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[ENH] survival prediction compositor - reducers to tabular probabilistic regression #161

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merged 67 commits into from
Jan 31, 2024

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@fkiraly fkiraly commented Dec 28, 2023

This PR adds two survival prediction compositors which take probabilistic supervised regressor (including possibly a survival capable regressor) and create survival predictors - i.e., reducers from survival prediction to probabilistic supervised regression.

The two compositors added are common simple baselines in survival regression:

  • FitUncensored - subsets to uncensored data and fits on the subsample
  • ConditionUncensored - adds C as column in fit, and fills 0 (uncensored) for the same column in predict-like methods.

Depends on #157

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codecov bot commented Dec 28, 2023

Codecov Report

Attention: 116 lines in your changes are missing coverage. Please review.

Comparison is base (86cc53b) 64.82% compared to head (949b743) 63.93%.

❗ Current head 949b743 differs from pull request most recent head 84d612d. Consider uploading reports for the commit 84d612d to get more accurate results

Files Patch % Lines
skpro/survival/coxph.py 20.40% 39 Missing ⚠️
skpro/survival/compose/_reduce_cond_unc.py 31.81% 30 Missing ⚠️
skpro/regression/base/_base.py 48.97% 17 Missing and 8 partials ⚠️
skpro/survival/compose/_reduce_uncensored.py 40.90% 13 Missing ⚠️
skpro/regression/compose/_pipeline.py 27.27% 8 Missing ⚠️
skpro/regression/base/_delegate.py 50.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #161      +/-   ##
==========================================
- Coverage   64.82%   63.93%   -0.89%     
==========================================
  Files         110      114       +4     
  Lines        5705     5870     +165     
  Branches     1069     1087      +18     
==========================================
+ Hits         3698     3753      +55     
- Misses       1722     1825     +103     
- Partials      285      292       +7     

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@fkiraly fkiraly changed the title [ENH] survival prediction compositor - fit on uncensored data [ENH] survival prediction compositor - reducers to tabular probailistic Dec 28, 2023
@fkiraly fkiraly changed the title [ENH] survival prediction compositor - reducers to tabular probailistic [ENH] survival prediction compositor - reducers to tabular probabilistic regression Dec 29, 2023
@fkiraly fkiraly merged commit e151a8c into main Jan 31, 2024
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enhancement implementing algorithms Implementing algorithms, estimators, objects native to skpro module:survival&time-to-event module for time-to-event prediction aka survival prediction
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