Giorgio Gilestro
c9c4d927ad
The two Flaticon icons (licensed via GG's paid subscription) are now committed as SVG source and rasterised at 2048 px by make_figs.py via rsvg-convert (~6000 DPI at the placed size - print-lossless), keeping every figure a pure function of the script plus committed sources. The 512 px CDN PNGs are gone; a clear error names the librsvg dependency if rsvg-convert is missing. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
638 lines
32 KiB
Python
638 lines
32 KiB
Python
"""Publication figures for the PNAS draft — unified, lettered, codename-free.
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Renders fig1 (the experimental-programme schematic) and re-plots every data panel directly from the
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committed results artifacts (figs/fig2.pdf .. fig7.pdf): no experiment codenames, no suptitles, no per-panel headline titles
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(interpretation lives in the captions), bold panel letters, one consistent style. The per-experiment
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figures under results/ remain the exploratory versions; these are the manuscript's.
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Usage: python paper/pnas/make_figs.py
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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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ROOT = Path(__file__).resolve().parents[2]
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sys.path.insert(0, str(ROOT / "figures"))
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sys.path.insert(0, str(ROOT / "src"))
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import os
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os.chdir(ROOT) # load_bundle uses repo-relative paths
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from _figlib import load_bundle, mean_ci # noqa: E402
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OUT = ROOT / "paper" / "pnas" / "figs"
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plt.rcParams.update({
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"font.size": 8, "axes.labelsize": 8.5, "legend.fontsize": 7, "legend.frameon": False,
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"lines.markersize": 3.6, "axes.spines.top": False, "axes.spines.right": False,
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})
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def letter(ax, s, x=-0.14):
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ax.text(x, 1.02, s, transform=ax.transAxes, fontsize=12, fontweight="bold", va="bottom")
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def save(fig, name):
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OUT.mkdir(exist_ok=True)
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fig.savefig(OUT / f"{name}.pdf", bbox_inches="tight")
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plt.close(fig)
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print("wrote", OUT / f"{name}.pdf")
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def _icon(svg_name: str):
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"""Rasterise a committed icon SVG at 2048 px (print-lossless at the ~0.3 in placed size).
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Requires ``rsvg-convert`` (librsvg). The SVGs are the committed source of truth; no derived
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PNGs are kept in the repo.
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"""
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import subprocess
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import tempfile
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svg = OUT / "icons" / svg_name
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with tempfile.NamedTemporaryFile(suffix=".png") as f:
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try:
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subprocess.run(["rsvg-convert", "-w", "2048", "-h", "2048", "-o", f.name, str(svg)],
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check=True, capture_output=True)
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except FileNotFoundError as e:
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raise RuntimeError("rsvg-convert (librsvg) is required to rasterise the icon SVGs "
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"for fig1a") from e
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return plt.imread(f.name)
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# ---------------------------------------------------------------- fig 1: experimental programme
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def fig1a():
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from matplotlib.patches import FancyBboxPatch
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# (name, architecture, guarantee, edge, cell face, header fill, header text colour, icon)
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# Icons: Flaticon #2347052 (green pea, for Mendel) and #10479785 (robot) as committed SVGs,
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# used under GG's paid Flaticon licence; rasterised at build time by _icon().
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TIERS = [
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("Biological model", "Wright\u2013Fisher simulator (NumPy)", "closed forms \u00b7 bitwise-reproducible",
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"#4e8d4e", "#eef6ec", "#c5e0bd", "#2d5b2d", "pea.svg"),
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("Trained networks", "RNN \u00b7 MLP \u00b7 VAE on a synthetic oracle;\nconvolutional VAE on MNIST",
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"sign-level tests \u00b7 exact oracles", "#5b9bc9", "#eff6fb", "#c9e2f2", "#1f4e79",
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"robot.svg"),
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("Language models", "LoRA specialists on Qwen 0.5B & 7B;\nexact-match verifier",
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"seed-replicated signs", "#3c6ea5", "#e7eef8", "#adc8e8", "#1d3f66", "robot.svg"),
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]
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ROWS = [
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("Grounding = immigration",
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"fresh verified samples from a\nfixed external source enter the\ntraining mix every generation",
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["immigration\u2013drift equilibrium:\n$g \\approx 0.05$ retains $\\geq$95% diversity;\nobservation floor $1-e^{-mp}$",
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"collapse & rescue in every\narchitecture; MNIST: dry 30$\\to$1 modes,\n10% grounding holds 30/30;\nestimator-bias learning kernel",
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"LIT:established at LLM scale in\nprior work (refs. 21, 30);\nnot re-run here"]),
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("Recombination = sex",
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"a child inherits from several\nparents, reassembling variants\nthat arose in different lineages",
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["blending conservation law\n(first-order cancellation);\nunion-operator gain; Fisher\u2013Muller",
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"merge rescues two forgetting\nspecialists ($\\approx$0.50 $\\to$ 0.955)",
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"merged specialists beat every parent\n(5 seeds at 0.5B; 7B); routing vs\naveraging: the headroom rule"]),
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("Epistasis (entangled skills)",
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"a variant's fitness contribution\ndepends on the variants present\nat the other loci",
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["NK landscapes: outbreeding\ndepression; directed sex restores\nthe gain; mate-pool breadth optimum",
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None,
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"bred-and-screened offspring beat\nthe blind blend in every seed\n(hard, unsaturated tasks)"]),
