ff244df0ea
post-release
2020-04-06 22:31:51 +08:00
0ee95a5e73
Update ( #1419 )
2020-04-04 01:22:16 +08:00
b94d3da84f
[Docs] Fix doc build doesn't work for nn.tensorflow and nn.mxnet ( #1413 ) ( #1417 )
...
* fix
* lint
* fix
2020-04-03 20:33:54 +08:00
e1d90f9b5e
update version
2020-03-30 16:21:04 +00:00
4a281ff3e6
Merge branch 'master' into 0.4.x
2020-03-30 16:14:14 +00:00
e4cc81852d
[Windows] fix compilation issues on vs2015 ( #1405 )
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* [Windows] fix compilation issues on vs2015
* fix test
2020-03-30 22:08:26 +08:00
e9440acb06
[TF] TF backend fix and new logic to choose backend ( #1393 )
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* TF backend fix and new logic to choose backend
* fix
* fix
* fix
* fix
* fix backend
* fix
* dlpack alignment
* add flag
* flag
* lint
* lint
* remove unused
* several fixes
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-03-30 18:45:17 +08:00
4b4186f87d
[Sampler] Change argument type of fanout from list to dict ( #1403 )
2020-03-30 15:52:46 +08:00
e3a9a6bba8
add an optional include_dst_in_src argument ( #1401 )
2020-03-30 12:06:12 +08:00
af61e2fbb4
[Feature] Support nn modules for bipartite graphs. ( #1392 )
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* init gat
* fix
* gin
* 7 nn modules
* rename & lint
* upd
* upd
* fix lint
* upd test
* upd
* lint
* shape check
* upd
* lint
* address comments
* update tensorflow
Co-authored-by: Quan Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-03-29 16:48:38 +08:00
67cb7a43a0
[Feature] Deprecate multigraph ( #1389 )
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* Deprecate multi-graph
* Handle heterograph and edge_ids
* lint
* Fix
* Remove multigraph in C++ end
* Fix lint
* Add some test and fix something
* Fix
* Fix
* upd
* Fix some test case
* Fix
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-03-28 21:31:24 +08:00
3efb5d8ecf
[NN] Add HeteroGraphConv module for cleaner module definition ( #1385 )
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* 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
bbfff8ce76
[Feature] Casting between DGLGraph and DGLHeteroGraph ( #1391 )
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* [Feature] Casting between DGLGraph and DGLHeteroGraph
* lint
* address comments
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-03-27 13:34:55 +08:00
b9c65e91ef
[BUG] Another fix on remove edges when all edges are removed ( #1386 )
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* [BUG] Another fix on remove edges when all edges are removed
* fix mxnet
2020-03-23 19:04:52 +08:00
d27b485912
[BUG] Fix remove_edges crashing with empty edge ID tensors ( #1384 )
2020-03-22 21:09:44 +08:00
a0721405cf
[BUGFIX] don’t import dgl in the package. ( #1382 )
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* 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
10253a5c07
[BUGFIX] Fix is_multigraph in the construction from scipy coo matrix ( #1357 )
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* fix is_multigraph in from_coo.
* add tests for partition.
* fix.
* Revert "add tests for partition."
This reverts commit cb8c8555da3e0c70a482c2d639adce2943475bfc.
* fix everywhere from_scipy_sparse_matrix is used.
2020-03-22 00:30:27 -07:00
0f40c6e49c
[Hetero] Replace card with num_nodes
...
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-03-20 16:56:53 +08:00
4af02022b2
[Bug] Multiple fixes ( #1374 )
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* multiple fixes
* lint
* lint x2
2020-03-19 11:19:44 +08:00
0a51dc5435
[Bug] Fix dsttype in GraphSAGE minibatch model ( #1371 )
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* fix for new ntype API for blocks
* adding two new interfaces
2020-03-18 23:57:03 +08:00
6111ea4665
[Model] RGCN mini-batch training; Better bipartite graph support ( #1337 )
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* change the model to use node embedding only
* minibatch training
* add readme
* small fix
* backward-compatible
* backward compatible
* modify to_block; rgcn changed
* fix
* fix transform
* fix bug in unittest script
* docstring
* fix lint
* add tests
* address comments; fix offline eval
* gitignore
2020-03-16 18:58:06 +08:00
3938b399d9
[BUGFIX] metis partition should generate a subgraph to the original graph. ( #1352 )
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* fix a partition.
* add comments.
2020-03-12 10:43:08 +08:00
1a584ced11
[Feature] Improve the speed of to_bidirected ( #1327 )
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* make graph symmetric
* call gklib routine.
