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
- 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
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
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
The decisive experiment from the external review. 39 LoRA parent pairs
(0.5B, 3 seeds) on three axes decorrelated by construction: conflict
(contradictory conventions on shared prompts, private budgets fixed),
compat (same prompts, SAME convention — overlap without conflict), and
duration (weight divergence, zero conflict). Six pre-merge predictors;
primary outcome = merge penalty (parent potential − merged achieved).
League table (Spearman vs penalty, n=39): functional measures predict
(dis_raw +0.460, epi_conf +0.446, p<0.005); geometry collapses
(delta_cos +0.03, delta_l2 +0.17 n.s.); gradient alignment weak (−0.35);
performance ~0. The first grid's apparent geometry win (+0.60) was an
overlap/volume artifact — the compat control axis (added for exactly
this) exposed and killed it: same overlap and data volume, zero penalty.
Honest riders in the README: confidence weighting does not beat raw
disagreement as a rank predictor (pre-registered internal prediction not
confirmed; it does double the conflict/compat level contrast), and
|rho|~0.45 is bounded by 0.5B merge-outcome noise (7B is the firm-up).
Also: micro-batched gradient accumulation (OOM fix on the shared 16GB
GPU), exact r-space LoRA-delta geometry (brute-force-verified test,
151 green), systemd-run runbook lesson (tmux dies with the SSH session
scope on this box).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
llm_speciation (new kind; src/llm/speciation.py): E13 in LLM weights.
LoRA children share the frozen base's coordinates, so merge failure is
functional by construction. CONFLICT (ambiguous sort prompts learned
under opposite conventions — the BDM structure): function-specific
hybrid breakdown — merged coherence 0.02-0.08 falls below BOTH parents
(~0.2) on the conflicted function; and in the de-confounded `add` design
(private budget fixed, conflict added on top; 3 seeds after a
single-seed pilot showed one anomalous point) the merge's private-family
accuracy shows NO trend with conflict — the damage is surgical, not
global. DURATION (over-trained disjoint specialists, 1->12 epochs): the
merge improves (0.84->0.94) and stays above the best parent — the MLP
"no emergent isolation" null generalises; relevant to the
expert-training-duration report (2607.11997), with the epistasis
prediction left to the decisive experiment.
Multi-seed firm-up (seeds threaded into specialist caches; `seeds:` list
support in the runner; fixed test sets): all three recombination claims
hold with CIs — merges beat every specialist (5 seeds, ties
0.647±0.027 > best spec 0.592±0.009; worst-family 0.28 vs <=0.16); union
0.274±0.026 > fusion 0.174±0.102 on hard (3 seeds); directed 0.221±0.026
> soup. NEW finding: fusion is seed-FRAGILE where headroom exists
(CI ±0.10) while routing/directed selection are stable (±0.026) — the
union/selection operators win on reliability, not just mean.
Figures (llm_speciation 3-panel; llm_seeds 3-panel with 95% CI), READMEs,
+1 convention test (150 green), make llm-speciation / llm-seeds targets.
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
A new analytic experiment on an orthogonal evolution-of-sex axis: not the
recombination RATE (E9) but the population's mating STRUCTURE. Agents on a
ring recombine with a second parent drawn from a window of breadth b
(b->0 monogamous/isolation-by-distance, b=1 promiscuous/panmictic), under
local selection, swept against NK ruggedness K.
Finding: the optimal mate-pool breadth SHRINKS as skills get more
entangled. Wide/promiscuous merging wins the champion on additive
landscapes (K<=3, b=0.6), but on rugged ones (K>=6) it prematurely
converges to a worse champion and an intermediate breadth (b~0.35) wins;
pure monogamy over-fragments. Throughout, promiscuity monotonically lifts
the population MEAN but destroys diversity and parallel exploration. The
design rule extends E9: merge widely for additive skills, keep
island-structured sub-populations for entangled ones — a merging-native
axis the panmixia-assuming literature lacks.
