b34a1e63d4
Update subgraph.py ( #2754 )
2021-03-17 18:15:30 +08:00
3c8382f6b6
Fix typos in zero-in-degree ( #2750 )
2021-03-14 19:13:59 +08:00
0b47e86803
[Example] Add DimeNet(++) for Molecular Graph Property Prediction ( #2706 )
...
* [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
c88fca5055
[Feature] Add edge coarsening for homogeneous undirected graphs ( #2691 )
...
* finish graph matching gpu version
* use C++ shuffle
* finish graph matching
* fix bug
* fix bug
* change name and use swap
* upt
* fix format problem
* fix format problem
* stronger test
* upt
* upt
* change python api
* upt
* upt
* format check
* upt
* upt
* fix bug
Co-authored-by: Tong He <hetong007@gmail.com >
2021-03-09 16:35:27 +08:00
a1f59c3b68
[Feature] QM9Edge Dataset Support ( #2704 )
...
* [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
7380d61eb9
[NN] Support Unidirectional Bipartite Graphs in CFConv ( #2674 )
...
* Update
* update
* Update
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-03-03 16:35:07 +08:00
d0638b1ea9
[Example] Update the example of distributed GNN training of RGCN ( #2709 )
...
* support gpu training.
* remove unnecessary arguments.
* update README.
* update time measurement.
* add zero_grad.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-03-01 12:00:15 -08:00
062f59a8f6
fix small typo bug ( #2708 )
...
Co-authored-by: Zihao Ye <expye@outlook.com >
2021-02-28 17:37:13 +08:00
99751d4960
[Doc] Rename block to message flow graph ( #2702 )
...
* rename block to mfg
* revert
* rename
2021-02-25 18:26:19 +08:00
7ab3d993a4
Change the absolute path to relative one in part_config.json ( #2690 )
...
* Update partition.py
* fix lint.
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2021-02-24 16:12:19 -08:00
1686106390
change __repr__ ( #2696 )
...
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-02-25 00:21:00 +08:00
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
7298173ac1
[Doc]Improve docstring for GINDataset ( #2676 )
...
* add docstring for gin
* update doc
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-02-23 15:14:10 +08:00
174dd18905
[hotfix] A bunch of fix for SetTransformer ( #2658 )
...
* upd
* lint
* upd
* fix
* fix
* upd
* upd
* fix
* warning
* upd
* upd
2021-02-23 14:19:51 +08:00
80c26877de
[Bug Fix] Fix munmap bug in sparse optimizer ( #2675 )
...
* Fix munmap bug
* lint
* update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal >
2021-02-22 11:33:44 +08:00
16e324daf3
[Bug Fix] Add warning for invalid input graph of edge UDF ( #2682 )
...
* Add warning for invalid graph of edge UDF
* lint
Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal >
2021-02-22 10:12:40 +08:00
72a16b22e4
[bugfix] Fix the behavior of select_topk ( #2688 )
...
* fix
* lint
* lint
2021-02-21 18:52:35 +08:00
e6bf54cdcb
[Feature] Support aggregate multiple edge features in to_simple. ( #2623 )
...
* upd
* fix
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* fix
* refactor
* upd test
* large feat_len or n in segment reduce
* lint
2021-02-21 10:05:42 +08:00
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
0fc649523b
[Doc] Distributed heterogeneous graph training ( #2654 )
...
* update DistGraph docstrings.
* add user guide.
* add doc string.
* fix.
* fix.
* fix.
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-02-19 10:48:05 -08:00
453d358d2c
[Doc] Fix docs for sparse optimizer ( #2680 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-02-19 14:07:35 +08:00
dda103d9f6
Fix bug in EdgeConv implementation ( #2669 )
...
* Update edgeconv.py
* update edgeconv to builtin
* add explanation on why ReLU is not there
* remove redundant code
2021-02-19 13:07:21 +08:00
d93a975997
revert ( #2672 )
2021-02-19 12:05:42 +08:00
0cbaa1fbcb
[Doc] Make the docstring of nn.glob more informative. ( #2649 )
...
* upd
* fix weight and sum
* upd sortpool
2021-02-12 12:29:22 +08:00
9e630101a1
fix and lots of tests ( #2650 )
2021-02-12 11:40:05 +08:00
cf8a3fb305
[hotfix] Address the performance issue of topk. ( #2628 )
...
* upd
* fix
* upd
* upd
* udp
* upd
* upd
* upd
* upd
* upd
* upd
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-02-11 00:00:39 +08:00
8ccb8206bf
[Doc] Update docs to motivate the use of set_batch_num_nodes and set_batch_num_edges ( #2630 )
...
* fix doc
* update docstring for transformation on batch graph
* update cn guide
* fix format
* update rst
2021-02-08 14:43:24 +08:00
bc3a532f5e
[Sampling] Implement dgl.to_block() for the GPU ( #2339 )
...
* Add start of to_block gpu implementation
* Pull in more changes from 0.4.2 cuda_to_block
* Move more code to IdArray
* Refactor DeviceNodeMapMaker
* Updates
* get compiling
* Integrate to_block
* Fix ID allocation
* Minor fixes
* Cleanup cuda calls to use cuda_common
* Reduce kernel calls
* Lint cleanup
* Expand documentation
* Remove unused function
* Rename variables for consistency
* Add doxygen comments
* Fix file extension
* Remove raw asynccopy for deviceapi
* Remove unused function
* Fix block/tile configuration
* Add cuda_device_common.cuh
* Add basic hashtable
* Migrate part of hashtable
* Refactor to use external hashtable
* Make functions members
* Format hash table functions
* Migrate duplicate filling
* Move last function over
* Refactor with cu file
* lint c++ code
* Move context check to C++ code
* Use macro switch
* Add missing files
* Update docstring
* update docs
* Move atomic functions
* Refactor hashtable
* Fix linting
* Expand docs
* Fix mismatched argument names
* Switch doxygen comments from using @param to \param
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-02-08 13:00:43 +08:00
98ac391ed9
[Doc] Large graph training tutorials ( #2595 )
...
