56bbf9cb6d
[Distributed][Example] Distributed training for unsupervised graphsage ( #1853 )
...
* Standalone can run
* fix
* Add save
* Fix
* Fix
* Fix
* Fix
* debug
* test
* test
* Fix
* Fix
* log
* Fix
* fix
* Profile
* auto sync grad
* update
* add test for unsupervised dist training
* upd
* Fix lr
* Fix update
* sync
* fix
* Revert "fix"
This reverts commit d5caa7398b36125f6d6e2c742a95c6ff4298c9e9.
* Fix
* unsupervised
* Fix
* remove debug
* Add test case for dist_graph find_edges()
* Fix
* skip tensorflow test for find_edges
* Update readme
* remove some test
* upd
* Update partition_graph.py
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-24-210.ec2.internal >
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2020-08-01 12:24:55 -07:00
34a067eaa0
[bugfix] Fix the memory leak issue of Cluster GAT under 0.5 kernel and simplify the bipartite GAT. ( #1908 )
...
* uipd
* upd
* upd
* upd
* upd
2020-08-02 00:59:27 +08:00
b347590a37
[Dataset] Citation graph ( #1902 )
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* citation graph
* GCN example use new citatoin dataset
* mxnet gat
* triger
* Fix
* Fix gat
* fix
* Fix tensorflow dgi
* Fix appnp, graphsage for mxnet
* fix monet and sgc for mxnet
* Fix tagcn
* update sgc, appnp
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-01 19:25:50 +08:00
4be4b13424
[Distributed] add copy_partitions.py ( #1866 )
...
* fix bugs.
* eval on both vaidation and testing.
* add script.
* update.
* update launch.
* make train_dist.py independent.
* update readme.
* update readme.
* update readme.
* update readme.
* generate undirected graph.
* rename conf_file to part_config
* use rsync
* make train_dist independent.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-115.us-west-2.compute.internal >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-07-31 11:11:56 -07:00
8b64037eea
[Example] cluster-gat for ogb ( #1875 )
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* cluster-gat for ogb
* Fix new graph
* Inference using minibatch style
* update readme
* Update params
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-186.ec2.internal >
Co-authored-by: Zihao Ye <expye@outlook.com >
2020-08-01 00:09:15 +08:00
dbb028acc8
[Dataset] Builtin knowledge graph dataset ( #1881 )
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* buildin knowledge graph dataset
* upd
* docstring
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Tong He <hetong007@gmail.com >
2020-07-30 23:37:33 +08:00
68a978d4de
[Model] Fixes JTNN for 0.5 ( #1879 )
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* jtnn and fixes
* make metagraph a method
* fix test
* fix
2020-07-30 13:36:08 +08:00
aee1067941
[Dataset] RDF dataset with DGL-Dataset template ( #1869 )
...
* update rdf builtin dataset
* Fix
* use new dataset
* fix
* rdf dataset using new framework
* tf work
* Fix mxnet
* Fix tensorflow
* Fix mxnet
* Update
* upd
* update some docstring
* clean some dead code
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-07-30 09:12:00 +08:00
15411d932c
[Example] Fix some example after graph refactor. ( #1884 )
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* Update cluster GCN README
We do not need to build metis right now.
We can use builtin metis.
* Fix gcmc mxnet
* Fix graphwriter
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal >
2020-07-29 22:07:47 +08:00
44089c8b4d
[Refactor][Graph] Merge DGLGraph and DGLHeteroGraph ( #1862 )
...
