d9a2d74167
[Performance][Feature] Implement edge excluding in EdgeDataLoader on GPU ( #3226 )
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* Update filter code
* Add unit tests
* Fixes
* Switch to indices
* Rename functions
* Fix linting
* Fix whitespace
* Add doc
* Fix heterograph
* Change workspace allocation
* Fix linting
* Fix docs in filter.py
* Add todo
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-08-20 02:47:48 +00:00
a0390dde93
[Feature] Add dgl.utils.is_sorted_srcdst() ( #2685 )
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* Add dgl.utils.is_sorted_srcdst
* Fix linting issues
* delete blank line
* Specify datatype to index tensor in test
* Force integer conversion
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-07-02 11:29:24 +08:00
acd21a6d60
[Feature] Support direct creation from CSR and CSC ( #3045 )
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* csr and csc creation
* fix
* fix
* fixes to adj transpose
* fine
* raise error if indptr did not match number of nodes
* fix
* huh?
* oh
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-25 10:05:47 +08:00
a7e941c379
[Feature] Add support for sparse embedding ( #2451 )
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* Add sparse embedding for dgl and update rgcn example
* upd
* Fix
* Revert "Fix"
This reverts commit 4da87cdfb8b8c3506b7fc7376cd2385ba8045c2a.
* Fix
* upd
* upd
* Fix
* Add unitest and update impl
* fix
* Clean up rgcn example code
* upd
* upd
* update
* Fix
* update score
* sparse for sage
* remove model sparse
* upd
* upd
* remove global norm
* revert delete model_sparse.py
* update according to comments
* Fix doc
* upd
* Fix test
* upd
* lint
* lint
* lint
* upd
* upd
* clean up
Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal >
2021-01-28 00:26:49 +08:00
0c2a2ea1e2
[Bugfix] Handle a Corner Case of Batching after Removing Nodes/Edges ( #2465 )
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* Update
* Update
* Update
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-01-05 22:22:03 +08:00
00edb94982
[Performance] Accelerate batching ( #2363 )
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* speed up batching
* more fix
* lint
* fix
2020-11-24 17:39:00 +08:00
2ce426d956
[Bug] add_edges() crashes if the input tensor is empty ( #2100 )
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* [Bug] add_edges() crashes if the input tensor is empty
* lint
* fix
2020-08-24 16:04:41 +08:00
f13b9b6212
[Doc] Scan the API docs and make many changes ( #2080 )
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* WIP: api
* dgl.sampling, dgl.data
* dgl.sampling; dgl.dataloading
* sampling packages
* convert
* subgraph
* deprecate
* subgraph APIs
* All docstrings for convert/subgraph/transform
* almost all funcs under dgl namespace
* WIP: DGLGraph
* done graph query
* message passing functions
* lint
* fix merge error
* fix test
* lint
* fix
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2020-08-20 23:26:49 +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
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
b9ef70e5ac
[Distributed] Set the number of threads correctly to speed up ( #1976 )
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* temp fix omp.
* set server threads.
* add CAPI to set up OMP threads.
* fix.
* fix.
* update namesapce.
* set cpi properly.
* allow to config num worker threads.
* set #threads.
* fix.
2020-08-08 19:30:53 -07:00
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
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
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
nv-dlasalle