660f356e06
Merge branch 'master' of github.com:zzhang-cn/dgl into 0.2.x
2019-03-08 17:07:42 -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
c4082bef7e
add cython ext
2019-03-08 15:15:15 -05:00
2f6222283c
update conda meta
2019-03-08 14:30:32 -05:00
d8fe6debb2
fix branch name in conda
2019-03-08 11:28:22 -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
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
98ff82e527
[Doc] Tutorial for GAT ( #400 )
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* 9_gat.py
* readme
* Update 9_gat.py
* Update 9_gat.py
* fix format
2019-02-20 22:50:55 -05:00
bfe3e9d64a
[Feature] Add switch readonly state interface ( #389 )
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* fix rgcn tutorial
* small fix
* add switch readonly state interface
* remove trailing ws
* fix
* fix
* change signature
* change signature
* remove trailing ws
* upd
* upd interface
* upd
* rm trailing ws
* reformat
* trailing space
* upd
2019-02-20 18:51:56 -05:00
111a4aa754
[Bugfix] Fix the SSE tutorial in CI. ( #401 )
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* fix.
* add check.
* fix assert.
2019-02-20 14:55:18 -08:00
6e7f3f3d24
Find OpenMP in CMake ( #402 )
2019-02-20 17:00:15 -05:00
bd9171d6cd
[Doc Fix] Fix group_apply_edges docs display
2019-02-21 00:19:39 +08:00
2e1cbd5d68
[Feature] Random walk traces generation ( #392 )
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* random walk traces generation
* remove outdated comments
* oops put in the wrong place
* explicit inline
* moving rand_r to util
* moving random walk to public function
* per-thread seed and openmp support
* type cast styles
2019-02-20 10:41:59 -05:00
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
220a1e68fb
[BUG] Fixing bug in pickling readonly graphs ( #397 )
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* fixing bug in pickling readonly graphs
* multigraph test coverage
* fixing lint (??????)
* another lint
* is_readonly interface
2019-02-19 00:14:11 -05:00
788d8dd4ad
[Model]PPI dataloader and inductive learning script. ( #395 )
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* 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
59ec7a9c93
MSBuild instructions ( #393 )
2019-02-14 11:56:32 -05:00
40afdf7cd5
[Bugfix] Remove unnecessary assert in from_scipy_sparse_matrix ( #391 )
2019-02-13 17:45:22 -05:00
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
29dd22e666
[Model] Support Multi-GPU for Transformer model ( #356 )
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* multi-process version of transformer
* lots of fix
* fix bugs and accum gradients for multiple batches
* many fixes
* minor
* upd
* set torch device
* fix bugs
* fix and minor
* comments and clean up
* uncomment viz code
2019-02-11 20:17:45 -05:00
1c63dd4f52
[Doc] fix the comment error of edge_id in graph.h ( #382 )
2019-02-11 13:14:47 -05:00
51293a3273
[Data] reddit data loader ( #372 )
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* reddit data loader
* upload to S3
* update
* add self loop
* address comments
* fi
2019-02-08 10:53:39 -08:00
5b9147c464
[Feature] Edge Group Apply API ( #358 )
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* add rtfd
* rrr
* update
* change env
* temp fix
* update
* fix
* fix
* add
* conf
* Move file_pattern from Makefile to conf.py
* remove yml
* fix
* fix
* fix
* fix
* remove yml
* remove yml
* add doc docker
* add dgl install script
* change name
* change dockerfile
* fix
* name
* add
* fix
* fix
* fix
* fix
* fix docker
* delete sphinx.py for doc-build backend
* Add softmax to test backend
* Add group apply function and tests
* Delete unnecessary file
* Update comments and test
* Fix lint
* remove unused bucketing code
* group apply edge bucketing code
* gen degree bucket schedule for group apply edge
* schedule and graph code
* fix compiling
* fix
* fix lint
* naming
* harder test case
* fix comments
* more comments
* tweak function name
2019-02-03 11:14:52 -05:00
9cd0df7dde
[Doc] Update README in MXNet GCN. ( #373 )
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* update readme.
* Revert "update readme."
This reverts commit cd5ea512059adadfcb22a615a2c42bba12f334a8.
* update.
2019-02-02 21:59:07 -08:00
12d706300c
[Hotfix] fixing zero shaped tensor problems for PyTorch 1.0.0 in JTNN example ( #371 )
2019-01-31 21:07:09 -05:00
dedfd908c6
[Fix] Fix link in batched graph blog ( #367 )
2019-01-26 11:04:05 -05:00
1989f8f43c
fix broken link ( #366 )
2019-01-26 23:17:55 +08:00
3cbfc25a32
[Tutorial] Batched Graph Classification ( #360 )
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* batched_graph_classification
* Fix
* Fix
* update tutorial with new dataset
* Final
* Fix doc for dataset
* small fix
2019-01-25 15:13:52 -05:00
abf12fc757
[Data] Synthetic dataset for graph classificaiton ( #364 )
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* minigc dataset
* more comments
* sphinx
2019-01-25 10:47:47 -05:00
525bb61245
[Doc] Fix a typo ( #365 )
2019-01-25 10:41:37 -05:00
Minjie Wang