* Merge
* [Graph][CUDA] Graph on GPU and many refactoring (#1791 )
* change edge_ids behavior and C++ impl
* fix unittests; remove utils.Index in edge_id
* pass mx and th tests
* pass tf test
* add aten::Scatter_
* Add nonzero; impl CSRGetDataAndIndices/CSRSliceMatrix
* CSRGetData and CSRGetDataAndIndices passed tests
* CSRSliceMatrix basic tests
* fix bug in empty slice
* CUDA CSRHasDuplicate
* has_node; has_edge_between
* predecessors, successors
* deprecate send/recv; fix send_and_recv
* deprecate send/recv; fix send_and_recv
* in_edges; out_edges; all_edges; apply_edges
* in deg/out deg
* subgraph/edge_subgraph
* adj
* in_subgraph/out_subgraph
* sample neighbors
* set/get_n/e_repr
* wip: working on refactoring all idtypes
* pass ndata/edata tests on gpu
* fix
* stash
* workaround nonzero issue
* stash
* nx conversion
* test_hetero_basics except update routines
* test_update_routines
* test_hetero_basics for pytorch
* more fixes
* WIP: flatten graph
* wip: flatten
* test_flatten
* test_to_device
* fix bug in to_homo
* fix bug in CSRSliceMatrix
* pass subgraph test
* fix send_and_recv
* fix filter
* test_heterograph
* passed all pytorch tests
* fix mx unittest
* fix pytorch test_nn
* fix all unittests for PyTorch
* passed all mxnet tests
* lint
* fix tf nn test
* pass all tf tests
* lint
* lint
* change deprecation
* try fix compile
* lint
* update METIDS
* fix utest
* fix
* fix utests
* try debug
* revert
* small fix
* fix utests
* upd
* upd
* upd
* fix
* upd
* upd
* upd
* upd
* upd
* trigger
* +1s
* [kernel] Use heterograph index instead of unitgraph index (#1813 )
* upd
* upd
* upd
* fix
* upd
* upd
* upd
* upd
* upd
* trigger
* +1s
* [Graph] Mutation for Heterograph (#1818 )
* mutation add_nodes and add_edges
* Add support for remove_edges, remove_nodes, add_selfloop, remove_selfloop
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
* upd
* upd
* upd
* fix
* [Transfom] Mutable transform (#1833 )
* add nodesy
* All three
* Fix
* lint
* Add some test case
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* fix
* triger
* Fix
* fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
* [Graph] Migrate Batch & Readout module to heterograph (#1836 )
* dgl.batch
* unbatch
* fix to device
* reduce readout; segment reduce
* change batch_num_nodes|edges to function
* reduce readout/ softmax
* broadcast
* topk
* fix
* fix tf and mx
* fix some ci
* fix batch but unbatch differently
* new checkk
* upd
* upd
* upd
* idtype behavior; code reorg
* idtype behavior; code reorg
* wip: test_basics
* pass test_basics
* WIP: from nx/ to nx
* missing files
* upd
* pass test_basics:test_nx_conversion
* Fix test
* Fix inplace update
* WIP: fixing tests
* upd
* pass test_transform cpu
* pass gpu test_transform
* pass test_batched_graph
* GPU graph auto cast to int32
* missing file
* stash
* WIP: rgcn-hetero
* Fix two datasety
* upd
* weird
* Fix capsuley
* fuck you
* fuck matthias
* Fix dgmg
* fix bug in block degrees; pass rgcn-hetero
* rgcn
* gat and diffpool fix
also fix ppi and tu dataset
* Tree LSTM
* pointcloud
* rrn; wip: sgc
* resolve conflicts
* upd
* sgc and reddit dataset
* upd
* Fix deepwalk, gindt and gcn
* fix datasets and sign
* optimization
* optimization
* upd
* upd
* Fix GIN
* fix bug in add_nodes add_edges; tagcn
* adaptive sampling and gcmc
* upd
* upd
* fix geometric
* fix
* metapath2vec
* fix agnn
* fix pickling problem of block
* fix utests
* miss file
* linegraph
* upd
* upd
* upd
* graphsage
* stgcn_wave
* fix hgt
* on unittests
* Fix transformer
* Fix HAN
* passed pytorch unittests
* lint
* fix
* Fix cluster gcn
* cluster-gcn is ready
* on fixing block related codes
* 2nd order derivative
* Revert "2nd order derivative"
This reverts commit 523bf6c249bee61b51b1ad1babf42aad4167f206.
* passed torch utests again
* fix all mxnet unittests
* delete some useless tests
* pass all tf cpu tests
* disable
* disable distributed unittest
* fix
* fix
* lint
* fix
* fix
* fix script
* fix tutorial
* fix apply edges bug
* fix 2 basics
* fix tutorial
Co-authored-by: yzh119 <expye@outlook.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-7-42.us-west-2.compute.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-1-5.us-west-2.compute.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal >
2020-07-28 14:30:41 +08:00
bcb988bdea
[Distributed] Small fix on launch script ( #1867 )
...
