GitLab

* attach positive.

* add neg_deg_sample.

* add comment.

* add neg_deg_sample for eval.

* change the edge sampler.

* rename edge sampler in KG.

* allow specifying chunk size and negative sample size separately.

* fix bugs in KG.

* add check in sampler.

* add more checks.

* fix

* add comment.

* add comments.

* accel edge sampling.

* measure sampling time.

* attach positive.

* add neg_deg_sample.

* fix a minor bug.

* remove unnecessary code.

* Revert "add neg_deg_sample."

This reverts commit 45f3c08c87e33589563ca7e6a3ec91cb1239910e.

* Revert "attach positive."

This reverts commit 503d7821555b69b7ccfed55ce8b87ee24fff852d.
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* hot fix

* Fix docs

* Fix ArrayHeap float overflow bug

* Fix

* Clean some dead code

* Fix

* FIx

* Add some comments

* run test

current samplers only support working on CPU

* Add weight based edge sampler

* Can run, edge weight work.
TODO: test node weight

* Fix node weight sample

* Fix y

* Update doc

* Fix syntex

* Fix

* Fix GPU test for sampler

* Fix test

* Fix

* Refactor EdgeSampler to act as class object not function that it
can record its own private states.

* clean

* Fix

* Fix

* Fix run bug on kg app

* update

* update test

* test

* Simply python API and fix some C code

* Fix

* Fix

* Fix syntex

* Fix

* Update API description

* add replacement for edge sampler

* Now edge sampler support replacement and no-replacement

* Fix

* Fix

* change kg/app to use edge sampler with replacement config

* Update replacement algo

* Fix syntax

* Update

* Update
Co-authored-by: Da Zheng <zhengda1936@gmail.com>

* Add weight based edge sampler

* Can run, edge weight work.
TODO: test node weight

* Fix node weight sample

* Fix y

* Update doc

* Fix syntex

* Fix

* Fix GPU test for sampler

* Fix test

* Fix

* Refactor EdgeSampler to act as class object not function that it
can record its own private states.

* clean

* Fix

* Fix

* Fix run bug on kg app

* update

* update test

* test

* Simply python API and fix some C code

* Fix

* Fix

* Fix syntex

* Fix

* Update API description

* edge sampler return head nodes and tail nodes.

* edge subgraph.

* use VecToIdArray

* example.

* fix compile error.

* optimizer for sampling all negative edges.

* allow to disable checking false negative.

* fix lint.

* fix docstring.

* fix for comment.

* add comments.

* find the existence of negative edges.

* add comment.

* fix test.

* PBG negative edge sampler.

* add a positive edge to make it regular, handle last batch.

* exclude all positive edges in the parent graph.

* just uniformly sample negative nodes.

* fix lint.

* shuffle one-side nodes of positive edges.

* just uniformly sample negative nodes.

* change the data type.

* address comment.

* remove commented code.

* moving heterograph index to another file

* node view

* python interfaces

* heterograph init

* bug fixes

* docstring for readonly

* more docstring

* unit tests & lint

* oops

* oops x2

* removed node/edge addition

* addressed comments

* lint

* rw on frames with one node/edge type

* homograph with underlying heterograph demo

* view is not necessary

* bugfix

* replace

* scheduler, builtins not working yet

* moving bipartite.h to header

* moving back bipartite to bipartite.h

* oops

* asbits and copyto for bipartite

* tested update_all and send_and_recv

* lightweight node & edge type retrieval

* oops

* sorry

* removing obsolete code

* oops

* lint

* various bug fixes & more tests

* UDF tests

* multiple type number_of_nodes and number_of_edges

* docstring fixes

* more tests

* going for dict in initialization

* lint

* updated api as per discussions

* lint

* bug

* bugfix

* moving back bipartite impl to cc

* note on views

* fix

* add edge sampler.

* add test and run.

* add negative sampling.

* remap the edge subgraph vid.

* negative graph excludes edges of positive edgs.

