MachineSex

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Author	SHA1	Message	Date
Giorgio Gilestro	6f8cef1ac5	main: keep only what reproduces the manuscript; everything else lives on dev Removed from main (all preserved on the dev branch): the arXiv build and its sources, design documents (blueprint, results summary, review responses, essay drafts), tasks/ and CLAUDE.md, the cover letter and reference tooling, two unused manuscript figures, and every experiment that feeds no figure or number in the paper: the collapse null, the sexual-vs-asexual lineage, the NK speciation variant, the 0.5B single-seed LLM prototypes, the compose and society experiments with their calibration and pilot runs, and their configs, runners, tests, figure scripts and PBS jobs. Their result bundles are moved to results/_archive/ (ignored) so the parquets stay on disk. Also: plot_llm_speciation reads the s{seed}/ layout; the mating-breadth plot writes under its bundle name; Makefile targets reduced to the kept experiments; REPRODUCING.md and README point to dev for the rest. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm	2026-09-13 17:07:23 +01:00
Giorgio Gilestro	a40ace1821	second review round: tempered claims, robust statistics, corrected technical statements Analyses (figures/stats_llm_epistasis.py, committed + reproducible): condition-clustered bootstrap CIs (functional measures exclude zero: dis_raw [+0.04,+0.69], conf-weighted [+0.02,+0.68]; gradient alignment [-0.59,-0.06]; geometry straddles zero), PAIRED predictor contrasts (not individually significant — stated), leave-one-condition-out held-out prediction (functional replicates, geometry ~0, performance baseline unstable), three outcome references (ordering sensitive to reference — reported, with the mechanism), between/within-axis decomposition (within-conflict identification impossible by design; the compat axis identifies), and seed-level paired reliability (routing/directed beat soup 3/3 seeds incl. one catastrophic soup failure; CI-width fragility claim withdrawn). Renames and corrections: "decisive experiment" -> "controlled predictive test"; "operational epistasis" -> "confidence-weighted functional conflict (proposed proxy)"; "functional by construction" -> "controls a major source of coordinate mismatch / conflict-associated" (module, configs, READMEs, figures); SI proposition's "chord" defined precisely (endpoint-loss interpolation, invariant) vs the path (not invariant) + no-global-optimality caveat (removable = lower bound, residual = upper); snowball count != performance cliff distinction added; claims table gains four rows (grid finding / weighting NOT supported / functional-vs- all-geometry not established / operator choice open); §1 ladder states the prediction rung as a bounded small-model result. paper/response-to-review-2.md: point-by-point, opening with the bookkeeping correction (E13b/c were in the reviewed draft — revised interpretation, not new results). READMEs rewritten around the four analyses with the chronology (prospective/adaptive/post-hoc) disclosed. 151 tests green. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v	2026-09-06 17:55:46 +01:00
Giorgio Gilestro	287d2326cc	epistasis_predicts: functional conflict, not weight geometry, predicts merge failure pre-merge The decisive experiment from the external review. 39 LoRA parent pairs (0.5B, 3 seeds) on three axes decorrelated by construction: conflict (contradictory conventions on shared prompts, private budgets fixed), compat (same prompts, SAME convention — overlap without conflict), and duration (weight divergence, zero conflict). Six pre-merge predictors; primary outcome = merge penalty (parent potential − merged achieved). League table (Spearman vs penalty, n=39): functional measures predict (dis_raw +0.460, epi_conf +0.446, p<0.005); geometry collapses (delta_cos +0.03, delta_l2 +0.17 n.s.); gradient alignment weak (−0.35); performance ~0. The first grid's apparent geometry win (+0.60) was an overlap/volume artifact — the compat control axis (added for exactly this) exposed and killed it: same overlap and data volume, zero penalty. Honest riders in the README: confidence weighting does not beat raw disagreement as a rank predictor (pre-registered internal prediction not confirmed; it does double the conflict/compat level contrast), and \|rho\|~0.45 is bounded by 0.5B merge-outcome noise (7B is the firm-up). Also: micro-batched gradient accumulation (OOM fix on the shared 16GB GPU), exact r-space LoRA-delta geometry (brute-force-verified test, 151 green), systemd-run runbook lesson (tmux dies with the SSH session scope on this box). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v	2026-09-06 17:19:46 +01:00

