文件历史

41 次代码提交

作者 SHA1 备注 提交日期
Da Zheng e36c5db614 [Distributed] Simplify distributed API (#2775)
* 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
Da Zheng bb54206620 remove pyinstrument. (#2772)
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
2021-03-21 20:27:12 -07:00
Roger Tu 93074dd358 Bug fix for RGCN Link Prediction Example Exceeding Specified Epochs (#2757)
* Address bug where epochs exceed specified limit

* fix spacing
2021-03-17 14:29:45 +08:00
Da Zheng d0638b1ea9 [Example] Update the example of distributed GNN training of RGCN (#2709)
* support gpu training.

* remove unnecessary arguments.

* update README.

* update time measurement.

* add zero_grad.

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Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
2021-03-01 12:00:15 -08:00
Da Zheng 28b0a76618 [Example] Provide instructions of setting up passwordless SSH login. (#2707) 2021-02-27 18:34:46 -08:00
Ligeng Zhu 6568d0aaf6 [Example] Recommend NFS over copy files (#2689)
* Update README to use NFS, rather than copying files

* Update README.md

* Update README.md

* Update README.md

* Add ParMetis

* Update README.md

* fix directory.

* fix

* redo.

* fix.

* update.

* add more descriptions

Co-authored-by: Da Zheng <zhengda1936@gmail.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
2021-02-25 20:20:52 +08:00
Da Zheng 0526b885ee [Distributed] Fix the path for distributed partitioning. (#2700)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal>
2021-02-24 20:41:41 -08:00
Da Zheng ff64bd0de8 add warning for a bug in README (#2665) 2021-02-16 00:16:40 -08:00
Da Zheng e4ff484494 [Distributed] Distributed METIS partition (#2576)
* add convert.

* fix.

* add write_mag.

* fix convert_partition.py

* write data.

* use pyarrow to read.

* update write_mag.py

* fix convert_partition.py.

* load node/edge features when necessary.

* reshuffle nodes.

* write mag correctly.

* fix a bug: inner nodes in a partition might be empty.

* fix bugs.

* add verify code.

* insert reverse edges.

* fix a bug.

* add get node/edge data.

* add instructions.

* remove unnecessary argument.

* update distributed preprocessing.

* fix readme.

* fix.

* fix.

* fix.

* fix readme.

* fix doc.

* fix.

* update readme

* update doc.

* update readme.

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2021-02-08 17:19:18 -08:00
xiang song(charlie.song) 48d357b8f6 Fix numbers (#2641)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal>
2021-02-08 14:05:30 +08:00
xiang song(charlie.song) 23afe911b2 [Bug Fix] Fix several sparse optimizer bugs (#2596)
* Fix pytorch TCP kvstore bug

* lint

* Fix

* upd

* Fix lint

* Fix

* trigger

* fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal>
2021-02-05 11:49:41 +08:00
xiang song(charlie.song) a7e941c379 [Feature] Add support for sparse embedding (#2451)
* Add sparse embedding for dgl and update rgcn example

* upd

* Fix

* Revert "Fix"

This reverts commit 4da87cdfb8b8c3506b7fc7376cd2385ba8045c2a.

* Fix

* upd

* upd

* Fix

* Add unitest and update impl

* fix

* Clean up rgcn example code

* upd

* upd

* update

* Fix

* update score

* sparse for sage

* remove model sparse

* upd

* upd

* remove global norm

* revert delete model_sparse.py

* update according to comments

* Fix doc

* upd

* Fix test

* upd

* lint

* lint

* lint

* upd

* upd

* clean up

Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal>
2021-01-28 00:26:49 +08:00
Da Zheng 25ac334403 [Distributed] Heterogeneous graph support (#2457)
* Distributed heterograph (#3)

* heterogeneous graph partition.

* fix graph partition book for heterograph.

* load heterograph partitions.

* update DistGraphServer to support heterograph.

* make DistGraph runnable for heterograph.

* partition a graph and store parts with homogeneous graph structure.

