8b266f5001
[doc] use tqdm from tqdm.auto ( #7191 )
2024-03-04 16:43:15 +08:00
c76a43ca39
Update doc network_emb.py ( #6559 )
2023-11-16 10:25:20 +08:00
eb40ed550a
[Model] Add Node explanation for Heterogenous PGExplainer Impl. ( #6050 )
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Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com >
2023-09-14 10:42:23 +08:00
9ef80a6e54
[BugFix] remove non-existent arg ( #6188 )
2023-08-22 11:43:49 +08:00
d5ae1ea05f
[BugFix] add input/output shape check in GatedGraphConv ( #6119 )
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Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com >
2023-08-09 19:16:46 +08:00
19c7e5afc0
[NN] Add EGT Layer ( #6056 )
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Co-authored-by: rudongyu <ru_dongyu@outlook.com >
2023-08-02 14:14:08 +08:00
416e2425b1
[Misc] Further polish gcn2conv.py ( #6046 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-63.ap-northeast-1.compute.internal >
2023-07-27 13:13:50 +08:00
6af55f18cd
Update gcn2conv.py ( #6020 )
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Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2023-07-26 12:11:33 +08:00
70ad508367
[Model] Add Node explanation for Homogenous PGExplainer Impl. ( #5839 )
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Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-07-10 14:17:39 +08:00
b51fb6f6a5
[NN] Refactor SpatialEncoder3d ( #5894 )
2023-06-29 11:39:03 +08:00
e47a02793f
[NN] Refactor DegreeEncoder, SpatialEncoder and PathEncoder ( #5799 )
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Co-authored-by: rudongyu <ru_dongyu@outlook.com >
2023-06-09 16:34:55 +08:00
b0308c8525
[Model] Implemented PGExplainer for Heterogeneous graph ( #5739 )
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Co-authored-by: kxm180046 <kxm180046@utdallas.edu >
Co-authored-by: Kunal Mukherjee <kunmukh@gmail.com >
2023-06-07 13:42:36 +08:00
484fabdcc1
[Model] Implemented PGExplainer for Homogeneous graph ( #5550 )
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Co-authored-by: kxm180046 <kxm180046@utdallas.edu >
Co-authored-by: Infinity_X <Infinity_X@sinomo.net >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-05-10 20:31:48 +08:00
c4c9b830ae
[NN] GatedGCNConv ( #5654 )
2023-05-06 18:20:06 +08:00
d6c12f0714
[NN] Fix #5642 ( #5652 )
2023-05-06 13:03:20 +08:00
ea706cae58
[Model] Update cugraph-ops models for 23.04 release ( #5540 )
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Co-authored-by: schmidt-ju <79865721+schmidt-ju@users.noreply.github.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
Co-authored-by: peizhou001 <110809584+peizhou001@users.noreply.github.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-16-19.ap-northeast-1.compute.internal >
2023-05-04 17:11:22 +08:00
c0f346e754
[Model] Implemented SubgraphX Explainer for Heterogeneous graph ( #5530 )
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Co-authored-by: kxm180046 <kxm180046@utdallas.edu >
Co-authored-by: Nick Baker <ndbaker1@outlook.com >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-04-21 14:05:02 +08:00
f41934df87
[Sparse] Add conversion between DGLGraph and SparseMatrix. ( #5553 )
2023-04-20 18:00:34 +08:00
b58416f76a
[NN] Refine the API of GraphormerLayer ( #5565 )
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Co-authored-by: rudongyu <ru_dongyu@outlook.com >
2023-04-19 16:36:25 +08:00
bb1f8850e5
[NN] Refactor the Code Structure of GT ( #5100 )
2023-04-14 11:50:14 +08:00
f1b0a07984
[NN] add egatconv edge_weight ( #5539 )
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Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-04-13 20:54:42 +08:00
97286f98d3
[NN] Add EdgeGAT operator ( #5282 )
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Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2023-04-09 22:54:49 +08:00
29e6661523
[Optimization] Optimize bias term in GatConv layer ( #5466 )
2023-04-05 23:17:10 +08:00
d45eafd47f
[NN] add gatconv edge_weight ( #5503 )
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Co-authored-by: venzino-han <venzino.han@buzzvil.com >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-03-31 19:53:49 +08:00
89b321b847
[Misc] Rename number_of_edges and number_of_nodes to num_edges and num_nodes. ( #5488 )
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* nn-only
* data-only
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-63.ap-northeast-1.compute.internal >
2023-03-28 12:58:54 +08:00
ae4a5b7394
[Feature] Add state_dict, load_state_dict, param_groups to dgl.optim.SparseGradOptimizer ( #5311 )
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* init update
* all get/set optm_state
* add unit tests
* add docstring
* fix for multiple embeddings
* move embedding methods to private