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("The composed society",
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"selection, recombination,\ndiversity preservation and\ngrounding on one population",
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["four-arm ablation: grounding, sex,\ndiversity each removed\n$\\to$ three distinct failures",
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None,
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"OPEN"]),
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("Speciation",
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"reproductive isolation: diverged\nlineages no longer produce\nviable (mergeable) offspring",
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["BDM incompatibility model:\nisolation cliff; quadratic snowball",
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"barrier decomposition under\npermutation+rescaling; conflict\nsweep 0.97$\\to$0.03; emergent null",
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"convention conflict $\\to$ hybrid\nbreakdown; duration null; pre-merge\npredictive test (13 cond. $\\times$ 3 seeds)"]),
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]
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TAGS = [("Fig. 2A", "Fig. 2B", None),
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("Fig. 4", "Table S2", "Fig. 3A\u2013B"),
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("Fig. 5", None, "Table S2"),
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("Fig. 6", None, None),
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("Fig. 7A\u2013B", "Fig. 7C\u2013D", "Figs. 7E\u2013F, 3C\u2013D")]
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fig, ax = plt.subplots(figsize=(11.4, 5.3))
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ax.set_axis_off()
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ax.set_xlim(0, 1)
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ax.set_ylim(0, 1)
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ax.text(0.0, 0.995, "A", fontsize=13, fontweight="bold", va="top")
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x0, gap, sep = 0.205, 0.008, 0.02 # sep: extra gutter between theory and the AI pair
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cw = (1.0 - x0 - sep) / 3
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xs = [x0, x0 + cw + sep, x0 + 2 * cw + sep]
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row_h, row_top = 0.157, 0.805
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from matplotlib.offsetbox import AnnotationBbox, OffsetImage
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for j2, (name, arch, guarantee, edge, face, headfill, textcol, icon) in enumerate(TIERS):
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x = xs[j2]
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xc = x + cw / 2 - 0.02 # text centred left of the icon slot
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ax.add_patch(FancyBboxPatch((x + gap, 0.825), cw - 2 * gap, 0.155,
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boxstyle="round,pad=0.004", fc=headfill, ec=edge, lw=1.6))
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ax.text(xc, 0.966, name, ha="center", va="top", fontsize=9.5,
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fontweight="bold", color=textcol)
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ax.text(x + cw / 2 - 0.026, 0.922, arch, ha="center", va="top", fontsize=6.6,
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linespacing=1.3, color=textcol)
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ax.text(xc, 0.833, guarantee, ha="center", va="bottom", fontsize=6.4,
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style="italic", color=textcol, alpha=0.85)
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img = _icon(icon)
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ax.add_artist(AnnotationBbox(OffsetImage(img, zoom=28.0 / img.shape[0]),
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(x + cw - gap - 0.024, 0.902), frameon=False))
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for i2, (label, definition, cells) in enumerate(ROWS):
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tags = TAGS[i2]
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y1 = row_top - i2 * row_h
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y0 = y1 - row_h + 2 * gap
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yc = (y0 + y1) / 2
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ax.text(0.0, y1 - 0.014, label, ha="left", va="top", fontsize=8, fontweight="bold")
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ax.text(0.0, y1 - 0.054, definition, ha="left", va="top", fontsize=6.2,
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style="italic", color="#555", linespacing=1.35)
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for j2, cell in enumerate(cells):
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x = xs[j2]
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edge = TIERS[j2][3]
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face = TIERS[j2][4]
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if cell is None:
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ax.add_patch(FancyBboxPatch((x + gap, y0), cw - 2 * gap, y1 - y0,
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boxstyle="round,pad=0.004", fc="white", ec="#bbbbbb",
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lw=0.8, ls=(0, (3, 2))))
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ax.text(x + cw / 2, yc, "adds no discriminating test\nat this tier", ha="center",
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va="center", fontsize=6.4, style="italic", color="#999", linespacing=1.35)
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elif cell.startswith("LIT:"):
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ax.add_patch(FancyBboxPatch((x + gap, y0), cw - 2 * gap, y1 - y0,
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boxstyle="round,pad=0.004", fc="white", ec="#bbbbbb",
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lw=0.8, ls=(0, (3, 2))))
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ax.text(x + cw / 2, yc, cell[4:], ha="center", va="center",
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fontsize=6.4, style="italic", color="#777", linespacing=1.35)
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elif cell == "OPEN":
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ax.add_patch(FancyBboxPatch((x + gap, y0), cw - 2 * gap, y1 - y0,
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boxstyle="round,pad=0.004", fc="white", ec=edge,
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lw=0.8, ls=(0, (3, 2))))
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ax.text(x + cw / 2, yc, "open \u2014 the stated gap", ha="center", va="center",
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fontsize=6.6, style="italic", color=edge)
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else:
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ax.add_patch(FancyBboxPatch((x + gap, y0), cw - 2 * gap, y1 - y0,
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boxstyle="round,pad=0.004", fc=face, ec=edge, lw=0.9))
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ax.text(x + cw / 2, yc + 0.008, cell, ha="center", va="center",
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fontsize=6.4, linespacing=1.35)
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if tags[j2]: # where the result lives (the ToC role)
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ax.text(x + cw - gap - 0.005, y0 + 0.006, tags[j2], ha="right", va="bottom",
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fontsize=5.6, style="italic", color=edge)
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save(fig, "fig1a")
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# ------------------------------------------------------- fig 1B: society in space -> in time
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BLUE, GREEN, GOLD = "#4292c6", "#41ab5d", "#d4a017"
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def _robot(ax, x, y, fc="#e8eef5", dots=(), lost=(), w=0.52, h=0.52):
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"""A friendly robot head with capability dots beneath (gold = the rare skill)."""
