文件历史

110 次代码提交

作者 SHA1 备注 提交日期
Zhou Fang 337b155970 [Doc] fix tutorial - blitz 4 link prediction (#2726)
The number of edges should be same as posive eids.

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-03-18 14:36:58 +08:00
Quan (Andy) Gan 99751d4960 [Doc] Rename block to message flow graph (#2702)
* rename block to mfg

* revert

* rename
2021-02-25 18:26:19 +08:00
Quan (Andy) Gan 71d53d9eef add thumbnails for tutorials (#2695)
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2021-02-23 20:33:35 +08:00
Quan (Andy) Gan da2f690a5a [Doc] Clarify link prediction tutorial (#2673)
* link prediction clarification

* fix
2021-02-23 19:41:54 +08:00
Minjie Wang 8a07ab7737 [Doc] Tutorials re-organization (#2683)
* reorg

* change titles

* rm some stale API doc; minor fix

* fix docs

* add warning

* rm new-tutorial run in ci

* lint
2021-02-20 17:42:45 +08:00
Quan (Andy) Gan 9e04a52abd [Doc] Reorganize tutorial (#2678) 2021-02-19 13:49:13 +08:00
Tong He a9f8f2589c [Doc] Update GraphDataLoader in our docs (#2504)
* update graphdataloader in docs

* fix

* update examples

* fix sagpool

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
2021-01-11 13:11:19 +08:00
Mufei Li 492ad9be81 [Fix] Avoid Overloading Nonzero for PyTorch Backend (#2434)
* Update gatedgraphconv.py

* Update entity_classify.py

* Update data-process.rst

* Update reading_data.py

* Update data-process.rst

* Update utils.py

* Update knowledge_graph.py

* Update entity_classify.py

* Update rdf.py

* Update entity_classify_mb.py

* Update test_classify.py

* Update tensor.py

* Update sparse.py

* Update entity_classify_mp.py

* Update 6_line_graph.py
2020-12-20 13:12:17 +08:00
cruyffturn 95dc971b7d [Doc] Some functions used in the tutorial are deprecated (#2398)
* Some functions used in the tutorial are deprecated

I'm receiving register_message_func and register_reduce_func are deprecated error. I have updated the code such that message and reduce functions are passed to g.send and g.recv

* Update 3_pagerank.py.bak

Co-authored-by: Zihao Ye <expye@outlook.com>
2020-12-09 13:11:10 +08:00
Mufei Li edb978772c [Doc, UG, Tutorial] Misc Fix (#2376)
* Update

* Update

* Update

* Update

* Update
2020-11-30 13:40:10 +08:00
Jinjing Zhou 4125f63e72 Update docs (#2123)
* Remove SSE

* Update env_var.rst
2020-08-28 20:35:36 +08:00
Jinjing Zhou ef78d675e9 Fix docs (#2073)
* remove mxnet tutorial

* remove sse

* fix docs
2020-08-20 15:37:50 +08:00
Mufei Li 100d932865 Update (#2062)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-1-5.us-west-2.compute.internal>
2020-08-19 17:42:48 +08:00
Mufei Li be444e52d9 [Doc/Feature] Refactor, doc update and behavior fix for graphs (#1983)
* Update graph

* Fix for dgl.graph

* from_scipy

* Replace canonical_etypes with relations

* from_networkx

* Update for hetero_from_relations

* Roll back the change of canonical_etypes to relations

* heterograph

* bipartite

* Update doc

* Fix lint

* Fix lint

* Fix test cases

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix test

* Fix

* Update

* Use DGLError

* Update

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* rewrite sanity checks

* delete unnecessary checks

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Fix

* Update

* Fix

* Update

* Fix

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
2020-08-18 04:26:29 +08:00
Xiangkun Hu 001d793711 [Dataset] SSTDataset (#1918)
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.

