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Manuscript revision and pending experiment work, snapshot before restructuring

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Clarity pass over the main text (36-item audit), Discussion rewrite and cut,
acknowledgements, Souly et al. as ref 62, lettered SI panels, model section
moved under Results; plus the untracked curriculum/society/compose/smol
configs, runners, figures, stats and tests that the SI already cites.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
This commit is contained in:
Giorgio Gilestro 2026-09-13 16:54:09 +01:00
parent e4804adabc
commit 84124de143
450 changed files with 52813 additions and 1202 deletions
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19
figures/plot_E5.py
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@ -15,7 +15,7 @@ import matplotlib.pyplot as plt
import numpy as np
sys.path.insert(0, str(Path(__file__).parent))
from _figlib import load_bundle, savefig # noqa: E402
from _figlib import load_bundle, savefig, letter_axes # noqa: E402
def main(results_dir: str = "results/E5") -> None:
@ -30,14 +30,14 @@ def main(results_dir: str = "results/E5") -> None:
# Panel 1: H trajectories
ax = axes[0]
series = [("greedy", 1.0, "#d62728", "greedy"),
("qd", 1.0, "#ff7f0e", "qd (α=1)"),
("qd", 2.0, "#1f77b4", "qd (α=2)"),
("qd", 1.0, "#ff7f0e", "quality-diversity (α=1)"),
("qd", 2.0, "#1f77b4", "quality-diversity (α=2)"),
("none", 1.0, "#2ca02c", "none (grounding only)")]
for mode, a, c, lab in series:
s = arm(mode, a).groupby("generation")["heterozygosity"].mean()
ax.plot(s.index, s.values, color=c, label=lab)
ax.set(xlabel="generation", ylabel="heterozygosity $H$",
title="Greedy collapses; QD maintains diversity")
title="Greedy collapses;\nquality-diversity maintains diversity")
ax.legend(frameon=False, fontsize=8)
# Panel 2: stationary H vs alpha for qd, with greedy/none reference lines
@ -45,19 +45,19 @@ def main(results_dir: str = "results/E5") -> None:
qd = df[(df["mode"] == "qd") & (df["generation"] >= last)]
st = qd.groupby("novelty_alpha")["heterozygosity"].agg(["mean", "sem"])
ax.errorbar(st.index, st["mean"], yerr=1.96 * st["sem"], fmt="-o",
color="#ff7f0e", capsize=3, label="qd")
color="#ff7f0e", capsize=3, label="quality-diversity")
for mode, c in (("greedy", "#d62728"), ("none", "#2ca02c")):
h = arm(mode, 1.0)
h = h[h["generation"] >= last]["heterozygosity"].mean()
ax.axhline(h, ls="--", color=c, label=f"{mode}")
ax.set(xlabel=r"novelty exponent $\alpha$", ylabel="stationary $H$",
title="QD maintains H above greedy for all α")
title="Quality-diversity keeps $H$\nabove greedy for all α")
ax.legend(frameon=False, fontsize=9)
# Panel 3: stationary support size per arm
ax = axes[2]
arms = [("greedy", 1.0, "greedy"), ("qd", 0.5, "qd α=0.5"),
("qd", 1.0, "qd α=1"), ("qd", 2.0, "qd α=2"), ("none", 1.0, "none")]
arms = [("greedy", 1.0, "greedy"), ("qd", 0.5, "quality-diversity α=0.5"),
("qd", 1.0, "quality-diversity α=1"), ("qd", 2.0, "quality-diversity α=2"), ("none", 1.0, "none")]
labels, vals, errs, colors = [], [], [], []
palette = {"greedy": "#d62728", "qd": "#ff7f0e", "none": "#2ca02c"}
for mode, a, lab in arms:
@ -70,9 +70,8 @@ def main(results_dir: str = "results/E5") -> None:
xticks=range(len(labels)))
ax.set_xticklabels(labels, rotation=25, ha="right", fontsize=8)
fig.suptitle("E5 — quality-diversity selection maintains diversity where greedy "
"fixes it", y=1.02)
fig.tight_layout()
letter_axes(fig)
savefig(fig, results_dir, "E5")