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 )
...
* change the signature of node/edge filter
* upd filter
2018-11-22 13:00:36 -05:00
deb653f8dc
[Runtime] Scheduler and Executor ( #140 )
...
* 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 )
...
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 )
...
[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 )
...
* 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
7fe6d0c857
[Doc] Refactor API doc ( #128 )
...
* refactor API doc; add markup link in tutorials
* fix readme
2018-11-08 22:57:16 -05:00
bd0e4fa0b3
[MXNet][API] move to the new API ( #123 )
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* move gat to the new api.
* fix gcn.
* update sse.
* fix dgl core.
* update sse.
* fix small bugs in dgl core.
* fix mxnet tests.
* retrigger
* address comments and fix more bugs.
* fix
* fix tests.
2018-11-08 10:00:47 -08:00
2319167444
[API] Graph traversal ( #103 )
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* bfs, dfs and topological traversal
* dfs and test cases
* Conflicts:
python/dgl/graph.py
src/graph/graph.cc
src/graph/graph_op.cc
* documentation
* requested changes
* Conflicts:
Jenkinsfile
examples/pytorch/gcn/gcn.py
examples/pytorch/gcn/gcn_spmv.py
python/dgl/graph.py
python/dgl/graph_index.py
src/graph/graph.cc
src/graph/graph_op.cc
* Conflicts:
Jenkinsfile
python/dgl/graph_index.py
* fix lint errors
* fix lint errors
* fix lint errors
* fix test cases
* requested changes
* traversal interface
* [Bug] fixed a typo that caused syntax error (#120 )
* WIP
* bfs nodes generator works
* topological traversal
* WIP: dfs_edges
* dfs edges
* dfs labeled edges
* utest for traversal
* fix lint
* fix utest
* code clean
* changes as requested
2018-11-08 10:14:19 -05:00
7241a9c008
[Backend] backend interface ( #109 )
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* backend interface
* small fix
* more comments to the data type dict
* WIP
* convert_to and narrow
* WIP
* pytorch and numpy backend; WIP on mxnet backend
* mxnet backend
* narrow
* Fix all usages
* fix for mx
* fix for mx
* fix mx
* fix mx
* fix mx
* fix mx
* fix mx
* fix mx
* fix mx
* revert jenkins
* add sparse_matrix api
* sparse matrix api
* some fixme
* Fix as requested
2018-11-04 21:42:39 -05:00
b420a5b5b3
[Model] Fix broken CDGNN example ( #111 )
...
* pretty printer
* Conflicts:
python/dgl/data/sbm.py
* refined line_graph implementation
* fix broken api calls
* small fix to trigger CI
* requested change
2018-11-05 07:14:01 +08:00
b355d1eddf
[API] Apply nodes & apply edges ( #117 )
2018-11-04 01:22:53 -04:00
1a2b306f55
[Bug] fix bug in nodes() that does not return int64 tensor ( #116 )
2018-11-03 00:00:29 -04:00
68ec624782
[API][Doc] API change & basic tutorials ( #113 )
...
* Add SH tutorials
* setup sphinx-gallery; work on graph tutorial
* draft dglgraph tutorial
* update readme to include document url
* rm obsolete file
* Draft the message passing tutorial
* Capsule code (#102 )
* add capsule example
* clean code
* better naming
* better naming
* [GCN]tutorial scaffold
* fix capsule example code
* remove previous capsule example code
* graph struc edit
* modified: 2_graph.py
* update doc of capsule
* update capsule docs
* update capsule docs
* add msg passing prime
* GCN-GAT tutorial Section 1 and 2
* comment for API improvement
* section 3
* Tutorial API change (#115 )
* change the API as discusses; toy example
* enable the new set/get syntax
* fixed pytorch utest
* fixed gcn example
* fixed gat example
* fixed mx utests
* fix mx utest
* delete apply edges; add utest for update_edges
* small change on toy example
* fix utest
* fix out in degrees bug
* update pagerank example and add it to CI
* add delitem for dataview
* make edges() return form that is compatible with send/update_edges etc
* fix index bug when the given data is one-int-tensor
* fix doc
2018-11-02 17:19:14 -04:00
2ecd2b23ec
[Frame] Support slice type indexing; optimize dgl.batch ( #110 )
...
