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

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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claim withdrawn).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
This commit is contained in:
Giorgio Gilestro 2026-09-06 17:55:46 +01:00
parent 1ae950cb7c
commit a40ace1821
17 changed files with 418 additions and 95 deletions
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6
src/llm/epistasis.py
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@ -1,4 +1,4 @@
"""The decisive experiment: does an operational EPISTASIS measure predict merge success PRE-merge?
"""A controlled predictive test: does a pre-merge FUNCTIONAL-CONFLICT measure predict merge damage?
The external review's bar (2026-08-11): population-genetic quantities must *predict*, not re-describe —
forecast merge success **before merging**, and beat existing predictors. This module builds a grid of
@ -11,7 +11,9 @@ The theory-derived predictor — and its built-in ablation. A raw functional-dis
two parents is, by our own theory, the WRONG measure: disjoint specialists disagree hugely (one knows,
one is ignorant) yet merge perfectly — harmless *complementation*. The Dobzhansky–Muller analogue is
**bilateral confident contradiction**: both parents confidently produce different answers to the same
input. So the operational epistasis measure is confidence-weighted disagreement,
input. So the framework-motivated measure is **confidence-weighted functional conflict** — a proposed proxy
for merge-relevant interactions (bilateral confident contradiction measures incompatible endpoint
behaviour, not non-additive interaction effects in the strict biological sense):
epi_conf = E_probe[ conf_A · conf_B · 1(ans_A != ans_B) ], conf = exp(mean token logprob),

9
src/llm/speciation.py
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@ -1,8 +1,11 @@
"""LLM-tier model speciation (E13 in language-model weights) — the conflict cliff + the duration null.
The real-LLM image of E13, with a structural bonus: LoRA deltas live in the frozen base's coordinate
system, so there is **no permutation/rescaling ambiguity by construction** — any merge failure here is
*functional* incompatibility, the residual isolated architecturally (no alignment step needed).
The real-LLM image of E13, with a structural advantage: LoRA deltas live in the frozen base's
coordinate system, which controls a major source of coordinate mismatch (no alignment step needed) and
so allows a cleaner test of conflict-associated merge failure. Note the honest boundary: a failure of
delta-averaging can still reflect nonlinear interaction, scaling, or capacity — shared coordinates
remove the permutation explanation, they do not make every failure evidence of incompatible functional
requirements.
Two knobs, mirroring the MLP experiment: