8651be54c2
[Perf] Accelerate block_compute when all nodes are invoked. ( #434 )
...
* 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 )
...
* 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
fb4246e564
[Feature]Uniform layer-wise sampler ( #416 )
...
* 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
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 )
...
* 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
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
bfe3e9d64a
[Feature] Add switch readonly state interface ( #389 )
...
* 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
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
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
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
929742b588
[Feature] Reimplement Immutable graph index in DGL ( #342 )
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* init.
* it's compiled.
* add immutable graph constructor.
* add immutable graph API.
* fix.
* impl get adjacency matrix.
* fix.
* fix graph_index from scipy matrix.
* add neighbor sampling.
* remap vertex ids.
* fix.
* move sampler test.
* fix tests.
* add comments
* remove mxnet-specific immutable graph.
* fix.
* fix lint.
* fix.
* try to fix windows compile error.
* fix.
* fix.
* add test.
* unify Graph and ImmutableGraph.
* fix bugs.
* fix compile.
* move immutable graph.
* fix.
* remove print.
* fix lint.
* fix
* fix lint.
* fix lint.
* fix test.
* fix comments.
* merge GraphIndex and ImmutableGraphIndex.
* temp fix.
* impl GetAdj.
* fix lint
* fix.
* fix.
* fix.
* fix.
* fix.
* use csr only for readonly graph.
* Revert "use csr only for readonly graph."
This reverts commit 8e24bb033af8504531b22849de5b7567b168e0d5.
* remove code.
* fix.
* fix.
* fix.
* fix.
* fix.
* fix.
* address comments.
* fix for comments.
* fix comments.
* revert.
* move test_graph_index to compute.
* fix.
* fix.
* impl GetAdj for coo.
* fix.
* fix tests.
* address comments.
* address comments.
* fix comment.
* address comments.
* use lambda.
* other comments.
* address comments.
* modify the semantics of edges.
* fix order.
* use DGLIdIter
* fix.
* remove NotImplemented.
* revert some code.
2019-01-17 09:59:53 +08:00
3a868eb04b
[Feature] Max readout and consecutive labeling for networkx ( #341 )
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* Max readout and consecutive labeling
* Delete test_readout.py
* Delete test_basics.py
* Test case and fix
* Recover accidentally removed file
* Fix import order
* Fix test case
* Fix
* Fix
* Fix
* Fix
* Fix
* revert
* Fix
* Fix
* Fix
2019-01-10 12:58:05 -05:00
e19cd62ecd
[Test] Unify tests for different backends ( #333 )
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* test basics
* batched graph & filter, mxnet filter fix
* frame and function; bugfix
* test graph adj and inc matrices
* fixing start = 0 for mxnet
* test index
* inplace update & line graph
* multi send recv
* more tests
* oops
* more tests
* removing old test files; readonly graphs for mxnet still kept
* modifying test scripts
* adding a placeholder for pytorch to reserve directory
* torch 0.4.1 compat fixes
* moving backend out of compute to avoid nose detection
* tests guide
* mx sparse-to-dense/sparse-to-numpy is buggy
* oops
* contribution guide for unit tests
* printing incmat
* printing dlpack
* small push
* typo
* fixing duplicate entries that causes undefined behavior
* move equal comparison to backend
2019-01-05 23:32:33 -05:00
Da Zheng