Author

SHA1

Message

Date

Giorgio Gilestro

6f8cef1ac5

main: keep only what reproduces the manuscript; everything else lives on dev

Removed from main (all preserved on the dev branch): the arXiv build and
its sources, design documents (blueprint, results summary, review responses,
essay drafts), tasks/ and CLAUDE.md, the cover letter and reference tooling,
two unused manuscript figures, and every experiment that feeds no figure or
number in the paper: the collapse null, the sexual-vs-asexual lineage, the
NK speciation variant, the 0.5B single-seed LLM prototypes, the compose and
society experiments with their calibration and pilot runs, and their
configs, runners, tests, figure scripts and PBS jobs. Their result bundles
are moved to results/_archive/ (ignored) so the parquets stay on disk.

Also: plot_llm_speciation reads the s{seed}/ layout; the mating-breadth
plot writes under its bundle name; Makefile targets reduced to the kept
experiments; REPRODUCING.md and README point to dev for the rest.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm

2026-09-13 17:07:23 +01:00

Giorgio Gilestro

a40ace1821

second review round: tempered claims, robust statistics, corrected technical statements

Analyses (figures/stats_llm_epistasis.py, committed + reproducible):
condition-clustered bootstrap CIs (functional measures exclude zero:
dis_raw [+0.04,+0.69], conf-weighted [+0.02,+0.68]; gradient alignment
[-0.59,-0.06]; geometry straddles zero), PAIRED predictor contrasts (not
individually significant — stated), leave-one-condition-out held-out
prediction (functional replicates, geometry ~0, performance baseline
unstable), three outcome references (ordering sensitive to reference —
reported, with the mechanism), between/within-axis decomposition
(within-conflict identification impossible by design; the compat axis
identifies), and seed-level paired reliability (routing/directed beat
soup 3/3 seeds incl. one catastrophic soup failure; CI-width fragility
claim withdrawn).

Renames and corrections: "decisive experiment" -> "controlled predictive
test"; "operational epistasis" -> "confidence-weighted functional
conflict (proposed proxy)"; "functional by construction" -> "controls a
major source of coordinate mismatch / conflict-associated" (module,
configs, READMEs, figures); SI proposition's "chord" defined precisely
(endpoint-loss interpolation, invariant) vs the path (not invariant) +
no-global-optimality caveat (removable = lower bound, residual = upper);
snowball count != performance cliff distinction added; claims table
gains four rows (grid finding / weighting NOT supported / functional-vs-
all-geometry not established / operator choice open); §1 ladder states
the prediction rung as a bounded small-model result.

paper/response-to-review-2.md: point-by-point, opening with the
bookkeeping correction (E13b/c were in the reviewed draft — revised
interpretation, not new results). READMEs rewritten around the four
analyses with the chronology (prospective/adaptive/post-hoc) disclosed.
151 tests green.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v

2026-09-06 17:55:46 +01:00

Giorgio Gilestro

287d2326cc

epistasis_predicts: functional conflict, not weight geometry, predicts merge failure pre-merge

The decisive experiment from the external review. 39 LoRA parent pairs
(0.5B, 3 seeds) on three axes decorrelated by construction: conflict
(contradictory conventions on shared prompts, private budgets fixed),
compat (same prompts, SAME convention — overlap without conflict), and
duration (weight divergence, zero conflict). Six pre-merge predictors;
primary outcome = merge penalty (parent potential − merged achieved).

League table (Spearman vs penalty, n=39): functional measures predict
(dis_raw +0.460, epi_conf +0.446, p<0.005); geometry collapses
(delta_cos +0.03, delta_l2 +0.17 n.s.); gradient alignment weak (−0.35);
performance ~0. The first grid's apparent geometry win (+0.60) was an
overlap/volume artifact — the compat control axis (added for exactly
this) exposed and killed it: same overlap and data volume, zero penalty.
Honest riders in the README: confidence weighting does not beat raw
disagreement as a rank predictor (pre-registered internal prediction not
confirmed; it does double the conflict/compat level contrast), and
|rho|~0.45 is bounded by 0.5B merge-outcome noise (7B is the firm-up).

Also: micro-batched gradient accumulation (OOM fix on the shared 16GB
GPU), exact r-space LoRA-delta geometry (brute-force-verified test,
151 green), systemd-run runbook lesson (tmux dies with the SSH session
scope on this box).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v

2026-09-06 17:19:46 +01:00

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