b49cd0952f
[Bugfix] Fix feature type of 'ENZYMES' in TUDataset ( #2800 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Hide implementations that may cause confusions to the user
* fix number of classes in Amazon Cobuy datasets
* add four papers
* fix feature type of TU dataset
* fix readme
* remove commented codes
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-04-01 14:36:55 +08:00
1f4c0b7193
Fix processing of QM9EdgeDataset ( #2801 )
2021-04-01 10:13:51 +08:00
bcffdb82c9
[Example] Add implementation of mvgrl ( #2739 )
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* [Example ]add mvgrl
* [Doc] add mvgrl to readme
* add more comments
* fix typos
* replace tab with space
* [doc] replace tab with space
* [Doc] fix a typo
* fix minor typos
* fix typos
* fix typos
* fix typos
* fix typos
* fix
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-03-22 21:20:21 +08:00
0b47e86803
[Example] Add DimeNet(++) for Molecular Graph Property Prediction ( #2706 )
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* [example] arma
* update
* update
* update
* update
* update
* [example] dimenet
* [docs] update dimenet
* [docs] update tf results
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-03-09 17:08:59 +08:00
a1f59c3b68
[Feature] QM9Edge Dataset Support ( #2704 )
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* [Feature] Support QM9Edge Datset
* Update qm9_edge.py
* disable tqdm
* Update qm9_edge.py
* Update qm9_edge.py
* Update qm9_edge.py
* Update qm9_edge.py
* Update qm9_edge.py
* Update qm9_edge.py
* Update qm9_edge.py
* remove preprocessing part
* add comparisons in qm9.py
* [docs] add qm9edge dataset
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-03-09 14:51:21 +08:00
7298173ac1
[Doc]Improve docstring for GINDataset ( #2676 )
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* add docstring for gin
* update doc
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-02-23 15:14:10 +08:00
b1840f49fa
[Dataset] Change the Data Type of the Node Features in GINDataset/TUDataset from Float64 to Float32 ( #2592 )
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* Update
* Update
* Update
* update
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Tong He <hetong007@gmail.com >
2021-02-03 21:00:45 +08:00
20d49771df
[Feature] Add reverse edges in CitationGraphDataset ( #2588 )
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* [Feature] Add reverse edges in CitationGraphDataset
* fix bug
* fix bug
* fix bug
* Update python/dgl/data/citation_graph.py
Co-authored-by: Xiangkun Hu <huxk_hit@qq.com >
* fix notes
* fix notes
* fix bugs
* solve requested changes
* fix bug
* fix bug
Co-authored-by: Xiangkun Hu <huxk_hit@qq.com >
2021-02-02 15:52:43 +08:00
12f6429616
remove hash_func from dataset object ( #2572 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-27 18:49:40 +08:00
c45f6eb575
[Bugfix] Fix duplicate edges in Coauthor Dataset #2553 ( #2569 )
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* fix
* address comment
2021-01-26 15:30:27 +08:00
25ac334403
[Distributed] Heterogeneous graph support ( #2457 )
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* Distributed heterograph (#3 )
* heterogeneous graph partition.
* fix graph partition book for heterograph.
* load heterograph partitions.
* update DistGraphServer to support heterograph.
* make DistGraph runnable for heterograph.
* partition a graph and store parts with homogeneous graph structure.
* update DistGraph server&client to use homogeneous graph.
* shuffle node Ids based on node types.
* load mag in heterograph.
* fix per-node-type mapping.
* balance node types.
* fix for homogeneous graph
* store etype for now.
* fix data name.
* fix a bug in example.
* add profiler in rgcn.
* heterogeneous RGCN.
* map homogeneous node ids to hetero node ids.
* fix graph partition book.
* fix DistGraph.
* shuffle eids.
* verify eids and their mappings when loading a partition.
* Id map from homogneous Ids to per-type Ids.
* verify partitioned results.
* add test for distributed sampler.
* add mapping from per-type Ids to homogeneous Ids.
* update example.
* fix DistGraph.
* Revert "add profiler in rgcn."
This reverts commit 36daaed8b660933dac8f61a39faec3da2467d676.
* add tests for homogeneous graphs.
* fix a bug.
* fix test.
* fix for one partition.
