Giorgio Gilestro
2d8f661924
"Model" now means an AI model everywhere; the Wright-Fisher construct is "the
biological model" throughout (19 occurrences): tier header, section title (now
"The biological model, and where trained learners depart from it"), Table 1
support column ("Exact" -> "Closed form"; "Analytic model" -> "Biological
model"), Results, Discussion, Methods ("Biological-model tier"), and all
figure captions. "Exact" survives only in technical noun phrases (exact-match
verifier, exact oracle, exact equilibrium, exact recovery); the abstract's
"exactly Wright-Fisher" is now "literally Wright-Fisher".
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
41 lines
3.2 KiB
Markdown
41 lines
3.2 KiB
Markdown
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**2026-08-11 — Stop padding time estimates.** GG: "You generally massively overestimate the time it
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takes to do some work... You're fast." Phase-1 items I scoped as "Week 1" took ~an hour. Rule: state
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what will be done and in what order; give a duration only when compute-bound (training walltime), and
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base it on measured runtimes, not human-project heuristics.
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**2026-08-11 — Correspondence is not identity; interpretation is not prediction (manuscript reviews).**
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The external review's core corrections, to internalise for all paper claims: (1) distinguish
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interpretation / explanation / prediction and claim only the level the evidence supports; (2) a
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minimal model being exactly Wright-Fisher does not make real training "literally" WF — our own
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learning-kernel result says otherwise (cite it against ourselves); (3) name the operator every claim
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is about (output-mean vs weight-average vs max-with-oracle vs routing are different objects with
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different budgets); (4) don't write "nobody has / none imports" — invite no priority disputes; say
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"to our knowledge" and state the positive contribution; (5) negative results (E13b) are strengths —
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lead with them; (6) "control theory" needs states/controls/dynamics/rule or it's a "framework".
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**2026-08-11 — tmux does NOT survive SSH disconnects on this machine.** The tmux server starts inside
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the SSH session's systemd scope and gets reaped on logout (lost ~20 min of the epistasis grid; GG:
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"SSH disconnected"). Reliable pattern here: `systemd-run --user --collect --unit=<name>
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--working-directory="$PWD" bash -c '<cmd>'` — lands in user@.service (kept alive by the desktop
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session), survives disconnects; check with `systemctl --user is-active <name>`, logs via redirect.
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**2026-08-11 — Internal deliberations must not leak into reader-facing prose.** GG (on the
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convergence paragraph): it "carries all the ghosts of our internal brainstorming that should be
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completely alien to the readers (this is, alas, a recurring problem with your writing)." The pattern:
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strategic concerns from the working process (priority anxieties -> "we cite for priority of
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publication"; calibration debates -> "the honest statement"; positioning battles -> "nobody has")
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surface as defensive or self-referential prose. Rule: before finalising any reader-facing passage,
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ask "does understanding this sentence require knowing how we worked?" If yes, rewrite it as a plain
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statement about the literature or the result. Confident papers situate; they do not litigate.
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(Promoted to a general rule in the global ~/.claude/CLAUDE.md, 2026-08-11 — it applies to all
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reader-facing prose in every project.)
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## Terminology: "model" is overloaded in this project (2026-09-07)
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In the PNAS manuscript and figures, "model" must mean an AI model. The settled term for the
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pop-gen construct is **"the biological model"** (GG decision, 2026-09-07) — used everywhere
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("the multi-locus biological model", "Biological-model tier"), never "minimal model",
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"analytic model", or "exact model"; GG also vetoed "(exact)" as a tier label (the guarantee
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line "closed forms · bitwise-reproducible" carries that content). Support level formerly
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"Exact" is now "Closed form". Keep "exact" only in technical noun phrases (exact-match
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verifier, exact oracle, exact equilibrium, exact recovery).
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