* update DistGraph server&client to use homogeneous graph.

* shuffle node Ids based on node types.

* load mag in heterograph.

* fix per-node-type mapping.

* balance node types.

* fix for homogeneous graph

* store etype for now.

* fix data name.

* fix a bug in example.

* add profiler in rgcn.

* heterogeneous RGCN.

* map homogeneous node ids to hetero node ids.

* fix graph partition book.

* fix DistGraph.

* shuffle eids.

* verify eids and their mappings when loading a partition.

* Id map from homogneous Ids to per-type Ids.

* verify partitioned results.

* add test for distributed sampler.

* add mapping from per-type Ids to homogeneous Ids.

* update example.

* fix DistGraph.

* Revert "add profiler in rgcn."

This reverts commit 36daaed8b660933dac8f61a39faec3da2467d676.

* add tests for homogeneous graphs.

* fix a bug.

* fix test.

* fix for one partition.

* fix for standalone training and evaluation.

* small fix.

* fix two bugs.

* initialize projection matrix.

* small fix on RGCN.

* Fix rgcn performance (#17)

Co-authored-by: Ubuntu <ubuntu@ip-172-31-62-171.ec2.internal>

* fix lint.

* fix lint.

* fix lint.

* fix lint.

* fix lint.

* fix lint.

* fix.

* fix test.

* fix lint.

* test partitions.

* remove redundant test for partitioning.

* remove commented code.

* fix partition.

* fix tests.

* fix RGCN.

* fix test.

* fix test.

* fix test.

* fix.

* fix a bug.

* update dmlc-core.

* fix.

* fix rgcn.

* update readme.

* add comments.

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Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-62-171.ec2.internal>

* fix.

* fix.

* add div_int.

* fix.

* fix.

* fix lint.

* fix.

* fix.

* fix.

* adjust.

* move code.

* handle heterograph.

* return pytorch tensor in GPB.

* remove some tests in example.

* add to_block for distributed training.

* use distributed to_block.

* remove unnecessary function in DistGraph.

* remove distributed to_block.

* use pytorch tensor.

* fix a bug in ntypes and etypes.

* enable norm.

* make the data loader compatible with the old format.

* fix.

* add comments.

* fix a bug.

* add test for heterograph.

* support partition without reshuffle.

* add test.

* support partition without reshuffle.

* fix.

* add test.

* fix bugs.

* fix lint.

* fix dataset.

* fix for mxnet.

* update docstring.

* rename to floor_div

* avoid exposing NodePartitionPolicy and EdgePartitionPolicy.

* fix docstring.

* fix error.

* fixes.

* fix comments.

* rename.

* rename.

* explain IdMap.

* fix docstring.

* fix docstring.

* update docstring.

* remove the code of returning heterograph.

* remove argument.

* fix example.

* make GraphPartitionBook an abstract class.

* fix.

* fix.

* fix a bug.

* fix a bug in example

* fix a bug

* reverse heterograph sampling.

* temp fix.

* fix lint.

* Revert "temp fix."

This reverts commit c450717b9f578b8c48769c675f2a19d6c1e64381.

* compute norm.

* Revert "reverse heterograph sampling."

This reverts commit bd6deb7f52998de76508f800441ff518e2fadcb9.

* fix.

* move id_map.py

* remove check

* add more comments.

* update docstring.

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Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-62-171.ec2.internal>
2021-01-24 19:18:00 -08:00
Mufei Li 492ad9be81 [Fix] Avoid Overloading Nonzero for PyTorch Backend (#2434)
* Update gatedgraphconv.py