* fix for standalone training and evaluation.
* small fix.
* fix two bugs.
* initialize projection matrix.
* small fix on RGCN.
* Fix rgcn performance (#17 )
Co-authored-by: Ubuntu <ubuntu@ip-172-31-62-171.ec2.internal >
* fix lint.
* fix lint.
* fix lint.
* fix lint.
* fix lint.
* fix lint.
* fix.
* fix test.
* fix lint.
* test partitions.
* remove redundant test for partitioning.
* remove commented code.
* fix partition.
* fix tests.
* fix RGCN.
* fix test.
* fix test.
* fix test.
* fix.
* fix a bug.
* update dmlc-core.
* fix.
* fix rgcn.
* update readme.
* add comments.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-202.us-west-1.compute.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-62-171.ec2.internal >
* fix.
* fix.
* add div_int.
* fix.
* fix.
* fix lint.
* fix.
* fix.
* fix.
* adjust.
* move code.
* handle heterograph.
* return pytorch tensor in GPB.
* remove some tests in example.
* add to_block for distributed training.
* use distributed to_block.
* remove unnecessary function in DistGraph.
* remove distributed to_block.
* use pytorch tensor.
* fix a bug in ntypes and etypes.
* enable norm.
* make the data loader compatible with the old format.
* fix.
* add comments.
* fix a bug.
* add test for heterograph.
* support partition without reshuffle.
* add test.
* support partition without reshuffle.
* fix.
* add test.
* fix bugs.
* fix lint.
* fix dataset.
* fix for mxnet.
* update docstring.
* rename to floor_div
* avoid exposing NodePartitionPolicy and EdgePartitionPolicy.
* fix docstring.
* fix error.
* fixes.
* fix comments.
* rename.
* rename.
* explain IdMap.
* fix docstring.
* fix docstring.
* update docstring.
* remove the code of returning heterograph.
* remove argument.
* fix example.
* make GraphPartitionBook an abstract class.
* fix.
* fix.
* fix a bug.
* fix a bug in example
* fix a bug
* reverse heterograph sampling.
* temp fix.
* fix lint.
* Revert "temp fix."
This reverts commit c450717b9f578b8c48769c675f2a19d6c1e64381.
* compute norm.
* Revert "reverse heterograph sampling."
This reverts commit bd6deb7f52998de76508f800441ff518e2fadcb9.
* fix.
* move id_map.py
* remove check
* add more comments.
* update docstring.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-202.us-west-1.compute.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-62-171.ec2.internal >
2021-01-24 19:18:00 -08:00
2c6d071617
[Feature] QM9 Dataset Support ( #2521 )
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* [Model] MixHop for Node Classification task
* [docs] update
* [docs] update
* [fix] remove seed option
* [fix] update readme
* [feature] support qm9 dataset
* [style] update
* [docs] fix the details
* [fix] indexing only support int
* [style] update
* [fix] multiple backends support
* [docs] add qm9
* [fix] Z type: float32 -> int32
* [fix] Z type: int32 -> long
* [docs] add ref
* [docs] fix
* [docs] update
* [docs] update
* [fix] test eval
* [docs] fix example
Co-authored-by: xnuohz@126.com <ubuntu@ip-172-31-44-184.us-east-2.compute.internal >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-01-21 01:33:30 +08:00
9a9a06eb2f
[Bug Fix] Fix undefined var bug in LegacyTUDataset ( #2543 )
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* [Bug Fix] Fix undefined var bug in LegacyTUDataset
* upt
* [Bug Fix] Fix cache file name bug in TUDataset
Co-authored-by: Tong He <hetong007@gmail.com >
2021-01-19 13:58:01 +08:00
21e90cbf48
[Doc] Fix number of classes in Amazon Cobuy datasets ( #2488 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update gnn_benckmark.py
* Hide implementations that may cause confusions to the user
* fix number of classes in Amazon Cobuy datasets
2021-01-05 13:08:05 +08:00
4464b9734c
Fix kg dataset len() ( #2475 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-59-204.ec2.internal >
2020-12-31 23:33:21 +08:00
492ad9be81
[Fix] Avoid Overloading Nonzero for PyTorch Backend ( #2434 )
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* 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
9d7bf4ea89
Fix citation data loading ( #2421 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-25.ec2.internal >
2020-12-14 14:58:01 +08:00
fcf1193579
[Doc] Hidden implementations that may cause confusion to the user. ( #2378 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
* remove chapter numbers
* Update data.rst
* image in dataset userguide
* update links using ref
* modify the link of save_graphs and load_graphs in dataset user guide
* move image to s3 server.
