GitLab

* merge

* format

* rename

* sort

* sort

* update

* update

* update

* Update tests/utils/checks.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

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Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* rename

* sort

* rename

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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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* [Misc] Auto-format tests.

* more

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* rename

* remove test transpose

* udpate

* rename

* cleanup

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* overwrite default_collate_fn

* Update dataloader.py

* Update dataloader.py

* Update dataloader.py

* Update dataloader.py

* Update test_dataloader.py

* revert the test code being reverted in #4956

* 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
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Co-authored-by: rudongyu <ru_dongyu@outlook.com>

* 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>

* 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
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Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* fix unit test

* oops

* Add biased multi-head attention module (dense)

* fix lint issues

* refine according to dongyu's comments
Co-authored-by: rudongyu <ru_dongyu@outlook.com>

* [Fix]Support HGT mini-batch

* [Test] Update HGT test

* [Conv] nightly update conv

* [Conv] nightly update

* 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
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* add a learned laplacian positional encoder

* leverage black to beautify the python code

* refine according to dongyu's comments
Co-authored-by: rudongyu <ru_dongyu@outlook.com>

* [Model] Heterogeneous graph support for GNNExplainer (#1)

* add HeteroGNNExplainer

* GNNExplainer for heterogeenous graph

* fix typo

* variable name cleanup

* added HeteroGNNExplainer test

* added doc indexing for HeteroGNNExplainer

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
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* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
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* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
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* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
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* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update python/dgl/nn/pytorch/explain/gnnexplainer.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update gnnexplainer.py

Change DGLHeteroGraph to DGLGraph, and specified parameter inputs

* Added ntype parameter to the explainer_node call

* responding to @mufeili's comment regarding restoring empty lines at appriopiate places to be consistent with existing practices

* responding to @mufeili's comment regarding restoring empty lines at appriopiate places that were missed in the last commit

* docstring comments added based on @mufeili suggestions

* indorporated @mufeili requested changes related to docstring model declaration.

* example model and test_nn.py added for explain_graphs

* explain_nodes fixed and fixed the way hetero num nodes and edges are handled

* white spaces removed

* lint issues fixed

* explain_graph model updated

* explain nodes model updated

* minor fixes related to gpu compatability

* cuda support added

* simplify WIP

* _init_masks for ennexplainer updated to match heterographs

* Update

* model simplified and docstring comments updated

* nits: docstring udpated

* lint check issues updated

* lint check updated

* soem formatting updated

* disabling int32 testing for GNNExplainer

* Update
Co-authored-by: Kangkook Jee <kangkook.jee@gmail.com>
Co-authored-by: ahadjawaid <94938815+ahadjawaid@users.noreply.github.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: kxm180046 <kxm180046@utdallas.edu>
Co-authored-by: Kunal Mukherjee <kunmukh@gmail.com>
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* metapath2vec package

* fix bugs --metapath2vec package

* add unittest and fix bugs

* fix pyling messages

* del init.py

* fix bugs

* modify metapath2vec and add deepwalk

* metapath2vec module

* Update

* Update

* rollback to initial metapath2vec

* Update

* Update

* Update

* Update
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
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* metapath2vec package

* fix bugs --metapath2vec package

* add unittest and fix bugs

* fix pyling messages

* del init.py

* fix bugs

* modify metapath2vec and add deepwalk

* deepwalk module

* del metapath2vec files

* Update

* Update

* Update

* Update

* Update

* Fix
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* fix

* Update hetero.py

* why did i remove this
Co-authored-by: Xin Yao <xiny@nvidia.com>

* rgcn-ogbn-mag

* Add link in README.md

* correct code-format,add the reset_parameters function to the HeteroEmbedding module

* add the annotation in hetero.py

* add a unit test

* modify format

* Update
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
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* Fix doc and default settings for RelGraphConv

* Add unit test

* Split msg in two lines to pass CI-lint

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>

* enhance EGATConv| nfeats as tuples

* egatconv modified for bipartite graphs

* modified docstrings

* added/modified unittests for EGATConv

* Update egatconv.py

* rectified lint errors
Co-authored-by: rijulizer <riju.mukherjee@gmail.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* add label propagation module

* fix prev bug in example

* add dgn

* fix linting and doc issues

* update label propagation & dgn

* update label propagation & dgn

* update example

* fix unit test

* fix agg heritage issue

* fix agg issue

* fix lint

* fix idx

* fix lp gpu issue

* Update

* Update
Co-authored-by: mufeili <mufeili1996@gmail.com>

* Update

* Update

* Update

* Update
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* add EGNN & PNA

* fix egnn issues

* fix pna issues

* update pna conv

* add doc strings

* update pnaconv

* fix unused args issue

* fix moment aggregation issue
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* radius graph

* remove trailing whitespaces from docs

* disable invalid name for transform func

* disable radius graph module invalid name

* move pylint disable before init

* fix missing nodes from point set

* update docs indexing

* add compute mode as optional param

* radius graph test

* remove trailing whitespaces

* fix precision when comparing tensors
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* WIP: TypedLinear and new RelGraphConv

* wip

* further simplify RGCN

* a bunch of tweak for performance; add basic cpu support

* update on segmm

* wip: segment.cu

* new backward kernel works

* fix a bunch of bugs in kernel; leave idx_a for future

* add nn test for typed_linear

* rgcn nn test

* bugfix in corner case; update RGCN README

* doc

* fix cpp lint

* fix lint

* fix ut

* wip: hgtconv; presorted flag for rgcn

* hgt code and ut; WIP: some fix on reorder graph

* better typed linear init

* fix ut

* fix lint; add docstring

* modify hetero

* modify rst document

* update hetero

* update hetero

* update hetero

* update hetero

* Update

* Update

* Update

* Update

* 20220216

* Update

* Update

* Fix
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: ShelkerX <925089962@qq.com>

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix lint

* lint

* Update

* Update

* lint fix

* Fix CI

* Fix

* Fix CI

* Update

* Fix

* Update

* Update

* Update ginconv.py

* Update test_nn.py
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* Update

* Update

* Update

* Update

* Update

* CI

* CI

* CI
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

* Fix a bug in TWIRLS, add unittest

* reformatting the code

* modify unittest for TWIRLS
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

* Update

* Update

* Fix

* Update

* Update

* update

* Fix test

* CI

* CI

* add

* fix optional docing

* fix

* lint

* add normalized by edge weight

* add test

* fix

* lint

* fix docs

* fix

* fix docs

* Update

* Fix

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* lint fix

* lint fix

* Fix lint

* Update

* Fix CI

* Fix CI

* Fix

* CI

* Fix

* Update

* Fix

* Fix

* Fix CI

* Fix CI

* [Model][Core] GATv2

* lint

* gatv2conv.py

* lint

* lint

* style and docs

* lint

* gatv2conv fix
Co-authored-by: Shaked Brody shakedbr@campus.technion.ac.il <shakedbr@tangerine.cslcs.technion.ac.il>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>