docs(dead-ends): foreclose two DE-44 kill-tests — adaptive PI (DE-55) + invivo-F-prior (DE-56)

data/validation/pi_fprior_killtests_2026-07-07.json

@@ -0,0 +1,34 @@
+{
+  "date": "2026-07-07",
+  "context": "Two pre-registered cheap kill-tests for the DE-44 'survivors' (calibrated-UQ PI-recalibration; invivo-F-prior). Both foreclosed. Local macOS public-clone stack; deltas are stack-internal (baseline reproduces the ~2.74 band).",
+  "pi_adaptive_conformal_killtest": {
+    "question": "Does any per-drug difficulty signal predict |log10 meta fold-error|, so a normalized/adaptive conformal PI could be tighter than the flat /÷12.9 while holding coverage under Invariant #5 (calibrate on train, not holdout)?",
+    "current_pi": {"method": "split_conformal", "q90_meta_log10": 1.111, "fold": 12.9, "holdout_coverage_at_nominal_0.90": 0.9533, "calibration": "train n=67"},
+    "spearman_rho_error_vs_signal": {
+      "div_eng_ml": -0.035, "div_eng_meta": -0.002, "div_ml_meta": -0.057,
+      "n_ad_flags": -0.051, "abs_log_meta": -0.069, "meta_cmax": 0.056, "not_in_ad": -0.061,
+      "mc_parameter_uncertainty_halfwidth": 0.039
+    },
+    "mondrian_by_compound_type": {
+      "verdict": "DEAD — widens +86%",
+      "reason": "n=67 split into acid/base/neutral/zwitterion (14/23/27/3); finite-sample conformal quantile ceil((n+1)(1-a)) lands at ~class-max at small n, so per-class q exceeds the pooled 90th pct. Train-calibrated per-class q (base 1.356, neutral 1.545) > global 1.100.",
+      "train_q90_by_class": {"acid": 1.112, "base": 1.356, "neutral": 1.545, "zwitterion": "INF (n=3<9)"}
+    },
+    "verdict": "WALLED — max |rho| = 0.069 across all obs-free signals incl. MC parameter-uncertainty. The structural model-form error (~60pp of the spread, not in the MC) is per-drug non-discriminable (confirms DE-41). The flat /÷12.9 PI is near-optimal under Invariant #5; its 0.953 over-coverage is the safe direction and cannot be honestly tightened (would require holdout-tuning or a non-existent adaptive signal)."
+  },
+  "invivo_f_prior_killtest": {
+    "question": "Does an in-vivo F prior (xgboost_bioavailability.json, scaffold-CV R2=-0.09) applied via the measured-F routing at shrinkage w improve the holdout meta AAFE? (DE-44 pre-registered: rises +0.02-0.08 => kill.)",
+    "baseline_meta_aafe": 2.7428,
+    "meta_aafe_by_w": {"0.0": 2.7428, "0.25": 2.6852, "0.5": 2.6459, "1.0": 2.7360},
+    "delta_vs_baseline": {"0.25": -0.0576, "0.5": -0.0969, "1.0": -0.0068},
+    "surprise": "AAFE FELL (not rose) at w=0.25/0.5 — the pre-registered surprise branch. Investigated with placebo controls.",
+    "placebo_controls_at_w0.5": {
+      "real_fpred_delta": -0.0969,
+      "constant_geomean_delta": -0.1328,
+      "shuffled_fpred_delta": -0.1160,
+      "interpretation": "CONST and SHUFFLED reproduce AND EXCEED the real per-drug F improvement => zero per-drug F information (real is slightly WORSE than shuffled). The improvement is a pure flat-scalar median-bias-null."
+    },
+    "mechanism": "f_eng geomean 0.148 vs Fpred geomean 0.424; median(Fpred/f_eng)=2.57 (upscale). The engine systematically under-predicts F, so any upward F scalar nulls that median bias -> AAFE dips; a constant does it cleanest. This is DE-42 (flat scalar nulls median F, not dispersion) shown directly on the meta.",
+    "verdict": "KILLED (triple-dead): (1) the effect is the DE-42 flat-scalar artifact, placebo-proven, zero per-drug F info (DE-28 re-confirmed); (2) the scalar is a holdout-fit median-bias correction = Invariant #8 forbidden ('fudge to Cmax loss, any form'); (3) even the best (constant) delta -0.133 is within the bootstrap CI half-width ~0.42 and does not generalize (prospective F-under-call differs; DE-42 over-tail flip)."
+  }
+}

docs/research/dead-ends.md

@@ -474,6 +474,26 @@ Artifacts: `scripts/probe_liver_zonation.py`, `tests/integration/test_liver_zona
 
