Add `node2vec` wrapper to cugraph #2093

betochimas · 2022-02-23T18:24:32Z

Helps close #2058, when combined with #2085. Requires #2085 to be merged before merging, as the cugraph implementation requires the pylibcugraph node2vec wrapper

…bcugraph Pylibcugraph wrappers for cugraph dev

…bcugraph Branch 22.04 fea node2vec pylibcugraph

…idsai#2089 is merged

…bcugraph Branch 22.04 fea node2vec pylibcugraph

codecov-commenter · 2022-02-23T20:13:40Z

Codecov Report

Merging #2093 (dacbba8) into branch-22.04 (ab72ed5) will increase coverage by 0.29%.
The diff coverage is 94.35%.

@@               Coverage Diff                @@
##           branch-22.04    #2093      +/-   ##
================================================
+ Coverage         73.70%   73.99%   +0.29%     
================================================
  Files               155      157       +2     
  Lines             10373    10496     +123     
================================================
+ Hits               7645     7767     +122     
- Misses             2728     2729       +1

Impacted Files	Coverage Δ
python/cugraph/cugraph/sampling/random_walks.py	`96.55% <ø> (ø)`
python/cugraph/cugraph/sampling/node2vec.py	`91.11% <91.11%> (ø)`
python/cugraph/cugraph/tests/test_node2vec.py	`96.10% <96.10%> (ø)`
python/cugraph/cugraph/__init__.py	`100.00% <100.00%> (ø)`
python/cugraph/cugraph/sampling/__init__.py	`100.00% <100.00%> (ø)`
python/cugraph/cugraph/structure/graph_classes.py	`78.53% <0.00%> (+0.52%)`	⬆️
.../cugraph/tests/test_edge_betweenness_centrality.py	`84.93% <0.00%> (+0.60%)`	⬆️
...graph/cugraph/tests/test_betweenness_centrality.py	`83.01% <0.00%> (+0.62%)`	⬆️
python/cugraph/cugraph/tests/test_graph_store.py	`100.00% <0.00%> (+1.56%)`	⬆️
python/cugraph/cugraph/tests/test_utils.py	`75.55% <0.00%> (+4.44%)`	⬆️

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Fetching from 22.04 after random walk bug was merged

betochimas · 2022-02-25T16:10:16Z

rerun tests

Automatically clone raft when the raft pinned tag changes (rapidsai#2087)

cjnolet · 2022-02-25T21:26:26Z

rerun tests

python/cugraph/cugraph/sampling/node2vec.py

python/pylibcugraph/pylibcugraph/node2vec.pyx

jnke2016 · 2022-03-02T17:07:29Z

python/pylibcugraph/pylibcugraph/tests/test_node2vec.py

+# are contained in Simple_1
+_test_data = {"karate.csv": {
+                  "seeds": cp.asarray([0, 0], dtype=np.int32),
+                  "paths": cp.asarray([0, 8, 33, 29, 26, 0, 1, 3, 13, 33],


I think this is good for now but I am a little concern with this approach of testing because of the randomness of the results.

did you make sure there are only 2 paths with depth 5 starting from seed 0?

Even if it is the case, the testing seems hardcoded and only a few seeds are tested.

An alternative approach could be to pick random seeds and verify the accuracy of the paths by checking the predecessors. To illustrate this, let's take the first path
[0, 8, 33, 29, 26]. you verify that 0 is a predecessor of 8, then 8 being a predecessor of 33 and so on... but I am not sure how to easily do this without involving cugraph.

This approach of testing was also in the cugraph level, but yes when this was done I did not check that the walks taken were in fact valid, just putting placeholder values and focusing on making sure the start of each path was each of the seeds. I've since made the testing more robust on the cugraph side, but for pylibcugraph it's more complicated, I'm still figuring that out right now but I can include a FIXME or add an issue to revisit later

…bcugraph Branch 22.04 fea node2vec pylibcugraph

Update for building

…bcugraph Branch 22.04 fea node2vec pylibcugraph

betochimas · 2022-03-08T22:06:21Z

rerun tests

acostadon

Great job on this. Testing especially.

betochimas · 2022-03-09T16:07:07Z

rerun tests

rlratzel

This is looking good, thanks. I have a few comments below based on what I found so far. Aside from that, I'd also like to look into the renumbering comments Joseph posted so I may have a follow-up review.

python/cugraph/cugraph/sampling/node2vec.py

python/cugraph/cugraph/tests/test_node2vec.py

python/pylibcugraph/pylibcugraph/node2vec.pyx

Include commits made mar 8-9

…testing

rlratzel

I noticed one other minor change to make, plus verifying the renumbering questions, then it looks ready to approve.

