274e1082f5
[Doc] API doc string for many components ( #245 )
...
* builtin function docstring
* init docstring
* view docstring
* add init to index and fix
* node /edge feature
* Example -> Examples
* fix func hyperlink
* traversal
* fix
* from/to_networkx docstring
* minor
* fix duplicate label
* comment about tensor framework
* from scipy sparse matrix
* fix format errors
2018-12-04 17:52:00 -05:00
7cca500787
[Doc] Computing with DGLGraph ( #212 )
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* Docs for graph computing
* Docs for graph computing
* Fix
* WIP
* update the docstring
2018-12-04 16:51:46 -05:00
c99f423718
[Sampler] extend sampler ( #238 )
2018-12-04 16:46:26 -05:00
455ea48570
[Bugfix] Conversion between networkx and DGLGraph ( #244 )
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* copy feature to networkx
* fix to_network for multi-graph
* test case for nx conversion
* iterate over Index returns plain int instead of numpy.int64
* fix from_network multi-edge bug
2018-12-04 16:19:11 -05:00
a5a35d1f7a
[Sampler] improve random shuffle performance in sampler ( #228 )
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* fix.
* make it generic.
* add the API.
* fix.
* remove mxnet.
2018-12-04 09:24:32 -08:00
dafe46710b
[Bug][MXNet] fix an API in immutable graph index. ( #233 )
2018-12-04 00:37:18 -05:00
b1e8d95e99
[Doc] LGNN tutorial ( #210 )
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* tutorial notebook added
* lg tutorial cleaned up
* dataset scaffold
* move dataloader to data
* fix model
* remove todo
* utils seperated
* [model]line graph new implementation + tutorial + binary sub graph dataset
* [tutorial] line graph sphinx scaffold
* [tutorial] lgnn tutorial improved
* [tutorial] remove notebook
* [tutorial] fix lg and gcn links
* [tutorial] fix random seed
* [tutorial]fix
* WIP
* code refactor done
* new mini dataset; remove utils code
* fix
* word fix
* fix link
* minor fix
* minor fix
* minor fix
2018-12-03 17:59:50 -05:00
2c170a8c17
[Graph][Bugfix] Fix the API of map_to_subgraph_nid ( #226 )
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* correct vid mapping API.
* fix sse.
2018-12-03 17:16:35 -05:00
b0c76d48be
[Bug] fix __slots__ in view.py ( #230 )
2018-12-03 13:28:22 -05:00
52ed09a392
[Bug] Fix inplace update ( #221 )
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* inplace write row op and executor
* update scheduler and graph to use inplace write
* fix
* fix bug
* test case for inplace
* fix bugs for inplace apply node/edge
* fix comments
* th.allclose -> U.allclose
2018-12-02 19:14:39 -05:00
5680f8dc13
[DOC] Documentation strings for graph mutation, queries, and subgraphing ( #207 )
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* docstrings for graph mutation & queries
* [Doc] contrib.sampler. (#200 )
* subgraph docs
* updates
2018-12-02 14:41:25 -05:00
57daf9c9a6
[Graph] small fix on the all index ( #219 )
2018-12-02 13:39:04 -05:00
57b07fce92
[Model] Accelerate SSE ( #172 )
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* lazy eval edge ids.
* parallelize node id lookup.
* fix a bug.
* use mxnet for index.
* use update_all in the subgraph training.
* sample neighbors.
* Revert "parallelize node id lookup."
This reverts commit e661f69bb06cb5a7c246f0e106f245e27800e220.
* update README.
* cache subgraphs.
* support all degrees.
* cache adj in CPU.
* fix a bug in sse.
* print.
* raise error on mutable graphs.
* measure train time per epoch.
* fix a bug in graph_index.
* remove readonly in DGLSubGraph.
* cache subgraph properly.
* accelerate getting adjacency.
* split infer.
* lazy eval edges.
* specify inference mode.
* update for new sampler.
* use new mxnet sampling api.
* fix indent.
* remove profiling code.
* remove mxnet from sampler.
* return a lambda function for graph edges.
* add docs for immutable subgraph.
* Revert "return a lambda function for graph edges."
This reverts commit 0de5d7f100e230c518a3fb8976a6227f474d09ee.
* get parent_eid.
