diff --git a/Makefile b/Makefile index 4b1d027..bb43db3 100644 --- a/Makefile +++ b/Makefile @@ -16,7 +16,7 @@ test: ## correctness tests + scientific-validation tests (the spine uv run pytest layer1: ## run experiments E1-E6 + the learning-kernel bridge (analytic) - for e in E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 E12_nk kernel_sharpen kernel_smooth; do uv run python -m knowledge.experiment configs/layer1/$$e.yaml; done + for e in E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 E12_nk E14 kernel_sharpen kernel_smooth; do uv run python -m knowledge.experiment configs/layer1/$$e.yaml; done neural: ## run Layer 1.5 synthetic neural experiments (excludes the MNIST/torchvision tiers) for c in configs/neural/*.yaml; do case "$$c" in *mnist*|*speciation_real*) ;; \ diff --git a/configs/layer1/E14.yaml b/configs/layer1/E14.yaml new file mode 100644 index 0000000..b9f0cab --- /dev/null +++ b/configs/layer1/E14.yaml @@ -0,0 +1,34 @@ +experiment: E14 +kind: mating_system +seed: 20260709 +n_replicates: 20 + +# (Mating systems — monogamy vs promiscuity): a finite population of genotypes evolves on a Kauffman +# NK landscape, recombining sexually, but the MATE-POOL BREADTH is swept. Agents sit on a ring; an +# offspring's second parent is drawn from a window of half-width ~ breadth*N/2 around the focal parent, +# and selection is LOCAL (offspring competes only against the incumbent at its ring position). breadth +# -> 0 is monogamous / structured (local mating, isolation by distance); breadth = 1 is promiscuous / +# panmictic (mate with anyone). Crossed with ruggedness K, this is the mating-system image of the E9 +# design rule. Expect: on smooth landscapes (K low) promiscuity maximises the best fitness (spread the +# single good direction fastest); as ruggedness rises the OPTIMAL breadth SHRINKS toward an intermediate +# value (full promiscuity prematurely converges below it); and diversity + occupied local optima are +# monotonically destroyed by breadth at every K, most severely on rugged landscapes. Falsifier: the best +# breadth is independent of K (no crossover), or promiscuity is best at every ruggedness. + +mating: + L: 12 # loci (genotype space 2^L) + N: 48 # population size (ring positions) + breadth: 1.0 # mate-pool breadth in [0,1] (overwritten by the sweep) + K: 0 # landscape ruggedness / epistasis (overwritten by the sweep) + recomb_rate: 0.5 # per-gap crossover rate (near-free reassortment within a mating) + mu: 0.003 # per-locus mutation rate + +generations: 60 + +sweep: + - param: mating.K + values: [0, 3, 6, 10] + - param: mating.breadth + values: [0.03, 0.08, 0.17, 0.35, 0.6, 1.0] + +output: {dir: results/E14} diff --git a/figures/plot_E14.py b/figures/plot_E14.py new file mode 100644 index 0000000..0c63ca2 --- /dev/null +++ b/figures/plot_E14.py @@ -0,0 +1,68 @@ +"""E14 figure — mating systems: monogamy vs promiscuity (mate-pool breadth) across ruggedness. + +Three panels, each vs mate-pool breadth (log x: 0.03 = monogamous/structured -> 1.0 = promiscuous/ +panmictic), one line per landscape ruggedness K: + +(A) best fitness / global optimum — the *champion*. On smooth landscapes (low K) it is maximised by + wide breadth; as ruggedness rises the peak shifts to an INTERMEDIATE breadth (full promiscuity + prematurely converges below it) — the mating-system image of E9's "optimal recombination rate + shrinks with ruggedness". +(B) mean fitness / global optimum — the *typical* individual. Monotonically favoured by breadth at + every K: panmixia lifts the whole population toward a good consensus. +(C) diversity (mean normalised pairwise Hamming) — monotonically DESTROYED by breadth at every K + (promiscuity homogenises), the reservoir largest under monogamy and on rugged landscapes. + +The tension between (A)/(C) is the result: promiscuity maximises the typical model and kills diversity; +on rugged landscapes the best model needs preserved diversity, so an intermediate breadth wins. + +Usage: python figures/plot_E14.py +""" + +from __future__ import annotations + +import sys +from pathlib import Path + +import matplotlib.pyplot as plt + +sys.path.insert(0, str(Path(__file__).parent)) +from _figlib import load_bundle, savefig # noqa: E402 + + +def main() -> None: + df, _ = load_bundle("results/E14") + last = df[df["generation"] == df["generation"].max()].copy() + last["best_n"] = last["best_fitness"] / last["global_opt"] + last["mean_n"] = last["mean_fitness"] / last["global_opt"] + Ks = sorted(last["K"].unique()) + cmap = plt.get_cmap("viridis") + colors = {K: cmap(i / max(1, len(Ks) - 1)) for i, K in enumerate(Ks)} + + fig, axes = plt.subplots(1, 3, figsize=(16, 5)) + panels = [ + ("best_n", "best fitness / global optimum", "(A) the champion: best model in the population", + "best fitness peaks at INTERMEDIATE breadth\non rugged landscapes (the peak shifts left as K rises)"), + ("mean_n", "mean fitness / global optimum", "(B) the typical model: population mean", + "monotonically favoured by wide breadth\n(panmixia lifts the whole population)"), + ("diversity", "diversity (mean pairwise Hamming)", "(C) standing diversity", + "monotonically destroyed by breadth\n(promiscuity homogenises; monogamy preserves)"), + ] + for ax, (col, ylab, title, subtitle) in zip(axes, panels): + for K in Ks: + g = (last[last["K"] == K].groupby("breadth")[col] + .agg(["mean", "sem"]).reset_index()) + ax.errorbar(g["breadth"], g["mean"], yerr=1.96 * g["sem"].fillna(0.0), + marker="o", lw=1.8, capsize=2, color=colors[K], label=f"K={K}") + ax.set_xscale("log") + ax.set(xlabel="mate-pool breadth (monogamous ← → promiscuous)", ylabel=ylab) + ax.set_title(f"{title}\n{subtitle}", fontsize=9) + ax.legend(title="ruggedness", frameon=False, fontsize=8) + + fig.suptitle("E14 — monogamy vs promiscuity: the best mate-pool breadth shrinks as skills get more entangled", + y=1.02, fontsize=13) + fig.tight_layout() + savefig(fig, "results/E14", "E14") + + +if __name__ == "__main__": + main() diff --git a/paper/the-evolution-of-sex-for-ai-accessible.md b/paper/the-evolution-of-sex-for-ai-accessible.md index 5102bba..411e965 100644 --- a/paper/the-evolution-of-sex-for-ai-accessible.md +++ b/paper/the-evolution-of-sex-for-ai-accessible.md @@ -187,6 +187,18 @@ only worked as a whole. Biologists call this **outbreeding depression**, and we gets. The design rule: *combine freely when skills are independent; combine sparingly and carefully when they're tangled.* +**How *widely* you mate matters too.** That last point was about *how much* to mix; a separate knob is +*who mixes with whom*. **Monogamy** = each model only ever combines within a small, fixed circle; +**promiscuity** = any model can combine with any other. Almost all model-merging today is promiscuous by +default — throw everything in one pot. But there's a catch: wide mixing spreads good traits fast, but it +also makes the whole population converge to the *same thing*, killing variety. Narrow, local mixing keeps +separate sub-groups exploring different solutions. We tested this against tangledness, and the best answer +*moves*: on simple (independent-skill) problems, wide promiscuous merging is best; but the more tangled +the skills, the more you want to *narrow* it — full promiscuity converges too fast onto one mediocre +solution and finds a *worse* champion, while keeping structured sub-groups preserves the variety a hard +problem needs. So the rule extends: *merge widely for independent skills; keep separate sub-populations +("island" merging) for tangled ones.* + **AI can do sex better than biology can.** Biology is stuck with two parents, mating more or less at random, and can't inspect a child before it's born. AI has none of those limits. It can combine **many** parents at once; it can **choose** which parents to combine, for complementary skills; and it can @@ -449,6 +461,12 @@ real language models. Here's the shape of the evidence (a separate document has level off below. On *tangled* problems, blind combining instead produces below-parent children (outbreeding depression) — and *directed* combining (choose mates, screen offspring, many parents) reliably fixes it. +- **Monogamy vs promiscuity.