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Paper-wide rename: the pop-gen construct is "the biological model"; "(exact)" dropped

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"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
This commit is contained in:
Giorgio Gilestro 2026-09-07 13:08:58 +01:00
parent f1970728cf
commit 2d8f661924
7 changed files with 67 additions and 63 deletions
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14
paper/pnas/build.py
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@ -23,13 +23,13 @@ OUT = HERE / "body.tex"
FIGURES: dict[str, tuple[list[str], str]] = {
"fig1": (["paper/pnas/figs/fig1a.pdf", "paper/pnas/figs/fig1b.pdf"],
"(A) The experimental programme. Each population-genetic abstraction (Table 1) is tested at up "
"to three tiers, ordered left to right by increasing realism: an exact "
"Wright--Fisher simulator over knowledge distributions (closed forms; bitwise-reproducible), "
"to three tiers, ordered left to right by increasing realism: a biological model (a "
"Wright--Fisher simulator over knowledge distributions; closed forms, bitwise-reproducible), "
"trained neural networks measured against exact oracles (recurrent, feedforward, and "
"variational-autoencoder generators on a synthetic mode universe, and a convolutional VAE on "
"MNIST), and language models (LoRA specialists on Qwen bases at 0.5B and 7B, scored by an "
"exact-match verifier). Colour separates the two categories: the population-genetic theory "
"tier in blue, the two AI-model tiers in oranges. The same abstractions are carried across "
"exact-match verifier). Colour separates the two categories: the biological model in blue, "
"the two AI-model tiers in oranges. The same abstractions are carried across "
"all three. Rows are the framework's mechanisms, each defined at the left margin; filled "
"cells name the experiments run at each tier, and each carries, in its corner, the figure "
"or table where that result is reported, so this figure doubles as a map of the paper. Each claim is tested at the cheapest tier that "
@ -48,7 +48,7 @@ FIGURES: dict[str, tuple[list[str], str]] = {
"grounding."),
"fig2": (["paper/pnas/figs/fig2.pdf"],
"Grounding is immigration. (A) Stationary diversity against the grounding fraction in the "
"minimal inheritance model: simulation (points, 95\\% CI) matches the exact immigration--drift "
"biological model: simulation (points, 95\\% CI) matches the exact immigration--drift "
"equilibrium (dashed). The equilibrium is smooth in $g$; $g \\approx 0.05$ marks the "
"operational threshold retaining 95\\% of source diversity in this setting (red line, "
"bootstrap CI shaded); the hollow point at $g=0$ is a finite-time value (the true equilibrium "
@ -56,7 +56,7 @@ FIGURES: dict[str, tuple[list[str], str]] = {
"generation on its own output (rows: generations 0--15 of an ungrounded lineage) collapse "
"toward a single blurred mode; 10\\% grounding holds all thirty modes (quantified in SI)."),
"fig4": (["paper/pnas/figs/fig4.pdf"],
"Recombination in the minimal model: blending inheritance and the Fisher--Muller effect. "
"Recombination in the biological model: blending inheritance and the Fisher--Muller effect. "
"(A) Expected rare-capability survival in a child refit from $K$ uncorrelated parents: the "
"output-mean (blending) stays at the single-parent level --- the first-order cancellation --- "
"while the union operator (strongest source per item, renormalised, oracle-identified) rises "
@ -81,7 +81,7 @@ FIGURES: dict[str, tuple[list[str], str]] = {
"preservation strands it lower. (B) Population diversity. (C) The self-consumption signature: "
"conformity minus true fitness (mean $\\pm$ 95\\% CI, 12 replicates)."),
"fig7": (["paper/pnas/figs/fig7.pdf"],
"Model speciation at three tiers. (A) Analytic model: hybrid fitness tracks the parents while "
"Model speciation at three tiers. (A) Biological model: hybrid fitness tracks the parents while "
"lineages are compatible, then falls to inviability; the denser the incompatibilities, the "
"earlier the fall. (B) The isolation cliff: probability of hybrid inviability against "
"divergence, by incompatibility density. (C) Trained networks: the merge error barrier between "