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from matplotlib.patches import Arc, Circle, FancyBboxPatch
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ax.add_patch(FancyBboxPatch((x - w / 2, y - h / 2), w, h, boxstyle="round,pad=0.03",
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fc=fc, ec="#445", lw=1.1))
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for dx in (-w / 4.5, w / 4.5):
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ax.add_patch(Circle((x + dx, y + h / 7), w / 9, fc="white", ec="#445", lw=0.7))
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ax.add_patch(Circle((x + dx, y + h / 7), w / 24, fc="#334", ec="none"))
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ax.add_patch(Arc((x, y - h / 7), w / 2.4, h / 3.2, theta1=195, theta2=345, ec="#445", lw=1.0))
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ax.plot([x, x], [y + h / 2 + 0.03, y + h / 2 + 0.10], color="#445", lw=1.1)
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ax.add_patch(Circle((x, y + h / 2 + 0.135), 0.04, fc="#445", ec="none"))
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marks = [(c, False) for c in dots] + [(c, True) for c in lost]
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n = len(marks)
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for i, (c, is_lost) in enumerate(marks):
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cx = x + (i - (n - 1) / 2) * 0.19
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cy = y - h / 2 - 0.17
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if is_lost:
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ax.add_patch(Circle((cx, cy), 0.07, fc="white", ec=c, lw=0.9, ls=(0, (2, 2))))
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ax.text(cx, cy - 0.005, "\u00d7", ha="center", va="center", fontsize=6, color=c)
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else:
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ax.add_patch(Circle((cx, cy), 0.07, fc=c, ec="none"))
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def fig1b():
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from matplotlib.patches import Circle, FancyArrowPatch
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W, H = 11.4, 4.75
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fig, ax = plt.subplots(figsize=(W, H))
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ax.set_xlim(0, W)
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ax.set_ylim(0, H)
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ax.set_aspect("equal")
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ax.set_axis_off()
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ax.text(0.05, H - 0.05, "B", fontsize=13, fontweight="bold", va="top")
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def arrow(p, q, color="#666", lw=1.2, style="-|>", shrink=2.0, ls="-"):
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ax.add_patch(FancyArrowPatch(p, q, arrowstyle=style, mutation_scale=10, color=color,
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lw=lw, linestyle=ls, shrinkA=shrink, shrinkB=shrink))
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# ---------------- left: a society in space (contemporaries exchanging messages)
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cx, cy, r = 2.45, 2.95, 0.95
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dotsets = [(BLUE, GOLD), (GREEN,), (BLUE, GREEN), (GOLD, GREEN), (BLUE,)]
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pos = []
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for i, ds in enumerate(dotsets):
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a = np.pi / 2 + i * 2 * np.pi / 5
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x, y = cx + r * np.cos(a) * 1.4, cy + r * np.sin(a) * 0.95
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pos.append((x, y))
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_robot(ax, x, y, dots=ds)
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for i, j2 in [(0, 2), (1, 3), (2, 4), (0, 3), (1, 4)]:
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arrow(pos[i], pos[j2], color="#99a", lw=0.9, style="<|-|>", shrink=26, ls=(0, (4, 2)))
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ax.text(pos[0][0] + 0.72, pos[0][1] + 0.38, "hi!", fontsize=8, ha="center",
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bbox=dict(boxstyle="round,pad=0.25", fc="white", ec="#99a", lw=0.8))
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clk = (0.55, 4.33)
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ax.add_patch(Circle(clk, 0.21, fc="white", ec="#445", lw=1.1))
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ax.plot([clk[0], clk[0]], [clk[1], clk[1] + 0.13], color="#445", lw=1.0)
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ax.plot([clk[0], clk[0] + 0.10], [clk[1], clk[1]], color="#445", lw=1.0)
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ax.text(clk[0], clk[1] - 0.34, "one moment", ha="center", fontsize=7, style="italic",
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color="#555")
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ax.text(2.45, 0.80, "a society in space", ha="center", fontsize=11, fontweight="bold")
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ax.text(2.45, 0.50, "contemporaries exchanging messages \u2014 multi-agent systems, agent economies",
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ha="center", fontsize=7.2, style="italic", color="#555")
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ax.text(2.45, 0.24, "information is passed on, but not easily stored: it fades with the conversation",
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ha="center", fontsize=7.2, style="italic", color="#555")
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# ---------------- middle: the shift of perspective
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arrow((4.60, 2.75), (5.95, 2.75), color="#445", lw=2.0, style="-|>")
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ax.text(5.27, 2.91, "the same ecosystem,\nseen along its time axis", ha="center",
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va="bottom", fontsize=8, style="italic", color="#334", linespacing=1.3)
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# ---------------- right: a society in time (a pedigree)
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axx = 6.8
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arrow((axx, 4.55), (axx, 1.25), color="#445", lw=1.3)
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for gy, lab in [(4.05, "gen 0"), (2.80, "gen 1"), (1.60, "gen 2")]:
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ax.text(axx - 0.12, gy, lab, ha="right", va="center", fontsize=7.5, color="#445")
