6124667f42
[Model] Refactor the sampling examples ( #498 )
...
* reorganize sampling code.
* speedup gcn_ns.
* speed up gcn_cv
* fix graphsage_cv.
* undo the modification.
* accel training.
* update readme.
2019-04-17 01:31:14 -07:00
a3febc061b
[Model] Add GIN Model ( #471 )
...
* add gin model
* convert dataset.py to data_ont_the_fly way and put it into dgl.data module
* convert dataset.py to data_ont_the_fly way and put it into dgl.data module
python code checked
* modified document and reference TUDataset; checked python part and bypass cpp part due to error
* change tensor to numpy in dataset and transform in collate@Dataloader
* Change minor format issue
Change minor format issue
* moved logging; adjusted tqdm etc
2019-04-17 14:57:07 +08:00
fb6af16f83
[BUG] Fix crash during Cython build ( #500 )
2019-04-17 14:18:22 +08:00
06e22f1ee4
[Test] Disable unittest for shared memory temporarily ( #497 )
...
* disable tests.
* import unittest.
2019-04-16 16:27:23 -07:00
b89dcce16c
[RPC] Refactoring networking APIs ( #496 )
...
* Refactoring network API
* update demo
* update
* update demo
* update demo
* add num_sender
* update
* fix lint
* fix lint
* fix lint
* update
2019-04-16 16:33:29 +08:00
688a9228a8
fix. ( #491 )
2019-04-11 15:38:35 -07:00
e2e04329a6
[BUG] Update URL for JTNN dataset
2019-04-11 22:23:34 +08:00
c69dbbb736
[Bug Fix] Fix TUDataset Processing bug ( #489 )
...
* add graph classification dataset
* add node label
* add TUDataset
* Modify to consistent with Qi Huang's implementation
* add docs
* Add docs
* Fix change of environment variable
* Update tu.py
* Update tu.py
* Fix error when add node with np.int64
* Fix processing bug
2019-04-11 19:30:50 +08:00
00fc680aae
[Dataset] Add TUDataset ( #473 )
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* add graph classification dataset
* add node label
* add TUDataset
* Modify to consistent with Qi Huang's implementation
* add docs
* Add docs
* Fix change of environment variable
* Update tu.py
* Update tu.py
* Fix error when add node with np.int64
2019-04-10 09:37:53 -04:00
039a711da1
[Model] fix self-edge bug in GCN and GAT. ( #482 )
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* Update gcn_mp.py
* Update train.py
* Update train.py
* Update train.py
* Update gat_batch.py
* Update gat_batch.py
* Update gcn_mp.py
2019-04-10 09:04:19 -04:00
fa887f69f4
[Model] Add APPNP model ( #480 )
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* [Model] Add APPNP model
* update
* Revert "update"
This reverts commit a8e42d19c8b421fb382305a8f04d7426e78ea53c.
* update
* Update appnp.py
2019-04-09 19:54:09 +08:00
bfdd1eaa44
[Feature] Create shared memory graph store. ( #468 )
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* accelerate gcn_ns.
* add timing.
* run infer with whole graph.
* distributed gcn_ns.
* reconstruct gcn_ns.
* minor fix.
* change graphsage_cv for numa.
* fix #OMP threads.
* accelerate graphsage_cv.
* fix a weird bug.
* add profiler in graphsage_cv.
* accelerate graphsage_cv.
manually aggregate neighbors' embeddings with pull.
* load csr directly in gcn_ns_sc.
* parallel sort for graph index.
* Revert "parallel sort for graph index."
This reverts commit 86fe2c7117fe5e56b0d481b39849c258b166945b.
* run gcn_ns_sc on GPUs.
* acc gcn_cv_sc.
* change gcn_cv for numa.
* fix gcn_cv to use numa and gpu.
* improve graphsage_cv to use numa and gpu.
* improve gcn_ns.
* improve graphsage_cv.
* init shared memory graph store.
* fix.
* enable init ndata.
* improve tests.
* add bidirectional communication.
* link to rt.
* fix compilation error.
* fix shared memory init.
* use MessageQueue for inter-process communication.
* reconstruct immutable graph csr.
* fix gcn.
* load csr to shared memory.
* fix minor bugs.
* add comments.
* refactor SharedMemory.
* fix bugs in ImmutableGraph.
* create CSR graph from shared memory.