* SSTDataset

* Update tree.py
2020-08-03 19:15:28 +08:00
Quan (Andy) Gan 68a978d4de [Model] Fixes JTNN for 0.5 (#1879)
* jtnn and fixes

* make metagraph a method

* fix test

* fix
2020-07-30 13:36:08 +08:00
Minjie Wang 44089c8b4d [Refactor][Graph] Merge DGLGraph and DGLHeteroGraph (#1862)
* Merge

* [Graph][CUDA] Graph on GPU and many refactoring (#1791)

* change edge_ids behavior and C++ impl

* fix unittests; remove utils.Index in edge_id

* pass mx and th tests

* pass tf test

* add aten::Scatter_

* Add nonzero; impl CSRGetDataAndIndices/CSRSliceMatrix

* CSRGetData and CSRGetDataAndIndices passed tests

* CSRSliceMatrix basic tests

* fix bug in empty slice

* CUDA CSRHasDuplicate

* has_node; has_edge_between

* predecessors, successors

* deprecate send/recv; fix send_and_recv

* deprecate send/recv; fix send_and_recv

* in_edges; out_edges; all_edges; apply_edges

* in deg/out deg

* subgraph/edge_subgraph

* adj

* in_subgraph/out_subgraph

* sample neighbors

* set/get_n/e_repr

* wip: working on refactoring all idtypes

* pass ndata/edata tests on gpu

* fix

* stash

* workaround nonzero issue

* stash

* nx conversion

* test_hetero_basics except update routines

* test_update_routines

* test_hetero_basics for pytorch

* more fixes

* WIP: flatten graph

* wip: flatten

* test_flatten

* test_to_device

* fix bug in to_homo

* fix bug in CSRSliceMatrix

* pass subgraph test

* fix send_and_recv

* fix filter

* test_heterograph

* passed all pytorch tests

* fix mx unittest

* fix pytorch test_nn

* fix all unittests for PyTorch

* passed all mxnet tests

* lint

* fix tf nn test

* pass all tf tests

* lint

* lint

* change deprecation

* try fix compile

* lint

* update METIDS

* fix utest

* fix

* fix utests

* try debug

* revert

* small fix

* fix utests

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* upd

* trigger

* +1s

* [kernel] Use heterograph index instead of unitgraph index (#1813)

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* upd

* trigger

* +1s

* [Graph] Mutation for Heterograph (#1818)

* mutation add_nodes and add_edges

* Add support for remove_edges, remove_nodes, add_selfloop, remove_selfloop

* Fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* upd

* upd

* upd

* fix

* [Transfom] Mutable transform (#1833)

* add nodesy

* All three

* Fix

* lint

* Add some test case

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* fix

* triger

* Fix

* fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* [Graph] Migrate Batch & Readout module to heterograph (#1836)

* dgl.batch

* unbatch

* fix to device

* reduce readout; segment reduce

* change batch_num_nodes|edges to function

* reduce readout/ softmax

* broadcast

* topk

* fix

* fix tf and mx

* fix some ci

* fix batch but unbatch differently

* new checkk

* upd

* upd

* upd

* idtype behavior; code reorg

* idtype behavior; code reorg

* wip: test_basics

* pass test_basics

* WIP: from nx/ to nx

* missing files

* upd

* pass test_basics:test_nx_conversion

* Fix test

* Fix inplace update

* WIP: fixing tests

* upd

* pass test_transform cpu

* pass gpu test_transform

* pass test_batched_graph

* GPU graph auto cast to int32

* missing file

* stash

* WIP: rgcn-hetero

* Fix two datasety

* upd

* weird

* Fix capsuley

* fuck you

* fuck matthias

* Fix dgmg

* fix bug in block degrees; pass rgcn-hetero

* rgcn

* gat and diffpool fix
also fix ppi and tu dataset

* Tree LSTM

* pointcloud

* rrn; wip: sgc

* resolve conflicts

* upd

* sgc and reddit dataset

* upd

* Fix deepwalk, gindt and gcn

* fix datasets and sign

* optimization

* optimization

* upd

* upd

* Fix GIN

* fix bug in add_nodes add_edges; tagcn

* adaptive sampling and gcmc

* upd

* upd

* fix geometric

* fix

* metapath2vec

* fix agnn

* fix pickling problem of block

* fix utests

* miss file

* linegraph

* upd

* upd

* upd

* graphsage

* stgcn_wave

* fix hgt

* on unittests

* Fix transformer

* Fix HAN

* passed pytorch unittests

* lint

* fix

* Fix cluster gcn

* cluster-gcn is ready

* on fixing block related codes

* 2nd order derivative

* Revert "2nd order derivative"

This reverts commit 523bf6c249bee61b51b1ad1babf42aad4167f206.

