[REVIEW] Experimental versions of GPU accelerated Kernel and Permutation SHAP #3126

dantegd · 2020-11-09T16:51:22Z

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GPUtester · 2020-11-09T16:51:50Z

Please update the changelog in order to start CI tests.

View the gpuCI docs here.

JohnZed

I just looked at the C++/CUDA so far. Looks good to me! Will comment on python later today.

cpp/include/cuml/explainer/kernel_shap.hpp

cpp/src/shap/kernel_shap.cu

Co-authored-by: John Zedlewski <[email protected]>

…kshap

codecov-io · 2020-11-11T07:50:54Z

Codecov Report

Merging #3126 (454180d) into branch-0.17 (6cc3d1f) will increase coverage by 1.02%.
The diff coverage is 96.02%.

@@               Coverage Diff               @@
##           branch-0.17    #3126      +/-   ##
===============================================
+ Coverage        70.99%   72.02%   +1.02%     
===============================================
  Files              198      205       +7     
  Lines            15745    16396     +651     
===============================================
+ Hits             11178    11809     +631     
- Misses            4567     4587      +20

Impacted Files	Coverage Δ
python/cuml/common/import_utils.py	`56.00% <62.50%> (+0.56%)`	⬆️
python/cuml/experimental/explainer/common.py	`92.18% <92.18%> (ø)`
python/cuml/experimental/explainer/base.py	`95.74% <95.74%> (ø)`
python/cuml/experimental/explainer/kernel_shap.pyx	`97.26% <97.26%> (ø)`
...n/cuml/experimental/explainer/permutation_shap.pyx	`97.97% <97.97%> (ø)`
python/cuml/__init__.py	`100.00% <100.00%> (ø)`
python/cuml/experimental/explainer/__init__.py	`100.00% <100.00%> (ø)`
python/cuml/experimental/linear_model/lars.pyx	`96.51% <0.00%> (ø)`
python/cuml/experimental/linear_model/__init__.py	`100.00% <0.00%> (ø)`
... and 7 more

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JohnZed

Looking good! I think splitting up the logic of 1-2 of the big functions would be handy. And it'd be great to add more unit tests for the utility functions, but really lookin good!

cpp/include/cuml/explainer/kernel_shap.hpp

cpp/src/shap/kernel_shap.cu

python/cuml/common/import_utils.py

python/cuml/experimental/explainer/common.py

python/cuml/experimental/explainer/kernel_shap.pyx

python/cuml/test/experimental/test_explainer_shap.py

JohnZed

Looking great! I think we're ready for a merge to experimental. I added very tiny suggestions and questions, but I think they'll be quick.

python/cuml/experimental/explainer/permutation_shap.pyx

cpp/include/cuml/explainer/permutation_shap.hpp

JohnZed · 2020-12-01T03:37:19Z

cpp/include/cuml/explainer/permutation_shap.hpp

+ *
+ * @param[in]  handle          cuML handle
+ * @param[out] out             generated data [on device] [dim = (2 * ncols * nrows_bg + nrows_bg) * ncols]
+ * @param[in] background       background data [on device] [dim = ncols * nrows_bg]


column major?

cpp/src/explainer/kernel_shap.cu

JohnZed · 2020-12-01T04:14:21Z

cpp/test/sg/shap_kernel.cu

+typedef MakeKSHAPDatasetTest<double> MakeKSHAPDatasetTestD;
+TEST_P(MakeKSHAPDatasetTestD, Result) {
+  ASSERT_TRUE(test_sampled_X);
+  // disabled due to a sporadic cuda 10.1 fail (by one value in one case!)


can you add an issue for this?

python/cuml/common/import_utils.py

python/cuml/experimental/explainer/base.py

python/cuml/test/experimental/test_explainer_kernel_shap.py

Co-authored-by: John Zedlewski <[email protected]>

dantegd · 2020-12-01T19:55:57Z

rerun tests

JohnZed

Looks good! I think the random state question can be deferred and improved over time.