- src/knowledge/mating_system.py + experiment.py dispatch (kind: mating_system)
- configs/layer1/E14.yaml (breadth x K sweep, 20 reps, bitwise-reproducible)
- figures/plot_E14.py; results/E14/ (figure, README, manifest, resolved config)
- tests/test_mating_system.py (+5, 147 green); make layer1 wired
- folded into both papers (full + accessible) as the third §5 result
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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>
New analytic result for the evolution-of-sex paper: how far can two lineages
diverge before recombination (model merging) stops working? Frames merge failure
as biological reproductive isolation via Bateson-Dobzhansky-Muller
incompatibilities. src/knowledge/speciation.py, kind: speciation, on the E7-E11
genotype machinery (pure seeded NumPy, bitwise-reproducible; no external
simulator whose separate RNG would break that).
- BDM construction (E12.yaml): ancestor + two lineages substituting disjoint loci
(each parent adaptive, incompatibility-free), a fraction rho of cross-lineage
pairs are BDMIs. Sweeping divergence d reproduces the predicted
compatible -> outbreeding depression -> hybrid inviability curve; the isolation
cliff moves to lower d as epistasis density rises (iso at d=20: 0.00/0.03/0.50
for rho 0.1/0.25/0.5); incompatibilities snowball ~ (d/2)^2 (Orr-Turelli).
- NK variant (E12_nk.yaml): parents = hill-climbed local optima; the epistasis
wedge — recombination gain flips 0 -> -0.13 and OD rate 0 -> 0.90 as ruggedness
K rises. At matched divergence, mergeability is governed by epistasis, the axis
no divergence-only ML merge predictor captures.
plot_E12.py (3-panel), +7 tests (138 green), README with honest positioning
(concedes the empirical phenomenon to Pari 2024 / Zhou 2026 + permutation
artefacts to Git Re-Basin; claims the predictive theory + the epistasis wedge).
Wired into make layer1.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The easy task families saturated 7B (strings & arith at 1.00), so the earlier
7B nulls — moe: fusion 0.87 > union 0.84; directed ~= soup — could not separate
"refinements don't help at scale" from "tasks too easy at 7B". Adds a hard task
variant (hard: true in tasks.py: multi-step lists, Caesar ciphers / letter
transforms, multi-step & larger arithmetic; same family labels and answer
formats, threaded through make_tasks/train_specialist/runners; hard specialists
cache separately as spec_*_hard) and re-runs both experiments at 7B on Imperial
CX3 (one L40S, 24 min, unsaturated: arith ~0.48, strings 0.67, lists 0.34).
Both nulls flip back to the 0.5B ordering:
- Union beats fusion again: routing 0.500 > fusion 0.40 (soup 0.392 / ties
0.400), the same 10-pt margin as 0.5B. Fusion dilutes the fragile strings
specialist so hard (0.665 -> soup 0.300) that soup even trails the best single
specialist (0.425); routing keeps it intact (0.670).
- Directed selection beats soup again: 0.492 > 0.392 (+10 pts), recovering most
of routing's benefit from one deployable merged model (lifts strings to 0.630).
Correction to the earlier interpretation: the llm_moe_hpc "regime flip" and the
llm_directed_hpc "no headroom" null were driven by TASK SATURATION, not base
capability. The operative variable is headroom — "merge, don't average" (union >
fusion) and "directed sex" (selection > single blend) hold whenever there is room
to lose to dilution: a weak base (0.5B) OR hard tasks at a strong base (7B-hard).
Fusion only wins in the degenerate corner where easy tasks let a strong base
compose to the 1.00 ceiling. Vindicates E8's max > mean in real 7B weights once
saturation is controlled.
Default (easy) task behaviour is unchanged (hard defaults False). +1 hard-task
test (131 green). Excludes the 0.5B smoke bundle (a pipeline gate, not a
deliverable). Results in results/llm_{moe,directed}_hard_hpc/ (parquet gitignored).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Adds the "directed sex" operator (E10) the moe regime-flip pointed to: don't
commit to one a-priori blend — breed a population of recombinant offspring
(specialists merged at Dirichlet-sampled weights), score each on a held-out
validation split with the verifier, and keep the fittest, reported on a fresh
test split. Two breeding objectives: best-overall and best-worst-family.
src/llm/directed.py + kind llm_directed, reusing the cached specialists.
