文件历史

114 次代码提交

作者 SHA1 备注 提交日期
VoVAllen bf6d0025aa [Bugfix] fix gpu manual choice for capsule example (#164) 2018-11-21 22:01:24 -05:00
Da Zheng 5f89cd662e Fix the convergence problem in SSE. (#162)
* 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
Zihao Ye 53b9a4bdbc [DOC][Model] Update Tree-LSTM (#152)
* update tree lstm

* tree_lstm (new interface)

* simplify pop

* merge qipeng(root)

* upd tree-lstm & tutorial

* upd model

* new capsule tutorial

* capsule for new API

* fix deprecated API

* New tutorial and example

* investigate gc problem

* add viz code

* new capsule tutorial

* remove ipynb

* move u_hat

* add link

* add requirements.txt

* remove ani.save

* update ci to install requirements

* utf-8

* change seed

* graphviz requirement

* accelerate

* little format

* update some markup
2018-11-14 22:29:59 -05:00
Da Zheng 2389df8155 [API] Subgraph sampling API. (#138)
* 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
Zihao Ye a9ffb59e66 [DOC][Model] Tree-LSTM example and tutorial (#146)
[DOC][Model] Tree-LSTM example and tutorial
2018-11-13 18:09:14 -05:00
VoVAllen 7cb50072a4 [Doc][Model] New Capsule Tutorial & Example (#143)
* new capsule tutorial

* capsule for new API

* fix deprecated API

* New tutorial and example

* investigate gc problem

* add viz code

* new capsule tutorial

* remove ipynb

* move u_hat

* add link

* add requirements.txt

* remove ani.save

* update ci to install requirements

* add graphviz
2018-11-12 12:43:13 -05:00
Minjie Wang 8ea359d125 [API] Message propagation APIs (#127)
* 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
Da Zheng bd0e4fa0b3 [MXNet][API] move to the new API (#123)
* 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
Zihao Ye 1eb17bb01f [Model] Adapt Tree-LSTM to new interface (#122)
* tree_lstm (new interface)

* simplify pop
2018-11-08 10:31:55 -05:00
GaiYu0 2319167444 [API] Graph traversal (#103)
* 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
GaiYu0 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
Minjie Wang b355d1eddf [API] Apply nodes & apply edges (#117) 2018-11-04 01:22:53 -04:00
Minjie Wang 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
Mufei Li 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
VoVAllen d0ea98befa [Model] Capsule (#95)
* add capsule example

* clean code

* better naming

* better naming

* Clean Codes based on pytorch MNIST example

* Clean codes

* Add README
2018-10-26 23:56:13 -04:00
Da Zheng 9e9a9488f1 [GraphIndex] Immutable graph index using MXNet CSRArray (#86)
* 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
Minjie Wang 3e76bcc052 remove anonymous repr 2018-10-18 21:43:40 -04:00
Minjie Wang 6cbdf37c37 Merge branch 'master' into cpp 2018-10-18 15:29:20 -04:00
Minjie Wang 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
Da Zheng 5567f4a4d9 [BACKEND] Add MXNet backend. (#77)
* 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
GaiYu0 f31b6fd2b4 Update README.md 2018-10-14 11:11:14 +08:00
GaiYu0 8738ebfa8a README.md 2018-10-14 11:08:14 +08:00
GaiYu0 0a6d720c30 fix build failure 2018-10-10 12:43:05 +08:00
GaiYu0 885f5e7313 Merge branch 'cpp' of https://github.com/jermainewang/dgl into line-graph 2018-10-09 16:08:18 +08:00
Minjie Wang 1f0f57b300 fix bug in treelstm 2018-10-08 17:29:28 +00:00
Gan Quan ec4216dda8 [MODEL] junction tree vae example (#70)
* junction tree vae example