* update
* update
* update
* update
2020-07-27 13:44:14 +08:00
ec2e24be6d
[Feature] Slice dstnode features in NN modules ( #1838 )
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* slice dstdata from srcdata within nn module
* a bunch of fixes
* add comment
* fix gcmc layer
* repr for blocks
* fix
* fix context
* fix
* do not copy internal columns
* docstring
2020-07-25 21:57:49 +08:00
0fb615b9a6
[Example] Several updates on deepwalk ( #1845 )
...
* fix bug
* fix bugs
* add args
* add args
* fix bug
* fix a typo
* results
* results
* results
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-07-22 23:26:30 +08:00
562871e76b
[Distributed] add distributed evaluation. ( #1810 )
...
* add eval.
* extend DistTensor.
* fix.
* add barrier.
* add more print.
* add more checks in kvstore.
* fix lint.
* get all neighbors for eval.
* reorganize.
* fix.
* fix.
* fix.
* fix test.
* add reuse_if_exist.
* add test for reuse_if_exist.
* fix lint.
* fix bugs.
* fix.
* print errors of tcp socket.
* support delete tensors.
* fix lint.
* fix
* fix example
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal >
2020-07-22 00:40:14 -07:00
523fa4dfc2
Adding MWE-GCN for ogb/ogbn-proteins ( #1803 )
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* 07132020_cleaned
* Update README.md
* Create README.md
* Update README.md
* Update README.md
* further cleaning
* further cleaning
* Update README.md
* Update README.md
* Update README.md
* Update README.md
* Update README.md
* Update README.md
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-170.us-west-2.compute.internal >
Co-authored-by: Zihao Ye <expye@outlook.com >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2020-07-20 22:23:13 +08:00
5c92f6c218
[RPC] Rpc exit with explicit invocation ( #1825 )
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* exit client
* update
* update
* update
* update
* update
* update
* update
* update test
* update
* update
* update
* update
* update
* update
* update
* update
* update
2020-07-20 14:56:26 +08:00
20734637f0
[Distributed] Fix partition ( #1821 )
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* fix partition and print timing.
* fix lint.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal >
2020-07-17 16:03:37 -07:00
df3683a234
fix ( #1817 )
2020-07-17 17:46:20 +08:00
63feb47c26
[Example] Update Links for Supervised Community Detection with Graph Neural Networks ( #1816 )
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* Update README.md
* Update README.txt
2020-07-17 17:13:25 +08:00
ca9d3216d0
[Distributed] Distributed launching script ( #1772 )
...
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix launch script.
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2020-07-16 10:20:57 -07:00
cda0abf75a
[Distributed] add the standalone mode in DistGraph ( #1800 )
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* add standalone mode
* add comments.
* add tests for sampling.
* fix.
* make the code to run the standalone mode
* fix
* fix
* fix readme.
* fix.
* fix test
Co-authored-by: Chao Ma <mctt90@gmail.com >
2020-07-14 23:46:25 -07:00
a1472bcff6
[Distributed] Run distributed graph server inside DGL ( #1801 )
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* run dist server in dgl.
* fix bugs.
* fix example.
* check environment variables and fix lint.