Result — refinements pay off in proportion to how far the uniform soup is from
optimal:
- 0.5B (soup dilutes): directed selection beats soup on the bred objective —
directed_overall 0.69 > soup 0.64; directed_balanced worst-family 0.37 > 0.26.
Riders: single-objective selection trades off the other axis (overall-breed
tanks lists to 0.17); a global blend still trails per-input routing (0.74).
- 7B (Imperial CX3, soup already composes to ceiling on near-saturated families,
strings/arith 1.00): directed ~= soup (0.868 ~ 0.873, marginally below via a
val/test overfit gap) — no fitter offspring to breed.
Through-line across all four LLM runs: "merge, don't average" and its refinements
(routing, directed selection) are weak-base / suboptimal-default phenomena — they
help at 0.5B and are inert at 7B. Honest limitation kept in the writeup: the 7B
families are near-saturated, which caps the headroom; a harder unsaturated
benchmark is the fair next test.
Also folds in the two llm_moe local manifest/config files missed in 8da0dac.
+3 directed unit tests (130 green). Results in results/llm_directed{,_hpc}/
(parquet gitignored).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Adds the union-preserving recombination operator that llm_merge lacked (E8's max,
not mean): keep each specialist LoRA intact and SELECT the right one per prompt
(MoE router: oracle, or training-free nearest-centroid over base embeddings) or
per module (max_merge = winner-take-all by delta norm). src/llm/moe.py, kind
llm_moe, reuses the cached specialists.
Result — a clean regime boundary for "merge, don't average":
- 0.5B: union wins. Routing 0.74 / worst-family 0.43 > soup 0.64 / 0.26, with no
dilution (recovers each specialist's own-family peak). E8's max > mean in real
weights, because at a weak base averaging dilutes.
- 7B (Imperial CX3, L40S, 9 min): the ordering INVERTS. Fusion wins — soup 0.87 >
routing 0.84 > max_merge 0.78. Routing is capped at the best parent per family;
fusion blends and, given a capable base, COMPOSES beyond any parent (soup lists
0.62 > spec 0.57). Selection can't synthesise better than its best component;
averaging-that-composes can.
So "merge, don't average" (E4/E8) is a weak-parent / small-model law, not
universal: union wins under dilution, fusion wins under composition. Refines E8
(its additive-landscape max>mean assumed no compositional headroom). The operator
to want is fusion-that-composes + offspring selection = the directed-sex ideal
(E10) — the natural next experiment.
Honest riders: the learned router is trivially perfect (lexically-distinct
families), and router-free max_merge is the weakest union (not input-adaptive).
+2 router unit tests (127 green). Results in results/llm_moe{,_hpc}/ (parquet
gitignored per the reproducibility contract).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Re-ran the specialist-merge experiment at a capable base (Qwen2.5-7B-Instruct,
200 tests/family) on one L40S GPU of Imperial's CX3 HPC (8 min walltime). The
two caveats the 0.5B prototype left marginal are now resolved:
- "exceeds every parent overall" is clean: both merges 0.87 vs best specialist
0.77 (+10 pts), and above every specialist on every family.
- dilution vanishes: at 0.5B averaging diluted the lists-specialist
(0.43->0.26); at 7B the merge beats it (0.62>0.57). Dilution was a
small-model artefact -- a capable base composes rather than dilutes, which
softens E4's "merge, don't average" once the parents are strong.
The figure title is now data-driven (reports ">" for 7B, "~" for 0.5B).
Adds the hpc/ smoke job script and the llm_merge walltime trim. Results synced
to results/llm_merge_hpc/ (parquet gitignored per the reproducibility contract).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
First step from toy models toward real language models, on one 16 GB GPU.
New src/llm/ package: procedural task families + exact-match verifier
(tasks.py), batched eval (evaluate.py), LoRA specialisation (specialise.py,
manual answer-only SFT), weight-space merge via peft add_weighted_adapter
(merge.py: soup = averaged deltas, ties = sign-reconciled union), runner
(experiment.py, kind llm_merge). Base Qwen2.5-0.5B-Instruct (Apache-2.0);
three disjoint hard families (lists/strings/arith); one LoRA specialist each
(~90s total).