* passed torch utests again

* fix all mxnet unittests

* delete some useless tests

* pass all tf cpu tests

* disable

* disable distributed unittest

* fix

* fix

* lint

* fix

* fix

* fix script

* fix tutorial

* fix apply edges bug

* fix 2 basics

* fix tutorial

Co-authored-by: yzh119 <expye@outlook.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-7-42.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-1-5.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal>
2020-07-28 14:30:41 +08:00
Mufei Li 63feb47c26 [Example] Update Links for Supervised Community Detection with Graph Neural Networks (#1816)
* Update README.md

* Update README.txt
2020-07-17 17:13:25 +08:00
Quan (Andy) Gan 32ea1b20ef remove edge list creation (#1688) 2020-06-23 21:48:09 +08:00
xiang song(charlie.song) 42b0c38f81 [Kernel] Migrate traversal on adjlist to CSR (#1650)
* traversal to new framework

* add new

* Fix compile

* Pass test

* keep old version

* lint

* lint

* Fix

* Fix

* Fix compatability with new master

* Fix test and tutorials

* Update according to comments

* Fix test

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
2020-06-19 13:25:18 +08:00
Mufei Li 9779c02667 Fix tutorial (#1587) 2020-06-04 15:17:03 +08:00
Mufei Li 38b9c0f82f [DGL-LifeSci] Allow Generating Vocabulary from a New Dataset (#1577)
* Generate vocabulary from a new dataset

* CI"
2020-06-02 14:21:48 +08:00
Zihao Ye cfb24790ba [hotfix] Several bug fix for remove nodes/edges in DGLGraph. (#1521)
* upd

* upd

* better
2020-05-15 02:29:44 +08:00
Mufei Li 1b152bf524 [Doc & Tutorial] Fix dgl.batch and GAT (#1418)
* Update doc and tutorials

* Fix
2020-04-04 01:23:22 +08:00
xiang song(charlie.song) 67cb7a43a0 [Feature] Deprecate multigraph (#1389)
* Deprecate multi-graph

* Handle heterograph and edge_ids

* lint

* Fix

* Remove multigraph in C++ end

* Fix lint

* Add some test and fix something

* Fix

* Fix

* upd

* Fix some test case

* Fix

* Fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
2020-03-28 21:31:24 +08:00
Minjie Wang 2cdc4d3c1d [Doc] Patch tutorial (#1380)
* patched 1_first

* done 2_basics

* done 4_batch

* done 1_gcn, 9_gat, 2_capsule

* 4_rgcn.py

* revert

* more fix
2020-03-22 10:21:22 +08:00
Zihao Ye 93ac29ce34 [Refactor] Unify DGLGraph, BatchedDGLGraph and DGLSubGraph (#1216)
* upd

* upd

* upd

* lint

* fix

* fix test

* fix

* fix

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd tutorial

* upd

* upd

* fix kg

* upd doc organization

* refresh test

* upd

* refactor doc

* fix lint

Co-authored-by: Minjie Wang <minjie.wang@nyu.edu>
2020-03-05 18:03:57 +08:00
Jinjing Zhou c23a61bd5c fix s3 link (#1310) 2020-03-04 21:01:29 +08:00
Minjie Wang 5967d81782 [Doc] Re-organize API docs and tutorials (#1222)
* reorg tutorials and api docs

* fix
2020-01-26 21:26:34 +08:00
Mufei Li a199b58a6a Fix (#1195) 2020-01-12 02:47:29 +08:00
Minjie Wang 17aab8128a [Doc] update working with multiple backend section (#1128)
* update work with different backend section

* fix some warnings

* Update backend.rst

* Update index.rst

Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com>
2019-12-24 17:32:56 +08:00
John Andrilla 41114b8758 [Doc] Tree-LSTM in DGL, edit pass for readability (#1031)
* [Doc] Tree-LSTM in DGL, edit pass for readability

Edit for grammar and style. 
How about deleting the last line? "Besides, you..." It needs a transition or some context.