 ---
 
+### DE-55 — Adaptive / normalized conformal PI: no per-drug difficulty signal exists, so the flat /÷12.9 interval cannot be honestly tightened (2026-07-07)
+
+**Date:** 2026-07-07
+
+**The DE-44 "PI-recalibration" survivor, tested and foreclosed.** The user-facing 90% Cmax PI is a train-calibrated split-conformal interval (meta q90 = 1.111 → **/÷12.9**, holdout coverage **0.9533** at nominal 0.90). The over-coverage cannot be "fixed" by lowering q — that is tuning on the holdout (Invariant #5). The only honest tightening is **adaptive/normalized conformal**: give easy drugs a narrower interval via a per-drug difficulty signal σ(x). The pre-registered kill-test (Spearman ρ between |log10 meta fold-error| and σ) is **dead across every signal**: div(eng,ml)=−0.035, div(eng,meta)=−0.002, div(ml,meta)=−0.057, n_ad_flags=−0.051, |log meta|=−0.069, meta_cmax=+0.056, not_in_ad=−0.061, and — the specifically-named signal — **MC parameter-uncertainty half-width ρ=+0.039** (max |ρ|=0.069). Mechanistically airtight: the MC propagates *parameter* uncertainty only (~30% coverage at nominal 90%); the dominant ~60pp of the spread is **structural model-form error not in the MC**, and it is per-drug **non-discriminable** (confirms DE-41). **Mondrian-by-compound-type also DEAD** — it *widens* the mean interval **+86%**: splitting n=67 into acid/base/neutral/zwitterion (14/23/27/3) makes the finite-sample conformal quantile `ceil((n+1)(1−α))` land at ~the class maximum, so per-class train q (base 1.356, neutral 1.545) exceeds the pooled 1.100. **Verdict:** the flat /÷12.9 PI is near-optimal under Invariant #5; its 0.953 over-coverage is the *safe* direction. The PI is not broken (split-conformal already fixed the 30%-coverage MC PI) — it just cannot be adaptively narrowed because the error is unpredictable per-drug. Artifact `data/validation/pi_fprior_killtests_2026-07-07.json`.
+
+**Telltale if it returns:** "a normalized / CQR / Mondrian conformal will tighten the 13-fold PI." It will not — no per-drug difficulty signal predicts the error (ρ≈0 for all, incl. MC-CV), and small-n Mondrian widens it. Ship PI work only if a *new* orthogonal difficulty signal clears |ρ|≥0.3 first.
+
+---
+
+### DE-56 — invivo-F-prior: the pre-registered "surprise" (AAFE falls) is the DE-42 flat-scalar median-bias artifact, placebo-proven (2026-07-07)
+
+**Date:** 2026-07-07
+
+**The DE-44 `invivo-F-prior` test, run with placebo controls — killed, richer than predicted.** Applied the structure→F predictor (`xgboost_bioavailability.json`, target log10(F/100), **scaffold-CV R²=−0.09** — noise, DE-28) to the holdout via the measured-F routing at shrinkage w∈{0.25,0.5,1.0}. DE-44 pre-registered "AAFE **rises** +0.02–0.08 → kill." Instead the meta AAFE **fell**: 2.7428 → 2.685 (w=0.25) → **2.646** (w=0.5) → 2.736 (w=1.0) — non-monotonic, the surprise branch. **Placebo controls at w=0.5 resolve it decisively:** REAL per-drug F Δ=**−0.097**, but a **CONSTANT** F (geomean) Δ=**−0.133** and a **SHUFFLED** F (drug↔F match destroyed) Δ=**−0.116** both *reproduce and exceed* it. Per-drug F information is **zero** (real is *worse* than shuffled). **Mechanism:** f_eng geomean 0.148 vs Fpred 0.424, median k=**2.57** (upscale) — the engine systematically under-predicts F, so *any* upward F scalar nulls that median bias → AAFE dips; a constant does it cleanest. This is **DE-42** (flat scalar nulls median F, not dispersion) shown directly on the meta headline. **Triple-dead:** (1) the effect is the placebo-proven flat-scalar artifact, no F signal (re-confirms DE-28/42); (2) the scalar is a holdout-fit median-bias correction = **Invariant #8 forbidden** ("fudge to Cmax loss, any form"); (3) even the best (constant) −0.133 is within the bootstrap CI half-width ~0.42 and does not generalize (the prospective F-under-call differs, DE-54; DE-42's over-tail flip). Artifact `data/validation/pi_fprior_killtests_2026-07-07.json`.
+
+**Telltale if it returns:** "an in-vivo F prior improved the holdout AAFE by ~0.10." That drop is a **flat-scalar median-bias null**, not F information — a constant or shuffled F reproduces it, and the scalar is holdout-fit (Invariant #8) and non-generalizing. Any future F-prior must beat its own constant/shuffled placebo before it counts.
+
+---
+
 ## 3. When to consult this list
 
