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[REVIEW] Naive Bayes #1375

Merged
merged 108 commits into from
Feb 15, 2020
Merged

[REVIEW] Naive Bayes #1375

merged 108 commits into from
Feb 15, 2020

Commits on Nov 14, 2019

  1. Simple implementation of labelbinarizer using cupy and custom raw ker… 

    …nels
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  2. More progress on label_binarize and LabelBinarizer

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  3. Initial very simple version of LabelBinarizer complete.

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  4. Making progress on Dask pieces

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  5. Adding a basic pytest for label binarizer

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  6. Adding validation for unseen classes

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Commits on Nov 15, 2019

  1. Getting closer

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  2. Initial tests are passing for Dask-based labelbinarizer

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  3. Updating changelog

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  4. More style check fixes

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  5. Style fixes

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  6. Able to run simple end-to-end Naive Bayes pytest using cupy & pytorch… 

    … via dlpack.
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  7. turning print into assert

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  8. Getting a start on Dask naive bayes

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Commits on Nov 17, 2019

  1. Using cupy for sparse matrix multiply and moving to cuml main

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  2. Using sparse outut for binarized labels

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  3. Removing prints

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Commits on Nov 18, 2019

  1. Adding a simple performance comparison pytest for cupy vs pytorch vs … 

    …sklearn
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  2. Initial Dask naive_bayes impl w/ sparse df support (coo format like c… 

    …ugraph)
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Commits on Nov 19, 2019

  1. Checking in what I have for now. We need to get a better handle on ho… 

    …w we are going to accept distributed sparse arrays.
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  2. Fixing silly typo in kernel

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Commits on Nov 20, 2019

  1. Profiling pytorch vs cupy

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Commits on Nov 21, 2019

  1. Bunch of optimizations to NaiveBayes. Pulling a few custom kernels in… 

    …to a `cuml.prims` package
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  2. Getting naive bayes to build

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Commits on Nov 22, 2019

  1. Fixing label binarizer test

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  2. Tests for both sparse and dense in place

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  3. Adding pytest for partial fit

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  4. Removing pytorch import for CI

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Commits on Nov 26, 2019

  1. Merge branch 'branch-0.11' into fea-ext-naive_bayes 

    Conflicts:
	CHANGELOG.md
	python/cuml/dask/common/__init__.py
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Commits on Dec 3, 2019

  1. Inverting labels in prediction.

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  2. Matching sklearn exactly

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  3. Updates to naive bayes

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Commits on Dec 17, 2019

  1. Multinomial NB works end-to-end in Dask

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Commits on Dec 18, 2019

  1. Enabling support for cupy csr_matrix in train_test_split

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  2. Style fixes

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  3. Merge branch 'branch-0.12' into fea-ext-naive_bayes 

    Conflicts:
	python/cuml/dask/common/comms.py
	python/cuml/test/dask/test_nearest_neighbors.py
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  4. Updating tests

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  5. Some fixes to the dask naive bayes test. Needs to wait until the cupy… 

    … vstack/hstack PR is merged, unfortunately
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  6. Adjusting order of parts

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  7. Array parts now able to take iterable of arrays 

    '
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  8. Using scatter to propagate trained models for prediction.

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Commits on Dec 20, 2019

  1. Adding dask end to end test for multinomial naive bayes

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  2. Moving some imports around

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Commits on Jan 8, 2020

  1. Merge branch 'branch-0.12' into fea-ext-naive_bayes 

    Conflicts:
	CHANGELOG.md
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  2. Merge branch 'branch-0.12' into fea-ext-naive_bayes 

    Conflicts:
	CHANGELOG.md
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Commits on Jan 10, 2020

  1. Merge branch 'fea-ext-kmeans_score' into fea-ext-naive_bayes

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Commits on Jan 14, 2020

  1. Merge branch '012-dbg-pytest-umapdask' into fea-ext-naive_bayes

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  2. Using a factory pattern for now to create raw kernels of differing pr… 

    …ecision
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  3. Fixing style issues

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Commits on Jan 15, 2020

  1. A little cleanup

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  2. Adding type generics to cupy rawkernel. Adding tests for different ty… 

    …pes in naive bayes. Cleaning up naive bayes pytests
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  3. Updating labelbinarizer pytests to test sparse and dtype

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  4. Supporting sparse input to inverse_transform in LabelBinarizer

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  5. Fixing style issues

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Commits on Jan 16, 2020

  1. Merge branch 'branch-0.12' into fea-ext-naive_bayes

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  2. Re-adding colocated partitions import

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  3. Debugging dask errors in CI

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  4. Fixing bad import for debugging

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  5. proper import this time.