* use gklib version except in windows.
* minor errors.
* fix test.
* update doc.
* fix a compile error.
* fix.
* add comments for the new C API.
* fix a bug.
* address comments.
* fix compile error.
* fix comment.
2020-03-10 22:44:32 -07:00
988c8b20a4
[DOC] Improve the docstring of GATConv and new APIs ( #1339 )
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* upd
* upd
* upd
* upd
* upd
2020-03-11 01:14:22 +08:00
d98c71ef90
[DGL-KE] Clean up argument for DGL-KE ( #1325 )
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* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* clean up args
* change args for eval
* update
* update
* update
* update num_worker=8
* add num_proc=1
* update
* update
* add eval percent
* update
* update
* update
* save emb
* update
* update
* update
* update
* update
* remove neg_chunk_size
* update
* update
* update
* remove
* update
* remove
* change num_thread
2020-03-09 23:11:56 +08:00
0e153c4baf
[Feature] add metis partitioning to DGL ( #1308 )
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* add metis.
* add test.
* construct partition id.
* link to METIS github repo.
* update metis.
* add a tool for partitioning a graph.
* update metis.
* update.
* update.
* fix metis.
* fix lint
* fix indent.
* another way of building metis.
* disable metis in windows.
* test windows
* fix.
* disable metis for windows properly.
* fix for tensorflow.
* skip test for gpu.
* make graph symmetric
* address comments.
* more comments.
* fix compile
* fix a bug.
* add test.
* change the default #hops of HALO nodes.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-26-167.us-east-2.compute.internal >
2020-03-07 23:24:03 -08:00
a9520f71ce
[Model][Sampler] GraphSAGE model, bipartite graph conversion & remove edges API ( #1297 )
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* remove edge and to bipartite and graphsage with sampling
* fixes
* fixes
* fixes
* reenable multigpu training
* fixes
* compatibility in DGLGraph
* rename to compact_as_bipartite
* bugfix
* lint
* add offline inference
* skip GPU tests
* fix
* addresses comments
* fix
* fix
* fix
* more tests
* more docs and unit tests
* workaround for empty slice on empty data
2020-03-08 02:38:29 +08:00
ce6e19f233
[Bugfix] Allows node types with no inbound/outbound edges ( #1323 )
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* add num nodes in ctors
* fix
* lint
* addresses comments
* replace with constexpr
* remove function with rvalue reference
* address comments
2020-03-08 01:11:44 +08:00
09ade2f265
upd ( #1321 )
2020-03-06 14:17:48 +08:00
978ac41097
[NN] Fix RelGraphConv num_bases error message ( #1309 )
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* Fix RelGraphConv when num_bases is None
* Improve error message in when num_bases is wrong
* Fix integer modulo by zero exception when num_bases is 0
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-03-06 01:00:48 +08:00
e2db791312
[Feature] Import subpackge based on backend of dgl.nn ( #1305 )
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* automatically select nn backend
* rename load_backend to private
* switch to backend_name
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-03-05 19:59:45 +08:00
93ac29ce34
[Refactor] Unify DGLGraph, BatchedDGLGraph and DGLSubGraph ( #1216 )
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* 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
ce93330e34
[Doc] Fix the docstring of builtin functions. ( #1303 )
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* fix.
* fix.
* fix.
* fix cmake.