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p1, p2 = (8.0, 4.05), (9.5, 4.05)
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c1, c2 = (7.5, 2.80), (9.0, 2.80)
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g2 = (9.0, 1.60)
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_robot(ax, *p1, dots=(BLUE, GOLD))
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_robot(ax, *p2, dots=(GREEN, BLUE))
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_robot(ax, *c1, dots=(BLUE,), lost=(GOLD,))
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_robot(ax, *c2, dots=(BLUE, GREEN, GOLD))
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_robot(ax, *g2, dots=(BLUE, GREEN, GOLD))
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arrow((7.87, 3.51), (7.56, 3.29), color="#666")
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ax.text(7.42, 3.41, "inherit", ha="right", fontsize=7, style="italic", color="#555")
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arrow((8.15, 3.49), (8.85, 3.29), color="#666")
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arrow((9.40, 3.49), (9.13, 3.29), color="#666")
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ax.text(9.0, 3.39, "merge (sex)", ha="center", fontsize=7, style="italic", color="#555",
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bbox=dict(boxstyle="round,pad=0.12", fc="white", ec="none"))
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ax.text(7.5, 2.08, "rare skill lost", ha="center", fontsize=6.8, style="italic",
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color="#a33")
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arrow((9.0, 2.24), (9.0, 2.06), color="#666")
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globe = (10.55, 2.10)
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ax.add_patch(Circle(globe, 0.32, fc="#eaf4fb", ec="#2c7fb8", lw=1.2))
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from matplotlib.patches import Arc as _Arc
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ax.add_patch(_Arc(globe, 0.32, 0.64, theta1=90, theta2=270, ec="#2c7fb8", lw=0.8))
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ax.add_patch(_Arc(globe, 0.32, 0.64, theta1=270, theta2=90, ec="#2c7fb8", lw=0.8))
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ax.plot([globe[0] - 0.32, globe[0] + 0.32], [globe[1], globe[1]], color="#2c7fb8", lw=0.8)
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ax.text(globe[0], globe[1] - 0.44, "reality\n(verifier)", ha="center", va="top", fontsize=7,
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color="#2c7fb8", linespacing=1.2)
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arrow((10.22, 1.95), (9.38, 1.70), color="#2c7fb8", lw=1.2)
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ax.text(9.82, 2.03, "ground\n(immigrate)", ha="center", va="bottom", fontsize=7,
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style="italic", color="#2c7fb8", linespacing=1.2)
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ax.text(8.9, 0.80, "a society in time", ha="center", fontsize=11, fontweight="bold")
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ax.text(8.9, 0.50, "information is inherited, evolutionarily selected, and passed on again \u2014",
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ha="center", fontsize=7.2, style="italic", color="#555")
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ax.text(8.9, 0.24, "from parent model to child model \u2014 where population genetics applies",
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ha="center", fontsize=7.2, style="italic", color="#555")
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save(fig, "fig1b")
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# ---------------------------------------------------------------- fig 2: grounding + MNIST
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def fig2():
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from knowledge.analysis import critical_grounding, reduce_to_stationary
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from knowledge.metrics import heterozygosity
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from knowledge.truth import make_true_distribution
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df, cfg = load_bundle("results/E2")
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n = cfg["dynamics"]["n"]
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td = make_true_distribution(cfg["truth"]["K"], 1, "zipf", cfg["truth"]["tail_frac"],
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cfg["truth"]["zipf_s"], 0, tail_threshold=cfg["truth"]["tail_threshold"])
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H_star = heterozygosity(td.p_star)
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last = int(cfg["generations"] * 0.8)
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stat = df[df["generation"] >= last]
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fig, axes = plt.subplots(1, 2, figsize=(10.6, 3.5), gridspec_kw={"width_ratios": [1, 1.35]})
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ax = axes[0]
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st = reduce_to_stationary(stat, value_col="heterozygosity", replicate_col="replicate", last_frac=1.0)
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gg, Hm, Hci = mean_ci(stat, "g", "heterozygosity")
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nz = gg > 0
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ax.errorbar(gg[nz], Hm[nz], yerr=Hci[nz], fmt="o", color="#1f77b4", capsize=2, label="simulation")
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ax.plot(gg[~nz], Hm[~nz], "o", mfc="white", mec="#1f77b4")
|
||
m_of_g = stat.groupby("g")["m"].first().to_numpy()
|
||
m_grid = np.linspace(0, m_of_g.max(), 400)
|
||
|
||
def H_eq(m):
|
||
m = np.asarray(m, float)
|
||
return np.where(m <= 0, 0.0, H_star * m * (2 * n + m - 1) / (n + 2 * n * m + m * m))
|
||
|
||
ax.plot(m_grid / (n + m_grid), H_eq(m_grid), "k--", lw=1, label="exact equilibrium")
|
||
ax.axhline(H_star, ls=":", color="gray", lw=1, label="source diversity $H^*$")
|
||
r = critical_grounding(st, H_star=H_star, frac=0.95, seed=7)
|
||
ax.axvspan(r["ci_low"], r["ci_high"], color="#d62728", alpha=0.15)
|
||
ax.axvline(r["g_star"], color="#d62728", lw=1.1,
|
||
label=f"95%-retention threshold $g\\approx{r['g_star']:.3f}$")
|
||
ax.set(xlabel="grounding fraction $g = m/(n+m)$", ylabel="stationary diversity $H$")
|
||
ax.legend()
|
||
letter(ax, "A")
|
||
|
||
ax = axes[1]
|
||
from PIL import Image
|
||
im = np.asarray(Image.open("results/mnist_collapse/mnist_montage.png"))
