94ecb8eb96
[BUGFIX] copy graph index to shared memory. ( #634 )
...
* copy graph index to shared memory.
* fix.
* fix.
* fix.
* use a diff name for in-csr and out-csr.
* fix lint.
* remove print.
* add test.
* add comments.
2019-06-12 01:32:25 -07:00
411bcd7e6c
[BUGFIX] extand DGLGraph graph_data. ( #632 )
...
* enable tutorial test in CI.
* extand DGLGraph graph_data.
* update doc.
* Revert "enable tutorial test in CI."
This reverts commit cd774067180922bb6ae979bde4aecbffc61c8147.
* accept DGLGraph in graph store.
2019-06-09 17:22:04 -07:00
fc7775a20f
Define node/edge Ids in NodeFlow more clearly ( #628 )
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* add tests.
* distinguish layer-local nid and nodeflow nid.
* use numpy assert_array_equal and assert_allclose
* fix map_from_parent_nid
* fix test
* fix test.
* renmae remap.
* update doc.
* update doc.
* update doc.
* fix test.
* fix test.
2019-06-09 12:10:07 -07:00
dec8b49b5d
[Examples] Run all the examples ( #623 )
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* all pytorch examples
* scan through mxnet examples
* change reddit data
* tweak numerical range for unittest
* fix ci
* fix ci
* fix
* add seed to workaround
2019-06-09 00:26:13 -04:00
74e13eea61
[Model] Update GAT model code ( #622 )
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* fix gat code to use latest edge softmax module
* avoid transpose
* update README
* use edge_softmax op
* mxnet edge softmax op
* mxnet gat
* update README
* fix unittest
* fix ci
* fix mxnet nn test; relax criteria for prod reducer
2019-06-08 21:41:38 -04:00
01a4cc5b7b
[Graph] Add API to convert graph to simple graph ( #587 )
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* to simple
* WIP: multigraph flag
* graph index refactor; pass basic testing
* graph index refactor; pass basic testing
* fix bug in to_simple; pass torch test
* fix mx utest
* fix example
* fix lint
* fix ci
* poke ci
* poke ci
* WIP
* poke ci
* poke ci
* poke ci
* change ci workspace
* poke ci
* poke ci
* poke ci
* poke ci
* delete ci
* use enum for multigraph flag
2019-06-01 23:32:46 -04:00
e0ce190dfe
[Doc] Update README.MD of demo for distributed sampler ( #579 )
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* Update README.md for the demo of distributed sampler
* Update README.MD of demo for distributed sampler
2019-05-30 01:24:13 -04:00
e0004f7199
[Doc] sampler readme update. ( #581 )
2019-05-29 23:47:57 -04:00
08d4900fd1
Update README.md for the demo of distributed sampler ( #577 )
2019-05-28 17:24:33 +08:00
9aa5ffcab1
[DEMO] Update demo of distributed sampler ( #564 )
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* update
* update
* update demo
2019-05-26 12:10:53 +08:00
8f378d90ad
[BUGFIX] fix bugs for running GCN on giant graphs. ( #561 )
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* load mxnet csr.
* enable load large csr.
* fix
* fix.
* fix int overflow.
* fix test.
2019-05-25 11:09:33 -07:00
86d60a1ff6
[DEMO] Add Pytorch demo for distributed sampler ( #562 )
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* update
* update
* update
* add sender
* update
* remove duplicate cpde
2019-05-24 11:53:28 +08:00
924efc6520
[Perf] Improve performance of graph store. ( #554 )
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* fix.
* use inplace.
* move to shared memory graph store.
* fix.
* add more unit tests.
* fix.
* fix test.
* fix test.
* disable test.
* fix.
