faf8c71163
[Performance] Use segment operators for graph readout. ( #2361 )
...
* upd
* upd
* update
* upd
* upd
* upd
* fix
* lint
* lint
* pylint
* doc
2020-11-27 03:21:04 +00:00
317be7f188
[Bugfix] GINDataset check whether labels are all valid ( #2319 )
...
* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* check whether the original labels are valid
* add unit test for gin dataset
* bug of asscalar in mxnet<=1.6
* mxnet<=1.6 asscalar requires ndarray to be shaped (1,)
* skip gpu while testing datasets
* Update test_data.py
* test of gin dataset takes too much time
2020-11-27 03:17:22 +00:00
4286bd2b94
fix bug in flatten and is_unibipartite ( #2279 )
2020-11-27 03:17:12 +00:00
3f994308c0
[bugfix] Fix the behavior of min/max reducer for 1-dim dta. ( #2250 )
...
* udp
* add test
* udp
* fix mxnet
2020-11-27 03:17:12 +00:00
26757bd383
[HeteroGraph] Fix the failure of apply_nodes when the input function changes feature size for all nodes ( #2223 )
...
* Fix
* Fix
2020-11-27 03:17:11 +00:00
7d8522a29f
[Bug] fix cumsum on an empty array with prepend_zero returning an empty array ( #2179 )
...
* fix cumsum
* udp
Co-authored-by: Zihao <expye@outlook.com >
2020-09-11 18:23:44 +08:00
8f4594074b
[Hotfix] Fix degree bucket edge ordering ( #2176 )
...
* fix degree bucket edge ordering
* unit test
* fix
2020-09-11 14:16:52 +08:00
cbd55eb12f
[performance] Batch DGLGraph in C++ end. ( #2155 )
...
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* fix
* upd
* upd
* upd
* upd
* fix
* upd
Co-authored-by: VoVAllen <jz1749@nyu.edu >
2020-09-11 02:54:27 +08:00
ac570c1dae
[Bugfix] Fix flatten not wrapping unit graph ( #2170 )
...
* fix flatten not wrapping unit graph
* fix doc
2020-09-10 17:41:52 +08:00
c9c6171b9f
Revert "[Feature] Basic utils to handle raw data features ( #2102 )" ( #2147 )
...
This reverts commit 33a8bb93bfwmjlyjemaine@gmail.com >
2020-09-08 10:33:59 +08:00
ac5c79cdb8
[Bug] Fixes issues in feature pickling and transmission for subgraphs and blocks ( #2139 )
...
* bug fixes
* remove __deepcopy__; not sure what the behavior should be
* lint
* skip gpu test
* fix
* fix dist dataloader
* add comment
* remove assert
2020-09-03 12:48:59 +08:00
9eaace9216
rename create_format_ to create_formats_ ( #2126 )
2020-08-29 22:49:27 +08:00
642bdbaf04
[Traversal] Fall back to CPU for Graph Traversal as a Workaround ( #2115 )
...
* workaround
* Allow Test for Traversal on GPU Graphs
Co-authored-by: Ubuntu <ubuntu@ip-172-31-1-5.us-west-2.compute.internal >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2020-08-29 16:34:31 +08:00
3808dc950b
[hotfix] Disable hypersparse memory optimization. ( #2121 )
...
* upd
* upd
2020-08-28 15:07:53 +08:00
33a8bb93bf
[Feature] Basic utils to handle raw data features ( #2102 )
...
* add feature utils and add test for feature norm
* Add docstring and test
* upd
* dis able some test
* Update
* update doc string
* update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal >
2020-08-27 11:36:39 +08:00
2ce426d956
[Bug] add_edges() crashes if the input tensor is empty ( #2100 )
...
* [Bug] add_edges() crashes if the input tensor is empty
* lint
* fix
2020-08-24 16:04:41 +08:00
3af0e91c0e
[Frame] Fix for Column Index Device ( #2055 )
...
* Update frame.py
* add unit test
* fix test
* fix
* fix
* fix
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2020-08-19 16:10:52 +08:00
dacc7afeb2
[Convert] Reserve node/edge IDs in to_heterogeneous ( #2045 )
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* Fix
* Fix
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-18 23:16:33 +08:00
9088c63592
[Feature] Change the Default Value of transpose in DGLGraph.adj ( #2046 )
...
* Update adj
* Fix
2020-08-18 22:45:46 +08:00
47c96dd114
[Test] Remove Test for metapath_random_walk ( #2039 )
...