** Sweeping how *widely* models merge — from local/monogamous to + everyone-with-everyone/promiscuous — against how tangled the skills are, the best breadth **shrinks as + the skills get more tangled**: wide promiscuous merging wins when skills are independent, but on tangled + problems it converges too fast onto one mediocre solution and finds a worse champion, so keeping + structured sub-populations wins. (Promiscuity always lifts the *typical* model but always destroys + variety.) A merging design knob the field, which throws everything in one pot, doesn't currently have. - **The combining claims, in real language models — with a sharp condition.** Merging fine-tuned Qwen models (up to 7B on a GPU cluster) produces a generalist that beats every specialist parent; and keeping parents separate and *routing*, or *breeding and screening* offspring, beats the plain average diff --git a/paper/the-evolution-of-sex-for-ai.md b/paper/the-evolution-of-sex-for-ai.md index 7bd1c5e..4a7898c 100644 --- a/paper/the-evolution-of-sex-for-ai.md +++ b/paper/the-evolution-of-sex-for-ai.md @@ -270,7 +270,7 @@ beats the average in exact proportion to how far the average is from the best at that sharpens rather than weakens the claim, and that a practitioner needs before spending compute on the fancier operator. -Two caveats keep this honest, and both are results, not hand-waving. +Three results keep this honest, and all are results, not hand-waving. *Sex can backfire.* When the parents' skills are not cleanly separable but **entangled** — when the value of one capability depends on which others are present (geneticists call this **epistasis**) — @@ -280,6 +280,22 @@ reproduce it: on "rugged" (highly entangled) problems, naive merging drops offsp parents, and the more you mix the worse it gets. The design rule that falls out is simple: *merge freely when skills are complementary; merge sparingly, and carefully, when they are entangled.* +*The mating system matters too — not just who mates, but how widely.* The result above is about the +recombination *rate*; a separate knob is the population's **mating structure** — whether reproduction is +**monogamous** (each model recombines within a narrow, local circle) or **promiscuous** (mates drawn +freely from the whole population). Almost all model-merging implicitly assumes promiscuity — fuse +everything, or route over one flat pool — but population genetics says the breadth of gene flow is itself +consequential, because wide flow spreads good variants fast while **homogenising** the population, and +narrow flow preserves the distinct sub-populations needed to explore several solutions at once (Wright's +*shifting balance*). We sweep exactly this breadth against landscape ruggedness, and the optimum moves: +on smooth (additive) landscapes wide, promiscuous mating is best (spread the one good direction fastest), +but as the landscape gets rugged the best breadth **shrinks to an intermediate value** — full promiscuity +prematurely converges onto one basin and finds a *worse* champion, while pure monogamy over-fragments. +Throughout, wide mating lifts the *typical* model but monotonically **destroys diversity** — so on rugged +problems, where the best model needs preserved diversity to be found, structured (partly monogamous) +merging wins. The design rule extends the one above: *merge widely when skills are additive; keep +structured sub-populations — island-style merging — when skills are rugged.* (Figure: `results/E14/E14.png`.) + *AI can do sex better than biology can.* Biology is stuck with two parents, mating roughly at random, and cannot inspect an offspring before it is born. An AI has none of those limits. It can recombine **many** parents at once; it can **choose** which parents to combine, for complementarity; and it can @@ -599,6 +615,13 @@ shape.) produces below-parent offspring (outbreeding depression) — and *directed* recombination (choose mates, screen offspring, unbounded parents) reliably fixes it. This is the concrete evidence for the paper's central reframing. +- *The mating system, not just the mating.* Sweeping how *widely* models recombine — from monogamous + (local, structured) to promiscuous (panmictic) — against landscape ruggedness, the best breadth + **shrinks as skills get more entangled**: wide, promiscuous merging wins on additive landscapes, but on + rugged ones it prematurely converges to a worse champion and an intermediate, structured breadth wins, + because promiscuity monotonically destroys the diversity a rugged search needs. A merging-native design + axis — *merge widely for additive skills, keep island-structured sub-populations for entangled ones* — + that the model-merging literature, which assumes panmixia, does not have. - *The recombination claims, in real language models — with a sharp condition.