2020-03-04 11:38:05 -08:00
c23a61bd5c
fix s3 link ( #1310 )
2020-03-04 21:01:29 +08:00
1c4bfb62bb
[Performance] Replace np.array with np.asarray ( #1301 )
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* replace np.array with np.asarray
* fix
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
2020-03-03 20:45:41 +08:00
5dd35580f7
[Feature] Improve sampling speed; Better pickle/unpickle; other fixes ( #1299 )
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* improve performance of sample_neighbors
* some more improve
* test script
* benchmarks
* multi process
* update more tests
* WIP
* adding two API for state saving
* add create from state
* upd test
* missing file
* wip: pickle/unpickle
* more c apis
* find the problem of empty data array
* add null array; pickling speed is bad
* still bad perf
* still bad perf
* wip
* fix the pickle speed test; now everything looks good
* minor fix
* bugfix
* some lint fix
* address comments
* more fix
* fix lint
* add utest for random.choice
* add utest for dgl.rand_graph
* fix cpp utests
* try fix ci
* fix bug in TF backend
* upd choice docstring
* address comments
* upd
* try fix compile
* add comment
2020-03-02 23:16:05 +08:00
00ba409440
[DGL-KE] Distributed training of DGL-KE ( #1290 )
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* update
* change name
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* change worker number
* update
* update
* update
* update
* update
* update
* test
* update
* update
* update
* remove barrier
* max_step
* update
* add complex
* update
* chmod +x
* update
* update
* random partition
* random partition
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* change num_test_proc
* update num_thread
* update
2020-03-02 14:17:54 +08:00
c3a33407fe
[Feature] PinSAGE sampler ( #1249 )
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* [WIP] PinSAGE operators
* moved the edge remapping mess into C
* some docstrings
* lint
* lint x2
* lint x3
* skip gpu test on topk
* extend pinsage to any metapath
* lint x4
* addresses #1265
* add always_preserve (fixes #1266 ) and fix a silly bug
* disable gpu test on compaction
* lint
* fix a horrible bug and add more tests
* lint
* addresses comments
* lint
* bugfix
* addresses comments
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
2020-02-28 20:46:13 +08:00
37d992ecf6
[Bugfix] Fix no attribute num_edges bug in Nodeflow ( #1289 )
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* fix nodeflow bug when using builtin on edge data
* fix
2020-02-26 10:05:38 +08:00
ddf8c858e1
[KVStore] Small fix on kvstore ( #1284 )
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* update
* str to int
* update
* update
* update
* test remove sync
* update
* update
* update
* update
* update
* update
* update
* update
* clear
2020-02-23 15:43:34 +08:00
c7f6cf6282
[Bugfix] Consistent order for cross-type stack reducer ( #1267 )
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* WIP
* fix shape of stack reducer
* apply merge order by edge id for stack reducer
2020-02-18 13:54:11 +08:00
537d37c26c
[Misc] add requests as the package dependency ( #1268 )
2020-02-17 23:45:17 +08:00
f8d4264e5b
[Feature] Neighbor-hood based sampling APIs ( #1251 )
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* WIP: working on random choices
* light slice
* basic CPU impl
* add python binding; fix CreateFromCOO and CreateFromCSR returning unitgraph
* simple test case works
* fix bug in slicing probability array
* fix bug in getting the correct relation graph
* fix bug in creating placeholder graph
* enable omp
* add cpp test
* sample topk
* add in|out_subgraph
* try fix lint; passed all unittests
* fix lint
* fix msvc compile; add sorted flag and constructors
* fix msvc
* coosort
* COOSort; CSRRowWiseSampling; CSRRowWiseTopk
* WIP: remove DType in CSR and COO; Restrict data array to be IdArray
* fix all CSR ops for missing data array
* compiled
* passed tests
* lint
* test sampling out edge
* test different per-relation fanout/k values
* fix bug in random choice
* finished cpptest
* fix compile
* Add induced edges
* add check
* fixed bug in sampling on hypersparse graph; add tests
* add ascending flag
* in|out_subgraph returns subgraph and induced eid
* address comments
* lint
* fix
2020-02-17 21:25:21 +08:00
c7c0fd0e37
[Feature] Accessing node/edge types in UDFs. ( #1243 )
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* typed udf
* docstrings
2020-02-17 16:02:56 +08:00
b133abb82e
[KVStore] New kvstore used by DGL-KE ( #1263 )
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* new kvstore
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* test warning
* update
* update
* udpate
* update
* update
* update
* update
* small fix
* small fix
* get group count
* update
* update
* make file
* update
* use addr
* get id
* partition book
* update
* partition
* barrier
* update
* loop count
* update
* update
* update
* update
* update
* update
* update
* update
* update
* add mxnet demo
* update ip
* update
* update
* update
* random
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* fix lint
2020-02-17 13:39:13 +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
eeeb52f464
[Feature] Preference to COO for "hypersparse" unit graphs & graph compaction ( #1238 )
...
* unit graph that prefers coo queries
* auto detect coo preference
* forgot some functions
* disable lint on detect_prefer_coo
* reorg
* change comment
* lint
* fix
* move array_utils.h to src
* compact graph impl
* fix redundant copying in idhashmap
* docstring
* moving preference detection to C
* lint
* fix unit test & address comments
* hypersparse autorestrict
* docstring & fix
* revert copyto and asnumbits
* fix stupid bug
* lint
* leave a TODO for sorted COO
* fixing same node type mapping to different id in different graphs
* addresses comments
* made induced nodes a feautre column
* lint?
2020-02-04 22:39:28 +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
e4948c5cbc
fix regression in #1237 ( #1239 )
2020-02-03 11:50:06 +08:00
c167373e1e
[Doc] Fix the doc of NeighborSampler. ( #1236 )
...
* fix.
* fix.
2020-01-31 13:36:17 -08:00
Quan Gan