* address comment

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2020-06-30 13:34:50 +08:00
Quan (Andy) Gan 57d111f9e5 [Bug] Fix broken initialization in Reddit (#1634) 2020-06-14 03:08:40 +08:00
Mufei Li 36c7b77167 [LifeSci] Move to Independent Repo (#1592) 
* Move LifeSci

* Remove doc
 2020-06-05 21:28:24 +08:00
Quan (Andy) Gan 2b9d06b6e2 [Data] Retry downloading once if dataset initialization fails (#1520) 
* dataloader guard

* more fixes

* sets overwrite to true by default

* Update utils.py

* fix

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
 2020-06-03 17:21:05 +08:00
Mufei Li 90d2118da5 [Dataset] Change Cora Split (#1583) 
* Use new version of Cora

* Fix import
 2020-06-03 15:45:38 +08:00
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