* fix lint
2020-07-14 07:41:44 -07:00
7ea777e122
[Example] Fix HAN ( #1790 )
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* Fix
* Fix
* Fix
2020-07-11 17:29:19 +08:00
ac282a5e35
[Model][Hetero] HGT ( #1778 )
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* add HGT example
* Update README.md
* Update model.py
* Update train_acm.py
* Add comments
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-07-10 01:58:54 -07:00
d6b4e286b6
RGCN minibatch using homogeneous graph. ( #1745 )
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* minibatch rgcn
* minibatch based rgcn
* remove ogb
* lint
* Add sparse emb
* Fix
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-87-240.ec2.internal >
2020-07-07 00:26:10 +08:00
2f6ab43a1b
[Model] Pinsage example that uses sparse embedding update ( #1676 )
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* pinsage example that uses sparse embedding update
* add difference from paper
2020-07-06 12:45:48 +08:00
4ddd477f35
[Model] GraphSAGE inductive example ( #1741 )
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* graphsage inductive example
* fix
2020-07-03 11:32:06 +08:00
168a88e570
[Sampling] NodeDataLoader for node classification ( #1635 )
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* neighbor sampler data loader first commit
* more commit
* nodedataloader
* fix
* update RGCN example
* update OGB
* fixes
* fix minibatch RGCN crashing with self loop
* reverting gatconv test code
* fix
* change to new solution that doesn't require tf dataloader
* fix
* lint
* fix
* fixes
* change doc
* fix docstring
* docstring fixes
* return seeds and input nodes from data loader
* fixes
* fix test
* fix windows build problem
* add pytorch wrapper
* fixes
* add pytorch wrapper
* add unit test
* add -1 support to sample_neighbors & fix docstrings
* docstring fix
* lint
* add minibatch rgcn evaluations
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: Tong He <hetong007@gmail.com >
2020-07-02 16:31:05 +08:00
2c88f7c0b0
[Distributed] Split data to ensure data locality for multiple clients ( #1710 )
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* fix.
* fix tests.
* fix
* add tests.
* fix.
* have default rank.
* add comment.
* fix test.
* remove check
* simplify code.
* add test.
* split data evenly.
* simplify the distributed training code.
* add comments.
* add comments.
2020-07-01 13:03:40 -07:00
c8ec6ee5cc
[Example] Experimental results of deepwalk on ogb datasets ( #1729 )
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* ogb-deepwalk
* ?
* ?
* remove pyg
2020-07-01 14:45:12 +08:00
02d3197407
[Distributed] Pytorch example of distributed GraphSage. ( #1495 )
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* add train_dist.
* Fix sampling example.
* use distributed sampler.
* fix a bug in DistTensor.
* fix distributed training example.
* add graph partition.
* add command
* disable pytorch parallel.
* shutdown correctly.
* load diff graphs.
* add ip_config.txt.
* record timing for each step.
* use ogb
* add profiler.
* fix a bug.
* add train_dist.
* Fix sampling example.
* use distributed sampler.
* fix a bug in DistTensor.
* fix distributed training example.
* add graph partition.
* add command
* disable pytorch parallel.
* shutdown correctly.
* load diff graphs.
* add ip_config.txt.
* record timing for each step.
* use ogb
* add profiler.
* add Ips of the cluster.
* fix exit.
* support multiple clients.
* balance node types and edges.
* move code.
* remove run.sh
* Revert "support multiple clients."
* fix.
* update train_sampling.
* fix.
* fix
* remove run.sh
* update readme.
* update readme.
* use pytorch distributed.
* ensure all trainers run the same number of steps.
* Update README.md
Co-authored-by: Ubuntu <ubuntu@ip-172-31-16-250.us-west-2.compute.internal >
2020-06-28 13:09:40 +08:00
7ee72b668e
[Example] Experimental results on ogbl-citation & ogbl-ppa ( #1711 )
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* ogb-deepwalk
* update readme
* update readme
* update readme
* update readme
* ogbl-ddi
* readme
* citation&ppa
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-06-28 11:37:01 +08:00
f9fd3107ae
[Example] Experimental results over ogbl-ddi ( #1707 )
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* ogb-deepwalk
* update readme
* update readme
* update readme
* update readme
* ogbl-ddi
* readme
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-06-27 14:01:44 +08:00
8d16d4bb6b
[Example] Test deepwalk on ogb leaderboard ( #1689 )
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* ogb-deepwalk
* update readme
* update readme
* update readme
* update readme
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-06-25 23:09:47 +08:00
558673e139
[Model] PointNet and PointNet++ for point cloud ( #1510 )
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* commit patch
* commit patch
* pointnet basic
* fix data
* reorg
* reorg
* temp status
* remove validate set
* add partseg data and model
* partseg miou
* clean up
* fix loss
* network definition match paper
* fix
* fix miou
* update data format
* fix
* fix
* working pointnet ssg cls
* avoid some pytorch bug
* fix script
* update hyperparams
* add msg module
* try different dataset
* update new dataset info
* quick fix to subgraph
* fix speed
* update training
* update
* fix bs
* update docstring
* update
* update
* remove parallel reduction in fps
* switch to kernel fps, training is 30% faster
Co-authored-by: Ubuntu <ubuntu@ip-172-31-20-181.us-west-2.compute.internal >
2020-06-22 19:50:40 +08:00
8192b10b08
[Example] Sample-based GAT on ogbn-product dataset ( #1613 )
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* Add ogbn-product with GAT with GraphSAGE sampling
* Update Readme
* Add self loop
* update score
* Update score
* Fix
* Update
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-186.ec2.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Zihao Ye <expye@outlook.com >
2020-06-20 22:42:47 +08:00
3ebf26607e
correct PinSAGE knn example syntax ( #1617 )
...
