文件历史

119 次代码提交

作者 SHA1 备注 提交日期
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
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
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
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 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
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
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
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 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
Minjie Wang 3e76bcc052 remove anonymous repr 2018-10-18 21:43:40 -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
Minjie Wang 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
Gan Quan bc3f852dab [GRAPHINDEX] Multigraph support (#79)
* 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
Lingfan Yu 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
Gan Quan b2c1c4facd node/edge filtering (#80)
* node/edge filtering

* changing to tensor operations (what did i do???)

* ???
2018-10-16 21:37:43 -04:00
Gan Quan 16da76c4b4 fix #81 2018-10-16 10:39:50 -04:00
GaiYu0 e7679cf2e6 implement requested changes 2018-10-13 14:24:46 +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 3d38c2a93e small fix 2018-10-08 13:30:50 -04:00
GaiYu0 baf5906bab (non)-backtracking line graph 2018-10-08 08:04:25 +08:00
Lingfan Yu cdf7334cc6 Dockerfile and CI (#74)
* Test CPP branch CI (#2)

* Fix batching node-only graphs (#62)

* fixing batching with graphs with no edges

* oops forgot test

* fix readme

* Docker and Jenkins (#1)

* docker ci cpu

* install python packages

* docker ci gpu

* add readme

* use dgl cpu image

* run command in container as root

* use python3

* fix test case

* remove nose from docker file

* docker folder readme

* parallelize cpu and gpu

* top level stages

* comment out python2 related installation

* fix

* remove igraph

* building for cpp

* change building order

* export env in test stage

* withEnv

* run docker container as root

* fix test cases

* fix test cases

* minor

* remove old build
2018-10-07 19:18:43 -04:00
GaiYu0 905db29286 cpp lg 2018-10-07 22:25:45 +08:00
GaiYu0 596ca471a5 Merge branch 'cpp' of https://github.com/jermainewang/dgl into line-graph 2018-10-06 23:52:04 +08:00
GaiYu0 8a6d25ae69 Resolve conflicts in python/dgl/graph.py 2018-10-06 16:13:06 +08:00
Minjie Wang 72f6345515 Fix for subgraph test and some docs 2018-10-05 23:58:42 -04:00
Da Zheng b0e02e5b52 Update the subgraph (#73)
* update subgraph.

* update subgraph API.

* keep node embedding.
2018-10-05 22:17:33 -04:00
Minjie Wang c468e06867 some fix 2018-10-05 10:38:44 -04:00
GaiYu0 26dcfb5bc2 Merge branch 'cpp' of https://github.com/jermainewang/dgl into cpp
Conflicts:
	python/dgl/graph.py
2018-10-04 21:26:56 +08:00
GaiYu0 cc372e3774 sbm mixture 2018-10-04 21:22:41 +08:00
Minjie Wang fde4f581d2 gcn runnable 2018-10-03 21:05:19 -04:00
Minjie Wang 7d04c8c9f3 remove nonbatchable mode 2018-10-03 12:20:12 -04:00
Minjie Wang a8a4fcbaff quickly integrating with tree-lstm example 2018-09-24 23:42:56 -04:00
Minjie Wang 882e2a7be0 Graph batching. Support convert nx graph attrs 2018-09-24 21:34:51 -04:00
Minjie Wang 79f62400fe WIP: batch graphs 2018-09-21 14:53:25 -04:00
Minjie Wang 4aebfd7bd8 add merge graph; fix bug in from_networkx 2018-09-21 12:25:54 -04:00
Minjie Wang 7b5d4c5886 pass specialization test 2018-09-20 18:22:46 -04:00
Minjie Wang b2e4bdc03f passed basic test batching 2018-09-20 14:44:06 -04:00
Minjie Wang 44db98c4e0 remove nx inheritence 2018-09-19 22:49:14 -04:00
Minjie Wang 916d375ba3 Merge branch 'master' into cpp 2018-09-19 21:04:31 -04:00
Minjie Wang a1038eb1ee graph index 2018-09-19 21:02:15 -04:00
Lingfan Yu 9b0a01db41 Support list of msg or reduce func for update_all and send_and_recv (#58)
* support multiple fields in spmv

* finishing SPMV executor

* non-spmv case

* refactor code to give single mfunc rfunc a shortcut

* two test cases to test multiple msg/red func

* catching cases where msg uses anonymous field

* default ALL for update edge

* more corner case test

* print failed test

* delete print

* fix builtin max reducer
2018-09-19 20:49:29 -04:00
Minjie Wang c086d454d3 Use TVMContext 2018-09-16 16:56:29 -04:00
Minjie Wang b24daa6607 change to rel import within dgl 2018-09-16 16:14:37 -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
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
Gan Quan 5e75f5dbfc Fix reducing with 0 incoming messages (#48)
* fixing 0 degree reduces

* adopting accum=None semantics

* minor fix as per reviews

* TODO in test

* fix test
2018-08-24 11:51:05 -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