|
||
# Strip the baked-in title band and left label margin (raster text is unreadable at panel
|
||
# size); measured on the committed montage: boxes span y >= 69, x >= 75, row centres below.
|
||
top, left = 60, 68
|
||
ax.imshow(im[top:, left:], interpolation="bilinear")
|
||
for yc, g in zip((101.5, 191.5, 282.0, 372.5, 462.5), (0, 4, 8, 12, 15)):
|
||
ax.text(-10, yc - top, str(g), ha="right", va="center", fontsize=8.5)
|
||
ax.text(-0.055, 0.5, "generation", transform=ax.transAxes, rotation=90,
|
||
ha="center", va="center", fontsize=8.5)
|
||
ax.set_axis_off()
|
||
letter(ax, "B", x=-0.02)
|
||
save(fig, "fig2")
|
||
|
||
|
||
# ---------------------------------------------------------------- fig 4: blending vs union + Fisher–Muller
|
||
def fig4():
|
||
fig, axes = plt.subplots(1, 2, figsize=(10.6, 3.5))
|
||
|
||
df, _ = load_bundle("results/E4")
|
||
r0 = df[(df["g"] == 0.0) & (df["rho"] == 0.0)]
|
||
mx = r0.groupby("K_T")["surviving_max"].agg(["mean", "sem"])
|
||
mn = r0.groupby("K_T")["surviving_mean"].agg(["mean", "sem"])
|
||
ax = axes[0]
|
||
ax.errorbar(mx.index, mx["mean"], yerr=1.96 * mx["sem"], fmt="-o", color="#1f77b4",
|
||
capsize=2, label="union operator (strongest source)")
|
||
ax.errorbar(mn.index, mn["mean"], yerr=1.96 * mn["sem"], fmt="--s", color="#d62728",
|
||
capsize=2, label="output-mean (blending)")
|
||
ax.set(xlabel="number of parents", ylabel="rare capabilities surviving in the child",
|
||
xticks=sorted(r0["K_T"].unique()))
|
||
ax.legend()
|
||
letter(ax, "A")
|
||
|
||
df8, cfg8 = load_bundle("results/E8")
|
||
L = cfg8["society"]["L"]
|
||
d0 = df8[df8["rho"] == 0.0]
|
||
ax = axes[1]
|
||
for col, c, lab in [("best_parent", "#7f7f7f", "best single parent"),
|
||
("average", "#1f77b4", "blended average"),
|
||
("sexual", "#d62728", "recombined offspring")]:
|
||
k, m, ci = mean_ci(d0, "K_T", col)
|
||
ax.errorbar(k, m, yerr=ci, fmt="-o", color=c, capsize=2, label=lab)
|
||
ax.axhline(L, ls=":", color="green", lw=1, label="optimum")
|
||
ax.set(xlabel="number of parents", ylabel="offspring capability")
|
||
ax.legend()
|
||
letter(ax, "B")
|
||
save(fig, "fig4")
|
||
|
||
|
||
# ---------------------------------------------------------------- fig 5: rugged landscapes
|
||
def fig5():
|
||
fig, axes = plt.subplots(2, 2, figsize=(10.6, 6.8))
|
||
|
||
df9, _ = load_bundle("results/E9")
|
||
Ks = sorted(df9["K"].unique())
|
||
colors = plt.cm.viridis(np.linspace(0, 0.85, len(Ks)))
|
||
bp = df9.groupby("K")["best_parent"].mean()
|
||
ax = axes[0, 0]
|
||
for K, c in zip(Ks, colors):
|
||
s = df9[df9["K"] == K].groupby("rate")["mean_offspring"].mean() - bp[K]
|
||
ax.plot(s.index, s.values, "-o", color=c, label=f"$K$={K}")
|
||
ax.axhline(0, ls=":", color="gray", lw=1)
|
||
ax.set(xlabel="recombination rate", ylabel="mean offspring − best parent")
|
||
ax.legend(title="ruggedness", ncol=2)
|
||
letter(ax, "A")
|
||
|
||
df10, _ = load_bundle("results/E10")
|
||
ax = axes[0, 1]
|
||
for col, c, lab in [("global_opt", "green", "global optimum"),
|
||
("directed_sex", "#d62728", "screened recombination (directed)"),
|
||
("best_parent", "#7f7f7f", "best single parent"),
|
||
("random_sex", "#1f77b4", "blind recombination")]:
|
||
k, m, ci = mean_ci(df10, "K", col)
|
||
if col == "global_opt":
|
||
ax.plot(k, m, ":", color=c, label=lab)
|
||
else:
|
||
ax.errorbar(k, m, yerr=ci, fmt="-o", color=c, capsize=2, label=lab)
|
||
ax.set(xlabel="landscape ruggedness $K$", ylabel="offspring capability")
|
||
ax.legend()
|
||
letter(ax, "B")
|
||
|
||