* add more test for loading a csr graph.
* terminate graph store properly.
* allow initializing ndata in the graph store server.
* use RPC for inter-process communication.
* a script for loading a graph.
* allow customizing port.
* list all ndata and edata.
* support dtype.
* reorganize SharedMemoryGraphStore.
* fix ndata shape.
* reconstruct gcn_ns.
* print info.
* set omp in gcn_ns.
* reset sampling examples.
* fix lint.
* fix lint.
* reset gcn.
* disable shared memory in windows.
* fix.
* fix.
* reset changes.
* revert nodeflow changes.
* fix cmake.
* fix test.
* fix test.
* fix test.
* fix test.
* add comments.
* fix test.
* move vector out.
* fix lint.
* fix lint.
* move SharedMemory.
* update cmake.
* update comment.
* fix comments.
* Revert "update cmake."
This reverts commit 592445e37077f70a6e3f2e5245f9a3d086b04f3b.
* update cmake.
* add comments.
* rename.
* change the comment.
* fix a bug.
* rename.
* add comments.
* add comments.
* add init_edata.
* rewrite memory alloc.
* move vector to CSR.
* fix.
* init data.
* Revert "init data."
This reverts commit 2b217b9553911b7dd84a9f1d9b68430b5aa18e23.
* init data.
* init new columns correctly.
2019-04-08 12:09:02 -07:00
9565db6f9e
fix warning. ( #479 )
2019-04-06 09:55:58 +08:00
4ea42e3e08
fix gcn. ( #469 )
2019-04-05 10:56:09 -07:00
8058f1c579
[Fix] Update inner API of distributed sampler ( #478 )
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* update inner API of distributed sampler
* update
2019-04-05 10:00:36 +08:00
da3ab84c3c
Add demo for distributed sampler ( #474 )
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* add C++ rpc infrastructure and distributed sampler
* update
* update lint
* update lint
* update lint
* update
* update
* update
* updare
* update
* update
* update
* update serialize and unittest
* update serialize
* lint
* update
* update
* update
* update
* update
* update
* update unittest
* put Finalize() to __del__
* update unittest
* update
* delete buffer in Finalize
* update unittest
* update unittest
* update unittest
* update unittest
* update
* update
* fix small bug
* windows socket impl
* update API
* fix bug in serialize
* fix bug in serialzie
* set parent graph
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* fix
* fix windows compilation error
* fix windows error
* change API to lower-case
* update test
* fix typo
* update
* add SamplerPool
* add SamplerPool
* update
* update test
* update
* update
* update
* update
* add example
* update
* update
* add distributed sampler demo
* add index
* update demo of distributed sampler
* fix lower-case
* print subg index
* update README.md
* update
* remove --gpu args
2019-04-03 16:09:59 -07:00
9b4fb2fb32
[Doc]Fix 'git remote' command in contribution doc ( #470 )
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* fix docs remote instead of remove
* Update CONTRIBUTORS.md
2019-04-01 09:05:17 +08:00
5d494c6207
[RPC] add C++ RPC infrastructure and distributed sampler ( #465 )
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* add C++ rpc infrastructure and distributed sampler
* update
* update lint
* update lint
* update lint
* update
* update
* update
* updare
* update
* update
* update
* update serialize and unittest
* update serialize
* lint
* update
* update
* update
* update
* update
* update
* update unittest
* put Finalize() to __del__
* update unittest
* update
* delete buffer in Finalize
* update unittest
* update unittest
* update unittest
* update unittest
* update
* update
* fix small bug
* windows socket impl
* update API
* fix bug in serialize
* fix bug in serialzie
* set parent graph
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* fix
* fix windows compilation error
* fix windows error
* change API to lower-case
* update test
* fix typo
* update
* add SamplerPool
* add SamplerPool
* update
* update test
* update
* update
* update
* update
* add example
* update
* update
2019-03-29 16:48:45 +08:00
6066fee935
[Model][Feature] PinSage & Random Walk with Restart ( #453 )
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* random walk traces generation
* remove outdated comments
* oops put in the wrong place
* explicit inline
* moving rand_r to util
* pinsage-like model on movielens
* the code runs now
* support cuda
* using readonly graph
* moving random walk to public function
* per-thread seed and openmp support
* pinsage-like model on movielens
* the code runs now
* support cuda
* using readonly graph
* using C random walk
* removing profile decorators
* param initialization
* no grad
* leaky relu fixes everything
* train and save
* WIP
* WIP
* WIP
* seems to work
* evaluation output
* swapping order of val/test and train
* debug
* hyperparam tuning
* prior/training dataset split changes
* random walk reorg
* random walk with restart
* signed comparison fix
* migrating random walk to nodeflow
* Revert "migrating random walk to nodeflow"
This reverts commit f2565347cced7c912a58a529b257c033d9f375b7.