* added README and moved data to dropbox

* auto download; some fix in python3
2018-10-06 16:59:47 -04:00
GaiYu0 596ca471a5 Merge branch 'cpp' of https://github.com/jermainewang/dgl into line-graph 2018-10-06 23:52:04 +08:00
GaiYu0 52ed6a4507 train.py help 2018-10-06 16:27:16 +08:00
GaiYu0 cc372e3774 sbm mixture 2018-10-04 21:22:41 +08:00
Minjie Wang 8e71b64e2a gat runnable 2018-10-03 21:17:23 -04:00
Minjie Wang fde4f581d2 gcn runnable 2018-10-03 21:05:19 -04:00
GaiYu0 f52fc3fcdf experiment 6.1 2018-10-01 09:12:50 +08:00
GaiYu0 2b09281178 line graph 2018-10-01 09:12:35 +08:00
Minjie Wang d772d390b2 fix 2018-09-25 03:55:18 +00:00
Minjie Wang a8a4fcbaff quickly integrating with tree-lstm example 2018-09-24 23:42:56 -04:00
Minjie Wang 61fa3c6cf5 Builtin function and API changes (#53)
* WIP: API renaming

* API rewrite and node function refactor

* builtin functions

* builtin functions tested

* fix test

* send and recv spmv test

* WIP: fix examples

* Fix examples using new APIs
2018-09-01 13:38:01 -04:00
Minjie Wang 8c71f3f86d Fix treelstm CPU 2018-08-29 10:53:22 -04:00
Gan Quan b7eb16595f Fix 0deg update_to and Tree-LSTM model (#51)
* WIP

* WIP

* treelstm dataloader

* Main training loop.

* trainable treelstm script

* fix dependency

* cuda training

* Add tensorized topological traversal

* allowing update_to() with no incoming messages

* fixing partial cases
2018-08-28 11:57:08 -04:00
Lingfan Yu c42eac718f Fix batched graph edge order bug and other fixes (#50)
* fix dgl.batch edge ordering bug

* add graph batching test cases

* fix partial spmv ctx.

* add dataset generating for dgmg
2018-08-23 15:11:38 -04:00
Minjie Wang 6105e44142 Many fix and updates (#47)
* subgraph copy from

* WIP

* cached members

* Change all usage of id tensor to the new Index object; remove set device in DGLGraph;

* subgraph merge API tested

* add dict type reduced msg test
2018-08-22 12:25:05 -04:00
Lingfan Yu 1f16f29b20 bug fix 2018-08-16 19:31:43 +00:00
Lingfan Yu 96179b0c96 Deep Generative Models of Graphs (#14)
* model code for generative graphs

* batched version for dynamic graph generation using padding

* renaming function train back to forward

* remove old util function for padding DGMG

* override networkx clear to reset state, add dgl.nn

* Dynamic graph without batching

* use relative import path

* load dataset, pad batch

* bug fix

* experimental batch and unbatch

* dgmg batched version

* minor tweak

* move preprocessing padding into data loading

* batch graph test code

* minor

* batched graph class and test cases

* make dgl.nn.gcn a simple layer plus minor fix

* update dgmg model

* test forward using attribute field

* use frame append, minor changes

* moving networkx operations out of forward

* revert some changes

* remove structural immutability check
2018-08-16 14:05:50 -04:00
Minjie Wang ee241699e0 GAT model (#37)
* GAT model

* fix output projection to have only one head
2018-08-09 22:44:53 -04:00
Minjie Wang 0a78dbe12a Three DGL-GCN implementations (#35)
* synthetic dataset

* some fix

* gcn readme
2018-08-07 15:26:58 -04:00
Minjie Wang 2c489fadec SPMV specialization (#32)
* fix edge list order problem in cached graph.

* minor fix

* fix bug in edge iter

* SPMV works

* gcn spmv on CPU

* change gcn style

* fix cached graph performance; fixed gcn dataset bug

* reorg dir

* non-batch spmv; partial update problem with shape change

* fix reorder problem; finish gcn-batch impl

* pop API

* GPU context
2018-08-06 14:00:06 -04:00
Ivan Brugere 57f480f591 LSTM fix (#28)
Correctly handling lstm model creation
2018-07-13 01:05:59 -04:00
Minjie Wang c50b90cf7e Change recvfrom API; fix corner cases in issue20 (#25)
* Change ; fix corner cases in issue20

* Change recvfrom to recv
2018-07-12 11:22:38 -04:00
GaiYu0 345a472dc2 profile graph-tool, igraph, networkx and pagerank with spmv (#19) 2018-07-11 11:25:16 -04:00
Ivan Brugere 0d6504434b cleaning
cleaning and documentation
2018-07-10 15:57:57 -07:00
Ivan Brugere ef18dab2a1 initial ginipath
Initial example file for ginipath
2018-07-10 12:35:13 -07:00