* Update tutorials/models/2_small_graph/3_tree-lstm.py

* Update tutorials/models/2_small_graph/3_tree-lstm.py
2019-12-17 14:14:18 +08:00
John Andrilla f36a451420 [Doc] Old wines new title, edit for grammar and style (#1027)
* Old wines new title, edit for grammar and style

new descriptive title here and an edit pass @aaronmarkham

* Update tutorials/models/4_old_wines/README.txt
2019-12-16 11:24:58 +08:00
Da Zheng 48c7ec4427 [Doc] Fix gcn tutorial (#1080)
* don't have activation.

* add evaluation.

* address comment.
2019-12-10 02:10:51 -08:00
John Andrilla 7784f0668d [Doc] Small graphs readme.txt, edit pass (#1030)
* [Doc] Small graphs readme.txt, edit pass

Edit for grammar and style. Should this be an .rst on .txt?

* Update README.txt
2019-12-05 13:48:39 +08:00
John Andrilla 5fc7eb6d97 [Doc] Generative models, edit pass (#1035)
* [Doc] Generative models, edit pass

Edit for grammar and style. Can you clarify "Instead of and/or"?

* Update tutorials/models/3_generative_model/5_dgmg.py

* Update tutorials/models/3_generative_model/5_dgmg.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>

* Update tutorials/models/3_generative_model/5_dgmg.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>

* Update tutorials/models/3_generative_model/5_dgmg.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>

* Update tutorials/models/3_generative_model/5_dgmg.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>
2019-12-03 09:38:47 +08:00
John Andrilla f45178c334 [Doc] Generative models, edit for readability (#1033)
Edit pass for grammar and style
2019-12-02 14:54:10 +08:00
John Andrilla d6dfaa9b74 [Doc] Capsule network tutorial, edit pass (#1026)
Edited for grammar and style.
2019-12-01 22:26:51 +08:00
John Andrilla 10b104dd35 [Doc] Transformer tutorial, edit for readability (#1025)
Edit pass for grammar and style
2019-12-01 11:25:51 +08:00
John Andrilla a2b8d8e4e7 [Doc] Giant graph tutorial edit for grammar and style (#1020)
* Edit for readability

* giant_graph_readme edit for grammar

* NodeFlow and Sampling edit pass for grammar

* Update tutorials/models/1_gnn/9_gat.py

* Update tutorials/models/1_gnn/9_gat.py
2019-11-30 12:31:59 +08:00
John Andrilla dd09f15fa7 [Doc] Stochastic steady-state embedding (SSE) Edit for readability
Revisions for grammar and style
2019-11-30 11:37:17 +08:00
John Andrilla 22d4de77a0 [Doc] 6_line_graph.py Edit pass (#1003)
* Edit pass

Updates for grammar and readability

* Update tutorials/models/1_gnn/6_line_graph.py

* Update tutorials/models/1_gnn/6_line_graph.py

* Update tutorials/models/1_gnn/6_line_graph.py
2019-11-29 13:53:43 +08:00
John Andrilla 287f387b8c Edit for readability (#1002)
Grammar and style updates
2019-11-29 10:53:11 +08:00
John Andrilla 8ae9770f9b [Doc] Graph neural network and its variant Edit for grammar and style (#992)
* Edit for grammar and style

Improve readability

* Update tutorials/models/1_gnn/README.txt

Co-Authored-By: Aaron Markham <markhama@amazon.com>

* Update tutorials/models/1_gnn/README.txt

Co-Authored-By: Aaron Markham <markhama@amazon.com>
2019-11-28 15:44:58 +08:00
John Andrilla 7911dc8332 [Doc] Edit for grammar and style (#987)
* Edit for grammar and style

As with other tutorials, it would help the reader if you add a paragraph in the opening section about assumptions or prerequisites.