* cherry picking optimization from jtnn
* unbatch by slicing frames
* reduce pack
* oops
* support frame read/write with slices
* reverting to unbatch by splitting; slicing is unfriendly to backward
* replacing lru cache with static object factory
* replacing Scheme object with namedtuple
* remove comment
* forgot the find edges interface
* subclassing namedtuple
2018-11-01 00:03:06 -04:00
9827e48176
Support for adding nodes/edges after setting representations ( #114 )
...
* Fix
1. Fix two typos in gcn.py and gcn_spmv.py
2. Update README
* Fix GCN module
1. Update the outdated graph convolution layer class
2. Fix a bug in the code where dropout never works. Modules like dropout/batch norm depend on whether we are in the training stage or inference stage.
* Fix a bug in dropout
1. dropout depends on nn.Module.training
* Update GCN module
* Fix README
* Fix dropout & remove self.msg_field
* Fix
* Align with TF implementation
* Make g an argument for forward
* Remove features from the argument of GraphConv layer
* Support for create nodes/edges after setting representations
* Remove redundant commit
* Delete test_init_repr.py
* Test case for dynamic addition
* Base 'add_rows' upon 'append'
* Move test function
* Fix
* test by assertion
* changed add_rows to adding blank rows only; adding convert_to to backend
* moving test to basics
* oops mxnet
2018-10-29 23:33:54 -04:00
2758c24955
[NN] Fix GCN module ( #99 )
...
1. Update `examples/pytorch/gcn` and `python/dgl/nn/pytorch` based on the latest APIs
2. Add full support for dropout in `examples/pytorch/gcn` and `python/dgl/nn/pytorch`
3. Rename `GCN` class in `python/dgl/nn/pytorch` to be `GraphConvolutionLayer` class
4. Make node field an argument that can be configured by users in GraphConvolutionLayer
Note that adjacency normalization has not been supported yet in the examples.
2018-10-28 04:35:33 +08:00
9e9a9488f1
[GraphIndex] Immutable graph index using MXNet CSRArray ( #86 )
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* add immutable graph index.
* update ImmutableGraphIndex.
* add benchmarks of subgraph generation.
* fix node_subgraphs.
* use scipy synthetic data in immutable graph.
* create immutable_graph.
* use spmv in gcn.
* fix immutable graph index.
* update graph index.
* create ImmutableSubgraphIndex.
* return subgraph node and edge mapping.
* fix benchmark.
* add mapping to subgraph nid.
* test in_edges and out_edges.
* update benchmark.
* Fix immutable subgraph.
* complete in_edges and out_edges.
* fix benchmarks.
* add test on node_subgraphs
* add sse.
* construct subgraphs in parallel.
* add in/out degree(s).
* make immutable graph index backend-specific.
* implement has_edge(s) and edge_id(s).
* Revert "use spmv in gcn."
This reverts commit 9cfed5f5fb3dd2ed9b98745348b1c0e9731ed7f7.
* implement node_subgraphs in GraphIndex.
* fix sse.
* address comments.
* address comments.
* Update mxnet docker.
2018-10-26 11:28:25 -07:00
ff92812609
remove pytorch dependency in sbm.py ( #107 )
2018-10-25 20:22:41 -04:00
2046980231
[DOC] API tutorials ( #96 )
...
* setup sphinx-gallery; work on graph tutorial
* draft dglgraph tutorial
* update readme to include document url
* rm obsolete file
* Draft the message passing tutorial
2018-10-23 16:27:15 -04:00
70d475813c
[BUG] Fixing networkx conversion with 0 edges ( #94 )
...