Result (seed 1), reported honestly:
- STRONG/robust: the merges are the ONLY models competent across ALL
families -- worst-family ~0.25 vs <0.16 for every single specialist (the
Fisher-Muller "generalist assembled from specialists" signature, in real
LoRA weights).
- MARGINAL: "exceeds every parent overall" is only marginal at this scale
(soup 0.64 vs best specialist 0.63; ties 0.61 below it).
- CAVEAT VISIBLE: averaging dilutes peaks (lists specialist 0.43 -> merge
0.26) -- Layer-1's "merge, don't average" (E4) appearing in real weights.
The pipeline works end-to-end; the balance/retention half reproduces; the
strict overall-exceeds and soup-vs-ties distinction need scale (bigger base,
more/cleaner families, seeds, a dilution-resistant / offspring-selected
merge) -- the HPC step. Env: Python 3.14 + transformers 5.13 works;
note transformers-5.x apply_chat_template returns a dict. make env-llm /
make llm; adapters under gitignored models/llm/, base in the HF cache.
figures/plot_llm_merge.py, README, tests/test_llm.py (+3, 125 green).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The culmination. A finite population of agents (genotypes, L loci) evolves
on a rugged NK landscape that IS reality (knowledge/dynamic_society.py),
composing the four operators the whole study built toward: grounding,
directed recombination (sex), quality-diversity selection, and mutation.
Grounding is made load-bearing via the consensus-conformity (self-
consumption) mechanism (GG decision): selection acts on
g*true_fitness + (1-g)*conformity, where conformity = agreement with the
population's own consensus, so at g=0 the society optimises fitting-the-
crowd rather than reality.
4-arm ablation (12 reps), each breaking distinctly, only the full society
climbing (global_opt ~ 0.79):
- full 0.78 climbs to the optimum, diversity maintained longest
- no_sex 0.77 can't recombine to escape local optima
- no_diversity 0.74 greedy: collapses diversity fastest, worse local optimum
- no_grounding 0.48 self-consumption collapse to an unfit consensus
(trains on the crowd -> confident-but-wrong mean;
conformity-true gap ~ 0.5)
This integrates E1-E6 + the learning kernel + E7-E10 into one system and
shows the Lamarckian society needs ALL of grounding + directed sex +
diversity: on a rugged landscape you need diversity to explore basins, sex
to recombine them, and grounding to select on reality -- remove any one and
you fail differently. Closes the C3 vertical claim analytically; the LLM
rung remains the eventual empirical instantiation.
New: knowledge/dynamic_society.py, configs/layer1/E11.yaml, figures/
plot_E11.py, README, tests/test_dynamic_society.py (+5). kind:
dynamic_society dispatch; make layer1 wired. 122 tests green.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Deepen the sexual-reproduction frame before entering the full society, on
the two facets GG chose: landscape robustness and directed recombination.
Adds a Kauffman NK landscape (genotype.nk_fitness, tunable ruggedness),
finite n-parent crossover (genotype.crossover, per-gap recombination rate),
and hill-climb (parents = local optima = trained models).
E9 (recomb_landscape) -- the "why sex?" test: E8's dramatic super-parent
result used an ADDITIVE landscape. On rugged/epistatic landscapes, blindly
recombining local optima causes OUTBREEDING DEPRESSION -- offspring fall
below the parents, worse with both ruggedness and recombination rate (K=8,
free recomb: ~ -0.23), and the optimal recombination rate shrinks as
ruggedness grows. Design rule: merge freely when skills are complementary/
additive; sparingly (and with selection) when entangled.
E10 (directed_sex) -- directed sex beats biological sex: biology is stuck
with 2 random-mating parents and no offspring preview; an AI can choose
complementary mates, evaluate many recombinant offspring, keep the fittest,
and use unbounded parents (iterated recombine-then-select). Random
("biological") sex craters with ruggedness (0.66->0.51); directed sex
tracks/exceeds the best parent at every ruggedness -- converting the
outbreeding-depression catastrophe into a win. No biological analog.