* fix lint
* fix unit tests
* resolve comments
* merge master
2023-03-08 16:46:34 +08:00
a454734f16
[Misc] Follow up on the missing comment in PR#4989. ( #5437 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-63.ap-northeast-1.compute.internal >
Co-authored-by: Xin Yao <yaox12@outlook.com >
2023-03-08 13:32:21 +08:00
8d5d8962ad
[Refactor] Replace third_party/nccl with PyTorch's NCCL backend ( #4989 )
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* expose GeneratePermutation
* add sparse_all_to_all_push
* add sparse_all_to_all_pull
* add unit test
* handle world_size=1
* remove python nccl wrapper
* remove the nccl dependency
* use pinned memory to speedup D2H copy
* fix lint
* resolve comments
* fix lint
* fix ut
* resolve comments
2023-03-08 12:59:10 +08:00
bfd411d0d5
[Model] Add dgl.nn.CuGraphGATConv model ( #5168 )
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* add CuGraphGATConv model
* lintrunner
* update model to reflect changes in make_mfg_csr(), move max_in_degree to forward()
* simplify pytest markers
* fall back to FG option for large fanout
* update error msg
* add feat_drop and activation options
* add residual option
* Update python/dgl/nn/pytorch/conv/cugraph_gatconv.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/nn/pytorch/conv/cugraph_gatconv.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* reset res_fc
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Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-03-04 14:10:06 +08:00
45153fc078
[Model] Implemented SubgraphX Explainer for Homogeneous graph ( #5315 )
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* subgraphx commit
* nits
* newline eof added
* lint fix
* test script updated to use default values
* lint fix
* graphs that are used for test cases are updated to a small graph
* lint formatted
* test paramter adj to complete the test under 20s
* lint fixes
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Co-authored-by: kxm180046 <kxm180046@utdallas.edu >
2023-02-23 12:50:31 +08:00
bcf9923b32
[Model] Add dgl.nn.CuGraphSAGEConv model ( #5137 )
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* add CuGraphSAGEConv model
* fix lint issues
* update model to reflect changes in make_mfg_csr(), move max_in_degree to forward()
* lintrunner
* allow reset_parameters()
* remove norm option, simplify test
* allow full graph fallback option, add example
* address comments
* address reviews
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Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-02-22 13:43:28 +08:00
63ac788ff4
auto-reformat-nn ( #5319 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-63.ap-northeast-1.compute.internal >
2023-02-19 08:33:30 +08:00
19b3cea166
[Model] Update CuGraphRelGraphConv to use pylibcugraphops=23.02 ( #5217 )
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* update cugraph_relgraphconv
* update equality test
* update cugraph rgcn example
* update RelGraphConvAgg based on latest API changes
* enable fallback option to fg when fanout is large
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Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-02-15 20:11:20 +08:00
21733e903b
Documentation equation syntax fix for EGATConv ( #5284 )
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Some weird formatting occurred in the documentation for EGATConv, so this quick commit should fix that.
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-02-13 14:58:11 +08:00
b7042a141c
[BugFix] fix unexpected exception when agg_type is GCN and bias disabled ( #5127 )
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* [BugFix] fix unexpected exception when agg_type is GCN and bias is disabled
* Update sageconv.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2023-01-10 09:05:44 +08:00
e296c468b2
[Optimization] Optimize bias term in SageConv layer ( #4747 )
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* Optimize bias term in sageconv
* fix lint
* Remove bias sharing
* Update sageconv.py
Co-authored-by: Bartlomiej Gawrych <barlomiej.gawrych@intel.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2023-01-08 13:06:46 +08:00
ab0c0ec68f
[API Deprecation] Deprecate candidates in convert module ( #4988 ) ( #5115 )
2023-01-06 14:45:52 +08:00
dde5cf5d02
[Bug] Fix NN modules crashing with non-FP32 inputs ( reopen #4262 ) ( #4829 )
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* fix fp16 in nn modules
* fix lint
* remove the example
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2023-01-06 14:18:19 +08:00
cd817a1a00
[NN] Add SpatialEncoder and SpatialEncoder3d ( #4991 )
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* Add SpatialEncoder and SpatialEncoder3d
* Optimize the code execution efficiency
* Fixed certain problems according to Dongyu's suggestions.