 - Before writing a design spec for any accuracy improvement.

docs/research/experiment-log.md

@@ -10,6 +10,30 @@ Reverse-chronological. The project README carries only the **current** headline
 
 ---
 
+## 2026-07-07 — Two DE-44 kill-tests run: adaptive PI walled (DE-55), invivo-F-prior killed via placebo (DE-56)
+
+Ran the two cheap pre-registered kill-tests DE-44 flagged as "survivors to test," on the 107-holdout
+(local macOS public-clone; deltas are stack-internal). Both foreclosed.
+
+- **Adaptive/normalized conformal PI (DE-55):** the user-facing 90% Cmax PI is train-calibrated
+  split-conformal, meta q90=1.111 (/÷12.9), holdout coverage 0.9533. The over-coverage can't be lowered
+  without tuning on the holdout (Inv #5); the only honest tightening is adaptive-by-difficulty. Spearman
+  ρ(|log meta fold-error|, σ) is dead for every obs-free signal — divergence(×3), AD flags, magnitude,
+  and the specifically-named **MC parameter-uncertainty half-width ρ=0.039** (max |ρ|=0.069). Mondrian
+  by compound-type *widens* +86% (n=67 split → per-class conformal q lands at ~class-max). The flat
+  /÷12.9 PI is near-optimal under Inv #5; the structural error is per-drug non-discriminable (DE-41).
+- **invivo-F-prior (DE-56):** applied the structure→F predictor (R²=−0.09 noise) via measured-F routing
+  at shrinkage w. DE-44 pre-registered "AAFE rises → kill"; instead it **fell** (2.743 → 2.646 at w=0.5,
+  non-monotonic) — the surprise branch. **Placebo controls decided it:** a CONSTANT F (Δ−0.133) and a
+  SHUFFLED F (Δ−0.116) both reproduce/exceed the real per-drug F (Δ−0.097) → zero per-drug F info. It is
+  the DE-42 flat-scalar median-bias null (f_eng 0.148 vs Fpred 0.424, median k 2.57 upscale nulls the
+  engine's systematic F-under-call). Triple-dead: placebo-artifact + Invariant #8 (holdout-fit scalar =
+  fudge to Cmax loss) + within-CI + non-generalizing.
+
+The pre-registration + placebo discipline caught what would otherwise read as a "broke the ceiling"
+false positive (a −0.10 AAFE drop). No headline change (2.743). Artifact
+`data/validation/pi_fprior_killtests_2026-07-07.json`; DE-55, DE-56.
+
 ## 2026-07-06 — OATP1B1 ECM: closed the FLUX-1 auto-ECM xfail; +BSA PSu,inf formally deferred (data-blocked)
 
 A 3-agent investigation of "the one un-foreclosed accuracy lever" (diagnosis §9 — the +BSA /