Complete sexual-transmission picture: dramatic super-parent offspring when
skills are complementary (E8); outbreeding-depression risk when entangled
(E9); directed sex resolves the risk (E10). configs/layer1/{E9,E10}.yaml,
figures/plot_{E9,E10}.py, READMEs, +5 tests (117 green).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Enter the Lamarckian society with a robust theoretical frame. The single-
locus, fixed-p* model can only express recovery toward a ceiling; the
society's load-bearing claim is vertical -- capability that EXCEEDS any
component. Generalize knowledge to a distribution over genotypes (L
biallelic loci, K=2^L, additive fitness = # correct loci), reusing all the
K-mode machinery. The one new operator is recombination: free recombination
sends p -> product of per-locus marginals (linkage equilibrium).
E8 (star, kind: society) -- the vertical claim / Fisher-Muller: decorrelated
PARENTS (specialists, expert on their loci, agnostic elsewhere) are
recombined; sexual merge assembles a genotype fitter than any parent,
climbing to the optimum (12/12, a genotype no parent had) as parent count
grows and rho->0, while the best single parent (~8.7) and the mean-mixture
"model soup" (~11.6) plateau below. Reuses make_retention_matrix (locus
mastery replaces tail-item retention).
E7 (kind: genotype_lineage) -- the advantage of sex: a single population
adapts toward the optimum; the sexual lineage adapts faster than asexual
(clonal interference) by keeping loci in linkage equilibrium (LD->0 vs LD
spike). Honest scope: a speed advantage, not a permanent Muller's-ratchet
gap (subtle to force); E8 carries the headline.
Metaphor shift (per GG): the society is sexual reproduction with UNBOUNDED
parents, not teacher->pupil. Teacher->pupil caps at the ceiling; n-parent
recombination is combinatorial and generative, and unlike biology there is
no two-parent limit. Collapse = asexual degradation; the cure = sex. This
unifies E4 (merge != average) + E6 (irreversibility) under evolution-of-sex
theory and reaches ground Riis's single-locus n-grams cannot.
New: knowledge/{genotype,genotype_lineage,society}.py, configs/layer1/{E7,
E8}.yaml, figures/plot_{E7,E8}.py, READMEs, tests/test_genotype.py (+7).
experiment.py dispatch (kind in {genotype_lineage, society}); make layer1
wired. 112 tests green.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Revisiting Layer 1 against Layer 1.5 (and Riis 2026, arXiv:2604.08554):
neutral Wright-Fisher is a null that BOTH neural architectures deviate
from, in opposite directions. Add a learning kernel to the refit step,
p_{t+1} = T_theta(counts/n), with two population-genetics knobs -- reset u
(mutation toward a prior = smoothing) and temperature tau (sharpening =
mode-competition) -- both identity by default, so the histogram bridge and
all 68 scientific-validation/correctness tests are unchanged.
Result: neutral drift fails both neural models, oppositely.
- VAE regime (n=6000, K=30): neutral drift is inert (no collapse), yet the
real VAE collapsed to one mode. Sharpening tau=0.8 reproduces it -- the
estimator ADDS collapse pressure.
- RNN regime (n=200, K=256): neutral drives H->0, but the real RNN only
partially collapses. Mutation u=0.006 reproduces the H-floor -- the
estimator REMOVES collapse pressure. Honest caveat: uniform-mutation
overshoots the RNN's forward-KL, evidence its smoothing prior is
truth-like, not uniform (future refinement).
This mechanistically explains the architecture-generality result and the
softened neural g*, and develops the estimator axis Riis names as future
work. New: knowledge/kernel.py, configs/layer1/kernel_{sharpen,smooth}.yaml,
figures/plot_kernel.py (overlays analytic arms vs committed neural
endpoints), READMEs, tests/test_kernel.py (+6, 105 total green). Strategic
Riis positioning recorded in CLAUDE.md: concede "collapse=drift" as prior
art; lead with recombination, the kernel axis, and the Lamarckian society.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Confirms model collapse and its arrest by grounding on REAL images, not
just the synthetic sandbox. A conv VAE (the canonical generative-collapse
model) is retrained each generation on its own generated digits, with a
fraction g of fresh real MNIST mixed in. Modes = digit class x stroke-
thickness bin (K=30, Zipf, ~18 tail modes); the oracle is a frozen CNN +
deterministic thickness at 98.5% mode accuracy (30x30 confusion matrix
recorded in the manifest as the measurement-noise floor).