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Chao Ma <mctt90@gmail.com >
2020-06-15 15:47:00 +08:00
8531ee6aa6
Fix input data source ( #1612 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-52-181.ec2.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-06-10 16:08:43 +08:00
cbe4c28fea
Fix ( #1596 )
2020-06-07 16:43:36 +08:00
36c7b77167
[LifeSci] Move to Independent Repo ( #1592 )
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* Move LifeSci
* Remove doc
2020-06-05 21:28:24 +08:00
94c67203dc
[Example] Implement deepwalk by dgl and pytorch ( #1503 )
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* deepwalk
* add docstr, etc.
* add tested version
* some doc
* some doc
* add sample and some docs, fix a bug
* update speed
* update speed
* docs
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-06-04 23:35:52 +08:00
90d2118da5
[Dataset] Change Cora Split ( #1583 )
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* Use new version of Cora
* Fix import
2020-06-03 15:45:38 +08:00
e979685ad9
[Model] Add SIGN model to example ( #1571 )
...
* sign model
* mini-batch GPU eval & set default hyper-parameters
* add readme for sign
* minor
2020-05-31 17:15:01 +08:00
901e0c24d6
[Example][Optimization] Performance optimization for graphsage unsupervised example ( #1531 )
...
* test
* profile
* opt
* Some fix
* upd
* upd
* Add multigpu training support for graphsage unsupervised
* Add share neg
* Fix
* Add profile
* turn on eval
* upd
* Fix
* performance opt
Co-authored-by: Ubuntu <ubuntu@ip-172-31-12-103.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-14-53.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-29.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-50.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-52-181.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-87-240.ec2.internal >
2020-05-27 11:47:02 +08:00
0b902d032a
[Bug][Model] Bugfix in PinSAGE code ( #1533 )
2020-05-18 00:14:50 +08:00
7b6af87a90
Update ( #1534 )
2020-05-17 21:17:03 +08:00
ccd4eab04e
removing old pinsage implementation ( #1525 )
2020-05-15 11:37:27 +08:00
1e84168edd
[Model] PinSAGE model with new sampler ( #1334 )
...
* another first commit
* test commit
* porting to nowplaying
* fixes
* more updates
* update readme
* add performance
* update
* switch to return_uv
* update result
* Update examples/pytorch/pinsage/process_nowplaying_rs.py
Co-authored-by: Xiagkun Hu <huxk_hit@qq.com >
* update with comments
Co-authored-by: Xiagkun Hu <huxk_hit@qq.com >
2020-05-14 14:04:44 +08:00
9b34b1c22a
[Model] Spatial-temporal Graph Neural Networks for Traffic Prediction ( #1445 )
...
* stgcn_wave model
* fix readme
* rm data file
* split sensors2graph
* rm dead code
* fix README
* rename class
* rm seed & dead code
* Update README.md
* rm dead code & networkx
* add num_layer papram, make model structure adjustable
* fix
* add model structure controller string, make code easier to understand and make model strcture more flexible
* Update main.py
* Update model.py
* fix
* Update README.md
Co-authored-by: Ubuntu <ubuntu@ip-172-31-14-255.ap-northeast-1.compute.internal >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2020-05-12 07:25:39 -07:00
ed60f40123
[Model] OGB products submission ( #1512 )
2020-05-12 16:01:28 +08:00
xiang song(charlie.song)