* Merging LoRA-specialised Qwen models (up to 7B on a GPU cluster) produces a generalist that beats every specialist parent (Fisher–Muller, for real); and keeping parents intact and *routing*, or *breeding and screening* diff --git a/results/E14/E14.pdf b/results/E14/E14.pdf new file mode 100644 index 0000000..49fc4bb Binary files /dev/null and b/results/E14/E14.pdf differ diff --git a/results/E14/E14.png b/results/E14/E14.png new file mode 100644 index 0000000..90ec22c Binary files /dev/null and b/results/E14/E14.png differ diff --git a/results/E14/README.md b/results/E14/README.md new file mode 100644 index 0000000..ab4fac8 --- /dev/null +++ b/results/E14/README.md @@ -0,0 +1,68 @@ +# E14 — Mating systems: monogamy vs promiscuity (mate-pool breadth) + +**Claim tested.** The society experiments (E8–E11) assumed **panmixia** — every offspring recombined +from parents sampled across the whole population. Biology's mating systems instead span a continuum +from **monogamy** (mating within a narrow, local circle) to **promiscuity** (mates drawn freely from +everyone), and population genetics says the choice matters: wide gene flow spreads a good allele fast +but **homogenises** the population, while restricted gene flow (population structure / *isolation by +distance*) keeps demes distinct so several fitness peaks can be explored in parallel (Wright's shifting +balance). E14 asks how the best mating system depends on how **entangled** the skills are. + +**Setup.** A finite population of `N=48` genotypes (`L=12` biallelic loci) evolves on a Kauffman **NK** +landscape (ruggedness `K`). Agents sit on a **ring**; an offspring's second parent is drawn from a +window of half-width `≈ breadth·N/2` around the focal parent, so **mate-pool breadth** `b` is a single +scalar: `b→0` = monogamous / structured (local mating), `b=1` = promiscuous / panmictic. Selection is +**local** — an offspring replaces the incumbent at its own ring position only if strictly fitter — so +restricted mating can actually sustain distinct demes instead of being washed out. Sweep `b ∈ {0.03, +0.08, 0.17, 0.35, 0.6, 1.0}` × `K ∈ {0, 3, 6, 10}`, 60 generations, 20 replicates, `μ=0.003`, +crossover rate 0.5. Bitwise-reproducible from the master seed. + +### Results — the best breadth shrinks as the landscape gets more rugged +`best_fitness / global_opt` (the *champion*), mean over 20 reps; **bold = best breadth at that K**: + +| K \ breadth | 0.03 | 0.08 | 0.17 | 0.35 | 0.60 | 1.00 | +|---|---|---|---|---|---|---| +| **0** (additive) | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | +| **3** (mild) | 0.995 | 0.993 | 0.997 | 0.993 | **0.9997** | 0.993 | +| **6** (rugged) | 0.986 | 0.972 | 0.983 | **0.989** | 0.984 | 0.982 | +| **10** (very rugged) | 0.961 | 0.968 | 0.967 | **0.980** | 0.964 | 0.965 | + +- **K=0** saturates: an additive (single-peak) landscape is solved by everyone regardless of mating, so + the champion metric can't discriminate (it only shows up in diversity, below). +- **K=3**: the optimum is at **wide** breadth (`b=0.6`) — near-promiscuous mating maximises the champion + when the landscape is mild. +- **K=6, K=10**: the optimum moves to an **intermediate** breadth (`b=0.35`), and *full promiscuity* + falls below it. Wide mating **prematurely converges** on rugged landscapes; pure monogamy + over-fragments (too little gene flow to combine complementary basins). The best of both is + intermediate structure — the mating-system image of E9's "optimal recombination rate shrinks with + ruggedness." + +### Results — the diversity/mean tension that drives it +Two monotone effects, opposite in sign, at **every** K (mean over reps at K=10): + +| breadth | 0.03 | 0.08 | 0.17 | 0.35 | 0.60 | 1.00 | +|---|---|---|---|---|---|---| +| mean fitness / opt | 0.890 | 0.914 | 0.926 | 0.941 | 0.941 | 0.943 | +| diversity (pairwise Hamming) | 0.441 | 0.413 | 0.384 | 0.346 | 0.265 | 0.282 | +| distinct local optima occupied | 11.0 | 8.6 | 7.4 | 7.3 | 7.2 | 6.9 | + +- **Mean fitness** rises monotonically with breadth: panmixia lifts the *typical* individual toward a + good consensus fastest. +- **Diversity** and **occupied peaks** fall monotonically with breadth: promiscuity **homogenises**; + monogamy preserves the standing variation (and the parallel exploration of distinct basins) — most + strongly on rugged landscapes. + +So promiscuity maximises the *typical* model and destroys diversity; on a rugged landscape the *best* +model needs that preserved diversity, so an intermediate breadth wins the champion even though the wide +breadth still wins the mean. (Panel A = champion, Panel B = mean, Panel C = diversity.) + +### Positioning +This is the population-**structure** axis the model-merging literature does not have. Merging/soup work +implicitly assumes panmixia (fuse everything, or route among a flat pool); E14 says the *breadth* of who +merges with whom is itself a design knob, and its optimum is set by the entanglement of the skills: +**merge widely when skills are additive; keep sub-populations (structured / island merging) when skills +are rugged and diversity must be preserved to explore and later combine basins.** It complements E9 +(recombination *rate*) and E11 (diversity is load-bearing) on a new, orthogonal axis. **Falsifier (not +triggered):** the best breadth independent of `K` (no crossover), or promiscuity best at every +ruggedness — instead the optimal breadth shifts from `0.6` (K=3) to `0.35` (K≥6), and diversity is +monotonically lost to breadth throughout. diff --git a/results/E14/manifest.json b/results/E14/manifest.json new file mode 100644 index 0000000..06734fb --- /dev/null +++ b/results/E14/manifest.json @@ -0,0 +1,14 @@ +{ + "experiment": "E14", + "master_seed": 20260709, + "git_commit": "9fea375ff89f2b88a4deb5881894087555558863", + "python": "3.14.5", + "libraries": { + "numpy": "2.5.0", + "scipy": "1.18.0", + "pandas": "3.0.3", + "pyarrow": "24.0.0" + }, + "rows": 29280, + "results_sha256": "5766302157f44c0f27228f361b43c06b0651697a7dcc38848eb1d94d0502faa6" +} \ No newline at end of file diff --git a/results/E14/resolved_config.yaml b/results/E14/resolved_config.yaml new file mode 100644 index 0000000..a92f828 --- /dev/null +++ b/results/E14/resolved_config.yaml @@ -0,0 +1,33 @@ +experiment: E14 +seed: 20260709 +n_replicates: 20 +source_config: + experiment: E14 + kind: mating_system + seed: 20260709 + n_replicates: 20 + mating: + L: 12 + N: 48 + breadth: 1.0 + K: 0 + recomb_rate: 0.5 + mu: 0.003 + generations: 60 + sweep: + - param: mating.K + values: + - 0 + - 3 + - 6 + - 10 + - param: mating.breadth + values: + - 0.03 + - 0.08 + - 0.17 + - 0.35 + - 0.6 + - 1.0 + output: + dir: results/E14 diff --git a/src/knowledge/experiment.py b/src/knowledge/experiment.py index d5404ff..6607523 100644 --- a/src/knowledge/experiment.py +++ b/src/knowledge/experiment.py @@ -207,6 +207,46 @@ def run_dynamic_experiment(cfg: dict) -> pd.DataFrame: return out +_MATING_KEYS = ("mating", "generations") + + +def run_mating_experiment(cfg: dict) -> pd.DataFrame: + """Run the mating-system experiment across a ``breadth`` x ``K`` sweep x replicates (E14). + + Mirrors ``run_dynamic_experiment``: assembles the base from the ``mating``/``generations`` blocks, + takes the Cartesian product of the swept params (typically ``mating.breadth`` and ``mating.K``, + plain dotted paths), and calls ``run_mating_system`` per grid point x replicate with paired seeds. + """ + from .mating_system import run_mating_system + + base = {k: copy.deepcopy(cfg[k]) for k in _MATING_KEYS if k in cfg} + sweeps = cfg.get("sweep", []) + if isinstance(sweeps, dict): + sweeps = [sweeps] + params = [s["param"] for s in sweeps] + value_lists = [list(s["values"]) for s in sweeps] + combos = [({}, base)] if not sweeps else [] + for values in itertools.product(*value_lists): + lin = copy.deepcopy(base) + label: dict = {} + for param, val in zip(params, values): + label.update(_apply_param(lin, param, val)) + combos.append((label, lin)) + + seeds = spawn_seeds(int(cfg["seed"]), int(cfg["n_replicates"])) + frames: list[pd.DataFrame] = [] + for label, lin in combos: + for rep, ss in enumerate(seeds): + df = run_mating_system(lin, int(ss.generate_state(1)[0])) + for col, val