* Update test_randomwalk.py
* Update test_randomwalk.py
2020-08-18 11:19:31 +08:00
aa19df1bbb
[Bugfix] Fix batching isolated node types ( #2035 )
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* [Bugfix] Fix batching isolated ntypes
* fix test
* remove test.py
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-18 09:29:05 +08:00
be444e52d9
[Doc/Feature] Refactor, doc update and behavior fix for graphs ( #1983 )
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* Update graph
* Fix for dgl.graph
* from_scipy
* Replace canonical_etypes with relations
* from_networkx
* Update for hetero_from_relations
* Roll back the change of canonical_etypes to relations
* heterograph
* bipartite
* Update doc
* Fix lint
* Fix lint
* Fix test cases
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Update
* Fix test
* Fix
* Update
* Use DGLError
* Update
* Update
* Update
* Update
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Update
* Fix
* Update
* Fix
* Fix
* Fix
* Update
* Fix
* Update
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* rewrite sanity checks
* delete unnecessary checks
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Update
* Update
* Update
* Fix
* Fix
* Fix
* Update
* Fix
* Update
* Fix
* Fix
* Update
* Fix
* Update
* Fix
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2020-08-18 04:26:29 +08:00
cd48435206
[Transform] Docstring and subframes ( #1962 )
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* update knn graph docs
* more docs
* [Doc] transform module docstrings
* remove copy_ndata and copy_edata
* fix
* lint
* fix
* fix
* fix
* clean up docstrings
* fix docstring
* dtype specifications
* addresses comments
* fix
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-13 10:41:43 +08:00
6294677f8a
[hotfix] Set reduce results to all zero for nodes with zero in-degrees. ( #2011 )
2020-08-13 01:20:56 +08:00
5362908236
Fix save/load for old version files ( #1994 )
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* load hetero
* fix
* more error message
* add warning
* add alias to dgl namespace
* fix tests
2020-08-12 23:45:21 +08:00
5e34ca8bb5
[Feature] Lazy copy ndata, edata to device ( #1986 )
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* Lazy to device
* remove print
* lint
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* lint
* Fix
* Revert "Fix"
This reverts commit 615c9b8f80f5f6ee2ab43c849a22f0083deedf3b.
* Add test for frame lazy update
* disable tensorflow
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-08-12 13:04:47 +08:00
f5eb80d221
[Feature] Edge DataLoader for edge classification & link prediction ( #1828 )
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* clean commit
* oops forgot the most important files
* use einsum
* copy feature from frontier to block
* Revert "copy feature from frontier to block"
This reverts commit 5224ec963eb6a3ef1b6ab74d8ecbd44e4e42f285.
* temp fix
* unit test
* fix
* revert jtnn
* lint
* fix win64
* docstring fixes and doc indexing
* revert einsum in sparse bidecoder
* fix some examples
* lint
* fix due to some tediousness in remove_edges
* addresses comments
* fix
* more jtnn fixes
* fix
2020-08-11 18:00:58 +08:00
729ff2ef38
Fix the performance issue of graph partitioning in new DGLGraph ( #1934 )
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* fix perf.
* fix.
* accelerate metis.
* fix lint.
* use gklib.
* fix perf.
* fix.
* update metis.
* update launch script
* handle synchronized API.
* fix.
* fix example.
* fix dataloader.
* temp fix.
* temp fix omp.
* distinguish roles.
* initialize iterator of DistDataloader correctly.
* check the correctness of launch script.
* move feature copy to sampler.
* measure mem/network copy time.
* remove
* Revert "measure mem/network copy time."
This reverts commit 86cefdc14b7815fcf5aad6496af912dba48e4aa6.
* fix.
* fix
* fix.
* fix cmake.
* disable metis in windows.
* disable metis tests in windows.
* remove test for multigraph.
* fix test.
* fix.
* fix cmake.
* fix.
* revert.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-115.us-west-2.compute.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal >
2020-08-09 18:33:05 -07:00
18bfec24cf
[hotfix] Refactor edge softmax module ( #1967 )
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* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
2020-08-07 23:50:12 +08:00
22167f7203
[Refactor] Enable new kernel in all message passing APIs ( #1953 )
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* WIP: frame refactor
* new frame
* simple update_all builtin
* move all subgraph routines into the same file
* sddmm & spmm schedule; node & edge udf
* degree bucketing
* some tricky 0deg corner cases
* bug in frame append
* merge test_hetero_basics and test_basics
* some code rearange
* fix test_heterograph
* add mean spmm
* enable all builtin combinations
* pass gpu test
* pass pytorch tests
* wip
* fix some pt debugging codes
* fix bug in mxnet backward
* pass all mxnet utests
* passed tf tests
* docstring
* lint
* lint
* fix broadcasting bugs
* add warning and clamp for mean reducer
* add test for zero-degree mean
* address comments
* lint
* small fix
