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
The five priority fixes, in the PNAS draft and propagated to the
long-form document and results documentation:
1. The averaging proposition now proves what it claims: a FIRST-ORDER
cancellation of the multi-parent retention gain under output-mean
inheritance in the rare-item regime (n·p/K << 1), with the convexity
boundary stated (averaging's variance reduction can reduce extinction
outside that regime — the reviewer's argument) and the union
operator's renormalisation + oracle requirement explicit. "Adding
parents cannot help" deleted everywhere.
2. Grounding: g*~=0.05 restated as an operational threshold (equilibrium
smooth in g — no phase transition); m·p floor restated as
1−exp(−m·p) per-batch observation probability with
retention/occupancy/reintroduction distinguished; the deep-tail rule
de-categoricalised (stratified sampling; recombination recovers only
what parents retain).
3. Grounded INHERITANCE (data channel) separated from grounded
EVALUATION (fitness channel) in the society section; retitled to
"complementary contributions"; general joint necessity disclaimed.
Table 1 + v6 ledger updated.
4. Alignment contradiction removed everywhere ("cannot be an alignment
failure" -> the reviewer's formulation); abstract says "remaining
after permutation-and-rescaling alignment"; group = search space,
control recovery != global optimality; "specialisation is merge-safe"
-> "do not treat divergence/specialisation alone as evidence of
incompatibility".
5. Significance headline matched to the bounded evidence; seed-
dependence sensitivity added (per-seed rho stable +0.37..+0.53 for
functional measures, ~0 for geometry, gradient alignment
seed-UNSTABLE −0.11..−0.55 — reported as its own caveat; LOSO ranges
in stats script).
Presentation: review-process meta-language stripped; "exact" reserved
for closed forms ("analytic model" labels); headroom rule qualitative;
directed-sex phrasing per review; ratchet = consequence-level
correspondence; compact results table (Table 2) added. Response letter:
paper/response-to-review-3.md. Both PDFs rebuilt; 151 tests green.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
E13c (the symmetry defense): alignment now runs modulo the FULL
function-preserving unit symmetry group of a ReLU MLP (per-unit positive
rescaling via canonicalise_scale, composed with Re-Basin permutations;
sanity gate recovers a permuted-and-rescaled copy exactly). Verdict: the
full group removes the independent-init barrier (residual 0.001) and
essentially none of the conflict barrier (0.502 -> 0.497) — the residual
is functional, not a missed symmetry (answers arXiv:2606.23607). The
cliff gains a hybrid-fitness readout: merged accuracy 0.97 -> 0.03 with
conflict. Floor proposition drafted (paper/si-notes.md S1): endpoint
invariance + max(eps_A, eps_B) >= mu(S)/2 for any merged model under any
alignment group.
E13b (emergent divergence): pre-registered second reading — with NO
conflicting training signal (disjoint class specialists; rolled-input
conventions), residual is 0.000 at every divergence to t_div=3200, and
the merge RESCUES the forgetting specialists (parents 0.535/0.474 ->
merged 0.955; a sustained Fisher-Muller rescue at zero barrier).
Speciation in real weights requires functional conflict; it does not
emerge from compatible specialisation on shared ancestry. LLM-scale
over-specialisation (cf. 2607.11997) deferred to Phase-3 llm_speciation.
3-panel figure, READMEs, +2 tests (149 green), make mnist wired.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
The real-weight image of E12, and the answer to the mode-connectivity reviewer.
Small no-BN MLPs on MNIST, forked from a shared base and trained independently,
are weight-averaged; we measure the linear-mode-connectivity barrier before and
after in-house deterministic Git Re-Basin permutation alignment (neural/rebasin.py,
scipy linear_sum_assignment), decomposing it into removable (coordinate artefact)
and residual (reproductive isolation). kind: speciation_real.
Result (3 reps):
- shared (same task, shared fork): no barrier — trivially mergeable.
- independent (same task, different init): naive 0.056, alignment removes 98%
(residual 0.001) — the incompatibility is a coordinate artefact.
- conflict (conflicting label maps): naive 0.496, alignment removes 0% (residual
0.496) — genuine reproductive isolation. Because alignment demonstrably works on
the independent case, the conflict residual is real, not a failure to align.
- Isolation cliff (speciation_real_cliff): residual rises 0.00->0.13->0.19->0.28->
0.40->0.49 with the fraction of conflicting classes — the real-weight mirror of
E12's cliff; residual==naive throughout (functional, not coordinate).
rebasin.py sanity-gated (recovers a known permutation exactly). plot_speciation_real.py
(2-panel), +4 pure-NumPy tests (142 green), README with honest positioning vs
Git Re-Basin / Entezari / Frankle / Pari 2024 / Zhou 2026. Wired into make mnist
(needs torchvision).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