* fix links and ref
* Hide implementations that may cause confusions to the user
2020-12-03 13:09:19 +08:00
fe4ada23f9
Update knowledge_graph.py ( #2329 )
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The l in "bool" is lost.
Co-authored-by: Zihao Ye <expye@outlook.com >
2020-11-10 17:33:55 +08:00
5f19876358
[Bugfix] GINDataset check whether labels are all valid ( #2319 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* check whether the original labels are valid
* add unit test for gin dataset
* bug of asscalar in mxnet<=1.6
* mxnet<=1.6 asscalar requires ndarray to be shaped (1,)
* skip gpu while testing datasets
* Update test_data.py
* test of gin dataset takes too much time
2020-11-05 09:35:10 +08:00
269983dbcd
[Fix] typo ( #2265 )
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* upd
* upd
* upd
* upd
* upd
* fix OpenMP compatibility issues
* typo
* partition
* misc
* fix typo
* num_parts=1
* import torch
* long
* print info
* print info
* print info
* upd
* remove debug code
* revert partition.py
* fix cut count
* fix cut count
* Revert "fix cut count"
This reverts commit 10926b4fd48f45c8f1ddb58be7db6c22e653effd.
* Revert "fix cut count"
This reverts commit 76465283bef093a2b4209ad70dd15d2437b2ec8a.
* type of deprecate
* typo in deprecate info
* fix typo
* use cv for partitioning
* CE
* no message
* revert
* typo
* no message
* no message
* no message
* practice
* dmlc-core
* DGLGraph
Co-authored-by: yzh119 <expye@outlook.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-10-29 23:05:36 +08:00
8bbc84e04f
[bugfix] Fix crash due to unfound attribute ( #2262 )
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An unexpected `AttributeError` exception is launched whenever the user defines `save_dir` on `DGLDataset` instantiation and uses `self._save_dir` within `has_cache` method.
This commit fixes the issue.
2020-10-09 09:44:38 +08:00
0b00562d1f
Update gindt.py ( #2212 )
2020-09-18 19:49:50 +08:00
3234189b60
Fix hdfs error when writing big data ( #2186 )
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* update dmlc-core to latest
* fix hdfs
2020-09-12 23:58:36 +08:00
8a227bfa03
[Bugfix] fix TUDataset labelling issue ( #2165 ) ( #2173 )
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* [Bugfix] fix TUDataset labelling issue (#2165 )
* [Bugfix] fix TUDataset labelling issue (dmlc#2165)
* update docstring according to discussion
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-09-11 17:05:24 +08:00
a102db23bf
[Dataset] CoraFull dataset remove redundant reference ( #2172 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update gnn_benckmark.py
2020-09-11 15:15:06 +08:00
0cf99be378
hotfix ( #2163 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal >
2020-09-09 11:00:31 +08:00
c9c6171b9f
Revert "[Feature] Basic utils to handle raw data features ( #2102 )" ( #2147 )
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This reverts commit 33a8bb93bfwmjlyjemaine@gmail.com >
2020-09-08 10:33:59 +08:00
33a8bb93bf
[Feature] Basic utils to handle raw data features ( #2102 )
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* add feature utils and add test for feature norm
* Add docstring and test
* upd
* dis able some test
* Update
* update doc string
* update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal >
2020-08-27 11:36:39 +08:00
51ba662169
Fix GINDT and #2087 ( #2103 )
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* fix gindt
* ff
* fix
* minor fix
* fix
2020-08-26 15:53:45 +08:00
f13b9b6212
[Doc] Scan the API docs and make many changes ( #2080 )
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* WIP: api
* dgl.sampling, dgl.data
* dgl.sampling; dgl.dataloading
* sampling packages
* convert
* subgraph
* deprecate
* subgraph APIs
* All docstrings for convert/subgraph/transform
* almost all funcs under dgl namespace
* WIP: DGLGraph
* done graph query
* message passing functions
* lint
* fix merge error
* fix test
* lint
* fix
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2020-08-20 23:26:49 +08:00
83654fdc4e
fix tu dataset ( #2064 )
2020-08-19 18:25:56 +08:00
4edde000a4
Fix tree lstm ( #2052 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-63-129.ec2.internal >
2020-08-19 10:44:10 +08:00
3d65484323