* remove print.

* avoid sampling NodeFlow when expand_factor or num_hops is 0.

* fix a bug when excluding nodes in negative graph.

* support multigraph.

* exclude positive edges.

* fix memory leak.

* return subgraph object directly.

* fix many problems.

* add comments.

* address comments

* nonuniform sampler

* unit test

* test on out neighbors

* error checks

* lint

* fix

* clarification

* use macro switcher

* use empty array for uniform sampling

* oops

* Revert "oops"

This reverts commit a11f9ae707aaeb67fb5921c887a17d3711d5b04a.

* Revert "use empty array for uniform sampling"

This reverts commit 8526ce4cade89f2c1b09a08aca8830375ebafb31.

* re-reverting

* use a method

* rng refactor

* fix bugs

* unit test

* remove setsize

* lint

* fix test

* use explicit instantiation instead of inlining

* stricter test

* use tvm solution

* moved python interface to dgl.random

* lint

* address comments

* make getthreadid an inline function

* WIP: using object system for graph

* c++ side refactoring done; compiled

* remove stale apis

* fix bug in DGLGraphCreate; passed test_graph.py

* fix bug in python modify; passed utest for pytorch/cpu

* fix lint

* address comments

* WIP: array refactoring

* WIP: implementation

* wip

* most csr part

* WIP: on coo

* WIP: coo

* finish refactoring immutable graph

* compiled

* fix undefined ndarray copy bug; add COOToCSR when coo has no data array

* fix bug in COOToCSR

* fix bug in CSR constructor

* fix bug in in_edges(vid)

* fix OutEdges bug

* pass test_graph

* pass test_graph

* fix bug in CSR constructor

* fix bug in CSR constructor

* fix bug in CSR constructor

* fix stupid bug

* pass gpu test

* remove debug printout

* fix lint

* rm biparate grpah

* fix lint

* address comments

* fix bug in Clone

* cpp utests

* fix.

* add comments.

* fix sampler.

* update doc.

* fix.

* WIP

* header

* WIP .cc

* WIP

* transpose

* wip

* immutable graph .h and .cc

* WIP: nodeflow.cc

* compile

* remove all tmp dl managed ctx; they caused refcount issue

* one simple test

* WIP: testing

* test_graph

* fix graph index

* fix bug in sampler; pass pytorch utest

* WIP on mxnet

* fix lint

* fix mxnet unittest w/ unfortunate workaround

* fix msvc

* fix lint

* SliceRows and test_nodeflow

* resolve reviews

* resolve reviews

* try fix win ci

* try fix win ci

* poke win ci again

* poke

* lazy multigraph flag; stackoverflow error

* revert node subgraph test

* lazy object

* try fix win build

* try fix win build

* poke ci

* fix build script

* fix compile

* add a todo

* fix reviews

* fix compile

* accelerate gcn_ns.

* add timing.

* run infer with whole graph.

* distributed gcn_ns.

* reconstruct gcn_ns.

* minor fix.

* change graphsage_cv for numa.

* fix #OMP threads.

* accelerate graphsage_cv.

* fix a weird bug.

* add profiler in graphsage_cv.

* accelerate graphsage_cv.

manually aggregate neighbors' embeddings with pull.

* load csr directly in gcn_ns_sc.

* parallel sort for graph index.

* Revert "parallel sort for graph index."

This reverts commit 86fe2c7117fe5e56b0d481b39849c258b166945b.

* run gcn_ns_sc on GPUs.

* acc gcn_cv_sc.

* change gcn_cv for numa.

* fix gcn_cv to use numa and gpu.

* improve graphsage_cv to use numa and gpu.

* improve gcn_ns.

* improve graphsage_cv.

* init shared memory graph store.

* fix.

* enable init ndata.

* improve tests.

* add bidirectional communication.

* link to rt.

* fix compilation error.

* fix shared memory init.

* use MessageQueue for inter-process communication.

* reconstruct immutable graph csr.

* fix gcn.

