Chainer graph #398

knshnb · 2019-09-19T07:03:44Z

New features

New data(set) patterns
- sparse graph data(set)
- padding graph data(set) with coo matrix
New models
- sparse RelGCN
- sparse GIN
- GIN with coo matrix
New task
- semi-supervised node classification on large graphs
New datasets
- citation network (cora, citeseer)
- reddit

Dataset class

	Chemical	Network
adjacency matrix	`NumpyTupleDataset`	`PaddingGraphDataset`
scatter operation	`SparseGraphDataset`	`SparseGraphDataset`
sparse matmul	not supported	`PaddingGraphDataset (use_coo=True)`

still use PaddingGraphDataset for network padding pattern

.gitignore

chainer_chemistry/dataset/networkx_preprocessors/gin_reddit.py

chainer_chemistry/dataset/preprocessors/ggnn_preprocessor.py

chainer_chemistry/dataset/preprocessors/mol_preprocessor.py

chainer_chemistry/datasets/citation_network/citation.py

chainer_chemistry/models/prediction/node_classifier.py

corochann · 2019-09-19T08:18:54Z

chainer_chemistry/utils/train_utils.py

+                                  device=-1,
+                                  converter=None,
+                                  use_default_extensions=True,
+                                  resume_path=None):


MEMO. TODO (nakago) later: check again. can't we merge to run_train?

examples/network_graph/README.md

examples/qm9/train_qm9.py

examples/network_graph/train_network_graph.py

chainer_chemistry/models/ggnn.py

chainer_chemistry/models/gin.py

chainer_chemistry/models/prediction/padding_model_wrapper.py

corochann · 2019-09-20T06:49:51Z

updated comment

corochann · 2019-09-20T06:50:39Z

updated comment

corochann · 2019-09-20T07:21:02Z

Thank you! LGTM. I will check to run example later!

codecov-io · 2019-09-20T07:29:12Z

Codecov Report

Merging #398 into master will decrease coverage by 6.81%.
The diff coverage is 27.85%.

@@            Coverage Diff             @@
##           master     #398      +/-   ##
==========================================
- Coverage   91.22%   84.41%   -6.82%     
==========================================
  Files         229      234       +5     
  Lines       11049    11449     +400     
==========================================
- Hits        10080     9665     -415     
- Misses        969     1784     +815

corochann · 2019-09-25T02:36:48Z

@knshnb
If you can add some test, please add test (coverage test is failing now, since new functionality is not tested.) But I am going to merge this PR, even though in current condition after I confirmed example code works.

corochann

LGTM!! I checked cora, citeseer, and reddit learning works (I did not check whether the accuracy is comparable to paper yet though...).

todo later.
Memo: I'd like to modify dataset methods to handle dirpath using os.path.join so that it works with/without / at last.

corochann · 2019-09-25T04:22:24Z

examples/network_graph/README.md

+
+On the GPU:
+```angular2html
+PYTHONPATH=. python examples/network_graph/train_network_graph.py --dataset cora


I will add --device 0 later.

corochann · 2019-09-25T04:23:18Z

examples/network_graph/README.md

+On the GPU:
+```angular2html
+PYTHONPATH=. python examples/network_graph/train_network_graph.py --dataset cora
+```


todo later: I'd like to modify running this script from examples/network_graph instead of top directory.

todo later: I'd like to add --coo option explanation, which is necessary to run reddit dataset.

todo later: it seems gin_sparse and coo=true combination is not supported.

reddit dataset only works with --method gin and --coo true.

corochann · 2019-09-25T05:22:36Z

I will merge this PR!

Known TODO: #400 #401

corochann and others added 30 commits September 3, 2019 15:47

add dataset class which specifies batch method.

bd0a049

add files

b3ae8ef

adapt sparse relgcn to dataset class

58036a6

Fix variable name

b47448b

Support RelGCN in dataset class

ddd4c45

Refactor

a787329

Support GIN in dataset class

3ec27db

arrange directory structure

1a24f0c

change RelGCNUpdate interface

21dc6a9

support GINSparse

01e5484

concat node num option

1dd965c

padding converter for sparse pattern

121ff95

add cache directory to .gitignore

5995f2a

implement scatter general readout

8ab6b5b

store n_nodes in graph data

9639804

set weight tying option false by default in GIN

941645f

don't use relu in last layer of GIN

f81489f

fix constructor of SparseGraphData

1c43011

support training on cora dataset

adbe443

support training on citeseer dataset

72553d5

support training on reddit dataset

310d334

implement NodeClassifier

b2f322a

fix device

96e8cbc

fix on GPU

0af27f5

fix GIN

105d8d6

add dropout as command-line argment

f5fe033

add first_mlp to GINSparse

74f5f96

add reddit data to gitignore

892e0fc

support node classification on GIN (dense)

85aa52a

change commandline argment default values

7be3f4d

knshnb added 5 commits September 19, 2019 13:21

fix on GPU

f064792

fix variable name

0a9166f

add readme for train_network_graph

2e84983

add links of datasets to readme

4a51521

use NumpyTupleDataset chemical padding pattern

5ec8919

still use PaddingGraphDataset for network padding pattern

knshnb force-pushed the chainer-graph branch from 624f732 to 5ec8919 Compare September 19, 2019 07:18

corochann reviewed Sep 19, 2019

View reviewed changes

knshnb added 8 commits September 19, 2019 17:41

use NumpyTupleDataset in GGNN and RelGCN

86d88f2

add docstring

70aa90f

change network dataset directory under examples/

f1a8bf1

save NumpyTupleDataset

52470f8

change file name

628afa9

use mlp inside models

970401c

wrap padding pattern model by another Chain

337cbfd

Merge remote-tracking branch 'upstream/master' into chainer-graph

56c0fd7

corochann reviewed Sep 20, 2019

View reviewed changes

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chainer_chemistry/models/gin.py Show resolved Hide resolved

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chainer_chemistry/models/gin.py Outdated Show resolved Hide resolved

add reference to network datasets

86dab65

corochann reviewed Sep 20, 2019

View reviewed changes

chainer_chemistry/models/prediction/padding_model_wrapper.py Outdated Show resolved Hide resolved

knshnb added 3 commits September 20, 2019 16:11

delete unnecessary modification

dff0925

fix weight_tying option

d6be7f6

move padding model wrapper under example

56218b1

corochann approved these changes Sep 25, 2019

View reviewed changes

corochann merged commit 0aecad6 into chainer:master Sep 25, 2019

corochann added this to the 0.7.0 milestone Dec 9, 2019

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Chainer graph #398

Chainer graph #398

knshnb commented Sep 19, 2019 •

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corochann commented Sep 25, 2019

Chainer graph #398

Chainer graph #398

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knshnb commented Sep 19, 2019 • edited Loading

New features

Dataset class

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