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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claim withdrawn).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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4
configs/llm/speciation.yaml
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@ -4,8 +4,8 @@ seed: 1
n_replicates: 1
# LLM-tier model speciation (E13 in language-model weights; PNAS work order Phase 3). Two LoRA
# children from the same frozen base — so there is NO permutation/rescaling ambiguity by construction:
# any merge failure is functional incompatibility, isolated architecturally. Two sweeps:
# children from the same frozen base — which controls a major source of coordinate mismatch (no
# alignment step needed), allowing a cleaner test of conflict-associated merge failure. Two sweeps:
# conflict_fracs — the IMPOSED cliff: each child has a private disjoint family (A: strings,
# B: arith) plus a shared set of AMBIGUOUS sort prompts ("Sort the list [...]", no direction)
# answered ascending by A and descending by B (each convention harmless alone, contradictory