* load csr to shared memory.

* fix minor bugs.

* add comments.

* refactor SharedMemory.

* fix bugs in ImmutableGraph.

* create CSR graph from shared memory.

* add more test for loading a csr graph.

* terminate graph store properly.

* allow initializing ndata in the graph store server.

* use RPC for inter-process communication.

* a script for loading a graph.

* allow customizing port.

* list all ndata and edata.

* support dtype.

* reorganize SharedMemoryGraphStore.

* fix ndata shape.

* reconstruct gcn_ns.

* print info.

* set omp in gcn_ns.

* reset sampling examples.

* fix lint.

* fix lint.

* reset gcn.

* disable shared memory in windows.

* fix.

* fix.

* reset changes.

* revert nodeflow changes.

* fix cmake.

* fix test.

* fix test.

* fix test.

* fix test.

* add comments.

* fix test.

* move vector out.

* fix lint.

* fix lint.

* move SharedMemory.

* update cmake.

* update comment.

* fix comments.

* Revert "update cmake."

This reverts commit 592445e37077f70a6e3f2e5245f9a3d086b04f3b.

* update cmake.

* add comments.

* rename.

* change the comment.

* fix a bug.

* rename.

* add comments.

* add comments.

* add init_edata.

* rewrite memory alloc.

* move vector to CSR.

* fix.

* init data.

* Revert "init data."

This reverts commit 2b217b9553911b7dd84a9f1d9b68430b5aa18e23.

* init data.

* init new columns correctly.

* add C++ rpc infrastructure and distributed sampler

* update

* update lint

* update lint

* update lint

* update

* update

* update

* updare

* update

* update

* update

* update serialize and unittest

* update serialize

* lint

* update

* update

* update

* update

* update

* update

* update unittest

* put Finalize() to __del__

* update unittest

* update

* delete buffer in Finalize

* update unittest

* update unittest

* update unittest

* update unittest

* update

* update

* fix small bug

* windows socket impl

* update API

* fix bug in serialize

* fix bug in serialzie

* set parent graph

* update

* update

* update

* update

* update

* update

* fix lint

* fix lint

* fix

* fix windows compilation error

* fix windows error

* change API to lower-case

* update test

* fix typo

* update

* add SamplerPool

* add SamplerPool

* update

* update test

* update

* update

* update

* update

* add example

* update

* update

* random walk traces generation

* remove outdated comments

* oops put in the wrong place

* explicit inline

* moving rand_r to util

* pinsage-like model on movielens

* the code runs now

* support cuda

* using readonly graph

* moving random walk to public function

* per-thread seed and openmp support

* pinsage-like model on movielens

* the code runs now

* support cuda

* using readonly graph

* using C random walk

* removing profile decorators

* param initialization

* no grad

* leaky relu fixes everything

* train and save

* WIP

* WIP

* WIP

* seems to work

* evaluation output

* swapping order of val/test and train

* debug

* hyperparam tuning

* prior/training dataset split changes

* random walk reorg

* random walk with restart

* signed comparison fix

* migrating random walk to nodeflow

* Revert "migrating random walk to nodeflow"

This reverts commit f2565347cced7c912a58a529b257c033d9f375b7.

* add README and remove dataset

* new endpoint

* lint

* lint x2

* oops forgot test

* including bpr - better for baseline

* addressing fixes

* throwing random walks out from SamplerOp class

* forgot to move RandomWalk; why did this even work?