Does this refer to SageMaker Ground Truth feature? "...assigns its ground truth label..." If yes, phrase it thus: assigns its Amazon SageMaker Ground Truth label

* Update tutorials/basics/4_batch.py

* Update tutorials/basics/4_batch.py

* Update tutorials/basics/4_batch.py

topologies

* Update tutorials/basics/4_batch.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>
2019-11-27 13:56:11 +08:00
John Andrilla 8f7abb5fb0 [Doc] Edit for readability (#989)
* Edit for readability

Edit pass for grammar and style. 
* A great value-add would be to provide assumptions and prerequisites in the opening section. This helps readers understand what they need to have in place in order to make use of your tutorial steps.
* The wikidata knowledge graph could be improved with a smaller font for the Zuckerberg circle.

* Update tutorials/hetero/1_basics.py

* Update tutorials/hetero/1_basics.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>

* Update tutorials/hetero/1_basics.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>

* Update tutorials/hetero/1_basics.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>

* Update tutorials/hetero/1_basics.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>

* Update tutorials/hetero/1_basics.py

Co-Authored-By: Aaron Markham <markhama@amazon.com>
2019-11-21 22:06:52 +08:00
John Andrilla 409183bc56 [Doc] Edit for grammar and style (#986)
Can you add a link for the download to this sentence: You can also `download <location?>` and run the different code examples...
As with other tutorial topics, it would be helpful to add your assumptions or information in the opening section about prerequisites.
2019-11-21 14:04:20 +08:00
John Andrilla d2afe65ca8 [Doc] Edit for grammar and style (#985)
* Edit for grammar and style

In the opening paragraph, it would be helpful to provide some overall scenario and the prerequisites you expect readers to have completed before they start here. "This tutorial assumes you have already..." Add a link to Install DGL topic perhaps and any other framework or IDE or even specialized knowledge. With this context, you help readers to succeed by setting expectations.

Better to group all tutorials (this, PageRank with, Batched Graph, Working with) at the same level in the left navigation rail and all as subsections of DGL Basics.

* Update tutorials/basics/2_basics.py
2019-11-20 12:03:18 +08:00
xiang song(charlie.song) 82499e602b [Bug Fix] Fix package reliability bug of networkx (#949)
* upd

* fig edgebatch edges

* add test

* trigger

* Update README.md for pytorch PinSage example.

Add noting that the PinSage model example under
example/pytorch/recommendation only work with Python 3.6+
as its dataset loader depends on stanfordnlp package
which work only with Python 3.6+.

* Provid a frame agnostic API to test nn modules on both CPU and CUDA side.

1. make dgl.nn.xxx frame agnostic
2. make test.backend include dgl.nn modules
3. modify test_edge_softmax of test/mxnet/test_nn.py and
    test/pytorch/test_nn.py work on both CPU and GPU

* Fix style

* Delete unused code

* Make agnostic test only related to tests/backend

1. clear all agnostic related code in dgl.nn
2. make test_graph_conv agnostic to cpu/gpu

* Fix code style

* fix

* doc

* Make all test code under tests.mxnet/pytorch.test_nn.py
work on both CPU and GPU.

* Fix syntex

* Remove rand

* Add TAGCN nn.module and example

* Now tagcn can run on CPU.

* Add unitest for TGConv

* Fix style

* For pubmed dataset, using --lr=0.005 can achieve better acc

* Fix style

* Fix some descriptions

* trigger

* Fix doc

* Add nn.TGConv and example

* Fix bug

* Update data in mxnet.tagcn test acc.

* Fix some comments and code

* delete useless code

* Fix namming

* Fix bug

* Fix bug

* Add test for mxnet TAGCov

* Add test code for mxnet TAGCov

* Update some docs

* Fix some code

* Update docs dgl.nn.mxnet

* Update weight init

* Fix

* reproduce the bug

* Fix concurrency bug reported at #755.
Also make test_shared_mem_store.py more deterministic.

* Update test_shared_mem_store.py

* Update dmlc/core

* networkx >= 2.4 will break our examples

* Update tutorials/requirements

* fix selfloop edges

* upd version
2019-10-29 23:34:31 -04:00
John Andrilla 8d84865548 Voice and tone updates for readability (#938)
Simple editorial updates
2019-10-21 09:06:56 +08:00