dantegd · 2020-12-01T23:24:03Z

Removing automerge label while skipping the one test that is strangely slow in CI

dantegd added 3 commits November 9, 2020 10:44

FEA Separate kernel shap from shared shap branch for PR

fe99177

FIX Typos

52bfcd8

FIX Typos

5021358

dantegd added 2 - In Progress Currenty a work in progress CUDA / C++ CUDA issue Cython / Python Cython or Python issue New Algorithm For tracking new algorithms that will be added to our existing collection labels Nov 9, 2020

dantegd requested review from a team as code owners November 9, 2020 16:51

JohnZed reviewed Nov 10, 2020

View reviewed changes

dantegd and others added 4 commits November 10, 2020 22:15

FEA Add files to cmakelists

26f21e6

ENH small corrections and started incorporating PR review feedback

ee47596

ENH progress on remaining todos

2d51f8e

[FIX] typo

e3aa3af

Co-authored-by: John Zedlewski <[email protected]>

dantegd requested a review from a team as a code owner November 11, 2020 04:17

dantegd added 2 commits November 10, 2020 22:18

FIX Small function typo

14f0a8b

Merge branch '017-fea-kshap' of github.com:dantegd/cuml into 017-fea-…

18cec88

…kshap

dantegd added 9 commits November 11, 2020 11:22

ENH Multiple small enhancements and fixes

dffb7b9

ENH Use tags for device model detection

267468f

ENH data type changes

90f59c5

ENH Add pytest files

96baa48

ENH multiple enhancements, completed todos and fixes

5602f28

ENH naming, comments and code enhancements to C++ code

df5517f

ENH clang-format cleanup

ec8af23

ENH variable rename for clarity

204dbcf

ENH Add explainer common pytests

9189efa

JohnZed requested changes Nov 17, 2020

View reviewed changes

JohnZed removed the non-breaking Non-breaking change label Dec 1, 2020

dantegd added non-breaking Non-breaking change and removed non-breaking Non-breaking change labels Dec 1, 2020

JohnZed requested changes Dec 1, 2020

View reviewed changes

JohnZed added 4 - Waiting on Author Waiting for author to respond to review and removed 4 - Waiting on Reviewer Waiting for reviewer to review or respond labels Dec 1, 2020

dantegd changed the title ~~[REVIEW] Experimental versions of GPU accelerated Kernel and Permutation SHAP~~ [REVIEW] Experimental versions of GPU accelerated Kernel and Permutation SHAP [skip-ci] Dec 1, 2020

dantegd and others added 3 commits December 1, 2020 11:25

Update cpp/src/explainer/kernel_shap.cu

30242e6

Co-authored-by: John Zedlewski <[email protected]>

Update python/cuml/common/import_utils.py

6cfe98e

Co-authored-by: John Zedlewski <[email protected]>

Update python/cuml/experimental/explainer/base.py

2cd7d0e

Co-authored-by: John Zedlewski <[email protected]>

JohnZed added the non-breaking Non-breaking change label Dec 1, 2020

dantegd added 3 commits December 1, 2020 13:39

ENH incorporating PR review feedback

7c50130

FIX solve changelog conflict

d6ebad4

FIX clang format fixes

2e0374f

dantegd changed the title ~~[REVIEW] Experimental versions of GPU accelerated Kernel and Permutation SHAP [skip-ci]~~ [REVIEW] Experimental versions of GPU accelerated Kernel and Permutation SHAP Dec 1, 2020

dantegd mentioned this pull request Dec 1, 2020

[FEA] Follow up items for experimental GPU SHAP explainers #3224

Closed

14 tasks

JohnZed approved these changes Dec 1, 2020

View reviewed changes

JohnZed added 6 - Okay to Auto-Merge and removed 4 - Waiting on Author Waiting for author to respond to review labels Dec 1, 2020

dantegd added 5 - Ready to Merge Testing and reviews complete, ready to merge and removed 6 - Okay to Auto-Merge labels Dec 1, 2020

FIX reduce test size and case matrix of test that was slow in CI

3725127

dantegd mentioned this pull request Dec 2, 2020

[BUG] Analysis of pytest execution difference between running tests locally vs CI #3228

Closed

FIX c++ docstring fix

454180d

JohnZed merged commit 936995f into rapidsai:branch-0.17 Dec 2, 2020

JohnZed mentioned this pull request Dec 2, 2020

[FEA] Initial integration with SHAP - Python layer #2352

Closed

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[REVIEW] Experimental versions of GPU accelerated Kernel and Permutation SHAP #3126

[REVIEW] Experimental versions of GPU accelerated Kernel and Permutation SHAP #3126

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[REVIEW] Experimental versions of GPU accelerated Kernel and Permutation SHAP #3126

[REVIEW] Experimental versions of GPU accelerated Kernel and Permutation SHAP #3126

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