python/cugraph/cugraph/tests/test_node2vec.py

jnke2016

Looks good to me

BradReesWork · 2022-03-11T19:29:48Z

@gpucibot merge

Merged PR #2093 requires `pylibcugraph`. This PR adds `pylibcugraph` as a run dependency to the `cugraph` conda package. Authors: - Rick Ratzel (https://github.com/rlratzel) Approvers: - Jordan Jacobelli (https://github.com/Ethyling) URL: #2121

betochimas and others added 15 commits February 18, 2022 09:25

Feature from branch-22.04-node2vec without merging issues

a8c6634

Merge pull request #11 from betochimas/branch-22.04-fea-node2vec-pyli…

70bccbd

…bcugraph Pylibcugraph wrappers for cugraph dev

Initial commit to cugraph node2vec wrapper

226a2bc

Account for offsets to path_sizes change

9399259

Improved testing coverage

010f87a

Merge pull request #12 from betochimas/branch-22.04-fea-node2vec-pyli…

6b0b017

…bcugraph Branch 22.04 fea node2vec pylibcugraph

Description update

abe6eed

Testing update for both values of compress_result, will pass once rap…

7184312

…idsai#2089 is merged

Style edits

0495fc8

Testing based on random_walks suite

97f90b4

Testing more inline with C implementation

0b1886a

Merge pull request #13 from betochimas/branch-22.04-fea-node2vec-pyli…

16ecf4a

…bcugraph Branch 22.04 fea node2vec pylibcugraph

Implementation ready, testing outline for cugraph node2vec

f7cc0bb

Implementation plus testing, with exception on networkx graphs

e1a595c

Updated docstring

8d6aad4

betochimas requested a review from a team as a code owner February 23, 2022 18:24

betochimas added the feature request New feature or request label Feb 23, 2022

betochimas added this to the 22.04 milestone Feb 23, 2022

betochimas added the non-breaking Non-breaking change label Feb 23, 2022

betochimas added 2 commits February 24, 2022 09:33

Merge pull request #15 from rapidsai/branch-22.04

53d309a

Fetching from 22.04 after random walk bug was merged

Merge pull request #16 from rapidsai/branch-22.04

465c6b3

Fetching from 22.04 after random walk bug was merged

BradReesWork requested review from rlratzel, acostadon and jnke2016 February 24, 2022 18:39

Merge pull request #17 from betochimas/branch-22.04

494bdba

Automatically clone raft when the raft pinned tag changes (rapidsai#2087)

BradReesWork reviewed Mar 1, 2022

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betochimas and others added 6 commits March 2, 2022 09:39

Replaced source_array with seed_array

e035788

Merge pull request #19 from betochimas/branch-22.04-fea-node2vec-pyli…

19b06ce

…bcugraph Branch 22.04 fea node2vec pylibcugraph

Resolving part of PR review, mainly description and checks

44864e8

Merge pull request #20 from betochimas/branch-22.04

363ebbd

Update for building

Merge pull request #21 from betochimas/branch-22.04-fea-node2vec-pyli…

b06ccda

…bcugraph Branch 22.04 fea node2vec pylibcugraph

Testing now checks individual walks are valid

621dc95

acostadon approved these changes Mar 9, 2022

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betochimas and others added 3 commits March 9, 2022 15:59

Merge pull request #22 from betochimas/branch-22.04

154816c

Include commits made mar 8-9

More efficient node2vec testing, other review changes

bf1e221

CI checks + edits

9100f77

rlratzel mentioned this pull request Mar 10, 2022

[ENH] Add node2vec API to cugraph #2058

Closed

7 tasks

Made threshold vals for force atlas 2 consistent over cpp and python …

308984c

…testing

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Type edit in test_node2vec

dacbba8

betochimas requested a review from a team as a code owner March 11, 2022 17:52

rlratzel approved these changes Mar 11, 2022

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jnke2016 approved these changes Mar 11, 2022

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rapids-bot bot merged commit fab8f18 into rapidsai:branch-22.04 Mar 11, 2022

rlratzel mentioned this pull request Mar 16, 2022

Add pylibcugraph as a run dep to the cugraph conda package #2121

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Add `node2vec` wrapper to cugraph #2093

Add `node2vec` wrapper to cugraph #2093

betochimas commented Feb 23, 2022

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Add node2vec wrapper to cugraph #2093

Add node2vec wrapper to cugraph #2093

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BradReesWork commented Mar 11, 2022

Add `node2vec` wrapper to cugraph #2093

Add `node2vec` wrapper to cugraph #2093

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