mirrors / dmlc--dgl

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v0.1.2
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95 次代码提交

作者 SHA1 备注 提交日期
Minjie Wang 3564fdc5f1 [Bugfix][Model] fix treelstm model (#274) 
* fix bug after moving batcher out of dgl.data

* disable mx utest
 2018-12-06 23:52:50 -05:00
Da Zheng 7aa494b3bc [Bugfix][Doc] explain the batch dimension in the doc and many fix (#266) 
* add more unit tests for mxnet.

* fix.

* explain the batch dimension.

* update doc.

* disable unit tests on DFS.

* fix graph traversal.
 2018-12-06 00:48:57 -05:00
Da Zheng 063ed69cdf [BUGFIX] fix a bug in creating immutable graph index. (#251) 
* fix a bug in creating immutable graph index.

* fix for new changes in the backend API.

* fix for creating immutable graph index from coo matrix.

* retrigger
 2018-12-05 17:51:50 -05:00
Minjie Wang 2194b7dfa6 [Bugfix] edge order is not preserved when converting from edge list (#262) 2018-12-05 17:41:26 -05:00
VoVAllen cd907cddfa [Tutorial] Add sse tutorial & MXNet Tutorial CI (#252) 
* add sse tutorial

* add mxnet tutorial ci

* fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* Fix ci

* Fix ci

* Fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* fix ci

* Fix CI

Fix CI image

* permission fix

* fix a bug in the code.

* small fix

* fix doc

* fix ci

* shorten the iters

* fix

* remove extra file

* add load_backend api to dynamically switch to another backend

* try fix

* fix tutorial

* fix tutorial

* fix bug in tutorial
 2018-12-05 16:21:44 -05:00
Da Zheng 899d125bb1 Add tests for MXNet and throw NotImplementedError if not implemented (#258) 
* add more unit tests for mxnet.

* fix.
 2018-12-05 10:41:33 -08:00
Da Zheng 7c7cc7e0c2 [sampler] Adjust the sampler API for the future extension. (#243) 
* return seed ids.

* fix tests.

* implement.
 2018-12-05 10:05:10 -08:00
Minjie Wang 21255b6528 [Bugfix] tolist and dependencies in dgl.data (#239) 
* change Index.tolist -> Index.tonumpy; fix bug in traversal; remove dependencies in data

* fix import

* fix __all__ and some docstring
 2018-12-05 12:20:59 -05:00
Minjie Wang eafcb7e7f5 [Bugfix][MXNet] Fix edge order and builtin max bug in mx (#247) 
* Fix edge order and builtin max bug in mx

* fix as requested
 2018-12-05 01:32:54 -08:00
Lingfan Yu 455ea48570 [Bugfix] Conversion between networkx and DGLGraph (#244) 
* 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
Da Zheng 2c170a8c17 [Graph][Bugfix] Fix the API of map_to_subgraph_nid (#226) 
* correct vid mapping API.

* fix sse.
 2018-12-03 17:16:35 -05:00
Da Zheng 8918cce0b5 [MXNet] add unit tests for mxnet (#227) 
[MXNet] add unit tests for mxnet
 2018-12-03 11:04:11 -05:00
Lingfan Yu 52ed09a392 [Bug] Fix inplace update (#221) 
* 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
Minjie Wang 524e656dd6 [Bugfix] enable SPMV for multi-dimension node feature (#178) 
* Support multi-dimension node feature in SPMV

* fix as requested
 2018-11-26 11:12:28 -05:00
Minjie Wang b1eeb93449 [Bugfix][Runtime] Zero degree behaviors (#177) 
* 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
Minjie Wang 4dfe7547e8 Fix num_rows bug in batched_graph (#169) 2018-11-23 02:49:59 +08:00
Zihao Ye 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
Lingfan Yu 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
Minjie Wang 0ec1a492b3 [Frame] change num rows behavior (#163) 
* 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
Da Zheng 440aecee8f [Test] add tests for built-in functions (#159) 
* add spmv tests on mxnet.

* test backward.

* add tests for pull.

* use mxnet backend.

* address comment.

* add comments.
 2018-11-20 23:39:54 -05:00
Gan Quan e515f5311b [Frame] supporting partial row on first column and individual column initializers (#160) 
addresses issue #156
 2018-11-19 18:18:36 -05:00
Gan Quan 79a510252b Pickling support (#155) 
* 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
Gan Quan 05f464f824 [Bugfix] fix args with incontiguous node and edge tensor (#153) 2018-11-15 10:55:15 -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
Minjie Wang 048f6d7a30 [GraphIndex] refactor graph caching (#150) 
* refactor graph caching

* fix mx test

* fix typo
 2018-11-13 22:12:38 -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 a95459e3a2 [CI] Improved CI (#141) 
* change ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* nx package

* update ci

* update ci

* update ci

* fix

* mx dockerfile by zhengda

* python3.6->3.5

* update ci image

* add tutorial test

* fix ci

* fix ssl problem

* minor change

* small fix on traversal utest

* fix syntax

* add matplotlib in image

* fix

* update ci

* update ci
 2018-11-12 01:06:05 -05:00
Gan Quan 7cbb83db9f better bfs edge test (#142) 2018-11-11 23:09:39 -05:00
Gan Quan d6c80e0cf7 [API] bfs with edges (#132) 
* 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
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
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 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
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
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
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
Minjie Wang c9e3c6589f Merge branch 'cpp' of github.com:zzhang-cn/dgl into cpp 2018-10-18 22:44:37 -04:00
Minjie Wang 820c6b9ed6 Add lint script and fix cpplint errors 2018-10-18 22:44:29 -04:00
Lingfan Yu 49ea781cc3 Improve CI (#92) 
* gcn example test code

* GPU test

* use python3

* use functions

* gpu test use functions

* remove root

* use one script to run both cpu and gpu tests
 2018-10-18 22:42:25 -04:00
Minjie Wang 3e76bcc052 remove anonymous repr 2018-10-18 21:43:40 -04:00
Da Zheng 4af3f8bcc8 update the MXNet backend. (#89) 
* update mxnet.

* add get_tvmtype.

* remove undefined test.
 2018-10-18 12:49:13 -07:00
Minjie Wang 6cbdf37c37 Merge branch 'master' into cpp 2018-10-18 15:29:20 -04:00