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add SoftImpute and IterativeSVD to imputation #353

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merged 12 commits into from
Mar 30, 2022
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@xinyuejohn xinyuejohn commented Mar 13, 2022

PR Checklist

  • This comment contains a description of changes (with reason)
  • Referenced issue is linked
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

Description of changes

  1. Add SoftImpute, IterativeSVD, MatrixFactorization, and NuclearNormMinimization from fancyimpute as imputation methods.
  2. Add miceforest as imputation method.

Technical details

  • pyproject.toml has been updated to add fancyimpute and miceforest dependency.
  • two test data sets have been added which can be used to test imputation.
    test_impute_iris.csv only contains numerical data and test_impute_titanic.csv contains numerical data and non-numerical data.
  • ehrapy/preprocessing/init.py has been updated to add import.
  • tests/preprocessing/test_imputation.py has been updated to add corresponding tests.

@github-actions github-actions bot added the enhancement New feature or request label Mar 13, 2022
@xinyuejohn xinyuejohn requested a review from Zethson March 13, 2022 21:32
@xinyuejohn xinyuejohn marked this pull request as draft March 14, 2022 07:40
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Docstring needs to be updated.

update docstring.
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@Zethson Zethson left a comment

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Looks good on a first glance. Can this also be sped up with the Intel sklearn extension?

Think that @Imipenem should review this one.

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Zethson commented Mar 14, 2022

@xinyuejohn you also need to add this function to the docs.

@Zethson Zethson requested a review from Imipenem March 14, 2022 08:29
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Mostly minor stuff.

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@xinyuejohn xinyuejohn self-assigned this Mar 27, 2022
@xinyuejohn xinyuejohn added this to the 0.2 milestone Mar 27, 2022
@xinyuejohn xinyuejohn linked an issue Mar 27, 2022 that may be closed by this pull request
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Zethson commented Mar 28, 2022

Please add the imputation methods to the docs (usage.rst)

@github-actions github-actions bot added the chore label Mar 28, 2022
Signed-off-by: zethson <[email protected]>
@Zethson Zethson marked this pull request as ready for review March 28, 2022 17:00
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@Zethson It seems this has no more issues.

@Zethson Zethson merged commit 9fd599d into development Mar 30, 2022
@xinyuejohn xinyuejohn deleted the feature/imputation branch April 25, 2022 18:39
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Add more imputation methods
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