* large graph training tutorials
* add full graph link prediction update
* fix
* fix
* fix
* addressed comments
2021-02-07 17:55:49 +08:00
0346b0aa80
[Test] Add test for Cython and force rebuild when run setup.py ( #2635 )
2021-02-05 22:38:46 +08:00
3ca52b1e59
[Fix] Various Fix after Bug Bash ( #2620 )
...
* update
* Misc fix
* Update
2021-02-05 17:34:16 +08:00
23afe911b2
[Bug Fix] Fix several sparse optimizer bugs ( #2596 )
...
* Fix pytorch TCP kvstore bug
* lint
* Fix
* upd
* Fix lint
* Fix
* trigger
* fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal >
2021-02-05 11:49:41 +08:00
b1840f49fa
[Dataset] Change the Data Type of the Node Features in GINDataset/TUDataset from Float64 to Float32 ( #2592 )
...
* 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
fb4a0508c6
[bugfix] Solve the boundary issue in backward function of segment sum ( #2610 )
...
* upd
* trigger
* upd
2021-02-03 18:50:07 +08:00
47c9380555
[Performance] Fix Cython not being imported after switching to RTLD_LOCAL ( #2608 )
...
* fix
* ?
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-02-02 16:23:54 +08:00
20d49771df
[Feature] Add reverse edges in CitationGraphDataset ( #2588 )
...
* [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
3a19bbc508
fix doc ( #2604 )
2021-02-02 11:04:43 +08:00
db57809da1
[hotfix] Add data type check for kernels. ( #2598 )
...
* upd
* upd
2021-01-31 13:08:05 +08:00
1f6eba9ed3
[Bug] Heterogeneous graph convolution bugfix ( #2578 )
...
* fix heterograph conv
* remove test cases
* fix test
* fix test
* fix test
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-29 09:30:19 +08:00
e4ddafe951
[NN] add multihead in DotGatConv ( #2549 )
...
* add multihead in DotGatConv
* Fix spacing issue
* Add Unit test for dotgat
* Modified Unit test for dotgat
* Add transformer like divisor
* Update dotgatconv.py
Co-authored-by: Chen <chesirui@3c22fbe5458c.ant.amazon.com >
Co-authored-by: Zihao Ye <expye@outlook.com >
2021-01-28 21:05:10 +08:00
fb3c07094f
Revert part of #2563 ( #2584 )
2021-01-28 14:53:55 +08:00
878acdb0fc
Revert "Refactor code for retaining formats in message-passing. ( #2570 )" ( #2583 )
...
This reverts commit a613ad8806
2021-01-28 14:04:07 +08:00
7bab1365e2
[feature] Supporting half precision floating data type (fp16). ( #2552 )
...
* add tvm as submodule
* compilation is ok but calling fails
* can call now
* pack multiple modules, change names
* upd
* upd
* upd
* fix cmake
* upd
* upd
* upd
* upd
* fix
* relative path
* upd
* upd
* upd
* singleton
* upd
* trigger
* fix
* upd
* count reducible
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* only keep related files
* upd
* upd
* upd
* upd
* lint
* lint
* lint
* lint
* pylint
* upd
* upd
* compilation
* fix
* upd
* upd
* upd
* upd
* upd
* upd
* upd doc
* refactor
* fix
* upd number
Co-authored-by: Zhi Lin <linzhilynn@gmail.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-42-78.us-east-2.compute.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-21-156.us-east-2.compute.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-01-28 11:21:58 +08:00
a7e941c379
[Feature] Add support for sparse embedding ( #2451 )
...
* Add sparse embedding for dgl and update rgcn example
* upd
* Fix
* Revert "Fix"
This reverts commit 4da87cdfb8b8c3506b7fc7376cd2385ba8045c2a.
* Fix
* upd
* upd
* Fix
* Add unitest and update impl
* fix
* Clean up rgcn example code
* upd
* upd
* update
* Fix
* update score
* sparse for sage
* remove model sparse
* upd
* upd
* remove global norm
* revert delete model_sparse.py
* update according to comments
* Fix doc
* upd
* Fix test
* upd
* lint
* lint
* lint
* upd
* upd
* clean up
Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal >
2021-01-28 00:26:49 +08:00
12f6429616
remove hash_func from dataset object ( #2572 )
...
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-27 18:49:40 +08:00
0855d25501
[NN] Support scalar edge weight for GraphConv, SAGEConv and GINConv ( #2557 )
...
* add edge weight in forward
* fix lint
* fix
* fix
* address comments
* add utils
* add util to normalize in gcn way
* fix lint
* add unittest
* fix lint
* fix docstring
* fix docstring
* address comments
* improve notation consistence
* use preferred fn
2021-01-26 23:34:12 +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
6c23fba8fa
[Doc][Org] move edge_softmax to functional ( #2442 )
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* move edge_softmax to functional
* change examples
* fixes
* revert
* fix
* fix
* remove
* fix
* test
* add init
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-26 12:46:37 +08:00
a613ad8806
Refactor code for retaining formats in message-passing. ( #2570 )
2021-01-25 16:55:16 +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
Mufei Li