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Commits on Jan 17, 2020

  1. Add pydocs for Naive Bayes & Distributed Naive Bayes 

    Add score, predict_proba, predict_log_proba
Add pytests for new functions.
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  2. Fixing style issues

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  3. Adding prims tests for classlabel prims 

    Updating kernel factory to use proper pydoc format
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Commits on Feb 5, 2020

  1. Merge branch 'branch-0.13' into fea-ext-naive_bayes

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Commits on Feb 6, 2020

  1. Some umap fixes. Setting seed to 50 for now to isolate why results ar… 

    …e still different. I believe it might be in the spectral clustering code, which doesn't provide a way to set a seed.
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Commits on Feb 11, 2020

  1. Some umap fixes. Setting seed to 50 for now to isolate why results ar… 

    …e still different. I believe it might be in the spectral clustering code, which doesn't provide a way to set a seed.
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  2. Many changes. Finally fixed nasty segmentaton fault from CuPy's incor… 

    …rect serialization
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  3. Naive Bayes tests are passing

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  4. Fixing style issues

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  5. Fixing CI issues

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  6. Sparse dask array conversion utility is complete. Unfortunately, they… 

    … cannot be computed until

cupy supports vstack and hstack.
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  7. Distributed label binarizer works with sparse dask arrays!

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  8. Removing support for sparse outputs in distributed label binarizer fo… 

    …r now. will add back when it is fully supported
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  9. Adding more documentation to Naive Bayes, along with distributed scor… 

    …e() function
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  10. Filling in remaining examples (label binarizer and naive bayes

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  11. Fixing style issues

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  12. Using rmm_cupy_ary for remaining cupy allocations

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  13. Style

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Commits on Feb 12, 2020

  1. Merge branch 'branch-0.13' of https://github.com/rapidsai/cuml into b… 

    …ranch-0.13
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  2. Merge branch 'branch-0.13' into fea-ext-naive_bayes

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  3. Fixing cpp style errors

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  4. More style errors

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  5. Updating copyrights to 2020

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  6. Properly closing resources

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  7. Merge branch 'branch-0.13' of https://github.com/rapidsai/cuml into b… 

    …ranch-0.13
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  8. Merge branch 'branch-0.13' into fea-ext-naive_bayes

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  9. Removing explicit seed settings (hsouldn't have been included in this… 

    … PR)
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  10. Referencing relevant issues

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  11. Creating note about remaining naive bayes variants

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  12. Adding rmm_cupy_ary everywhere.

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  13. Adjusting copyright year for new files

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Commits on Feb 14, 2020

  1. Fixing shared memory population bug

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  2. Updates based on review feedback

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  3. Fixing style issues

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  4. Allowing naive bayes functions to take both host and gpu memory throu… 

    …gh explicit conversion to rmm allocated GPU
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  5. Making sure class prior is on device

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  6. Patching local client as well

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  7. Patching the new to_sp_dask_array for the cupy serialization issue

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  8. Fixing naive bayes to use coo instead of csr.

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  9. Removing unused function.

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Commits on Feb 15, 2020

  1. Small fixes

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  2. Fixing style issues

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  3. Commenting out trustworthiness in c++ test for now, until we figure o… 

    …ut how trustworthiness seems to be causing the test to fail.
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  4. iUpdating cpp stylew for umap test

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  5. Three separate UMAP C++ tests: fit, transform, supervised fit

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  6. Fixing cpp style issues

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  7. Adjusting thresholds for umap

    @cjnolet
    cjnolet committed Feb 15, 2020
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  8. Style checking

    @cjnolet
    cjnolet committed Feb 15, 2020
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  9. Lowering threshold again

    @cjnolet
    cjnolet committed Feb 15, 2020
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