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ENH - Implement Cox with Efron estimate #159

Merged
merged 52 commits into from
Jun 8, 2023
Merged

ENH - Implement Cox with Efron estimate #159

merged 52 commits into from
Jun 8, 2023

Commits on May 17, 2023

  1. init commit

    @Badr-MOUFAD
    Badr-MOUFAD committed May 17, 2023
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Commits on May 23, 2023

  1. implem datafit

    @Badr-MOUFAD
    Badr-MOUFAD committed May 23, 2023
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  2. fix numba errors && unittest datafit

    @Badr-MOUFAD
    Badr-MOUFAD committed May 23, 2023
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  3. normalize df with n_samples

    @Badr-MOUFAD
    Badr-MOUFAD committed May 23, 2023
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  4. unittest Cox Estimator against lifeline

    @Badr-MOUFAD
    Badr-MOUFAD committed May 23, 2023
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  5. debug script

    @Badr-MOUFAD
    Badr-MOUFAD committed May 23, 2023
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  6. avoid ties

    @Badr-MOUFAD
    Badr-MOUFAD committed May 23, 2023
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Commits on May 24, 2023

  1. finding 0 or very small solution even for reg < 1

    @mathurinm
    mathurinm committed May 24, 2023
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  2. fix unittest: agree with lifeline

    @Badr-MOUFAD
    Badr-MOUFAD committed May 24, 2023
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  3. require lifelines in CI tests

    @Badr-MOUFAD
    Badr-MOUFAD committed May 24, 2023
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  4. Cox docs

    @Badr-MOUFAD
    Badr-MOUFAD committed May 24, 2023
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  5. more on docs cox

    @Badr-MOUFAD
    Badr-MOUFAD committed May 24, 2023
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  6. normalize as external param

    @Badr-MOUFAD
    Badr-MOUFAD committed May 24, 2023
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  7. dummy survival data docs

    @Badr-MOUFAD
    Badr-MOUFAD committed May 24, 2023
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  8. fix pydoctest

    @Badr-MOUFAD
    Badr-MOUFAD committed May 24, 2023
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  9. faster matmul && fix lifelines install in CI

    @Badr-MOUFAD
    Badr-MOUFAD committed May 24, 2023
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  10. preserve support of numba v0.56

    @Badr-MOUFAD
    Badr-MOUFAD committed May 24, 2023
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Commits on May 25, 2023

  1. make script debug reproducible

    @mathurinm
    mathurinm committed May 25, 2023
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  2. illustrate convergence failure of lifelines

    @mathurinm
    mathurinm committed May 25, 2023
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  3. fix

    @mathurinm
    mathurinm committed May 25, 2023
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Commits on May 27, 2023

  1. clean up

    @Badr-MOUFAD
    Badr-MOUFAD committed May 27, 2023
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  2. add support of sparse data

    @Badr-MOUFAD
    Badr-MOUFAD committed May 27, 2023
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  3. Merge branch 'main' of https://github.com/scikit-learn-contrib/skglm … 

    …into cox-estimator
    @Badr-MOUFAD
    Badr-MOUFAD committed May 27, 2023
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  4. use Weibull for tm

    @Badr-MOUFAD
    Badr-MOUFAD committed May 27, 2023
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  5. unittest Cox sparse data

    @Badr-MOUFAD
    Badr-MOUFAD committed May 27, 2023
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  6. clean ups

    @Badr-MOUFAD
    Badr-MOUFAD committed May 27, 2023
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Commits on May 30, 2023

  1. setups efron

    @Badr-MOUFAD
    Badr-MOUFAD committed May 30, 2023
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  2. compute val

    @Badr-MOUFAD
    Badr-MOUFAD committed May 30, 2023
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  3. implement grad and Hessian

    @Badr-MOUFAD
    Badr-MOUFAD committed May 30, 2023
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  4. implement A and A.T dot ops

    @Badr-MOUFAD
    Badr-MOUFAD committed May 30, 2023
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  5. filter out censored data

    @Badr-MOUFAD
    Badr-MOUFAD committed May 30, 2023
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  6. fix shapes bugs

    @Badr-MOUFAD
    Badr-MOUFAD committed May 30, 2023
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  7. fix dtype & fraction

    @Badr-MOUFAD
    Badr-MOUFAD committed May 30, 2023
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  8. unittest Efron datafit

    @Badr-MOUFAD
    Badr-MOUFAD committed May 30, 2023
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  9. unittest efron estimator

    @Badr-MOUFAD
    Badr-MOUFAD committed May 30, 2023
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Commits on May 31, 2023

  1. Merge branch 'main' of https://github.com/scikit-learn-contrib/skglm … 

    …into cox-efron
    @Badr-MOUFAD
    Badr-MOUFAD committed May 31, 2023
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  2. rm cox in api

    @Badr-MOUFAD
    Badr-MOUFAD committed May 31, 2023
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  3. typo docs Breslow

    @Badr-MOUFAD
    Badr-MOUFAD committed May 31, 2023
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  4. Efron for sparse data

    @Badr-MOUFAD
    Badr-MOUFAD committed May 31, 2023
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  5. add argument with_ties in dummy data

    @Badr-MOUFAD
    Badr-MOUFAD committed May 31, 2023
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  6. sample data from weibull

    @Badr-MOUFAD
    Badr-MOUFAD committed May 31, 2023
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Commits on Jun 7, 2023

  1. update docs

    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 7, 2023
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  2. Merge branch 'main' of https://github.com/scikit-learn-contrib/skglm … 

    …into cox-efron
    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 7, 2023
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Commits on Jun 8, 2023

  1. Merge branch 'main' of https://github.com/scikit-learn-contrib/skglm … 

    …into cox-efron
    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 8, 2023
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  2. fix links to docs

    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 8, 2023
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  3. typos

    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 8, 2023
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  4. example lifelines: data and compare sols

    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 8, 2023
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  5. example lifelines: speed up ratio

    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 8, 2023
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  6. example lifelines: check ties

    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 8, 2023
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  7. example lifelines: typos and reformulations

    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 8, 2023
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  8. example lifelines: fix heading

    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 8, 2023
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  9. fix format

    @Badr-MOUFAD
    Badr-MOUFAD committed Jun 8, 2023
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