Fix mxnet gin ( #2048 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-19 00:05:15 +08:00
be444e52d9
[Doc/Feature] Refactor, doc update and behavior fix for graphs ( #1983 )
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* 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
b35388020d
[Bugfix] fix vocab not saved bug in SSTDataset ( #2036 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update tree.py
2020-08-17 21:59:14 +08:00
c113a5a0d7
Update dgl_dataset.py ( #2021 )
2020-08-14 16:17:37 +08:00
5362908236
Fix save/load for old version files ( #1994 )
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* load hetero
* fix
* more error message
* add warning
* add alias to dgl namespace
* fix tests
2020-08-12 23:45:21 +08:00
e4b4fcffc2
hotfix ( #1987 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-10 22:06:25 +08:00
e75157738b
hotfix ( #1980 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-87-240.ec2.internal >
2020-08-09 11:25:13 +08:00
264d96cdf5
[bugfix] Fix a bunch of examples to be compatible with dgl 0.5 ( #1957 )
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* upd
* upd
* upd
* upd
* upd
* upd
* fix pinsage also
* upd
* upd
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-29-3.us-east-2.compute.internal >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-08 01:31:23 +08:00
22167f7203
[Refactor] Enable new kernel in all message passing APIs ( #1953 )
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* WIP: frame refactor
* new frame
* simple update_all builtin
* move all subgraph routines into the same file
* sddmm & spmm schedule; node & edge udf
* degree bucketing
* some tricky 0deg corner cases
* bug in frame append
* merge test_hetero_basics and test_basics
* some code rearange
* fix test_heterograph
* add mean spmm
* enable all builtin combinations
* pass gpu test
* pass pytorch tests
* wip
* fix some pt debugging codes
* fix bug in mxnet backward
* pass all mxnet utests
* passed tf tests
* docstring
* lint
* lint
* fix broadcasting bugs
* add warning and clamp for mean reducer
* add test for zero-degree mean
* address comments
* lint
* small fix
2020-08-07 15:40:25 +08:00
5d5436ba18
[Dataset] RedditDataset change data.train_mask to numpy array ( #1961 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update reddit.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-07 15:22:13 +08:00
78651016f4
[Hot fix][Dataset] knowledge graph dataset statistics output ( #1952 )
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* Hot fix
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-06 20:20:20 +08:00
13ea9ddb06
[Doc] Fix some format issues in dataset api doc ( #1951 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* update doc
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-06 16:51:46 +08:00
967ecb8064
[Dataset] Fix the docstring format for dgl.data section ( #1941 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* update data rst
* update data doc and docstring
* API doc rst for dataset
* docstring
* update api doc
* add url format
* update docstring
* update citation graph
* update knowledge graph
* update gc datasets
* fix index
* Rst fix (#3 )
* Fix syntax
* syntax
* update docstring
* update doc (#4 )
* final update
* fix rdflib
* fix rdf
Co-authored-by: HuXiangkun <huxk_hit@qq.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-06 14:47:49 +08:00
451ed6d836
[Dataset] SBMMixtureDataset ( #1920 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* SBMMixture dataset
* Update sbm.py
* fix example
* Update sbm.py
* Revert "Update sbm.py"
This reverts commit 066db5c89bd5e159981ae7cad1bfb883ea5db71d.
* Update sbm.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-04 15:06:53 +08:00
2c141229d5
[Dataset] RedditDataset ( #1914 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* RedditDataset
* Update reddit.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-03 23:49:22 +08:00
37aa99c510
[Dataset] GNNBenchmarkDataset ( #1912 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* gnn benchmark dataset
* Update gnn_benckmark.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-03 23:28:58 +08:00
001d793711
[Dataset] SSTDataset ( #1918 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* SSTDataset
* Update tree.py
2020-08-03 19:15:28 +08:00
Xiangkun Hu