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Add P1C7: Start-to-finish ML survival analysis chapter#175

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Add P1C7: Start-to-finish ML survival analysis chapter#175
adibender wants to merge 3 commits into
mainfrom
p1c7-start-to-finish

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Summary

Adds the new closing chapter of Part I (book/P1C7_mlsa.qmd, anchor #sec-ml-sa-pipeline) that draws together the foundational concepts of Parts I-IV into an end-to-end view of a machine learning survival analysis.

This addresses an open question from the intro-draft3 thread (PR #118): "I can see you uploaded a figure 'book/Figures/introduction/ml-sa-pipeline.png' but you haven't added to any chapters... survival task I guess is the only one that makes sense?" — the chapter is its own home for that figure.

Contents

  • Re-states the standard supervised-learning pipeline and identifies the survival-analysis-specific adaptation required at each step (figure @fig-ml-sa-pipeline, already tracked on main).
  • Carries a nine-step worked example on a hypothetical retrospective study of 30-day in-hospital mortality of COVID-19 patients with type 2 diabetes (CHESS dataset), adapted from @Dennis2020.
  • Wires P1C7 into _quarto.yml after P1C6_survtsk.qmd as the final chapter of Part I.

Notes

  • Source for the chapter content was book/_drafts/start-to-finish-for-P1C7.md (gitignored). I dropped the leading "Content moved out of intro §1.3" header note and applied the inline TODO suggestion ("research question" → "question of interest").
  • Cross-references all resolve: @sec-surv, @sec-eha, @sec-survtsk, @sec-rules, @sec-models-classical, @sec-boost, @sec-ranfor, @sec-ml, @Dennis2020. The draft used @sec-classical which I corrected to @sec-models-classical.
  • The ml-sa-pipeline.png and .svg figure files were originally included in PR Mainly chapters 1-3, with some other reviewer comments thrown in sorry #118 but never used; they were removed from intro-draft3 in commit a63a1b3 so that this PR is the canonical source. Since the figures had already been merged into main via Mainly chapters 1-3, with some other reviewer comments thrown in sorry #118, they are already tracked on this branch.

Test plan

  • Render book/P1C7_mlsa.qmd standalone — done locally, no warnings.
  • Full book build: confirm no broken cross-refs introduced by the new chapter being added to _quarto.yml.
  • Verify chapter ordering renders correctly: P1C5 → P1C6 → P1C7 → P2C8.

@adibender adibender marked this pull request as draft May 8, 2026 14:15
@adibender adibender marked this pull request as draft May 8, 2026 14:15
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