1fe0860750
[Bugfix] Fixes #2844 ( #2847 )
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Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-04-25 18:12:17 +08:00
c37e036432
[Bug Fix] Fix sparse opt bug ( #2859 )
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* Fix #2856
* upd
* Fix unitest
* upd
* upd
* upd
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-25.ec2.internal >
2021-04-25 13:40:21 +08:00
d76af4d4c1
[Distributed] Return the ID mapping in graph partitioning. ( #2857 )
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* return mapping.
* support heterogeneous graph.
* more test.
* fix lint.
* fix for diff backends.
* fix.
* fix.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-04-22 17:51:42 +08:00
bbebde4660
[Performance] Track sorted status of COO from creation ( #2645 )
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* Add row/col sorted flags
* improve sorting paths
* Remove print statement
* Keep track of sorted matrices
* Remove sort check in to_block
* Improve CPU sorted COO->CSR
* Handle the zero edge case
* Remove omp default clause to work with MSVC
* Update comments on sorted COO->CSR cpu implementatoin
* Expose sorted to python interface
* Make check_sorted default to false for dgl.graph()
* remove check sorted; add utests
* remove check_sorted flag
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-04-16 10:30:07 +08:00
e70138bbe4
[Performance][GPU] Enable GPU uniform edge sampling ( #2716 )
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* Start on uniform GPU sampling
* Save more work
* Get cu file compiling
* Update sampling
* More changes
* Get GPU sampling for uniform probabilities solved
* Fix batch tensor migration
* Fix
* update kernels
* expand blocking
* Undo testing change
* Cut down on sampling overhead
* Fix replacement
* Update unit tests
* Add option to gpu sample in graphsage
* Copy only csc to gpu
* Add ogbn support
* Fix linting
* Remove nvtx from sample
* Improve documentation and error checking
* Expand documentation
* Update assert checking
* delete extra space
* Use standard dataloader when dataset is a dictionary
* ogb -> ogbn
* Fix edge selection determinism
* Fix typos
* Remove nvtx
* Add comment for self.fanout_arrays and assert
* Fix linting
* Migrate to scalarbatcher
* Fix indentation
* Fix batcher
* Fix indexing
* Only use databatcher for GPU
* Convert to DGL NDArray to PyTorch Tensor
* Add optimization for PyTorch's F.tensor() for list of GPU tensors
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2021-04-14 18:55:09 -07:00
de5e8e2392
[Distributed] Fix a bug for graphs without node/edge data. ( #2838 )
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* fix.
* test distributed graph without node/edge data.
* remove some tests.
* fix lint
2021-04-12 22:35:01 -07:00
e83d0a8007
[Feature] Add kd-tree implementation (CPU) for kNN ( #2767 )
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* add submodule nanoflann
* finish python API for knn
* finish ndarray adaptor
* finish cpu-kdtree version of knn
* use openmp
* add endline
* upt
* upt
* fix format and code style
* upt
* add warning for gpu-cpu copy
* avoid contiguous copy
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Tong He <hetong007@gmail.com >
2021-04-09 17:39:34 +08:00
0fce09074d
[Distributed] Bind to the correct NIC ( #2798 )
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Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2021-04-08 17:56:30 -07:00
bfbbefa793
[Distributed] Fix a bug in multiprocessing sampling. ( #2826 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-73-81.ec2.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-04-08 01:29:33 -07:00
48b9ecd201
Fix discrepancy in dgl.dataloading.EdgeDataLoader ( #2819 )
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* fix discrepancy
* address comments
2021-04-07 16:08:14 +08:00
3301bd0bcc
bump nightly to 0.7 ( #2814 )
2021-04-06 13:51:26 +08:00
cfe6e70b7a
RGAT baseline for OGB-LSC node classification challenge ( #2810 )
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* RGAT baseline
* update links (data.dgl.ai hasn't refreshed yet)
* nvm still use dgl.ai domain
* descriptions
* actually it took less
* address comments
* stop worrying about cache
* update links
* oops
2021-04-05 18:21:18 +08:00
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
e36c5db614
[Distributed] Simplify distributed API ( #2775 )
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* remove num_workers.