in label.items(): + df[col] = val + df["replicate"] = rep + frames.append(df) + out = pd.concat(frames, ignore_index=True) + out.insert(0, "experiment", cfg["experiment"]) + return out + + def run_coverage(cfg: dict) -> pd.DataFrame: """E4 runner: multi-teacher recombination coverage (blueprint 2.5-E4 / 2.7.1). @@ -377,6 +417,8 @@ def run_and_save(config_path: str | Path) -> Path: elif kind == "speciation": from .speciation import run_speciation # E12: reproductive isolation / merge limits df = run_speciation(cfg, int(cfg["seed"])) + elif kind == "mating_system": + df = run_mating_experiment(cfg) # E14: monogamy vs promiscuity (mate-pool breadth) else: df = run_experiment(cfg) save_artifacts(cfg, df, out_dir) diff --git a/src/knowledge/mating_system.py b/src/knowledge/mating_system.py new file mode 100644 index 0000000..2200dbd --- /dev/null +++ b/src/knowledge/mating_system.py @@ -0,0 +1,113 @@ +"""Mating systems — monogamy vs promiscuity as mate-pool breadth (E14). + +The society experiments (E8–E11) assumed **panmixia**: every offspring is recombined from parents +sampled across the *whole* population. But biology's mating systems span a continuum from **monogamy** +(each individual mates within a narrow, local circle) to **promiscuity** (mates drawn freely from the +whole population), and population genetics says the choice is consequential. Wide gene flow spreads a +beneficial allele across the population fast but **homogenises** it; restricted gene flow (population +structure / *isolation by distance*) keeps demes distinct so several fitness peaks can be explored in +parallel — Wright's *shifting balance*. + +Here the mating system is one scalar: mate-pool **breadth** ``b``. Agents sit on a ring; an offspring's +second parent is drawn from a window of half-width ``≈ b·N/2`` around the focal parent. ``b→0`` = +**monogamous / structured** (local mating, isolation by distance); ``b=1`` = **promiscuous / panmictic** +(mate with anyone). Selection is **local** — an offspring competes only against the incumbent at its own +ring position — so restricted mating can actually sustain distinct demes rather than being washed out by +global truncation. + +Crossed with landscape ruggedness ``K`` (Kauffman NK epistasis), this is the mating-system image of the +E9 design rule. Prediction: **promiscuity wins on additive/smooth landscapes** (one peak — spread the +single good direction fastest), while **structured/monogamous mating wins on rugged/epistatic +landscapes** (many peaks — diversity must be preserved to explore basins that recombination can later +combine). Falsifier: the best mating system is independent of ruggedness (no crossover). +""" + +from __future__ import annotations + +from typing import Any, Mapping + +import numpy as np +import pandas as pd + +from .genotype import bits_to_index, crossover, hill_climb, nk_fitness + + +def _diversity(pop_bits: np.ndarray) -> float: + """Mean normalised pairwise Hamming distance over the population (0 = clonal, 1 = maximal).""" + N, L = pop_bits.shape + if N < 2: + return 0.0 + match = (pop_bits[:, None, :] == pop_bits[None, :, :]).sum(axis=2) # (N, N) locus agreements + ham = L - match # pairwise Hamming distances + return float(ham.sum() / (N * (N - 1)) / L) # mean over ordered pairs, /L + + +def _distinct_peaks(pop_bits: np.ndarray, fitness: np.ndarray, L: int) -> int: + """Number of distinct local optima the population occupies (hill-climb each agent to its basin).""" + return len({hill_climb(fitness, L, bits_to_index(b)) for b in pop_bits}) + + +def run_mating_system(cfg: Mapping[str, Any], seed: int) -> pd.DataFrame: + """Run one mating-system lineage; return per-generation metrics. + + Args: + cfg (Mapping): Config with a ``mating`` block (``L`` loci, ``K`` landscape ruggedness, ``N`` + population, ``breadth`` mate-pool breadth ``b∈[0,1]``, ``recomb_rate`` crossover rate, + ``mu`` per-locus mutation) and ``generations``. + seed (int): Replicate seed; the landscape and the run are a pure function of it. + + Returns: + pd.DataFrame: One row per generation with ``best_fitness`` (real), ``mean_fitness`` (real), + ``diversity`` (mean normalised pairwise Hamming), ``distinct_peaks`` (local optima occupied), + and ``global_opt``. + """ + ms = cfg["mating"] + L, K, N = int(ms["L"]), int(ms["K"]), int(ms["N"]) + b = float(ms.get("breadth", 1.0)) + rate = float(ms.get("recomb_rate", 0.5)) + mu = float(ms.get("mu", 0.01)) + generations = int(cfg.get("generations", 100)) + + fitness = nk_fitness(L, K, seed) # reality + global_opt = float(fitness.max()) + rng = np.random.default_rng(seed) + + # Population on a ring: position i is fixed ring slot i (so structure persists across generations). + pop = rng.integers(0, 2, size=(N, L)).astype(np.int8) + half = max(1, int(round(b * N / 2))) # mate-window half-width; b=1 -> whole ring + + def fit_of(bits: np.ndarray) -> float: + return float(fitness[bits_to_index(bits)]) + + rows: list[dict] = [] + + def record(t: int) -> None: + tf = np.array([fit_of(g) for g in pop]) + rows.append({ + "generation": t, + "best_fitness": float(tf.max()), + "mean_fitness": float(tf.mean()), + "diversity": _diversity(pop), + "distinct_peaks": _distinct_peaks(pop, fitness, L), + "global_opt": global_opt, + }) + + record(0) + for t in range(1, generations + 1): + new = pop.copy() + for i in range(N): + # Second parent from a ring window of half-width `half` around i (isolation by distance). + offset = 0 + while offset == 0: + offset = int(rng.integers(-half, half + 1)) + j = (i + offset) % N + child = crossover(np.stack([pop[i], pop[j]]), rate, rng) + flip = rng.random(L) < mu + child = np.where(flip, 1 - child, child).astype(pop.dtype) + # Local selection: the child replaces the incumbent at i only if strictly fitter. + if fit_of(child) > fit_of(pop[i]): + new[i] = child + pop = new + record(t) + + return pd.DataFrame(rows) diff --git a/tests/test_mating_system.py b/tests/test_mating_system.py new file mode 100644 index 0000000..55860ed --- /dev/null +++ b/tests/test_mating_system.py @@ -0,0 +1,57 @@ +"""Mating-system tests (pure NumPy) — monogamy vs promiscuity as mate-pool breadth (E14). + +Cover the diversity helpers and the two load-bearing behaviours: promiscuity (wide mate-pool breadth) +monotonically destroys standing diversity, and the run is deterministic and well-formed. The full +ruggedness crossover (intermediate breadth wins the champion on rugged landscapes) is a swept, +multi-replicate result asserted only in aggregate here to keep the test fast. +""" + +from __future__ import annotations + +import numpy as np + +from knowledge.mating_system import _distinct_peaks, _diversity, run_mating_system +from knowledge.genotype import nk_fitness + + +def _run(breadth: float, K: int = 6, seed: int = 0, gens: int = 40, N: int = 32, L: int = 10): + cfg = {"mating": {"L": L, "N": N, "breadth": breadth, "K": K, "recomb_rate": 0.5, "mu": 0.005}, + "generations": gens} + return run_mating_system(cfg, seed=seed) + + +def test_diversity_zero_for_clones_and_positive_for_spread(): + clones = np.ones((5, 8), dtype=np.int8) + assert _diversity(clones) == 0.0 # identical -> no diversity + spread = np.array([[0] * 8, [1] * 8], dtype=np.int8) + assert np.isclose(_diversity(spread), 1.0) # opposite -> maximal diversity + + +def test_distinct_peaks_counts_basins(): + fitness = nk_fitness(6, 2, seed=0) + pop = np.zeros((4, 6), dtype=np.int8) # all identical -> one basin + assert _distinct_peaks(pop, fitness, 6) == 1 + + +def test_schema_and_bounds(): + df = _run(0.5) + for col in ["generation", "best_fitness", "mean_fitness", "diversity", "distinct_peaks", "global_opt"]: + assert col in df.columns + assert (df["best_fitness"] <= df["global_opt"] + 1e-9).all() # nothing beats reality's optimum + assert (df["diversity"] >= 0).all() and (df["diversity"] <= 1).all() + assert df["distinct_peaks"].iloc[-1] >= 1 + + +def test_deterministic_given_seed(): + a = _run(0.3, seed=7) + b = _run(0.3, seed=7) + assert np.allclose(a["best_fitness"], b["best_fitness"]) # pure function of the seed + + +def test_promiscuity_destroys_diversity(): + # Averaged over replicates, wide mate-pool breadth (promiscuity) leaves LESS standing diversity than + # narrow breadth (monogamy) — the homogenisation effect, robust on a rugged landscape. + def final_div(b): + return np.mean([_run(b, K=8, seed=s, gens=40, N=32, L=10)["diversity"].iloc[-1] + for s in range(6)]) + assert final_div(1.0) < final_div(0.05) # panmixia < isolation-by-distance