df14, _ = load_bundle("results/E14")
|
||
last = df14[df14["generation"] == df14["generation"].max()].copy()
|
||
last["best_n"] = last["best_fitness"] / last["global_opt"]
|
||
K14 = sorted(last["K"].unique())
|
||
cmap = plt.get_cmap("viridis")
|
||
c14 = {K: cmap(i / max(1, len(K14) - 1)) for i, K in enumerate(K14)}
|
||
for ax, col, ylab, L in [(axes[1, 0], "best_n", "best fitness / optimum", "C"),
|
||
(axes[1, 1], "diversity", "population diversity", "D")]:
|
||
for K in K14:
|
||
g = last[last["K"] == K].groupby("breadth")[col].agg(["mean", "sem"]).reset_index()
|
||
ax.errorbar(g["breadth"], g["mean"], yerr=1.96 * g["sem"].fillna(0), fmt="-o",
|
||
color=c14[K], capsize=2, label=f"$K$={K}")
|
||
ax.set_xscale("log")
|
||
ax.set(xlabel="mate-pool breadth (monogamous → panmictic)", ylabel=ylab)
|
||
ax.legend(title="ruggedness")
|
||
letter(ax, L)
|
||
save(fig, "fig5")
|
||
|
||
|
||
# ---------------------------------------------------------------- fig 6: the society
|
||
def fig6():
|
||
df, _ = load_bundle("results/E11")
|
||
arms = [("full", "#2ca02c", "full system"),
|
||
("no_sex", "#ff7f0e", "no recombination"),
|
||
("no_diversity", "#9467bd", "no diversity preservation"),
|
||
("no_grounding", "#d62728", "no grounded evaluation")]
|
||
arms = [a for a in arms if a[0] in set(df["arm"].unique())]
|
||
g_opt = df["global_opt"].mean()
|
||
|
||
fig, axes = plt.subplots(1, 3, figsize=(11.4, 3.2))
|
||
panels = [("best_fitness", "best real fitness", "A"),
|
||
("diversity", "population diversity", "B"),
|
||
("conformity_true_gap", "conformity − true fitness", "C")]
|
||
for ax, (col, ylab, L) in zip(axes, panels):
|
||
for name, c, lab in arms:
|
||
sub = df[df["arm"] == name]
|
||
g, m, ci = mean_ci(sub, "generation", col)
|
||
ax.plot(g, m, "-", color=c, lw=1.6, label=lab)
|
||
ax.fill_between(g, m - ci, m + ci, color=c, alpha=0.15)
|
||
if col == "best_fitness":
|
||
ax.axhline(g_opt, ls=":", color="gray", lw=1, label="global optimum")
|
||
ax.legend()
|
||
ax.set(xlabel="generation", ylabel=ylab)
|
||
letter(ax, L)
|
||
save(fig, "fig6")
|
||
|
||
|
||
# ---------------------------------------------------------------- fig 7: speciation, three tiers
|
||
def fig7():
|
||
fig, axes = plt.subplots(2, 3, figsize=(11.4, 6.6))
|
||
|
||
bdm, _ = load_bundle("results/E12")
|
||
rhos = sorted(bdm["rho"].unique())
|
||
colors = plt.cm.viridis(np.linspace(0.15, 0.85, len(rhos)))
|
||
|
||
def agg(df, keys, value):
|
||
g = df.groupby(keys)[value].agg(["mean", "std", "count"]).reset_index()
|
||
g["se"] = g["std"] / np.sqrt(g["count"].clip(lower=1))
|
||
return g
|
||
|
||
ax = axes[0, 0]
|
||
par = agg(bdm, "divergence", "parent_fitness")
|
||
ax.plot(par["divergence"], par["mean"], "k--", lw=1.3, label="parents")
|
||
for rho, c in zip(rhos, colors):
|
||
g = agg(bdm[bdm["rho"] == rho], "divergence", "offspring_fitness")
|
||
ax.plot(g["divergence"], g["mean"], "-o", color=c, label=f"hybrid, density {rho:g}")
|
||
ax.fill_between(g["divergence"], g["mean"] - g["se"], g["mean"] + g["se"], color=c, alpha=0.15)
|
||
ax.axhline(0, color="#999", lw=0.7, ls=":")
|
||
ax.set(xlabel="parental divergence (substitutions)", ylabel="fitness")
|
||
ax.legend()
|
||
letter(ax, "A")
|
||
|
||
ax = axes[0, 1]
|
||
for rho, c in zip(rhos, colors):
|
||
g = agg(bdm[bdm["rho"] == rho], "divergence", "isolation")
|
||
ax.plot(g["divergence"], g["mean"], "-o", color=c, label=f"{rho:g}")
|
||
ax.set(xlabel="parental divergence (substitutions)", ylabel="P(hybrid inviable)", ylim=(-0.02, 1.02))
