Giorgio Gilestro
ab3dc10587
- paper/pnas -> paper/manuscript (venue-neutral)
- configs/layer1 -> configs/inheritance, src/knowledge -> src/inheritance
(imported as `inheritance`), make layer1 -> make inheritance; layer2 alias dropped
- inheritance and trained-network bundles named after the manuscript figure
they feed (fig2_grounding_sweep, figS3_rebaselining, ...), or descriptively
where they feed none; configs keep their `experiment:` value so parquet
hashes are unchanged, only output.dir moves
- figure scripts, SI figure sources, notebooks, REPRODUCING.md, README and the
SI Methods/tables updated; make clean no longer deletes tracked manifests;
reproduce.sh hashes the s{seed}/ layouts too
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
64 lines
2.4 KiB
Python
64 lines
2.4 KiB
Python
"""E1 figure: reproduce collapse (null model).
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Shows tail-first collapse under pure neutral drift: geometric H decay matching the
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analytic law, tail items dying faster than head items, support -> 1 and forward-KL
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diverging. Usage: python figures/plot_collapse_null.py [results/collapse_null]
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"""
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from __future__ import annotations
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import sys
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from pathlib import Path
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import matplotlib.pyplot as plt
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import numpy as np
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sys.path.insert(0, str(Path(__file__).parent))
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from _figlib import load_bundle, mean_ci, savefig # noqa: E402
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def main(results_dir: str = "results/collapse_null") -> None:
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df, cfg = load_bundle(results_dir)
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n = cfg["dynamics"]["n"]
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gens, Hmean, Hci = mean_ci(df, "generation", "heterozygosity")
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H0 = Hmean[0]
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analytic = H0 * (1.0 - 1.0 / n) ** gens
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m = df.groupby("generation").mean(numeric_only=True)
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fig, axes = plt.subplots(1, 3, figsize=(15, 4.2))
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# Panel 1: heterozygosity decay vs the analytic law
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ax = axes[0]
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ax.plot(gens, Hmean, color="#1f77b4", label="simulation (mean)")
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ax.fill_between(gens, Hmean - Hci, Hmean + Hci, color="#1f77b4", alpha=0.25)
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ax.plot(gens, analytic, "k--", label=r"$H_0(1-1/n)^t$")
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ax.set(xlabel="generation", ylabel="heterozygosity $H$",
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title=f"Geometric decay (n={n})")
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ax.legend(frameon=False)
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# Panel 2: tail-first — fraction of tail vs head items still alive
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ax = axes[1]
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ax.plot(m.index, m["tail_frac_alive"], color="#d62728", label="tail items alive")
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ax.plot(m.index, m["head_frac_alive"], color="#2ca02c", label="head items alive")
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ax.set(xlabel="generation", ylabel="fraction of items surviving",
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title="Tail dies first", yscale="log")
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ax.legend(frameon=False)
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# Panel 3: support collapse and KL divergence
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ax = axes[2]
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ax.plot(m.index, m["support_size"], color="#9467bd", label="support size")
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ax.set(xlabel="generation", ylabel="support size", yscale="log", title="Collapse")
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ax2 = ax.twinx()
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ax2.plot(m.index, m["forward_kl"], color="#ff7f0e", label="forward KL")
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ax2.set_ylabel(r"forward KL $D_{KL}(p^*\,\|\,p_t)$", color="#ff7f0e")
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ax.legend(loc="center right", frameon=False)
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fig.suptitle("E1 — distillation without grounding collapses, tail first", y=1.02)
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fig.tight_layout()
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savefig(fig, results_dir, "collapse_null")
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if __name__ == "__main__":
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main(*sys.argv[1:])
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