* remove num_workers.
* remove num_workers.
* remove num-servers.
* update error message.
* update docstring.
* fix docs.
* fix tests.
* fix test.
* fix.
* print messages in test.
* fix.
* fix test.
* fix.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal >
2021-03-29 19:19:23 -07:00
97863ab85b
[Distributed] Cleanup the process pool correctly when the process exits. ( #2781 )
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Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-03-29 14:53:51 -07:00
2952f3c473
Update subgraph.py ( #2784 )
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Co-authored-by: Zihao Ye <expye@outlook.com >
2021-03-29 14:58:39 +08:00
0576a33b7f
Update convert.py ( #2789 )
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Co-authored-by: Zihao Ye <expye@outlook.com >
2021-03-28 20:59:52 +08:00
e22087aa36
[BUG] fix for zero degree nodes ( #2786 )
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* fix for zero degree nodes
* Update python/dgl/ops/spmm.py
linting fix
Co-authored-by: Zihao Ye <zihaoye.cs@gmail.com >
Co-authored-by: Konstantin Sofeikov <konstantin.sofeikov@complyadvantage.com >
Co-authored-by: Zihao Ye <expye@outlook.com >
Co-authored-by: Zihao Ye <zihaoye.cs@gmail.com >
2021-03-25 22:09:53 +08:00
03482f0a4c
[NN] tf nn for edgeConv ( #2741 )
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* tf nn for edgeConv
* Auto stash before merge of "tf_working" and "origin/tf_working"
* clean up
* added test for edge_conv
* fix
* fix
* fix
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2021-03-25 13:44:07 +08:00
929d863447
[Feature] Sparse-sparse matrix multiplication, addition, and masking ( #2753 )
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* test
* more stuff
* add test
* fixes
* optimize algo
* replace unordered_map with arrays
* lint
* lint x2
* oops
* disable gpu csrmm tests
* remove gpu invocation
* optimize with openmp
* remove python functions
* add back with docstrings
* lint
* lint
* update python interface
* functionize
* functionize
* lint
* lint
2021-03-24 17:24:41 +08:00
6999f88f3f
[Model] Add random_start option for Farthest Point Sampler ( #2755 )
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* add random_start option for FPS
* change doc
* change from random_start to start_idx
* change error condition
* change error msg
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-03-22 21:53:46 +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
1789972c4b
[Bugfix] add default value for BlockSampler ( #2771 )
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* [Bugfix] add default value for BlockSampler
* [Doc] modify user_guide description about MultiLayerDropoutSample
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-03-22 14:02:27 +08:00
edf644633d
[performance] Optimize the association order of AXW in GraphSAGE. ( #2747 )
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* upd
* lint
* upd
* upd
* compatibility
* upd
* upd
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-03-19 01:41:33 +08:00
366cc7ebf3
[Pickle] Fix HeteroGraphConv pickle problem ( #2761 )
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* fix pickle problem
* lint
* add pickle tests
* fix
* fix
* fix
* fix
* fix for windows
2021-03-18 17:56:28 +08:00
09ef2c2c3d
[Doc] Add Pseudo Code for HeteroGraphConv ( #2729 )
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* Update
* Update
* Update
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-15-8.us-west-2.compute.internal >
2021-03-17 20:00:15 +08:00
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 )
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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
c88fca5055
[Feature] Add edge coarsening for homogeneous undirected graphs ( #2691 )
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* 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 )
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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
7380d61eb9
[NN] Support Unidirectional Bipartite Graphs in CFConv ( #2674 )
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* 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 )
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* 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 )
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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 )
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* 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 )
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* 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 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-02-25 00:21:00 +08:00
71d53d9eef
add thumbnails for tutorials ( #2695 )
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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 )
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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
174dd18905
[hotfix] A bunch of fix for SetTransformer ( #2658 )
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* 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 )
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* 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 )
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* 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 )
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* fix
* lint
* lint
2021-02-21 18:52:35 +08:00
e6bf54cdcb
[Feature] Support aggregate multiple edge features in to_simple. ( #2623 )
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* 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 )
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* 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 )
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* 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 )
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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 )
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* 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
Quan (Andy) Gan