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Manuscript revision and pending experiment work, snapshot before restructuring

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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
This commit is contained in:
Giorgio Gilestro 2026-09-13 16:54:09 +01:00
parent e4804adabc
commit 84124de143
450 changed files with 52813 additions and 1202 deletions
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24
Makefile
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@ -2,7 +2,8 @@
# reproducibility source of truth; every target runs inside it via `uv run`.
.PHONY: env env-neural env-mnist env-llm env-notebooks test layer1 layer2 neural mnist llm \
llm-epistasis llm-society figures paper-figures paper notebooks clean
llm-epistasis llm-society llm-society-calib llm-society-calib-b llm-society-v2-smoke \
figures paper-figures paper notebooks clean
env: ## build .venv from the committed lockfile
uv sync --extra dev
@ -50,6 +51,26 @@ llm-epistasis: ## the controlled predictive test (feeds paper Fig. 3C-D) + i
llm-society: ## the composed society at LLM scale (C3): pilot; the campaign runs on HPC
uv run python -m llm.experiment configs/llm/society.yaml
llm-society-calib: ## v2 society calibration gates (prereg §4): stage A (families), then B (C2/C3/C5)
uv run python -m llm.experiment configs/llm/society_v2_calib_a.yaml
@echo "Review the C1 table, fix the 12 families in society_v2_calib_b.yaml, then: make llm-society-calib-b"
llm-society-calib-b: ## v2 calibration stage B over the chosen 12 families: transmission, cross, consensus
uv run python -m llm.experiment configs/llm/society_v2_calib_b.yaml
mkdir -p configs/llm/_gen
uv run python - <<'EOF'
import yaml; c = yaml.safe_load(open("configs/llm/society_v2_calib_b.yaml"))
for st in ("cross", "consensus"):
c["stage"] = st; c["output"] = {"dir": f"results/llm_society_v2_calib_b_{st}"}
yaml.safe_dump(c, open(f"configs/llm/_gen/calib_{st}.yaml", "w"), sort_keys=False)
EOF
uv run python -m llm.experiment configs/llm/_gen/calib_cross.yaml
uv run python -m llm.experiment configs/llm/_gen/calib_consensus.yaml
llm-society-v2-smoke: ## v2 society loop smoke (4 families, 4 agents, 2 generations, all arms)
uv run python -m llm.experiment configs/llm/society_v2_smoke.yaml
uv run python figures/plot_llm_society.py results/llm_society_v2_smoke
llm-seeds: ## multi-seed firm-up (heavy): merge x5, moe-hard x3, directed-hard x3
uv run python -m llm.experiment configs/llm/merge_seeds.yaml
uv run python -m llm.experiment configs/llm/moe_hard_seeds.yaml
@ -69,6 +90,7 @@ paper-figures: ## regenerate the manuscript figures (Fig. 1-7) and rebuild t
paper: paper-figures ## figures + compile both PDFs (needs tectonic)
cd paper/pnas && tectonic main.tex && tectonic si.tex
uv run python paper/pnas/build_lay_legends.py && cd paper/pnas && tectonic figure_legends_for_students.tex
env-notebooks: ## add Jupyter for the walkthrough notebooks
uv sync --extra dev --extra notebooks