* add README and remove dataset
* new endpoint
* lint
* lint x2
* oops forgot test
* including bpr - better for baseline
* addressing fixes
* throwing random walks out from SamplerOp class
* forgot to move RandomWalk; why did this even work?
* removing legacy garbage
* add todo
* address comments
* stupid bug fix
* call ndarrayvector converter to handle traces
2019-03-29 13:01:18 +08:00
2dff1aba83
[Bugfix] Fix shape of test_relation tensor in RGCN ( #464 )
2019-03-28 14:34:07 -04:00
5033d94530
[News] Add GTC 2019 Tutorial as news in readme ( #462 )
2019-03-23 17:39:09 -04:00
341dbea0a1
[Bug] Fix unused prefetch switch for NeighborSampler and LayerSampler ( #457 )
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* forgot prefetch switch
* yet another stupid bug
2019-03-19 14:57:10 +08:00
33b9c38389
[Bugfix] fix bug in pickling ( #456 )
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* fix bug in pickling
* fix lint
2019-03-18 23:48:20 -04:00
6f603bbf8f
[BugFix] Fix performance bug in EdgeSoftmax ( #452 )
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* fix performance bug in EdgeSoftmax
* minor
2019-03-18 16:22:38 -04:00
681e5217dd
[Refactor] Sampler code refactor ( #454 )
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* refactored sampler code
* docstring
* fix tutorial
2019-03-18 10:41:35 -04:00
eb1acecd0d
[BugFix] Handle case when calling send with builtin message function ( #449 )
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* fix send with builtin bug
* test cases
* remove todo comment
2019-03-13 14:49:50 -04:00
d1d580ecc1
[feature & bugfix] adjacency_matrix_scipy, wrong order of edges in immutable graph. ( #437 )
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* fix rgcn tutorial
* small fix
* upd
* findedge/s
* upd
* upd
* upd
* upd
* add test
* remove redundancy
* upd
* upd
* upd
* upd
* add edge_subgraph
* explicit cast
* add test immutable subg
* reformat
* reformat
* fix bug
* upd
* hotfix
* subgraph docs
* fix adj mat
* fix edges() order
* add test
* revert
* upd
* fix
* upd
2019-03-12 23:57:13 -04:00
8f426250e9
switching to msbuild for conda windows ( #448 )
2019-03-13 10:39:41 +08:00
13272628b5
[Doc] added index [0] to torch.max ( #443 )
2019-03-08 18:29:16 -05:00
d3cd60142c
[Build] fix setup script to allow cython ext ( #444 )
2019-03-08 18:23:38 -05:00
32e0f74811
[Release] Update readme performance number ( #441 )
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* update README performance number
* news
2019-03-08 18:17:31 -05:00
2ade0ef96d
[Hotfix] fix cython bug ( #442 )
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* fix cython bug
* fix
* fix
2019-03-08 17:07:17 -05:00
cd4f0a2bfc
[Release] update version ( #440 )
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* update version
* update news
2019-03-08 11:12:16 -05:00
8651be54c2
[Perf] Accelerate block_compute when all nodes are invoked. ( #434 )
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* refactor.
* accelerate update_all in nodeflow.
* fix.
* refactor.
* fix lint.
* fix lint.
* reorganize.
* reorg.
* remove.
* add doc.
* impl block_incidence_matrix
* fix lint.
* fix.
* simple fix.
* fix test.
* fix interface.
* fix eid.
* fix comments.
