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3215 次代码提交

作者 SHA1 备注 提交日期
Minjie Wang 66676a548d [Bugfix] Fix bug in bfs and topo (#135)
* Fix bug in bfs and topo

* remove legacy codes
2018-11-10 20:34:17 -05:00
Minjie Wang 6d96a97f17 [Doc] docstring for SST dataset (#133) 2018-11-10 11:59:55 -05:00
Gan Quan 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
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
Gan Quan 72efb42718 [Bugfix] fixes NLTK dependency (#125) and #126 (#131) 2018-11-09 14:16:52 -05:00
Minjie Wang aa56835806 [Hotfix] hotfix for clang (#130) 2018-11-09 02:18:23 -05:00
Minjie Wang 7fe6d0c857 [Doc] Refactor API doc (#128)
* refactor API doc; add markup link in tutorials

* fix readme
2018-11-08 22:57:16 -05:00
Minjie Wang 3e43d7b8d2 [Test] Lower allclose precision (#129) 2018-11-08 22:52:22 -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
Minjie Wang 79ceccef43 [Doc] Fix missing file (#119) 2018-11-04 23:02:11 -05:00
Gan Quan 87ed21ec42 [Doc] Basic tutorials & two model tutorials (#118)
[Doc] Basic tutorials & two model tutorials
2018-11-04 22:57:05 -05:00
Minjie Wang 7241a9c008 [Backend] backend interface (#109)
* 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
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 1a2b306f55 [Bug] fix bug in nodes() that does not return int64 tensor (#116) 2018-11-03 00:00:29 -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
Gan Quan 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
Mufei Li 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
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
Da Zheng 0d6cd30be3 [CI] Enable mxnet CI. (#105)
* fix tests.

* enable mxnet CI.

* add mxnet tests.

* update jenkins.

* update mxnet docker image.
2018-10-26 12:04:41 -04:00
GaiYu0 ff92812609 remove pytorch dependency in sbm.py (#107) 2018-10-25 20:22:41 -04:00
Minjie Wang 9fd94b53ac fix capsule doc (#104) 2018-10-25 16:19:36 -04:00
Zihao Ye 53e7f731ca Merge pull request #98 from yzh119/master
[Doc] fixed installation document
2018-10-25 00:39:11 +08:00
yzh119 1d3de6452f fixed install doc 2018-10-25 00:35:14 +08:00
VoVAllen 81bbeb602f Merge branch 'capsule-tutorial' into master 2018-10-24 19:46:53 +08:00
VoVAllen 4fd359cbff Capsule docs 2018-10-24 19:25:33 +08:00
VoVAllen a50bbe58c2 Merge branch 'master' into master 2018-10-24 19:21:36 +08:00
VoVAllen 6c29aba4c9 build without execute 2018-10-24 19:13:19 +08:00
VoVAllen 30fb4b9b78 Merge pull request #6 from jermainewang/doc
Doc
2018-10-24 16:20:40 +08:00
Minjie Wang 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
VoVAllen 4d7b3ba841 Merge pull request #6 from jermainewang/doc
Doc
2018-10-23 14:09:34 +08:00
VoVAllen 9628481f69 Merge pull request #5 from jermainewang/master
Sync with upstream
2018-10-23 14:08:47 +08:00
Minjie Wang 9e92fe74c4 rm obsolete file 2018-10-22 16:21:56 -04:00
Minjie Wang 0efd2aad9c update readme to include document url 2018-10-22 16:12:04 -04:00
Minjie Wang 5552b60a86 draft dglgraph tutorial 2018-10-22 16:01:22 -04:00
Minjie Wang 797b20792f setup sphinx-gallery; work on graph tutorial 2018-10-22 14:58:45 -04:00
Chao Ma 3de203853c Change size_t to int
To fix the compiler error on Mac OSX:

/dgl/src/c_api_common.cc:27:16: error: conversion from 'tvm::runtime::TVMArgValue' to 'size_t' (aka 'unsigned long') is ambiguous
        size_t which = args[0];
2018-10-22 20:51:57 +08:00
VoVAllen 026d35c588 update capsule tutorials 2018-10-22 20:46:55 +08:00
VoVAllen d0313326c2 delete legacy codes 2018-10-22 17:35:14 +08:00
Gan Quan 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
VoVAllen 7bad9178ba add visualization~ 2018-10-20 21:34:53 +08:00
VoVAllen 8e2e1f98a1 [WIP]update tutorial 2018-10-20 21:34:07 +08:00
VoVAllen d87fea8273 add gcn toy case 2018-10-19 21:02:46 +08:00
VoVAllen 522030510d fix 2018-10-19 20:59:16 +08:00
VoVAllen 0a50711f18 add GCN toy case 2018-10-19 20:55:51 +08:00
VoVAllen eb45bc07a1 add toy case for GCN 2018-10-19 20:53:02 +08:00