* Update entity_classify.py

* Update data-process.rst

* Update reading_data.py

* Update data-process.rst

* Update utils.py

* Update knowledge_graph.py

* Update entity_classify.py

* Update rdf.py

* Update entity_classify_mb.py

* Update test_classify.py

* Update tensor.py

* Update sparse.py

* Update entity_classify_mp.py

* Update 6_line_graph.py
2020-12-20 13:12:17 +08:00
mszarma 62b4bbb494 [Fix] Enable mini-batch rgcn for CPU (#2345) 2020-11-16 17:27:54 +08:00
xiang song(charlie.song) 782527d481 Fix partition for 0.5.1 (#2187)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-24-210.ec2.internal>
2020-09-13 16:25:51 +08:00
Chao Ma e8273a8510 update README.md (#2138) 2020-09-02 15:42:28 +08:00
xiang song(charlie.song) 1e3fcc7c53 update comments (#2132)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
2020-08-31 13:23:43 +08:00
xiang song(charlie.song) 0435b74c48 [Hotfix] Fix layer norm (#2119)
* hotfix

* Fix Layer Norm

Co-authored-by: Ubuntu <ubuntu@ip-172-31-87-240.ec2.internal>
2020-08-28 11:20:33 +08:00
xiang song(charlie.song) 0052f1212b [Example] Rgcn distributed training (#1999)
* add entity_classify_dist

* upd

* update

* Fix

* Fix

* upd

* upd

* upd

* upd

* global eval

* Fix

* Fix

* Fix

* Fix

* FIx

* upd

* upd

* update

* support pytorch sparse embedding

* Fix

* Fix

* update Readme

* update with new API

* Fix

* update Readme

* add fanout for validation neighbor sampling

Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-24-210.ec2.internal>
Co-authored-by: Chao Ma <mctt90@gmail.com>
Co-authored-by: Da Zheng <zhengda1936@gmail.com>
2020-08-18 12:12:21 -07:00
Mufei Li be444e52d9 [Doc/Feature] Refactor, doc update and behavior fix for graphs (#1983)
* Update graph

* Fix for dgl.graph

* from_scipy

* Replace canonical_etypes with relations

* from_networkx

* Update for hetero_from_relations

* Roll back the change of canonical_etypes to relations

* heterograph

* bipartite

* Update doc

* Fix lint

* Fix lint

* Fix test cases

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix test

* Fix

* Update

* Use DGLError

* Update

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* rewrite sanity checks

* delete unnecessary checks

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Fix

* Update

* Fix

* Update

* Fix

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
2020-08-18 04:26:29 +08:00
xiang song(charlie.song) 4ef01dbb05 [Example] Rgcn support ogbn-mag dataset. (#1812)
* rgcn support ogbn-mag dataset

* upd

* multi-gpu val and test

* Fix

* fix

* Add support for ogbn-mag

* Fix

* Fix

* Fix

* Fix

* Add layer_norm

* update

* Fix merge

* Clean some code

* update Readme

* upd

Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-87-240.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
2020-08-09 15:56:15 +08:00
xiang song(charlie.song) dbb028acc8 [Dataset] Builtin knowledge graph dataset (#1881)
* 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
xiang song(charlie.song) 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
Minjie Wang 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>
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2020-07-28 14:30:41 +08:00
xiang song(charlie.song) d6b4e286b6 RGCN minibatch using homogeneous graph. (#1745)
* 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>
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2020-07-07 00:26:10 +08:00
hgalioulline 6c7c403914 [Feature] Filtered MRR metrics for R-GCN example (#1298)
* Add filtered metrics for R-GCN example

* Add new line to end of file

* Add evaluation protocol argument option for R-GCN example

* Update README

Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
2020-03-13 16:25:03 +08:00
Quan (Andy) Gan b05cb84a77 [BUG] Fixes #1262 (#1286) 2020-02-24 13:33:55 +08:00
Zihao Ye 7a80faf120 [Bugfix] Correct the loss function in RGCN model (#1217)
* upd

* upd

* fix

Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
2020-02-13 18:35:07 +08:00
Minjie Wang 1c91f460d3 [Hetero][Model] RGCN for heterogeneous input (#885)
* new hetero RGCN

