figure-ed8-discussion-models

Metadata

Status	done
Assigned	`agent-704`
Agent identity	`f51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e`
Created	2026-05-05T05:06:30.501270132+00:00
Started	2026-05-05T05:45:30.944018203+00:00
Completed	2026-05-05T06:08:28.446458156+00:00
Tags	`paper-prep,figure`, `eval-scheduled`
Eval score	0.83
└ blocking impact	0.75
└ completeness	0.95
└ constraint fidelity	0.85
└ coordination overhead	0.85
└ correctness	0.75
└ downstream usability	0.80
└ efficiency	0.90
└ intent fidelity	0.89
└ style adherence	0.80

Description

Produce ED8 (4 panels) — Discussion synthesis: feedback loop + D4Z4 model + recombination null + compartment-identity diagnostic. Two of the 4 are mechanistic schematics. Implement directly — do not decompose further.

File scope

paper_prep/figures/ed8/figure_ed8.{pdf,png,R/py}, caption.md, sources.tsv

Figure spec (excerpt from MANUSCRIPT_SKELETON.md ED8)

ED8 — Discussion synthesis: feedback loop, recombination null, mechanistic models

Panel	Content	Status	Source
ED8a	Causal feedback loop schematic (4 links, support level coded)	GENERATE	Schematic; `SURVEY_07 §1.6, §6 T-2`
ED8b	D4Z4-CTCF-lamin tethering schematic for C1 + 0–15 kb sharing-peak inset	GENERATE	Schematic + sequence-level distance histogram from §1.4 `SURVEY_07`
ED8c	Recombination map vs cross-arm affinity — all 39 arms (ρ = −0.43) and N=32 (ρ = 0.00, p = 0.98)	GENERATE	Lalli 2025 cM/Mb × `cross_arm_affinity_sequences.tsv` — `SURVEY_07 §1.7 prediction 2`; `SURVEY_10/11/12 §6 T-3`
ED8d	Compartment-identity-at-tips diagnostic (e1 distribution, 68% A; mean +0.007; vs Dip-C radial)	GENERATE	HG002 100 kb eigenvector + radial table — `SURVEY_07 §6 T-6`

Validation

All 4 panels; sources.tsv complete
Caption ≤ 200 words; ≥ 2 metrics with TSV paths
ED8c is the manuscript honest-null figure — must show the all-39-arm and N=32 fits side-by-side
PDF + PNG

Inputs

paper_prep/synthesis/MANUSCRIPT_SKELETON.md
paper_prep/surveys/SURVEY_07_integrated.md, SURVEY_10_11_12_limits_summary_lit.md

## Description
Produce ED8 (4 panels) — Discussion synthesis: feedback loop + D4Z4 model + recombination null + compartment-identity diagnostic. Two of the 4 are mechanistic schematics. Implement directly — do not decompose further.

## File scope
- `paper_prep/figures/ed8/figure_ed8.{pdf,png,R/py}`, `caption.md`, `sources.tsv`

## Figure spec (excerpt from MANUSCRIPT_SKELETON.md ED8)

### ED8 — Discussion synthesis: feedback loop, recombination null, mechanistic models
| Panel | Content | Status | Source |
|---|---|---|---|
| ED8a | Causal feedback loop schematic (4 links, support level coded) | GENERATE | Schematic; `SURVEY_07 §1.6, §6 T-2` |
| ED8b | D4Z4-CTCF-lamin tethering schematic for C1 + 0–15 kb sharing-peak inset | GENERATE | Schematic + sequence-level distance histogram from §1.4 `SURVEY_07` |
| ED8c | Recombination map vs cross-arm affinity — all 39 arms (ρ = −0.43) and N=32 (ρ = 0.00, p = 0.98) | GENERATE | Lalli 2025 cM/Mb × `cross_arm_affinity_sequences.tsv` — `SURVEY_07 §1.7 prediction 2`; `SURVEY_10/11/12 §6 T-3` |
| ED8d | Compartment-identity-at-tips diagnostic (e1 distribution, 68% A; mean +0.007; vs Dip-C radial) | GENERATE | HG002 100 kb eigenvector + radial table — `SURVEY_07 §6 T-6` |

## Validation
- [ ] All 4 panels; sources.tsv complete
- [ ] Caption ≤ 200 words; ≥ 2 metrics with TSV paths
- [ ] ED8c is the manuscript honest-null figure — must show the all-39-arm and N=32 fits side-by-side
- [ ] PDF + PNG

## Inputs
- `paper_prep/synthesis/MANUSCRIPT_SKELETON.md`
- `paper_prep/surveys/SURVEY_07_integrated.md`, `SURVEY_10_11_12_limits_summary_lit.md`

Depends on

Required by

Log

2026-05-05T05:41:39.951465528+00:00 Lightweight assignment: agent=Careful Programmer (f5143935), exec_mode=full, context_scope=task, reason=Figure implementation task requires careful, correctness-critical programming for publication-grade schematics and data visualizations; Careful Programmer has proven track record (83 tasks, 0.83 score) on similar implementation work.
2026-05-05T05:45:30.944022+00:00 Spawned by coordinator --executor claude --model opus
2026-05-05T05:45:54.078969443+00:00 Starting ED8 figure: 4 panels — feedback loop schematic, D4Z4-CTCF-lamin schematic, recombination null, compartment-identity diagnostic
2026-05-05T06:03:14.795333558+00:00 Created figure_ed8.{R,pdf,png}, caption.md, sources.tsv. Stats: per-arm rho all-46 = -0.35 (p=0.017), well-callable n=40 = -0.01 (p=0.97); compartment 63/92 A (68%), mean e1 = +0.0073.
2026-05-05T06:07:54.134715944+00:00 Validated: 4 panels render correctly (a=feedback loop schematic, b=D4Z4-CTCF-lamin schematic with 0-15 kb sharing-peak inset, c=honest-null scatter pair all-46 + N=40, d=e1 distribution histogram). PDF + PNG produced. caption.md ≈ 200 words; sources.tsv has 9 rows tracing all panels. Stats from real data tables (recombination_maps + cross_arm_affinity + assignments + compartment_analysis).
2026-05-05T06:08:16.912656661+00:00 Committed: 5d85355 — pushed to origin/wg/agent-704/figure-ed8-discussion-models
2026-05-05T06:08:28.446462154+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-05T06:12:35.007304380+00:00 PendingEval → Done (evaluator passed; downstream unblocks)