2020-08-07 15:40:25 +08:00
35c9473ba5
[HotFix] Fix add_reverse_edges ( #1960 )
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* Hot fix
* more test
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-07 13:07:06 +08:00
879e4ae5f2
[Transform] Add add_reverse_edges ( #1936 )
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* Add add_reverse_edges and is_simple_graph
Update to_bidirected
* remove is_simple_graph
* Fix lint
* to bidirected only support cpu
* support copy ndata
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-05 15:09:55 +08:00
d2ccd218cf
[hotfix] Allow creating graph from edges with restrict formats excluding coo. ( #1926 )
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* upd
* upd
* upd
* upd
2020-08-04 00:33:36 +08:00
b5be4f4bbf
[Dataset] Update dataset hash with deterministic function ( #1919 )
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* update hash with deterministic function
* update docstring
* add test on determination
2020-08-03 16:17:00 +08:00
03f251ced1
upd ( #1905 )
2020-07-31 20:13:24 +08:00
a28bfa9f5f
[hotfix] Activate kernel unittest for tensorflow ( #1895 )
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* upd
* upd
* upd
* upd
* upd
* trigger
* simplify unittest
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-07-31 19:57:53 +08:00
f4608c2227
[CUDA][Kernel] A bunch of int64 kernels for COO and CSR ( #1883 )
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* COO sort
* COOToCSR
* CSR2COO
* CSRSort; CSRTranspose
* pass all CSR tests
* lint
* remove int32 conversion
* fix tensorflow nn tests
* turn on CI
* fix
* addreess comments
2020-07-30 21:02:07 +08:00
444becf00a
[Misc] Move many deprecated codes to the deprecate folder ( #1893 )
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* some file movements
* move some codes to deprecated
* more deprecation
* lint
* remove useless test
2020-07-30 18:17:33 +08:00
68a978d4de
[Model] Fixes JTNN for 0.5 ( #1879 )
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* jtnn and fixes
* make metagraph a method
* fix test
* fix
2020-07-30 13:36:08 +08:00
2fa2b4534e
[Feature] Support higher order derivative for message passing. ( #1877 )
...
* upd
* fix typo
2020-07-28 23:11:06 +08:00
40950629b2
[Feature] Shared memory utilities ( #1807 )
...
* update
* update
* update
* update
* fix
* update
* fix
* update
* update
* win32
* update
* fix
* update
* update
* update
* updat
* update
* update
* fix
* update
* update
* update
* update
* update
* fix
* TODO
* 111
* fix
* minor fix
* minor fix
* fox
* Update shared_mem_manager.cc
* update
* update
* update
* update metis
* update metis
* update
Co-authored-by: VoVAllen <jz1749@nyu.edu >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-07-28 15:26:15 +08:00
44089c8b4d
[Refactor][Graph] Merge DGLGraph and DGLHeteroGraph ( #1862 )
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* 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
ec2e24be6d
[Feature] Slice dstnode features in NN modules ( #1838 )
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* slice dstdata from srcdata within nn module
* a bunch of fixes
* add comment
* fix gcmc layer
* repr for blocks
* fix
* fix context
* fix
* do not copy internal columns
* docstring
2020-07-25 21:57:49 +08:00
33abd2757b
[HeteroGraph] Metis partition for hetero ( #1843 )
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* metis for hetero
* fix partition
2020-07-22 16:31:10 +08:00
ea420c0abd
[Distributed] Reduce memory consumption in graph partitioning ( #1823 )
...
* save mem.
* save mem.
* reduce mem
* fix test
* fix lint
* fix test
* fix.
* fix.
* fix.
* fix.
* fix lint.
* fix backend operator.
* fix tensorflow operators.
* fix.
* revert change in mxnet operator.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal >
2020-07-18 06:53:48 -07:00
0e92dad69a
[Transfom] Add support for to_bidirected of heterogeneous graphs ( #1793 )
...
* code
* joint_union
* joint union pass all test
* test case for test_transform
* upd
* lint
* lint
* Fix
* list
* Fix
* Fix
* update to_bidirected impl
* Fix
* Fix
* upd
* remove joint_union
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-07-15 18:01:02 +08:00
a5722d02a4
[Transform] New ToSimple API ( #1789 )
...
* To simple
* lint
* upd
* more test
* fix
* Fix
* Fix
* add share edata
* doc
* Fix
* Fix
* Fix
* Fix
* lint
* lint
* Fix
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2020-07-15 13:45:32 +08:00
be53add4d1
relax ( #1802 )
2020-07-14 09:44:42 +08:00
bc209bff94
[bugfix] Fix the deterministic of kernel test and add documentation. ( #1799 )
...
* upd
* upd
* upd
* relax
* relax too
* upd
2020-07-14 04:22:31 +08:00
f25b1a064d
[Feature] Autograd of gspmm and gsddmm on PyTorch/MXNet/Tensorflow ( #1680 )
...
* init
* reverse(by minjie
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* gpu
* upd
* upd
* upd
* upd
* udp
* upd
* upd
* imidiot
* fix
* upd
* upd
* upd
* udp
* upd
* upd
* fix
* udp
* upd
* upd
* upd
* upd
* upd
* fix
* remove redundency
* upd
* upd
* upd
* cache
* upd
* upd
* upd
* upd
* upd
* udp
* upd
* trigger
* upd
* fix
* upd
* unused import
* upd
* upd
2020-07-13 23:21:22 +08:00
Zihao Ye