3 commits

Author	SHA1	Message	Date
Giorgio Gilestro	c435cfba6e	Reproducibility pass: figure map, one-command reproduce.sh, notebooks, Makefile gaps ... An audit of the figure pipeline found real sync gaps, now closed: - `paper/pnas/make_figs.py` (which draws every manuscript figure) was invoked by NO Makefile target or script - a manual step. Added `make paper-figures`. - `configs/llm/epistasis{,_compat}.yaml` were reachable from nothing at all, despite producing Fig. 3C-D. Added `make llm-epistasis` (+ its statistics). - `make figures` never regenerated the MNIST montage that Fig. 2B embeds; it now runs with the `mnist` target (it needs torch - it re-simulates). - Added `make llm-society`, `env-notebooks`, `notebooks`. New REPRODUCING.md is the authoritative map: every manuscript panel -> the artifact it plots -> the config that produced it -> that config's seed, plus the determinism policy (biological tier bitwise; GPU tiers statistical), the seed-provenance statement, and an artifact-hash verification snippet. All 44 committed bundles currently hash-match their manifests, and figure regeneration is pixel-identical (verified by comparison). reproduce.sh delivers the one-command reproduction the paper's Methods promises, writing REPRODUCED.md with recomputed hashes per bundle. Two executed notebooks: 01 builds the Wright-Fisher model from scratch and checks both closed forms interactively (runs in ~1 min on a laptop); 02 verifies artifact hashes then regenerates and displays all seven manuscript figures. Both execute end-to-end (`make notebooks`). Also pins `.python-version` to 3.14: the interpreter was previously unpinned, and a `uv sync` silently switched it to 3.11 mid-session (see tasks/lessons.md). README rewritten - it still described a Layer-1-only repo of E1-E6 and pointed at a figure_manifest.md that does not exist. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v	2026-09-07 15:50:50 +01:00
Giorgio Gilestro	840b6b00b3	Layer 1.5: architecture-general neural existence proof ... Re-scopes Layer 2 into a cheaper, architecture-general neural collapse proof before the LLM rung. Realises the same Wright–Fisher abstractions in real trained generative models on a fully-synthetic sandbox with an exact oracle, reusing knowledge.metrics/truth/seeding and the output contract so neural curves overlay the Layer-1 analytic curves. - src/neural/: synthetic token-grammar sandbox (lossless identity + stochastic style), ExactOracle, HistogramModel bridge, generation loop, experiment runner - HARD GATE passed: histogram lineage reproduces Layer 1 exactly (neutral decay, exact H_eq, tracks run_lineage) — tests/test_neural_validation.py - torch models: autoregressive RNN + MLP (VAE implemented, not yet fidelity- passing); determinism seeding derived from the SeedSequence stream - N0 bridge (neural g*=0.047 ≈ Layer-1 0.048), N1 collapse-in-weights, N2 phase boundary, N5 architecture-generality (collapse + grounding-rescue in histogram + RNN + MLP). Manifests/configs committed; parquet gitignored, hashes tracked - additive backward-compatible save_artifacts extension; Makefile neural targets Finding: neural smoothing partially resists H-collapse, so forward-KL and tail survival are the sharp neural collapse metrics (H is smooth, per Layer 1). 92 tests green. Remaining (tasks/todo.md): N4 merge, N2 refine, N3/N6, VAE fidelity, MNIST tier, figures. LLM/LoRA rung and C3 deferred. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-04 21:02:49 +01:00
Giorgio Gilestro	a6eb9b7512	Layer 1 core: Wright-Fisher knowledge-transmission model with E1-E2 ... 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>	2026-07-04 18:10:18 +02:00