Result (4 reps): dry (g=0) collapses to a single mode -- forward-KL
0.5->18, support 30->1, tail 1.0->0.06, H->0 -- while 10% grounding holds
all 30 modes (KL~0.6, full tail, H~0.9). Signs, not magnitudes (blueprint
3.5); the exact synthetic oracle stays the quantitative anchor. The VAE
needs ~10% grounding vs the synthetic histogram's ~5%, consistent with the
grounding finding that trained nets need more than the exact operator.
Plugs into the existing data-agnostic contract (metrics/grounding/output
reused verbatim): mnist_data (thickness bins, class x thickness bijection,
MnistSampler), mnist_oracle (ClassifierOracle + confusion matrix),
mnist_vae (ConvVAEGenerator), mnist_loop (run_mnist_lineage), kind=
mnist_lineage dispatch, MnistCfg/OracleCfg. Figures: plot_mnist (parquet-
only) + mnist_montage (eyeball diagnostic showing digits degenerate to one
blurry mode). make mnist / make env-mnist, kept out of the make neural
loop. 99 tests green (+5 torchvision-gated).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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>
configs/neural/{N0,N1,N2,N5}.yaml -> {bridge,collapse,grounding,architectures}.yaml,
results dirs likewise. Updated experiment/output.dir fields, comments/docstrings, and
docs; regenerated the four result manifests (now carrying the real git commit). No
functional path resolution referenced the codes (the Makefile globs configs/neural/*.yaml
and tests use inline configs), so nothing breaks. 92 tests green.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Finishes the Layer 1 analytical core. All six experiments run with honest,
publication-quality figures; 71 tests green.
- E3 region-matched grounding: `grounding.exercised` knob + per-region tail
survival. Matched holds the exercised region's tail (0.49) where uniform
spreads thin and lets it collapse (0.07).
- E4 multi-teacher recombination: `run_coverage` runner. Union coverage matches
U(K_T,rho,q) exactly. Finding: mean-mixture distillation shows NO surviving
benefit (a conservation law — 1/K_T dilution cancels the union gain); a
union-preserving max-merge (M2N2-style) does. E4 reports both operators.
- E5 QD vs greedy: greedy drives fixation (H~0.01); QD holds H at 0.48-0.88,
rising with the novelty exponent.
- E6 re-mint gate: `arm` multi-override sweep. Re-minting a collapsed lineage
locks in divergence of KL-to-original; gating on diversity prevents it.
- E2 analysis add-ons (from the companion work order, numbers verified): new
analysis.py (reduce_to_stationary, critical_grounding with bootstrap CI ->
g*=0.048, 95% CI [0.047,0.050]); tail_band_metrics + per-band logging; the
E2 figure rebuilt as a 2x2 (defined g*+CI, g=0 flagged as a finite-time
artifact, tail item-vs-mass, per-rarity-band panel). Uses truth-mass-weighted
tail coverage rather than the raw (martingale) tail_mass.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Scaffold plus the Layer 1 analytical core and the first two experiments.
- knowledge/: truth, metrics, teachers (2.7.1 shared-switch construction),
step, lineage, experiment, config, seeding (imported as `knowledge`).
- Validation spine green: neutral decay (Pred 1), fixation (Pred 2), exact
mutation-drift equilibrium (Pred 3), union coverage (Pred 5). 68 tests pass.
- E1 reproduces tail-first collapse. E2 delivers the headline: a grounding
phase boundary g* << 1, with stationary H tracking the exact H_eq closed
form (g=0.005 -> 68% of truth diversity; g=0.05 -> 96%).
- Reproducibility: uv venv from a hash-pinned uv.lock is the source of truth;
every run writes results.parquet + resolved_config.yaml + manifest.json
(lib versions, git commit, sha256). Figures and manifests tracked; the
large regenerable parquet is gitignored.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
