review-zoom-v7-slide08b-nearest-superpop-mds

Metadata

Status	done
Assigned	`agent-1119`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-07T19:42:44.212770860+00:00
Started	2026-05-07T19:45:02.685516052+00:00
Completed	2026-05-07T20:02:23.102657470+00:00
Tags	`review-zoom`, `review-zoom-v7`, `slide08`, `mds`, `superpopulation`, `eval-scheduled`
Eval score	0.94
└ blocking impact	0.94
└ completeness	0.97
└ constraint fidelity	0.55
└ coordination overhead	0.95
└ correctness	0.93
└ downstream usability	0.96
└ efficiency	0.91
└ intent fidelity	0.88
└ style adherence	0.90

Description

Rebuild slide 08b around Erik's requested metric. The current v6 view is bad and the previous within-population pairwise/centroid ideas are not acceptable.\n\nGoal:\n- Produce two slide-ready figures/assets:\n 1. An 'original type' MDS scatter plot with points labeled/colored by continental superpopulation labels, matching the older familiar MDS style as much as possible.\n 2. A violin/box/jitter distribution of distance from each subtelomeric MDS point to its nearest other point from the same continental superpopulation.\n\nCritical metric definition:\n- For each point in the MDS coordinate table with a continental group/superpopulation label, compute the Euclidean distance to every other point in the same superpopulation, exclude self, and keep the minimum.\n- Do not use centroids.\n- Do not use all-pairwise within-population distances as the primary metric.\n- Do not average a population point against all in-group points. This is nearest same-group neighbor distance only.\n\nImplementation guidance:\n- Locate the source MDS coordinate data behind s08a/s08b and the v3 08b work. If the plotted MDS is 2D, compute the main metric in plotted 2D MDS space; if prior scripts used cached 5D coordinates, document that and optionally report a secondary 5D sensitivity table, but the slide must be interpretable as MDS-space nearest-neighbor distance.\n- Use consistent continental group labels and colors.\n- Show sample sizes per superpopulation in the violin plot.\n- Include a concise note: lower values mean each subtelomere has a closer same-superpopulation neighbor in sequence-similarity MDS space.\n- Keep axes 1:1 on scatter and use readable labels.\n\nDeliverables:\n- Reproducible script(s), README, nearest-neighbor TSV, summary TSV, rendered PNG/PDF assets under slides/v2-review-zoom/_revision_assets/v7/08b_nearest_same_superpop_mds/.\n- SLIDE_PATCH.md with recommended insertion: likely split into two slides, first labeled superpopulation MDS, second nearest same-group distance distribution.\n- Validation note that no centroid/all-pairwise metric is used.\n\nDo not make final deck integration changes; leave that to review-zoom-v7-fanin-render.

Rebuild slide 08b around Erik's requested metric. The current v6 view is bad and the previous within-population pairwise/centroid ideas are not acceptable.\n\nGoal:\n- Produce two slide-ready figures/assets:\n  1. An 'original type' MDS scatter plot with points labeled/colored by continental superpopulation labels, matching the older familiar MDS style as much as possible.\n  2. A violin/box/jitter distribution of distance from each subtelomeric MDS point to its nearest other point from the same continental superpopulation.\n\nCritical metric definition:\n- For each point in the MDS coordinate table with a continental group/superpopulation label, compute the Euclidean distance to every other point in the same superpopulation, exclude self, and keep the minimum.\n- Do not use centroids.\n- Do not use all-pairwise within-population distances as the primary metric.\n- Do not average a population point against all in-group points. This is nearest same-group neighbor distance only.\n\nImplementation guidance:\n- Locate the source MDS coordinate data behind s08a/s08b and the v3 08b work. If the plotted MDS is 2D, compute the main metric in plotted 2D MDS space; if prior scripts used cached 5D coordinates, document that and optionally report a secondary 5D sensitivity table, but the slide must be interpretable as MDS-space nearest-neighbor distance.\n- Use consistent continental group labels and colors.\n- Show sample sizes per superpopulation in the violin plot.\n- Include a concise note: lower values mean each subtelomere has a closer same-superpopulation neighbor in sequence-similarity MDS space.\n- Keep axes 1:1 on scatter and use readable labels.\n\nDeliverables:\n- Reproducible script(s), README, nearest-neighbor TSV, summary TSV, rendered PNG/PDF assets under slides/v2-review-zoom/_revision_assets/v7/08b_nearest_same_superpop_mds/.\n- SLIDE_PATCH.md with recommended insertion: likely split into two slides, first labeled superpopulation MDS, second nearest same-group distance distribution.\n- Validation note that no centroid/all-pairwise metric is used.\n\nDo not make final deck integration changes; leave that to review-zoom-v7-fanin-render.

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Log

2026-05-07T19:42:44.185811919+00:00 Task paused
2026-05-07T19:43:48.924941712+00:00 Task published
2026-05-07T19:45:02.685520631+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-05-07T19:45:29.249185829+00:00 Starting work: inspect existing MDS sources and prior slide 08b assets before generating nearest same-superpopulation outputs.
2026-05-07T19:54:55.149860027+00:00 Generated v7 08b nearest same-superpopulation MDS assets, row-level TSV, summary TSV, README, validation note, and slide patch guidance.
2026-05-07T20:00:04.793157151+00:00 Validated: R script regenerates assets; nearest TSV has 15,668 rows, no missing labels, finite 2D distances, and no self-neighbor rows; summary TSV has 10 rows; git diff --check passes. No Cargo/package build manifest found at repository top levels, so validation used the R asset generator.
2026-05-07T20:01:43.227098642+00:00 Committed: c76d81f - pushed to remote branch wg/agent-1119/review-zoom-v7-slide08b-nearest-superpop-mds
2026-05-07T20:02:23.102666137+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-07T20:07:54.096674206+00:00 PendingEval → Done (evaluator passed; downstream unblocks)