* bgs running

* fix gpu

* am dataset

* fix bug in label preparation

* Fix AM training; add result

* rm sym link

* new embed layer; mutag

* mutag matched; other fix

* minor fix

* dataset refactor

* new data loading

* rm old files

* refactor

* docstring

* include literal nodes in AIFB dataset

* address comments

* docstring
2019-09-29 00:21:17 -04:00
Minjie Wang 708765f0a1 [NN] RGCN modules (#744)
* rgcn module

* support id input

* WIP: model codes

* use faster index select

* dropout

* self loop

* WIP: link prediction

* fix lint

* WIP: docs

* docstring

* docstring

* merge two child classes

* mxnet rgcn module

* fix lint

* fix lint

* fix rename bug

* add uniform edge sampler

* fix fn name

* docstring

* fix mxnet rgcn module

* fix mx rgcn

* enable test on cuda
2019-08-23 16:38:48 -04:00
Sahand 77c58289a7 [Bugfix][Model] Fixing RGCN evaluation bug (#778) 2019-08-20 15:54:03 -04:00
Quan (Andy) Gan 714f2e1ced fix node id dtype (#674) 2019-06-20 10:53:26 +08:00
Giuseppe Futia 2dff1aba83 [Bugfix] Fix shape of test_relation tensor in RGCN (#464) 2019-03-28 14:34:07 -04:00
Lingfan Yu d3c24cc25b [BugFix] Fix bug in RGCN data processing and use index_select to improve speed (#429)
* use index_select instead of __getitem__

* fix bug in dataset processing

* fix edge_type shape bug

* comments
2019-03-04 10:52:21 -05:00
Zihao Ye ae1806f651 [Bugfix] RGCN tutorial (#388)
* fix rgcn tutorial

* small fix

* upd
2019-02-15 11:14:56 +08:00
Giuseppe Futia 6c3dba867a [Tutorial] Update prerequisites of README (#380)
* Update prerequisites of README

* dependencies for pytorch models

* dependencies for mxnet models

* minor
2019-02-11 22:58:17 -05:00
brett koonce 707334ce85 minor spelling tweaks (#349)
* minor spelling tweaks

* Update CONTRIBUTORS.md
2019-01-10 12:02:31 -05:00
Gan Quan ac660f45ef [Doc] Readme (#265)
* [Doc] updated readme

* contribution guide change

* small edits

* add perf #

* Update README.md

* Update README.md

* add others...

* rewrite scalability

* model & code links

* some note for treelstm

* rewrite scalability
2018-12-06 00:31:04 -05:00
Minjie Wang e557ed89ff [Doc][Model] example folder doc and model summary (#259)
* update example readme

* mx example readme

* add results in readme

* mx rgcn readme
2018-12-05 14:35:14 -05:00
Lingfan Yu b98dc92c59 [Model] Relational GCN (#55)
* data preprocessing for rgcn

* edge subgraph

* WIP: RGCN

* use edge feature in spmv

* fix bugs

* match AIFB accuracy

* match mutag accuracy

* avoid materializing in featureless case

* remove untouched nodes and relabel nodes

* fix python list concatenate overhead

* sparsely store edge types

* refactor entity classify code for clean link prediction implementation

* further refactor code

* refactoring

* rgcn block decompose layers

* link predict dataset

* link predict model and eval code

* dropout, self-loop, regularization, etc, plus bug fixes

* update to new api

* dataset update

* bugs, WIP, need to impl early stopping and filtered metrics

* instruction to run, and minor

* group conv and early stop

* clean slow code

* some code comments

* use new api in model code

* change data preprocessing

* entity classify model

* WIP

* move dgl graph out of model

* hot fix for extract zip

* fix link predict model

* use latest dgl apis

* still have memory issue...

* bug fix and move inference to cpu

* move rgcn data processing to contrib

* th.allclose -> U.allclose

* minor change in readme

* fix memory issue in entity classify

* fix and testing code for link predict

* fix entity classify

* clean up

* fix comments

* revert erroneous git merge changes

* code clean up and more comments

* minor

* dependent package version
2018-12-03 13:01:27 -05:00