* fixing networkx conversion with 0 edges
* fixes as required
* remove obsolete comment
2018-10-21 23:15:45 -04:00
dce1f44d46
CI lint check ( #93 )
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* CI for lint check
* init submodule before run lint
* install ubuntu core for lint docker
* remove generator import in dgl
2018-10-18 23:50:24 -04:00
3683a774d5
Merge branch 'cpp' of github.com:jermainewang/dgl into cpp
2018-10-18 22:49:22 -04:00
f1ede61ffa
removing obsolete line_graph()
2018-10-18 22:49:05 -04:00
3e76bcc052
remove anonymous repr
2018-10-18 21:43:40 -04:00
fb6be9fbd7
[GraphIndex] Create graph index directly from scipy matrix. ( #87 )
...
* create synthetic data with scipy.
* changes as comments
2018-10-18 16:39:45 -04:00
4af3f8bcc8
update the MXNet backend. ( #89 )
...
* update mxnet.
* add get_tvmtype.
* remove undefined test.
2018-10-18 12:49:13 -07:00
6cbdf37c37
Merge branch 'master' into cpp
2018-10-18 15:29:20 -04:00
b9631912db
[Frame] Refactor frame. ( #85 )
...
* refactor frame codes
* fix unit test
* fix gcn example
* minor doc/message changes
* raise errors for non-exist columns in FrameRef; sanity check when append
* fix unittest; change error msg
* Add warning for none initializer
* fix unittest
* use warnings package
2018-10-18 15:08:21 -04:00
66261aee03
[Hotfix] Revert part of the send logic; disable the send twice test case; GCN on GPU works again. ( #88 )
2018-10-18 14:20:44 -04:00
bc3f852dab
[GRAPHINDEX] Multigraph support ( #79 )
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* multigraph support on graph index
* more tests
* multigraph flag, bugfix on clear & copy
* networkx interfaces
* including graph index tests in Jenkins
* node subgraph test
* edge subgraphs
* removing duplicates in pred/succ
* more explicit test and doc
* query source and destination from edge id
* subgraphindex
* renaming has_edge to has_edge_between, apply_edges adding eid
* send_on and send_and_recv_on
* DGLGraph edge subgraph
* merged send_on and send_and_recv_on
* change request
* removing hashmap
* creating multigraph by flag; mingw support
* changes per request
* reverting networkx auto multigraph discovery
* notes on send/send_and_recv on multigraphs
* changing test reducer from sum to max
* added a fixme note in spmv scheduler
2018-10-17 21:46:10 -04:00
750e50372a
Efficient send_and_recv ( #83 )
...
* python side send_and_recv shortcut
* common util function for c apis
* degree bucketing scheduler
* scheduler c apis
* cmake
* python side logics
* minor
* fix multiple msg/red func cases
* remove shell echo command in Jenkinsfile...
* fuse apply for send_and_recv
* fuse update func for update_all
* typo...
* handle anonymous
* add degree bucketing for entire graph
* degree bucketing executor
* minor
* style
* rename graph_mapping to recv_nodes
* fix some comments
2018-10-17 11:14:52 -04:00
b2c1c4facd
node/edge filtering ( #80 )
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* node/edge filtering
* changing to tensor operations (what did i do???)
* ???
2018-10-16 21:37:43 -04:00
16da76c4b4
fix #81
2018-10-16 10:39:50 -04:00
5567f4a4d9
[BACKEND] Add MXNet backend. ( #77 )
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* support mxnet.
* add mxnet version of GCN.
* rename mxnet.nd as F.
* add mxnet GAT.
* enable GPU for GCN.
* fix MXNet GCN train.
* Use adam to optimize GAT
* support more operators.
* support sparse arrays.
* update mxnet backend.
* support index_copy.
* remove NN.
* update mxnet backend.
* temp check in.
* fix data conversion.
* add test.
* clean up mxnet backend.
* update mxnet examples.
* Revert "remove NN."
This reverts commit d815d9a0ec619f9ce9099c48cd35db9d8e947483.
* temp disable MXNet version of NN.
2018-10-14 11:15:48 -04:00
e7679cf2e6
implement requested changes
2018-10-13 14:24:46 +08:00
eb46dc0018
Merge branch 'line-graph' of https://github.com/jermainewang/dgl into line-graph
2018-10-10 12:43:39 +08:00
Minjie Wang