* removing legacy garbage

* add todo

* address comments

* stupid bug fix

* call ndarrayvector converter to handle traces

* enable cython

* add helper function and data structure for void_p vector return

* move sampler from graph index to contrib.sampling

* WIP

* WIP

* refactor layer sampling

* pass tests

* fix lint

* fix graphsage

* remove comments

* pickle test

* fix comments

* update dev guide for cython build

* migrate to node-flow

* uniform layer sampler test cases

* more test cases

* documentations

* fix lint errors

* fix lint errors

* fix lint errors

* iota

* add asnumpy

* requested changes

* fix indptr error

* fix lint errors

* requested changes & fix lint errors

* fix lint errors

* fix LayerSampler unit test

* neighbor sampling draft

* val/test acc

* control variate draft

* control variate

* update

* fix new_history

* maintain aggregated history while updating new history

* preprocess the first layer, change push to pull

* update

* fix subg_degree

* nodeflow

* clear

* readme

* doc and unittest for self loop

* address comments

* rename

* update

* fix

* Update node_flow.py

* Update node_flow.py

* refactor graph conv

* docs & tests

* fix lint

* fix lint

* fix lint

* fix lint script

* fix lint

* Update

* Style fix

* Fix style

* Fix style

* Fix gpu case

* Fix for gpu case

* Hotfix edgesoftmax docs

* Handle repeated features

* Add docstring

* Set default arguments

* Remove dropout from nn.conv

* Fix

* add util fn for renaming

* revert gcn_spmv.py

* mx folder

* fix wierd bug

* fix mx

* fix lint

* fix.

* add check.

* fix assert.

* random walk traces generation

* remove outdated comments

* oops put in the wrong place

* explicit inline

* moving rand_r to util

* moving random walk to public function

* per-thread seed and openmp support

* type cast styles

* sample layer subgraphs.

* fix.

* fix.

* add layered subgraph.

* fix lint.

* fix.

* fix tutorial.

* fix.

* remove copy_to_parent.

* add num_layers

* move sampling code to sampler.cc

* fix.

* move subgraph construction out.

* Revert "move subgraph construction out."

This reverts commit 24b3d13b0d8ed5f91847ea75a7674ee8f7d45cff.

* change to NodeFlow.

* use NodeFlow in Python.

* use NodeFlowIndex.

* add node_mapping and edge_mapping.

* remove unnecessary code in SSE tutorial.

* Revert "remove unnecessary code in SSE tutorial."

This reverts commit 093f0413d5fa2e63ca5f80c46c80a126a9fb720c.

* fix tutorial.

* move to node_flow.

* update gcn cv updater.

* import NodeFlow.

* update.

* add demo code for vanilla control variate sampler.

* update.

* update.

* add neighbor sampling.

* return flow offsets.

* update node_flow.

* add test.

* fix sampler.

* fix graph index.

* fix a bug in sampler.

* fix map_to_layer_nid and map_to_flow_eid.

* fix apply_flow.

* remove model code.

* implement flow_compute.

* fix a bug.

* reverse the csr physically.

* add mini-batch test.

* add mini batch test.

* update flow_compute.

* add prop_flows

* run on specific nodes.

* test copy

* fix a bug in creating frame in NodeFlow.

* add init gcn_cv_updater.

* fix a minor bug.

* fix gcn_cv_updater.

* fix a bug.

* fix a bug in NodeFlow.

* use new h in gcn_cv_updater.

* add layer_in_degree and layer_out_degree.

* fix gcn_cv_updater for gpu.

* temp fix in NodeFlow for diff context.

* allow enabling/disabling copy back.

* add with-updater option.

* fix a bug in computing degree.

* add with-cv option.

* rename and add comments.

* fix lint complain.

* fix lint.

* avoid assert.

* remove assert.

* fix.

* fix.

* fix.

* fix.

* fix the methods in NodeFlow.

* fix lint.

* update SSE.

* remove gcn_cv_updater.

* correct comments for the schedulers.

* update comment.

* add map_to_nodeflow_nid

* address comment.

* remove duplicated test.

* fix int.

* fix comments.

* fix lint

* fix.

* replace subgraph with NodeFlow.

* move view.

* address comments.

* fix lint.

* fix lint.

* remove static_cast.

* fix docstring.

* fix comments.

* break SampleSubgraph.

* move neighbor sampling to sampler.cc

* fix comments.

* rename.

* split neighbor_list.

* address comments.

* fix.

* remove TODO.