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
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
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
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
faa1dc56fc
hot fix ( #1888 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-07-30 12:02:49 +08:00
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
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
41b905da71
Fix #1826 ( #1835 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-07-21 16:32:54 +08:00
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
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
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
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
57d111f9e5
[Bug] Fix broken initialization in Reddit ( #1634 )
2020-06-14 03:08:40 +08:00
36c7b77167
[LifeSci] Move to Independent Repo ( #1592 )
...
* Move LifeSci
* Remove doc
2020-06-05 21:28:24 +08:00
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
90d2118da5
[Dataset] Change Cora Split ( #1583 )
...
* Use new version of Cora
* Fix import
2020-06-03 15:45:38 +08:00
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
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
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
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
aa17d78af7
Fix ( #1478 )
2020-04-27 20:02:34 +08:00
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
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
09ade2f265
upd ( #1321 )
2020-03-06 14:17:48 +08:00
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
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
537d37c26c
[Misc] add requests as the package dependency ( #1268 )
2020-02-17 23:45:17 +08:00
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
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
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
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
a5a052b5bf
[Fix] Fix #1078 , #1077 and add nightly build to readme
2019-12-09 00:03:35 +08:00
35653ddd0a
[Fix] Fix karate due to networkx version change
2019-12-04 22:02:10 +08:00
45aa158408
Fix example code in saving graphs ( #1034 )
2019-11-22 13:38:58 +08:00
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
52c7ef49fc
[Model Zoo] AttentiveFP ( #955 )
...
* Update
* Fix style
* Update
* Update
* Fix
* Update
* Update
2019-10-26 01:57:34 +08:00
4eba1ce2a4
[Chemistry] Hot fix ( #953 )
...
* Hot fix
* CI
2019-10-25 15:05:21 +08:00
577cf2e63b
[Model Zoo] Refactor and Add Utils for Chemistry ( #928 )
...
* Refactor
* Add note
* Update
* CI
2019-10-22 00:47:45 +08:00
ae3102d3a2
[Dataset] Migration for Chemistry Datasets ( #926 )
...
* Update
* Update
2019-10-21 16:38:28 +08:00
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
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
54e1ef2e06
[Fix] Fix serialize NDArray when shape is 0 ( #884 )
...
* fix
* fix bugs
2019-09-28 19:21:38 +08:00
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
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
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
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
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
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
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
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
Tong He