2018-12-02 12:43:25 -05:00
5278220f85
update s3 links ( #215 )
2018-12-02 20:48:29 +08:00
53ea03ad82
[Doc] Fix doc bug and warning ( #213 )
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* fix dgmg tutorial indentation
* bug in incidence_matrix docstring
* remove print
2018-12-01 18:58:56 -05:00
0f121eeb76
[Doc] RGCN tutorial ( #206 )
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* rgcn tutorial
* data processing for rgcn
* many fix
* requirements for rgcn tutorial
* fix comments
* description of rgcn dataset
* author
* bug fix
* move all dataset to s3
2018-12-01 14:58:13 -05:00
cccc2339c1
[Dataset] update s3 links ( #209 )
2018-12-01 14:45:30 -05:00
91141a9826
[Dataset] Move file from dropbox to s3 (and fix ci fail due to sst dataset) ( #205 )
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* move file from dropbox to s3
* fix ci and move sst to s3
* remove blank line
2018-11-30 19:44:55 -05:00
c80dc5e012
[model] Tree-LSTM update & hotfix(dropbox link) ( #202 )
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* change the signature of node/edge filter
* upd filter
* Support multi-dimension node feature in SPMV
* stable version
* hotfix
* upd tutorial
* upd README
2018-11-30 19:39:49 -05:00
3a0f86a663
[Doc] data ( #198 )
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* Fix dataset
* Track data APIs
2018-11-30 11:40:22 -05:00
485f6d3abd
[Doc] udf ( #195 )
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* Docstring for udf
* Track udf docs
* Improve
* Improved
* Delete udf.py
* Improve
2018-11-30 00:38:58 -05:00
9e8261735f
[Doc] Minor doc update for mxnet/immutable_graph_index ( #194 )
2018-11-29 20:59:13 -05:00
41c9c3b94b
[Doc] Fix batched_graph doc ( #193 )
2018-11-29 12:23:10 -05:00
8dc6784b12
[Doc] docstring for BatchedDGLGraph + some fix ( #184 )
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* Update doc
* Update batched_graph.py
* Fix
* Fix
* Fix
* Fix
2018-11-29 09:53:16 -05:00
a8fa85c7d5
Conda builds ( #187 )
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* conda recipe
* switching to source build
* trying windows build
* wip
* windows build works
2018-11-29 02:21:53 -05:00
a0d0b1ea00
[Model] Fix + batched DGMG ( #175 )
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* DGMG with batch size 1
* Fix
* Adjustment
* Fix
* Fix
* Fix
* Fix
* Fix has_node and __contains__
* Batched implementation for DGMG
* Remove redundant dependency
* Adjustment
* Fix
* Add comments
2018-11-29 00:13:30 +08:00
5cda368d79
[Model] SBM hotfix ( #137 )
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* [Model]SBM hotfix
* [Model] remove backend in data
2018-11-27 11:58:03 -05:00
2c2b747808
[Install] pip install ( #180 )
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* add bdist_wheel build
* fix wheel build
* fix setup
* fix ci
* fix setup
* fix
* fix setup
* poke ci
* fix
* poke ci
* clean build
* fix ci
* addback the env
2018-11-27 00:47:01 -05:00
b82b8e2d2a
[Schedule] get rid of unnecessary graph.edges() call for v2v-spmv update_all ( #179 )
2018-11-27 00:37:03 -05:00
524e656dd6
[Bugfix] enable SPMV for multi-dimension node feature ( #178 )
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* Support multi-dimension node feature in SPMV
* fix as requested
2018-11-26 11:12:28 -05:00
b1eeb93449
[Bugfix][Runtime] Zero degree behaviors ( #177 )
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* fix recv nodes are all 0deg; fix hybriddict does not through keyerror properly
* fallback to apply_nodes when all nodes are 0deg; WIP on pull spmv 0deg
* new 0deg behavior
* new 0deg behavior
* update mx utest for pull-0deg
* fix mx
* fix mx
* get rid of unnecessary sort-n-unique
2018-11-25 22:33:08 -05:00
4dfe7547e8
Fix num_rows bug in batched_graph ( #169 )
2018-11-23 02:49:59 +08:00
23e2e83b5e
[API] change the signature of node/edge filter ( #166 )
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* change the signature of node/edge filter
* upd filter
2018-11-22 13:00:36 -05:00
deb653f8dc
[Runtime] Scheduler and Executor ( #140 )
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* executor api
* draft executor interface
* WIP
* revert changes to avoid conflict with api change
* core scheduling logic
* WIP: build graph adj
* incidence matrix for in edges
* support incidence matrix for partial recv nodes
* improve
* build adjmat in scheduler
* graph store
* get degree bucketing schedule
* connect to c++ degree bucketing
* conceptual executor creation code
* executor comments
* fix
* more executor comments
* WIP: full send_and_recv schedule
* most schedulers
* simplify scheduler
* executors
* runtime
* builtin function base class
* adj indices and shape
* completely refactor scheduler
* rename and move bundled out to function.py
* use_edge_feature in msg func
* rewrite scheduler
* node edge executor
* connect with graph api
* handle zero degree
* misc
* fix test cases
* fix a good many bugs...