2019-03-07 13:39:39 -08:00
ca2a7e1ca1
[Refactor] Nodeflow, sampling, CAPI ( #430 )
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* enable cython
* add helper function and data structure for void_p vector return
* move sampler from graph index to contrib.sampling
* WIP
* WIP
* refactor layer sampling
* pass tests
* fix lint
* fix graphsage
* remove comments
* pickle test
* fix comments
* update dev guide for cython build
2019-03-05 14:07:22 -05:00
27e0e547dd
[BUG] Graceful handling of random walking with no successors ( #433 )
2019-03-05 21:19:35 +08:00
d3c24cc25b
[BugFix] Fix bug in RGCN data processing and use index_select to improve speed ( #429 )
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* use index_select instead of __getitem__
* fix bug in dataset processing
* fix edge_type shape bug
* comments
2019-03-04 10:52:21 -05:00
fb4246e564
[Feature]Uniform layer-wise sampler ( #416 )
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* migrate to node-flow
* uniform layer sampler test cases
* more test cases
* documentations
* fix lint errors
* fix lint errors
* fix lint errors
* iota
* add asnumpy
* requested changes
* fix indptr error
* fix lint errors
* requested changes & fix lint errors
* fix lint errors
* fix LayerSampler unit test
2019-03-02 16:37:18 -08:00
a88f351174
[Doc] update doc string ( #426 )
2019-03-02 14:00:52 -05:00
3cc32a9775
[Feature] Reduce messages with scatter_add in PyTorch ( #427 )
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* implement pytorch spmm with gather and scatter add
* fix
* replace torch take with index_select
* comments
* comment about pytorch __getitem__ operator pitfall
* typo
2019-03-01 22:51:51 -05:00
fe44ffe5dc
[Doc] fix equation in nn.conv ( #425 )
2019-03-01 15:56:08 -05:00
dba2a5b628
[Doc] Add DGLSubGraph, and DGLGraph.readonly() interface to docs ( #421 )
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* fix rgcn tutorial
* small fix
* upd
* findedge/s
* upd
* upd
* upd
* upd
* add test
* remove redundancy
* upd
* upd
* upd
* upd
* add edge_subgraph
* explicit cast
* add test immutable subg
* reformat
* reformat
* fix bug
* upd
* hotfix
* subgraph docs
2019-03-01 10:10:24 -05:00
bea07b41b3
[Sampler] fix the API of neighbor sampler. ( #407 )
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* don't return aux_info.
* fix sampler test.
* fix sse.
* fix.
* add comment.
2019-02-28 13:45:21 -08:00
7e30382e4f
[Model][MXNet] neighbor sampling & skip connection & control variate & graphsage ( #322 )
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* neighbor sampling draft
* val/test acc
* control variate draft
* control variate
* update
* fix new_history
* maintain aggregated history while updating new history
* preprocess the first layer, change push to pull
* update
* fix subg_degree
* nodeflow
* clear
* readme
* doc and unittest for self loop
* address comments
* rename
* update
* fix
* Update node_flow.py
* Update node_flow.py
2019-02-28 13:29:51 -08:00
3f891b64b7
[Tutorial] Fix gat tutorial ( #420 )
2019-02-28 11:10:14 -05:00
724aa0caf0
[Feature] FindEdge/FindEdges for Immutable Graph ( #404 )
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* fix rgcn tutorial
* small fix
* upd
* findedge/s
* upd
* upd
* upd
* upd
* add test
* remove redundancy
* upd
* upd
* upd
* upd
* add edge_subgraph
* explicit cast
* add test immutable subg
* reformat
* reformat
* fix bug
* upd
2019-02-27 15:32:32 +08:00
c07ae34a99
[Bugfix] removing non-determinism in data loading ( #413 )
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[Bugfix] Removing non-determinism in data loading
2019-02-26 01:24:48 -05:00
565f0c88fc
[WIP] [NN] Refactor NN package ( #406 )
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* refactor graph conv
* docs & tests
* fix lint
* fix lint
* fix lint
* fix lint script
* fix lint
* Update
* Style fix
* Fix style
* Fix style
* Fix gpu case
* Fix for gpu case
* Hotfix edgesoftmax docs
* Handle repeated features
* Add docstring
* Set default arguments
* Remove dropout from nn.conv
* Fix
* add util fn for renaming
* revert gcn_spmv.py
* mx folder
* fix wierd bug
* fix mx
* fix lint
2019-02-25 18:41:21 -05:00
8c750170e8
[Model][Pytorch] GraphSAGE ( #403 )
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* simple implemention of GraphSAGE
* update the abstract method and `torch.nn` modules are more utilized
2019-02-22 15:48:53 -05:00
29dfa349fc
[Doc] update contributors ( #409 )
2019-02-22 14:56:02 -05:00
Da Zheng