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* [Sparse] Add sparse matrix C++ implementation

* Add documentation

* Update

* Minor fix

* Move Python code to dgl/mock_sparse2

* Move headers to include

* lint

* Update

* Add dgl_sparse directory

* Move src code to dgl_sparse

* Add __init__.py in tests to avoid naming conflict

* Add dgl sparse so in Jenkinsfile

* Complete docstring & SparseMatrix basic op

* lint

* Disable win tests

* edgewise mpops

* formatting

* black formatting

* isort

* fix lint

* remove typing module; address comments

* fix gpu ut; rename test file

* 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>

* 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>

* sample neighbors with masks

* oops

* refactor again

* remove

* remove debug code

* rename macro

* address comments

* more stuff

* remove

* fix

* try fix unit test

* oops

* fix test

* oops

* change name

* rename a lot of stuff

* oops

* ugh

* misc fixes

* lint

* address a lot of comments

* lint

* lint

* fix

* that was silly

* fix

* fix

* fix

* oops

* [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
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 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 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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>

* 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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Sparse] Add SparseMatrix unittest and fix docstring problem

* Minor fix

* Update

* check permission

* rm future annonations

* Skip create_from_csr and create_from_csc tests because Pytorch 1.9.0 does not have torch.sparse_csr_tensor
Co-authored-by: Israt Nisa <nisisrat@amazon.com>

* Add elementwise operators for diagonal matrix

* minor

* resolve ambiguity of ops

* lint check

* lint check

* lint check
Co-authored-by: Israt Nisa <nisisrat@amazon.com>

* 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
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* sddmm init

* SDDMM with N-D nonzero values

* drop support for vector shaped non zero elements

* address comments

* skip cpu test

* skip GPU test too
Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* Update

* lint

* Fix

* Update

* Update

* Update

* update

* Fix

* Update

* Fix

* Fix

* Fix

* CI

* Update

* Update

* Update

* update test
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* fix test stream

* init cusparse handle

* [Sparse] Add reduction operators

* Fix linting problem

* Fix linting problem

* Fix linting problem

* Fix docstring

* Fix test cases

* Fix linting problem

* Skip reduction unittests

* initial commit

* address comments

* lint check
Co-authored-by: Israt Nisa <nisisrat@amazon.com>

* [Sparse] Add Transposition

* Fix docstring

* Fix linting problem

* Minor fix

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

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* fix

* Update hetero.py

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

* add set_stream

* add .record_stream for NDArray and HeteroGraph

* refactor dgl stream Python APIs

* test record_stream

* add unit test for record stream

* use pytorch's stream

* fix lint

* fix cpu build

* address comments

* address comments

* add record stream tests for dgl.graph

* record frames and update dataloder

* add docstring

* update frame

* add backend check for record_stream

* remove CUDAThreadEntry::stream

* record stream for newly created formats

* fix bug

* fix cpp test

* fix None c_void_p to c_handle

* init

* Add api doc for sparse library

* support op btwn matrices with differnt sparsity

* Fixed docstring

* addresses comments

* lint check

* change keyword format to fmt
Co-authored-by: Israt Nisa <nisisrat@amazon.com>

[Feature] Added exclude_self and output_batch to knn graph construction (Issues #4323 #4316) (#4389)

* * Added "exclude_self" and "output_batch" options to knn_graph and segmented_knn_graph
* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information

* * Changed defaults on new knn_graph and segmented_knn_graph function parameters, for compatibility; pytorch/test_geometry.py was failing

* * Added test to ensure dgl.remove_self_loop function correctly updates batch information

* * Added new knn_graph and segmented_knn_graph parameters to dgl.nn.KNNGraph and dgl.nn.SegmentedKNNGraph

* * Formatting

* * Oops, I missed the one in segmented_knn_graph when I fixed the similar thing in knn_graph

* * Fixed edge case handling when invalid k specified, since it still needs to be handled consistently for tests to pass
* Fixed context of batch info, since it must match the context of the input position data for remove_self_loop to succeed

* * Fixed batch info resulting from knn_graph when output_batch is true, for case of 3D input tensor, representing multiple segments

* * Added testing of new exclude_self and output_batch parameters on knn_graph and segmented_knn_graph, and their wrappers, KNNGraph and SegmentedKNNGraph, into the test_knn_cuda test

* * Added doc comments for new parameters

* * Added correct handling for uncommon case of k or more coincident points when excluding self edges in knn_graph and segmented_knn_graph
* Added test cases for more than k coincident points

* * Updated doc comments for output_batch parameters for clarity

* * Linter formatting fixes

* * Extracted out common function for test_knn_cpu and test_knn_cuda, to add the new test cases to test_knn_cpu

* * Rewording in doc comments

* * Removed output_batch parameter from knn_graph and segmented_knn_graph, in favour of always setting the batch information, except in knn_graph if x is a 2D tensor
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-50-143.us-west-2.compute.internal>

* Fix doc and default settings for RelGraphConv

* Add unit test

* Split msg in two lines to pass CI-lint

* test ddp dataloader

* add pure_gpu for edgedataloader

* resolve ddp issue

* enable use for weighted neighbor sampler and biased random walk

* add unit tests

* fix for mxnet/tf

* fix typo

* Fix test_csrmm for tensor core

* unset allow tf32 flag

* update test unified tensor

* skip fp16 for CPU

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

* Add uva by default to embedding

* More updates

* Update optimizer

* Add new uva functions

* Expose new pinned memory function

* Add unit tests

* Update formatting

* Fix unit test

* Handle auto UVA case when training is on CPU

* Allow per-embedding decisions for whether to use UVA

* Address spares_optim.py comments

* Remove unused templates

* Update unit test

* Use dgl allocate memory for pinning

* allow automatically unpin

* workaround for d2h copy with a different dtype

* fix linting

* update error message

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

* Explicitly unpin tensoradapter allocated arrays

* Undo unrelated change

* Add unit test

* update unit test

* add pinned_by_dgl flag to NDArray::Container

* use dgl.ndarray for holding the pinning status

* update multi-gpu uva inference

* reinterpret cast NDArray::Container* to DLTensor* in MoveAsDLTensor

* update unpin column and examples

* add unit test for unpin column
Co-authored-by: Dominique LaSalle <dlasalle@nvidia.com>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>

* fix

* fix

* Update utils.py

* 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>

This reverts commit fdd1fe19.

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>

Prevent users from attempting to pin PyTorch non-contiguous tensors or views only encompassing part of tensor. (#3992)

* Disable pinning non-contiguous memory

* Prevent views from being converted for write

* Fix linting

* Add unit tests

* Improve error message for users

* Switch to pytest function

* exclude mxnet and tensorflow from inplace pinning

* Add skip

* Restrict to pytorch backend

* Use backend to retrieve device

* Fix capitalization in decorator
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* Explicitly unpin tensoradapter allocated arrays

* Undo unrelated change

* Add unit test

* update unit test

* Update

* Update

* Update

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