|
||
ax.legend(title="incompatibility density")
|
||
letter(ax, "B")
|
||
|
||
dec, _ = load_bundle("results/speciation_real")
|
||
order = [c for c in ["shared", "independent", "conflict"] if c in set(dec["condition"])]
|
||
g = dec.groupby("condition").agg(naive=("barrier_naive", "mean"),
|
||
res=("residual_scale", "mean")).reindex(order)
|
||
ax = axes[0, 2]
|
||
x = np.arange(len(order)); w = 0.38
|
||
ax.bar(x - w / 2, g["naive"], w, color="#9ecae1", label="before alignment")
|
||
ax.bar(x + w / 2, g["res"], w, color="#d62728", label="after alignment (residual)")
|
||
ax.set_xticks(x)
|
||
ax.set_xticklabels(["same task,\nshared start", "same task,\ndifferent start", "conflicting\ntasks"])
|
||
ax.set(ylabel="merge error barrier")
|
||
ax.legend()
|
||
letter(ax, "C")
|
||
|
||
cliff, _ = load_bundle("results/speciation_real_cliff")
|
||
cg = cliff.groupby("conflict_frac").agg(res=("residual_scale", "mean"),
|
||
hyb=("acc_merge_scale", "mean")).reset_index()
|
||
ax = axes[1, 0]
|
||
ax.plot(cg["conflict_frac"], cg["res"], "-o", color="#d62728", label="residual barrier")
|
||
ax2 = ax.twinx()
|
||
ax2.plot(cg["conflict_frac"], cg["hyb"], "-s", color="#2c7fb8", label="merged-model accuracy")
|
||
ax2.set_ylabel("merged accuracy", color="#2c7fb8")
|
||
ax2.tick_params(axis="y", labelcolor="#2c7fb8")
|
||
ax2.spines["right"].set_visible(True)
|
||
ax.set(xlabel="fraction of classes in conflict", ylabel="residual barrier")
|
||
l1, la1 = ax.get_legend_handles_labels(); l2, la2 = ax2.get_legend_handles_labels()
|
||
ax.legend(l1 + l2, la1 + la2, loc="center left")
|
||
letter(ax, "D")
|
||
|
||
rep, _ = load_bundle("results/llm_speciation")
|
||
|
||
def series(df, mode, model, metric):
|
||
sub = df[(df["mode"] == mode) & (df["model"] == model) & (df["metric"] == metric)]
|
||
g = sub.groupby("x")["accuracy"].mean().reset_index()
|
||
return g["x"], g["accuracy"]
|
||
|
||
ax = axes[1, 1]
|
||
x_, y_ = series(rep, "conflict", "parent_a", "ambig_asc")
|
||
ax.plot(x_, y_, "--o", color="#9ecae1", label="parent A, own convention")
|
||
x_, y_ = series(rep, "conflict", "parent_b", "ambig_desc")
|
||
ax.plot(x_, y_, "--o", color="#a1d99b", label="parent B, own convention")
|
||
x_, y_ = series(rep, "conflict", "merge_soup", "coherence")
|
||
ax.plot(x_, y_, "-s", color="#d62728", label="merge, best convention")
|
||
ax.set(xlabel="fraction of training in conflict", ylabel="accuracy, shared prompts")
|
||
ax.legend()
|
||
letter(ax, "E")
|
||
|
||
ax = axes[1, 2]
|
||
x_, y_ = series(rep, "duration", "merge_soup", "mean_private")
|
||
ax.plot(x_, y_, "-o", color="#d62728", label="merged model")
|
||
x_, y_ = series(rep, "duration", "parent_a", "strings")
|
||
ax.plot(x_, y_, "--o", color="#9ecae1", label="parent A, own task")
|
||
x_, y_ = series(rep, "duration", "parent_b", "arith")
|
||
ax.plot(x_, y_, "--o", color="#a1d99b", label="parent B, own task")
|
||
ax.set(xlabel="specialist training (epochs)", ylabel="accuracy", ylim=(0, 1.02))
|
||
ax.legend()
|
||
letter(ax, "F")
|
||
save(fig, "fig7")
|
||
|
||
|
||
# ---------------------------------------------------------------- fig 3: the language-model tier
|
||
def fig3():
|
||
import pandas as pd
|
||
from scipy.stats import spearmanr
|
||
|
||
fig, axes = plt.subplots(2, 2, figsize=(10.6, 6.6))
|
||
|
||
dfm, _ = load_bundle("results/llm_merge_seeds")
|
||
specs = sorted(m for m in dfm["model"].unique() if m.startswith("spec_"))
|
||
rows = []
|
||
for s, sub in dfm.groupby("seed"):
|
||
