Giorgio Gilestro
871bc39ec6
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>
37 lines
1.8 KiB
Makefile
37 lines
1.8 KiB
Makefile
# Layer 1 + Layer 1.5 automation. The uv venv (built from the committed uv.lock) is the
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# reproducibility source of truth; every target runs inside it via `uv run`.
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.PHONY: env env-neural env-mnist test layer1 layer2 neural mnist figures clean
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env: ## build .venv from the committed lockfile
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uv sync --extra dev
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env-neural: ## add the Layer 1.5 torch stack (GPU; Stage C onward)
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uv sync --extra dev --extra neural
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env-mnist: ## add torchvision for the real-MNIST confirmation tier
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uv sync --extra dev --extra neural --extra mnist
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test: ## correctness tests + scientific-validation tests (the spine of trust)
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uv run pytest
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layer1: ## run experiments E1-E6 + the learning-kernel bridge (analytic)
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for e in E1 E2 E3 E4 E5 E6 kernel_sharpen kernel_smooth; do uv run python -m knowledge.experiment configs/layer1/$$e.yaml; done
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neural: ## run Layer 1.5 synthetic neural experiments (excludes the heavy MNIST tier)
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for c in configs/neural/*.yaml; do case "$$c" in *mnist*) ;; \
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*) uv run python -m neural.experiment "$$c" ;; esac; done
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mnist: ## run the real-MNIST confirmation tier (needs env-mnist; downloads MNIST)
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uv run python -m neural.experiment configs/neural/mnist_collapse.yaml
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layer2: neural ## alias: Layer 1.5 is the current Layer-2 deliverable (LLM rung deferred)
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figures: ## regenerate figures from committed results
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for e in E1 E2 E3 E4 E5 E6; do MPLBACKEND=Agg uv run python figures/plot_$$e.py; done
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for p in figures/plot_*.py; do case "$$p" in */plot_E[1-6].py|*/_*) ;; \
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*) [ -e "$$p" ] && MPLBACKEND=Agg uv run python "$$p" ;; esac; done
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clean: ## remove caches and generated results (keeps committed manifests)
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rm -rf .pytest_cache **/__pycache__
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find results -type f ! -name '.gitkeep' -delete 2>/dev/null || true
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