Removed from main (all preserved on the dev branch): the arXiv build and
its sources, design documents (blueprint, results summary, review responses,
essay drafts), tasks/ and CLAUDE.md, the cover letter and reference tooling,
two unused manuscript figures, and every experiment that feeds no figure or
number in the paper: the collapse null, the sexual-vs-asexual lineage, the
NK speciation variant, the 0.5B single-seed LLM prototypes, the compose and
society experiments with their calibration and pilot runs, and their
configs, runners, tests, figure scripts and PBS jobs. Their result bundles
are moved to results/_archive/ (ignored) so the parquets stay on disk.
Also: plot_llm_speciation reads the s{seed}/ layout; the mating-breadth
plot writes under its bundle name; Makefile targets reduced to the kept
experiments; REPRODUCING.md and README point to dev for the rest.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
One self-contained README.md per results/ figure folder (Layer 1 E1-E6
and Layer 1.5 bridge/collapse/grounding/architectures/recombination):
plain-language claim, setup, a compact symbol glossary, a panel-by-panel
walkthrough, and the takeaway + falsifier. Auto-renders when browsing the
folder; carries the honest caveats (grounding's ruler reframing, the
excluded VAE).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Grounding refinement (18 reps): forward-KL is the operative neural
collapse metric, not H or tail-survival. The RNN's smoothing keeps
spurious tail modes alive, so tail_truth_mass_alive is flat/non-monotone
in g and H stays ~0.8 of H*; only forward-KL falls monotonically (dry
2.08 -> g=0.2: 0.75, paired t up to 3.3). The sharp g* << 1 is an
exact-operator feature carried by the histogram bridge (0.047); the
trained RNN confirms the SIGN and softens the sharpness (half the KL gap
closes by g~0.04, but full recovery needs g~0.19). Blueprint 3.5's
directional claim holds; the pre-registered 95%-of-H*/tail falsifier is
not met because those are the wrong metrics for a smoothing model.
Robustness: a fully-degenerate RNN can emit only invalid codewords, so
measure_distribution now returns a terminal-collapse sentinel (fixation
on the dominant mode) instead of crashing a long sweep. Edge test added
(94 tests green).
Figures: plot_{bridge,collapse,grounding,architectures,recombination}.py,
each a pure function of its committed bundle, wired into `make figures`
(glob plot_*.py minus plot_E[1-6]/_*). bridge sits on the exact H_eq
curve (g*=0.047); recombination shows max-merge rising while mean-distill
stays flat; architectures shows the collapse/rescue signs across
histogram/GRU/MLP.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
src/neural/recombine.py mirrors Layer-1 run_coverage but trains K_T specialist RNNs on
assignments from the exact shared-switch retention construction (K_T/rho/q clean; union
matches the closed form), then recombines the measured teacher distributions two ways:
mean (naive pooling) vs oracle-guided max-merge (per-mode strongest teacher, M2N2-style),
each followed by size-n resampling.
Result (8 reps): at rho=0, union rises 0.49->0.96 (supply matches closed form); analytic
surviving_max rises 0.043->0.087 while surviving_mean stays flat ~0.045 — the conservation
law (averaging cancels the union gain, max-merge realises it). At rho=1 (identical
teachers) union and max are flat. The lesson holds in the neural setting; trained-weight
columns show the same signs but noisier (smoothing inflates baseline; deep tail barely
clears n=200 resampling). torch-gated test added. 93 tests green.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