* remove old scheduler
* push and pull
* fix send recv
* c++ lint
* fix batched send recv
* hot fix for mxnet
* typo
* write back executor
* apply node edge
* clean up, doc string
* fix as requested
* refactor
* fix
* WIP
* WIP
* ir draft
* more on ir
* WIP: spmv schedule
* WIP
* recv schedule
* refactor
* WIP
* snr degree bucketing
* snr scheduler
* move prog to graph.py; rename
* unittest for send/recv
* remove some legacy codes
* WIP: update_all
* pass test_basics
* passed all current utests
* more utests; fix mx utest
* WIP: fixing zero deg initial value
* some tests
* fix 0deg problem
* fix mx
* fix mx
* some notes
* fix as requested
2018-11-22 12:15:50 -05:00
0ec1a492b3
[Frame] change num rows behavior ( #163 )
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* move initializer to column scheme; change num rows behavior
* poke mx ci
* fix mx utest in append
* fix bug in add edges
* utest for updating partial rows
* fix bug in from_networkx and from_scipy_matrix
* revert per-col initializer change
* fix pickle utest
2018-11-21 11:50:46 -05:00
5f89cd662e
Fix the convergence problem in SSE. ( #162 )
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* add a test.
* move file.
* debug
* add degree normalization.
* it can converge now.
* remove hidden_data.
* use readonly graph index.
* use subgraph loader.
* refactor code and remove intermediate data.
* split inference.
* mix cpu and gpu training.
* fix mxnet sparse_matrix constructor.
* convert tensor context.
* set up the prediction model.
* load mxnet csr directly.
* add timing.
* move test_sse.py to sse_batch.py
* fix the tensor version of SSE.
* update README.
2018-11-20 15:57:52 +08:00
e515f5311b
[Frame] supporting partial row on first column and individual column initializers ( #160 )
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addresses issue #156
2018-11-19 18:18:36 -05:00
79a510252b
Pickling support ( #155 )
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* pickling support
* resorting to suggested way of pickling
* custom attribute pickling check
* working around a weird pytorch pickling bug
* including partial frame case
* pickling everything now
* fix as requested
2018-11-16 17:19:20 -05:00
05f464f824
[Bugfix] fix args with incontiguous node and edge tensor ( #153 )
2018-11-15 10:55:15 -05:00
ed1854e800
[Bugfix] fix a potential context mismatch ( #154 )
2018-11-15 09:47:20 -05:00
2389df8155
[API] Subgraph sampling API. ( #138 )
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* add neighbor sampler.
* fix sampler.
* handle non-existing nodes differently in MapParentIdToSubgraphId.
* fix sampling tests.
* parallelize sampling.
* add more tests.
* fix a bug in subgraph loader.
* get number of sampled nodes directly.
* load mxnet CSR to DGLGraph directly.
* create graph from mxnet csr array directly.
* use subgraph loader in SSE.
* fix a bug in sampling.
* output framework tensor.
* fix.
* remove unnecessary code.
* fix tests.
* add SSE README.
* move to contrib.
* address comments.
* add tests.
2018-11-14 13:51:27 -08:00
048f6d7a30
[GraphIndex] refactor graph caching ( #150 )
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* refactor graph caching
* fix mx test
* fix typo
2018-11-13 22:12:38 -05:00
a9ffb59e66
[DOC][Model] Tree-LSTM example and tutorial ( #146 )
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[DOC][Model] Tree-LSTM example and tutorial
2018-11-13 18:09:14 -05:00
0452cc3c0c
[Bug] Transpose adj is not correctly cached ( #148 )
2018-11-12 22:15:45 -05:00
d6c80e0cf7
[API] bfs with edges ( #132 )
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* bfs with edges
* dfs toy test case
* clean up
* style fix
* bugfix
* updating docs for bfs_edges and readouts
2018-11-11 17:19:55 -05:00
a36d0841b5
removing 3.6 f-string ( #139 )
2018-11-11 14:43:15 -05:00
6d96a97f17
[Doc] docstring for SST dataset ( #133 )
2018-11-10 11:59:55 -05:00
40ca5de450
[API] Readout interfaces ( #124 )
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* fixing builtin src*edge shape mismatch
* bundled function refactor (?)
* fixing names
* readout prototype
* oops
* more fixes
* removing readout prototype
* sum_on() with SPMV, fixing batching with 0 edges
* readouts with segmented sum
* typo (??????)
* fixes NLTK dependency (#125 )
* misc fixes including #126 (pushing again)
* sanity check for mxnet
* fixes NLTK dependency (#125 ) and #126
* reverting to sum_nodes/edges
2018-11-10 11:35:34 -05:00
8ea359d125
[API] Message propagation APIs ( #127 )
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* add examples in traversal.py
* message propagate methods
* use the new message propagation for tree-lstm
* update to the new name
* update propagate API doc
* update doc
* add propagate utest
2018-11-09 15:04:57 -05:00
72efb42718
[Bugfix] fixes NLTK dependency ( #125 ) and #126 ( #131 )
2018-11-09 14:16:52 -05:00
Lingfan Yu