Giorgio Gilestro
ab3dc10587
- paper/pnas -> paper/manuscript (venue-neutral)
- configs/layer1 -> configs/inheritance, src/knowledge -> src/inheritance
(imported as `inheritance`), make layer1 -> make inheritance; layer2 alias dropped
- inheritance and trained-network bundles named after the manuscript figure
they feed (fig2_grounding_sweep, figS3_rebaselining, ...), or descriptively
where they feed none; configs keep their `experiment:` value so parquet
hashes are unchanged, only output.dir moves
- figure scripts, SI figure sources, notebooks, REPRODUCING.md, README and the
SI Methods/tables updated; make clean no longer deletes tracked manifests;
reproduce.sh hashes the s{seed}/ layouts too
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
27 lines
1.3 KiB
YAML
27 lines
1.3 KiB
YAML
experiment: E9
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kind: recomb_landscape
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seed: 20260705
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n_replicates: 24
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# (Landscape robustness / the "why sex?" question — the credibility centerpiece): E8 showed sex wins
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# on an ADDITIVE landscape, where recombination trivially helps. Does it survive EPISTASIS? Parents
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# are local optima ("trained models") of a Kauffman NK landscape whose ruggedness K (epistatic
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# interactions per locus) is swept with the recombination rate. Expect: on smooth/mildly-rugged
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# landscapes recombination helps; on rugged ones FREE recombination (rate~0.5) breaks co-adapted
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# blocks and offspring fall BELOW the parents (outbreeding depression); and the OPTIMAL recombination
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# rate shrinks as ruggedness grows. Design rule: merge freely when skills are complementary/additive;
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# merge sparingly when entangled. Falsifier: recombination rate has no effect, or free recombination
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# never underperforms the parents on rugged landscapes.
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society:
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L: 12
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n_parents: 6 # trained specialists = local optima of the landscape
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pop: 200 # recombinant offspring sampled per (K, rate, replicate)
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sweep:
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- param: K
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values: [0, 2, 4, 6, 8] # landscape ruggedness (epistasis): 0 = additive, high = rugged
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- param: rate
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values: [0.0, 0.05, 0.1, 0.2, 0.35, 0.5] # clonal -> free recombination
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output: {dir: results/figS10_rugged_landscapes}
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