2019-05-23 12:23:31 -07:00
49c4a9e4cc
[DEMO] Remove duplicate code for sampling ( #557 )
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* update
* update
* re-use single-machine code
* update
* use relative path
* update
* update
* update
* add __init__.py
* add __init__.py
* import sys, os
* fix typo
* update
2019-05-23 16:57:35 +08:00
28379f927f
[DEMO] Reproduce numbers of distributed training in AMLC giant graph paper ( #556 )
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* update
* update
* update
* update num_hops
* fix bug
* update
* report numbers of distributed training in AMLC giant graph paper
2019-05-23 14:23:14 +08:00
f99725adbc
all demo use python-3 ( #555 )
2019-05-23 10:38:05 +08:00
b2b8be25bb
[API] update graph store API. ( #549 )
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* add init_ndata and init_edata in DGLGraph.
* adjust SharedMemoryGraph API.
* print warning.
* fix comment.
* update example
* fix.
* fix examples.
* add unit tests.
* add comments.
2019-05-21 03:27:05 -07:00
cdfca992e1
[BUGFix] Improve multi-processing training ( #526 )
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* fix.
* add comment.
* remove.
* temp fix.
* initialize for shared memory.
* fix graphsage.
* fix gcn.
* add more unit tests.
* add more tests.
* avoid creating shared-memory exclusively.
* redefine remote initializer.
* improve initializer.
* fix unit test.
* fix lint.
* fix lint.
* initialize data in the graph store server properly.
* fix test.
* fix test.
* fix test.
* small fix.
* add comments.
* cleanup server.
* test graph store with a random port.
* print.
* print to stderr.
* test1
* test2
* remove comment.
* adjust the initializer signature.
2019-05-20 14:23:19 -07:00
d8c69d53e2
Fixing typo in JTNN after interface change ( #536 )
2019-05-16 09:43:03 +08:00
3a1392e641
[Model] add multiprocessing training with sampling. ( #484 )
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* reorganize sampling code.
* add multi-process training.
* speed up gcn_cv
* fix graphsage_cv.
* add new API in graph store.
* update barrier impl.
* support both local and distributed training.
* fix multiprocess train.
* fix.
* fix barrier.
* add script for loading data.
* multiprocessing sampling.
* accel training.
* replace pull with spmv for speedup.
* nodeflow copy from parent with context.
* enable GPU.
* fix a bug in graph store.
* enable multi-GPU training.
* fix lint.
* add comments.
* rename to run_store_server.py
* fix gcn_cv.
* fix a minor bug in sampler.
* handle error better in graph store.
* improve graphsage_cv for distributed mode.
* update README.
* fix.
* update.
2019-05-06 23:51:56 -07:00
e89519150f
disable pytorch reddit ( #512 )
2019-04-28 11:24:14 +08:00
2ff8ecfbac
update test_batch_size ( #510 )
2019-04-25 13:28:36 +08:00
3b96299a45
sampling ( #505 )
2019-04-23 12:14:38 +08:00
ad9da36add
[Model] Add DGI Model ( #501 )
2019-04-22 11:37:06 +08:00
fe7d5e9b8b
[Sampler] Change Distributed Sampler API ( #499 )
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* Change Distributed Sampler API
* fix lint
* fix lint
* update demo
* update
* update
* update
* update demo
* update demo
2019-04-22 09:41:47 +08:00
3f4645918d
[Model] Add edge dropout to APPNP ( #493 )
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* [Model] Add edge dropout to APPNP
[Model] Add edge dropout to APPNP
* [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.
* [Model] Add edge dropout to APPNP
[Model] Add edge dropout to APPNP
update
2019-04-18 20:58:28 +08:00
6124667f42
[Model] Refactor the sampling examples ( #498 )
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* 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 )
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* 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
b89dcce16c
[RPC] Refactoring networking APIs ( #496 )
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* 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
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
4ea42e3e08
fix gcn. ( #469 )
2019-04-05 10:56:09 -07:00
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
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
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
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
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
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
cdbeb17f2d
[Model] Simplifying Graph Convolutional Networks. ( #405 )
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* [Model] Simplifying Graph Convolutional Networks.
* - improve code stype (use nn.Linear)
- use `bias` option
- update hyperparameter and corresponding performance
2019-02-22 15:17:26 +08:00
f370e628cd
[Feature] add NodeFlow API ( #361 )
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* sample layer subgraphs.