ov = {m: sub[(sub["model"] == m) & (sub["metric"] == "overall")]["accuracy"].mean() for m in specs}
|
||
b = sub[sub["model"] == max(ov, key=ov.get)].copy(); b["model"] = "best_specialist"
|
||
rows.append(b)
|
||
dfm = pd.concat([dfm] + rows, ignore_index=True)
|
||
models = ["base", "best_specialist", "merge_soup", "merge_ties"]
|
||
labels = ["base", "best\nspecialist", "merged\n(average)", "merged\n(interference-aware)"]
|
||
ax = axes[0, 0]
|
||
x = np.arange(len(models))
|
||
for off, metric, c, lab in ((-0.19, "overall", "#2c7fb8", "overall"),
|
||
(0.19, "worst_family", "#d62728", "worst task family")):
|
||
vals, errs = [], []
|
||
for m in models:
|
||
v = dfm[(dfm["model"] == m) & (dfm["metric"] == metric)].groupby("seed")["accuracy"].mean()
|
||
vals.append(v.mean()); errs.append(1.96 * v.std(ddof=1) / max(1, np.sqrt(len(v))))
|
||
ax.bar(x + off, vals, 0.36, yerr=errs, capsize=2, color=c, label=lab)
|
||
ax.set_xticks(x); ax.set_xticklabels(labels, fontsize=7)
|
||
ax.set(ylabel="verifier accuracy")
|
||
ax.legend()
|
||
letter(ax, "A")
|
||
|
||
df7, _ = load_bundle("results/llm_moe_hard_hpc")
|
||
|
||
def acc7(model, metric):
|
||
r = df7[(df7["model"] == model) & (df7["metric"] == metric)]["accuracy"]
|
||
return float(r.iloc[0]) if len(r) else np.nan
|
||
specs7 = sorted(m for m in df7["model"].unique() if m.startswith("spec_"))
|
||
best7 = max(specs7, key=lambda m: acc7(m, "overall"))
|
||
models7 = [best7, "merge_soup", "merge_ties", "moe_oracle"]
|
||
labels7 = ["best\nspecialist", "merged\n(average)", "merged\n(interference-aware)", "routed\n(kept separate)"]
|
||
ax = axes[0, 1]
|
||
x = np.arange(len(models7))
|
||
for off, metric, c, lab in ((-0.19, "overall", "#2c7fb8", "overall"),
|
||
(0.19, "worst_family", "#d62728", "worst task family")):
|
||
ax.bar(x + off, [acc7(m, metric) for m in models7], 0.36, color=c, label=lab)
|
||
ax.set_xticks(x); ax.set_xticklabels(labels7, fontsize=7)
|
||
ax.set(ylabel="verifier accuracy")
|
||
ax.legend()
|
||
letter(ax, "B")
|
||
|
||
a = pd.read_parquet("results/llm_epistasis/results.parquet")
|
||
b = pd.read_parquet("results/llm_epistasis_compat/results.parquet")
|
||
dfe = pd.concat([a, b], ignore_index=True)
|
||
ax = axes[1, 0]
|
||
for mode, c, mk, lab in (("conflict", "#d62728", "o", "conflicting conventions"),
|
||
("duration", "#2c7fb8", "s", "divergence only"),
|
||
("compat", "#41ab5d", "^", "overlap, no conflict")):
|
||
sub = dfe[dfe["mode"] == mode]
|
||
ax.scatter(sub["epi_conf"], sub["merge_penalty"], c=c, marker=mk, s=26, alpha=0.75, label=lab)
|
||
ax.axhline(0, color="#999", lw=0.6)
|
||
ax.set(xlabel="pre-merge functional conflict (confidence-weighted)",
|
||
ylabel="merge penalty")
|
||
ax.legend()
|
||
letter(ax, "C")
|
||
|
||
preds = [("dis_raw", "raw\ndisagreement"), ("epi_conf", "conf-weighted\nconflict"),
|
||
("grad_cos", "gradient\nalignment"), ("delta_cos", "weight\ncosine"),
|
||
("delta_l2", "weight\ndistance"), ("cross_perf", "cross-task\naccuracy")]
|
||
ax = axes[1, 1]
|
||
rhos_ = [abs(spearmanr(dfe[c], dfe["merge_penalty"])[0]) for c, _ in preds]
|
||
cols = ["#fc9272", "#d62728", "#9ecae1", "#9ecae1", "#9ecae1", "#9ecae1"]
|
||
ax.bar(np.arange(len(preds)), rhos_, 0.6, color=cols)
|
||
ax.set_xticks(np.arange(len(preds)))
|
||
ax.set_xticklabels([l for _, l in preds], fontsize=6.5)
|
||
ax.set(ylabel="|Spearman ρ| vs merge penalty", ylim=(0, 0.8))
|
||
letter(ax, "D")
|
||
save(fig, "fig3")
|
||
|
||
|
||
if __name__ == "__main__":
|
||
for f in (fig1a, fig1b, fig2, fig3, fig4, fig5, fig6, fig7):
|
||
f()
|