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review-zoom-v9-broom-jaccard-method-slides

Review zoom v9: add broom cartoons for PHR bundle Jaccard method

Metadata

Statusdone
Assignedagent-1253
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Created2026-05-08T15:09:39.346559846+00:00
Started2026-05-08T15:12:03.172538133+00:00
Completed2026-05-08T15:23:07.702267695+00:00
Tagsreview-zoom, review-zoom-v9, methods, jaccard, phr-similarity, cartoons, deadline, eval-scheduled
Eval score0.96
└ blocking impact0.96
└ completeness0.97
└ coordination overhead0.97
└ correctness0.95
└ downstream usability0.98
└ efficiency0.96
└ intent fidelity0.92
└ style adherence0.95

Description

Add Erik's broom cartoons as a two-slide explanation of the PHR bundle comparison / Jaccard method. This should feed v9 fan-in before the final render.\n\nInput assets at repo root:\n- broom_1.png: single bundle at one subtelomere/chromosome end.\n- brooms_compare.png: overlapping/combined bundles representing the comparison between two chromosome ends.\n\nSlide intent and placement:\n- Insert these where the deck explains the method used to compare PHRs, near the PHR Jaccard workflow/method slides, before downstream community heatmaps/MDS if possible.\n- Use two slides, not one crowded slide.\n- Slide 1: introduce the concept of a chromosome-end bundle: the whole collection of HPRCv2 haplotype PHR paths assigned to a particular chromosome end. This is not a single reference interval; it is the population collection for that end.\n- Slide 2: explain the comparison metric: compare two chromosome-end bundles by intersection/union of variation graph nodes in the PGGB/ODGI graph. This graph-node Jaccard is the basis for the arm-level similarity/distance matrix and therefore for the heatmaps, Leiden communities, and MDS.\n\nWording constraints:\n- Say 'chromosome end' or 'subtelomere bundle' clearly.\n- Say 'variation graph nodes' or 'PGGB graph nodes' clearly.\n- Jaccard = intersection / union of graph nodes across the two chromosome-end bundles.\n- Note that self-comparisons need not be 1 if the bundle contains multiple heterogeneous haplotypes/paths; this is important background but keep it small.\n- Avoid overloading the slide with equations; the cartoon should do the work.\n\nDeliverables:\n- Local copied/processed assets under slides/v2-review-zoom/_revision_assets/v9/broom_jaccard_method/.\n- Optional slide-ready PNG previews or Typst snippet.\n- README with method wording and source asset paths.\n- SLIDE_PATCH.md telling review-zoom-v9-fanin-render exactly where to insert the two slides and what title/source/caption text to use.\n\nDo not edit final Typst deck directly; leave integration to review-zoom-v9-fanin-render.

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