* fix.
* fix.
* add layered subgraph.
* fix lint.
* fix.
* fix tutorial.
* fix.
* remove copy_to_parent.
* add num_layers
* move sampling code to sampler.cc
* fix.
* move subgraph construction out.
* Revert "move subgraph construction out."
This reverts commit 24b3d13b0d8ed5f91847ea75a7674ee8f7d45cff.
* change to NodeFlow.
* use NodeFlow in Python.
* use NodeFlowIndex.
* add node_mapping and edge_mapping.
* remove unnecessary code in SSE tutorial.
* Revert "remove unnecessary code in SSE tutorial."
This reverts commit 093f0413d5fa2e63ca5f80c46c80a126a9fb720c.
* fix tutorial.
* move to node_flow.
* update gcn cv updater.
* import NodeFlow.
* update.
* add demo code for vanilla control variate sampler.
* update.
* update.
* add neighbor sampling.
* return flow offsets.
* update node_flow.
* add test.
* fix sampler.
* fix graph index.
* fix a bug in sampler.
* fix map_to_layer_nid and map_to_flow_eid.
* fix apply_flow.
* remove model code.
* implement flow_compute.
* fix a bug.
* reverse the csr physically.
* add mini-batch test.
* add mini batch test.
* update flow_compute.
* add prop_flows
* run on specific nodes.
* test copy
* fix a bug in creating frame in NodeFlow.
* add init gcn_cv_updater.
* fix a minor bug.
* fix gcn_cv_updater.
* fix a bug.
* fix a bug in NodeFlow.
* use new h in gcn_cv_updater.
* add layer_in_degree and layer_out_degree.
* fix gcn_cv_updater for gpu.
* temp fix in NodeFlow for diff context.
* allow enabling/disabling copy back.
* add with-updater option.
* fix a bug in computing degree.
* add with-cv option.
* rename and add comments.
* fix lint complain.
* fix lint.
* avoid assert.
* remove assert.
* fix.
* fix.
* fix.
* fix.
* fix the methods in NodeFlow.
* fix lint.
* update SSE.
* remove gcn_cv_updater.
* correct comments for the schedulers.
* update comment.
* add map_to_nodeflow_nid
* address comment.
* remove duplicated test.
* fix int.
* fix comments.
* fix lint
* fix.
* replace subgraph with NodeFlow.
* move view.
* address comments.
* fix lint.
* fix lint.
* remove static_cast.
* fix docstring.
* fix comments.
* break SampleSubgraph.
* move neighbor sampling to sampler.cc
* fix comments.
* rename.
* split neighbor_list.
* address comments.
* fix.
* remove TODO.
2019-02-19 15:49:28 -08:00
788d8dd4ad
[Model]PPI dataloader and inductive learning script. ( #395 )
...
* Create ppi.py
* Create train_ppi.py
* Update train_ppi.py
* Update train_ppi.py
* Create gat.py
* Update train.py
* Update train_ppi.py
* Update ppi.py
* Update train_ppi.py
* Update ppi.py
* Update train_ppi.py
* Update train_ppi.py
* Update ppi.py
* Update train_ppi.py
* update docs and readme
2019-02-17 16:41:30 -05:00
1ea0bcf486
[Model] fix link & beam search ( #394 )
2019-02-17 13:32:36 -05:00
ae1806f651
[Bugfix] RGCN tutorial ( #388 )
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* fix rgcn tutorial
* small fix
* upd
2019-02-15 11:14:56 +08:00
91b7382378
[Model] update gat ( #390 )
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* update gat: add minus max for softmax
* small fix
2019-02-13 14:53:41 -05:00
6c3dba867a
[Tutorial] Update prerequisites of README ( #380 )
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* Update prerequisites of README
* dependencies for pytorch models
* dependencies for mxnet models
* minor
2019-02-11 22:58:17 -05:00
Da Zheng