MachineSex/README.md

The evolution of sex for artificial intelligence

A population-genetic framework for multigenerational model populations. Knowledge transmission between generations of learning agents is modelled literally as a Wright–Fisher process, not by analogy: a model's knowledge is a distribution p_t over K discrete items, a fixed true distribution p* has a rare tail, and each generational step is "sample from the parent (drift) + mix in fresh real samples (grounding/immigration) + refit". Model collapse is the loss of rare alleles under drift — and the remedies population genetics knows for drift (immigration, recombination, selection, population structure) become engineering levers for model populations.

The framework is developed at three tiers of increasing realism:

Tier	What it is	Hardware
Biological model	Wright–Fisher simulator over knowledge distributions; closed forms, bitwise reproducible	laptop
Trained networks	RNN / MLP / VAE on a synthetic mode universe with an exact oracle; convolutional VAE on MNIST	one GPU
Language models	LoRA specialists on Qwen2.5-Instruct (0.5B / 7B) with an exact-match verifier	one GPU / L40S

Reproduce

Start here: REPRODUCING.md — the authoritative map from every manuscript figure panel back to the artifact, config, and seed that produced it, plus the determinism policy and artifact-hash verification.

curl -LsSf https://astral.sh/uv/install.sh | sh   # one-time, if needed

./reproduce.sh          # env -> tests -> biological-model tier at committed seeds -> figures
./reproduce.sh --with-gpu   # ... and the trained-network + language-model tiers

Or tier by tier:

make env             # build .venv from the committed, hash-pinned uv.lock
make test            # correctness + closed-form scientific validation (the spine of trust)
make layer1          # the biological model: E1-E12, E14, learning kernel
make figures         # per-experiment figures, from committed parquets (no re-simulation)
make paper-figures   # the manuscript's Fig. 1-7 + rebuild the PDF body

make help is not defined, but every target carries a ## description — grep '##' Makefile.

Notebooks

make env-notebooks && jupyter lab notebooks/

• 01_biological_model.ipynb — builds the Wright–Fisher model from scratch, checks it against the closed forms (geometric diversity decay, the immigration–drift equilibrium), and derives the grounding threshold and its per-item observation floor. Runs on a laptop in under a minute.
• 02_paper_figures.ipynb — verifies artifact hashes, then regenerates and displays every manuscript figure from the committed artifacts.

Layout

src/knowledge/   biological-model tier (imported as `knowledge`)
src/neural/      trained-network tier
src/llm/         language-model tier
configs/         one YAML per experiment: layer1/ neural/ llm/ (each declares its master seed)
figures/         plot_*.py — per-experiment diagnostics, read results.parquet only
paper/pnas/      the manuscript: main.md, make_figs.py (Fig. 1-7), build.py, si.md
notebooks/       executable walkthroughs
hpc/             PBS job scripts for the 7B tier (Imperial CX3)
tests/           correctness + test_scientific_validation.py (the closed forms as assertions)
results/         run artifacts: results.parquet (gitignored) + resolved_config.yaml + manifest.json

Design documents: paper/blueprint.md (the normative build spec) and paper/results-summary.md (plain-language + technical summary of every result).

The engineering contract

• Reproducibility is a requirement, not a preference. The environment is a uv venv built from a committed, hash-pinned uv.lock; the biological-model tier is bitwise reproducible from a single master seed, and the GPU tiers are statistically reproducible with per-seed points reported.
• One master seed per config, with all sub-randomness derived via SeedSequence.spawn. No code touches global RNG state; a run is a pure function of its resolved config.
• No magic numbers in code. Every parameter lives in a YAML resolved at run time, and the resolved config is written next to the results.
• Every run writes the same triple: results.parquet + resolved_config.yaml + manifest.json (seed, git commit, library versions, row count, SHA-256 of the results).
• Every figure is a pure function of a committed artifact — figure scripts never re-simulate.
• The scientific-validation tests are the spine of trust. They assert that the simulator reproduces the closed forms to within 0.5%. If they fail, the science is wrong, not just the code.