* Fix an error about probability of division by zero in PathEcoder; Change certain designs in SpatialEncoder
* Fix a typo
* polish the docstring
* fix doc
* lint
Co-authored-by: Ubuntu <ubuntu@ip-172-31-14-146.ap-northeast-1.compute.internal >
Co-authored-by: rudongyu <ru_dongyu@outlook.com >
2023-01-03 14:02:14 +08:00
3db6604e67
[Fix core lib warning] Fix using torch.tensor for tensor conversion ( #5028 )
2022-12-15 13:50:33 +08:00
996c533149
[Model] Fix bug of gatv2 when input is block ( #5000 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-16-19.ap-northeast-1.compute.internal >
2022-12-12 15:32:48 +08:00
279e2e8fba
Add Graph Transformer Layer (Dense Computation) ( #4959 )
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* Add GraphTransformerLayer (dense)
* beautify the python code with black
* refine according to mufei's comments
* fix AttributeError in unit test
* rename module as GraphormerLayer
* fix name issue
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-12-07 16:23:14 +08:00
ba21295cd5
[Model] Update CuGraphRelGraphConv to use new bindings from pylibcugraphops ( #4965 )
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* update agg function with new bindings
* handle optional import in __init__
* raise error in RelGraphConvAgg when pylibcugraphops not imported
* Update tests/cugraph/cugraph-ops/test_cugraph_relgraphconv.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update tests/cugraph/cugraph-ops/test_cugraph_relgraphconv.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* use keyword args for readability
* add missing docstring to pass CI
* catch ImportError rather than ModuleNotFoundError
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-12-06 14:00:57 +08:00
93ecfa313a
[NN] Add PathEncoder ( #4956 )
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* Add PathEncoder to transformer.py
* add blank line at the and
* rename variabl sp to shortest_path
* Fixed corresponding problems
* Fixed certain bugs when running on CUDA
* changed clamp min from 0 to 1
Co-authored-by: Ubuntu <ubuntu@ip-172-31-14-146.ap-northeast-1.compute.internal >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-12-05 13:47:51 +08:00
611393021a
[API Deprecation] Remove candidates in DGLGraph ( #4946 )
2022-12-01 16:41:53 +08:00
16eba6e88c
[NN] Add biased multi-head attention module (dense) ( #4916 )
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* Add biased multi-head attention module (dense)
* fix lint issues
* refine according to dongyu's comments
Co-authored-by: rudongyu <ru_dongyu@outlook.com >
2022-11-20 14:55:25 +08:00
4ecd2c8585
[Model] Add dgl.nn.CuGraphRelGraphConv model ( #4826 )
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* added relgraphconv
* add tests for CuGraphRelGraphConv
* move test to tests directory
* update docs
* address PR review 1
* address PR review, continued
* remove stashing ctx.device
* make fanout optional
* fanout -> max_in_degree
* improve docstrings consistency
* initialize parameters directly in __init__
* get rid of shared memory size check
* improve docs
* format comments
* skip test case for regularizer=None
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com >
2022-11-18 14:04:51 +08:00
3132da2826
Deprecate ( #4864 )
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rename DGLHeteroGraph to DGLGraph
2022-11-15 10:01:01 +08:00
ee9887d66a
[Fix]Support HGT mini-batch ( #4664 )
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* [Fix]Support HGT mini-batch
* [Test] Update HGT test
* [Conv] nightly update conv
* [Conv] nightly update
2022-11-14 16:18:39 +08:00
9d9280cb0e
[NN] Add DegreeEncoder for graph transformer ( #4742 )
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* Add files via upload
This file will contain several utility modules for Graph Transformer. DegreeEncoder has been implemented in this file now.
* Update graph_transformer.py
* Update nn-pytorch.rst
Add graph_transformer.DegreeEncoder in Utility Modules
* Update test_nn.py
* Update __init__.py
* Update graph_transformer.py
* Update test_nn.py
* Update graph_transformer.py
fix unused import
* Update graph_transformer.py
add module doc-string
* Update graph_transformer.py
* Update graph_transformer.py
Co-authored-by: rudongyu <ru_dongyu@outlook.com >
2022-11-02 13:29:41 +08:00
Rhett Ying