0a51dc5435
[Bug] Fix dsttype in GraphSAGE minibatch model ( #1371 )
...
* 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 )
...
* 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 )
...
* fix a partition.
* add comments.
2020-03-12 10:43:08 +08:00
1a584ced11
[Feature] Improve the speed of to_bidirected ( #1327 )
...
* 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 )
...
* upd
* upd
* upd
* upd
* upd
2020-03-11 01:14:22 +08:00
d98c71ef90
[DGL-KE] Clean up argument for DGL-KE ( #1325 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* [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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* typed udf
* docstrings
2020-02-17 16:02:56 +08:00
b133abb82e
[KVStore] New kvstore used by DGL-KE ( #1263 )
...
* 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
a9dabcc769
[Feature] Random Walk for 0.5 ( #1209 )
...
* trying to refactor IndexSelect
* partial implementation
* add index select and assign for floats as well
* move to random choice source
* more updates
* fixes
* fixes
* more fixes
* adding python impl
* fixes
* unit test
* lint
* lint x2
* lint x3
* update metapath2vec
* debugging performance
* still debugging for performance
* tuning
* switching to succvec
* redo
* revert non-uniform sampler to use vector
* still not fast
* why does this crash with OpenMP???
* because there was a data race!!!
* add documentations and remove assign op
* lint
* lint x2
* lol what have i done
* lint x3
* fix and disable gpu testing
* bugfix
* generic random walk
* reorg the random walk source code
* Update randomwalks.h
* Update randomwalks_cpu.cc
* rename file
* move internal function to anonymous ns
* reorg & docstrings
* constant restart probability
* docstring fix
* more commit
* random walk with restart, tested
* some fixes
* switch to using NDArray for choice
* massive fix & docstring
* lint x?
* lint x??
* fix
* export symbols
* skip gpu test
* addresses comments
* replaces another VecToIdArray
* add randomwalks.h to include
* replace void * with template
2020-01-31 19:52:08 +08:00
f1a8f926a4
[Feature] Add environment variable to switch on/off MXNet set_np_shape ( #1207 )
...
* add env var
* Trigger CI
* simplification
* add doc
2020-01-20 13:54:14 +08:00
a00636a02b
[Tensorflow] Several nn & example ( #1191 )
...
* several nn example
* appnp
* fix lint
* lint
* add dgi
* fix
* fix
* fix
* fff
* docs
* 111
* fix
* change init
* change result
* tiaocan+1
* fix
* fix lint
* fix
* fix
2020-01-19 22:48:40 +08:00
31a7d50964
[Bug Fix] Add boundary check for heterograph build with card as input ( #1192 )
...
* Add boundary check for heterograph build with card as input
* Fix when u or v is empty
* fix test_kernel.py error print
* Revert "fix test_kernel.py error print"
This reverts commit a71c20292549c0ac62a5326c30669ca4bde8febc.
* Turn op validation check on graph and bipartite by default
* upd
* udp
* upd
* update test
2020-01-18 17:18:40 +08:00
86fe58ebb8
[Bug] Another fix on PyTorch memory leakage issue ( #1139 )
...
* another fix
* another try
* fix
* rewriting with kernel functions
* revert mxnet softmax changes
* lint fix
Co-authored-by: Zihao Ye <zihaoye.cs@gmail.com >
2020-01-14 22:54:19 +08:00
28a24414c8
[BUG] Fix empty heterograph creation with list & tuple ( #1188 )
...
* [BUG] Fix empty heterograph creation with list & tuple
* more fix
2020-01-09 22:40:27 +08:00
aa06e4579f
[Doc] Improve the docstring of several nn modules. ( #1187 )
...
* upd
* upd
* upd
* upd
* lint
* upd
* upd
* upd
* upd
* upd
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com >
2020-01-09 21:14:33 +08:00
3ef757dbff
[Feature] Pickle support for heterograph ( #1177 )
...
* [Feature] Pickle support for heterograph
* fix lint
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com >
2020-01-09 13:27:29 +08:00
ca302a13ac
[Feature] Add dgl.nn.*.Sequential for usability ( #1166 )
...
* upd
* upd
* upd
* upd
* lint
* upd
* upd
* upd
* upd
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com >
2020-01-09 12:39:22 +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
38d292e541
[KVStore] Fix memory leak bug. ( #1174 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
* add multiple NICs support for kvstore
* test
* fix lint
* update
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* update
* fix lint
* delete msg
* clear kv msg
* update
* update
* update
* update
* update
* update
* is not None
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
2020-01-06 19:47:54 +08:00
6d0a9c4297
[Fix issue] Fix issue 1170 ( #1171 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
* add multiple NICs support for kvstore
* test
* fix lint
* update
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* update
* fix lint
2020-01-05 14:31:41 +08:00
1022d5d64d
[KG] PBG's way of constructing negative edges ( #1159 )
...
* attach positive.
* add neg_deg_sample.
* add comment.
* add neg_deg_sample for eval.
* change the edge sampler.
* rename edge sampler in KG.
* allow specifying chunk size and negative sample size separately.
* fix bugs in KG.
* add check in sampler.
* add more checks.
* fix
* add comment.
* add comments.
2020-01-04 19:25:06 -08:00
61b78e6ee7
[Bug Fix]edge sample hotfix ( #1152 )
...
* hot fix
* Fix docs
* Fix ArrayHeap float overflow bug
* Fix
* Clean some dead code
* Fix
* FIx
* Add some comments
* run test
2019-12-30 19:42:57 -08:00
6731ea3af7
[KVStore] Reduce memory cost of kvstore ( #1156 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
* add multiple NICs support for kvstore
* test
* fix lint
* update
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
2019-12-30 20:25:32 +08:00
4f02bb751b
[KVStore] Made kvstore can support multiple NICs ( #1150 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
* add multiple NICs support for kvstore
* test
* fix lint
* update
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* update
* update
* update
* update
2019-12-30 15:17:31 +08:00
655d75688a
fix deprecation warning ( #1147 )
2019-12-28 12:42:16 +08:00
d57ff78da1
[Small Fix] Change default message queue size of communicator to 2GB ( #1140 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
2019-12-25 17:03:52 +08:00
e4ef8d1a80
[KVStore] API change of kvstore ( #1058 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
2019-12-24 17:05:15 +08:00
Quan (Andy) Gan