Loop 76: Negative-Result Informativeness Guide (F6)

Makefile

@@ -1,4 +1,4 @@
-.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter
+.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter classify-negative-informativeness
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -603,6 +603,12 @@ failed-candidate-report:
 		--out-md outputs/failed_candidate_report.md \
 		--validate-rejection-codes
 
+classify-negative-informativeness:
+	PYTHONPATH=src $(PYTHON) scripts/classify_negative_result_informativeness.py \
+		--input examples/negative_result_entry_example.json \
+		--out-json outputs/negative_result_informativeness_result.json \
+		--out-md outputs/negative_result_informativeness_result.md
+
 safe-publication-filter:
 	PYTHONPATH=src $(PYTHON) scripts/safe_publication_filter.py \
 		--input examples/safe_publication_filter_example_input.json \

docs/PROJECT_INDEX.md

@@ -236,6 +236,7 @@ First useful contribution: make the repo easier to maintain without lowering saf
 | [`docs/review/ASSAY_PREREGISTRATION.md`](review/ASSAY_PREREGISTRATION.md) | Candidate-selection pilot pre-registration template, not a protocol. |
 | [`docs/review/COLLABORATION_PLAYBOOK.md`](review/COLLABORATION_PLAYBOOK.md) | External collaboration modes and boundaries. |
 | [`docs/evidence/NEGATIVE_RESULT_ARCHIVE.md`](evidence/../evidence/NEGATIVE_RESULT_ARCHIVE.md) | Safe negative-result format. |
+| [`docs/evidence/NEGATIVE_RESULT_INFORMATIVENESS_GUIDE.md`](evidence/../evidence/NEGATIVE_RESULT_INFORMATIVENESS_GUIDE.md) | 7-dimension framework for classifying negative-result entries as informative/neutral/non-informative. |
 
 ## Core safety docs
 

docs/evidence/METRICS_CURRENT.md

@@ -5,7 +5,9 @@ Machine-readable snapshot: `outputs/metrics_snapshot.json` regenerated with `mak
 > **Purpose:** One authoritative table of current pipeline metrics. If any doc disagrees
 > with this file, this file wins. Updated whenever benchmark/benchmark config changes.
 >
-> **Last updated:** 2026-07-09 (Phase F safe-publication filter — v0.5.76)
+> **Last updated:** 2026-07-09 (Phase F negative-result informativeness — v0.5.77)
+> **New in v0.5.77:** Negative-result informativeness guide (F6) — comprehensive documentation defining 7-dimension informativeness framework for negative-result entries, with 14 examples across all 6 reason categories, before/after transformation pairs, and quick-reference checklist. CLI classifier (`scripts/classify_negative_result_informativeness.py`) that scores entries on 7 dimensions and produces informative/neutral/non-informative classification. 37 tests. 2796 total.
+>
 > **New in v0.5.76:** Safe-publication filter (F5) — CLI that reads candidate panel data with safety metadata and checks each candidate against publication safety constraints before external release. FAIL-CLOSED: defaults to reject unless all checks pass. Checks: dry_lab_only (must be true), proof_ladder_level (≤4), toxicity_screened, hemolysis_screened, dual_use_reviewed (all must be true). Produces structured JSON filter result and human-readable Markdown summary. 33 tests. 2758 total.
 >
 > **New in v0.5.75:** Failed-candidate report generator (F4) — CLI that reads candidate rejection data + taxonomy, produces structured JSON report with summary aggregation (by category, severity, stage, evidence impact) and human-readable Markdown summary. 26 tests. 2724 total.
@@ -62,7 +64,7 @@ Machine-readable snapshot: `outputs/metrics_snapshot.json` regenerated with `mak
 > **New in v0.5.31:** Added dipeptide-order features for sequence-order awareness. `dipeptide_order_score` achieves AUROC 0.7861 on AMP-vs-scrambled discrimination — the strongest order-dependent feature in the pipeline. Only 7/31 features survive scrambling (amphipathicity/helix-wheel + dipeptide). All composition features are purely position-independent (exactly 0.5000 AUROC on scrambled test).
 > **New in v0.5.30:** Easy baseline benchmark added — charge density alone (AUROC 0.8166) outperforms the full pipeline ensemble (0.7792) on AMP-vs-Swiss-Prot-decoy discrimination. Honest finding documented: expected because pipeline optimizes for safety, not raw discrimination.
 > **New in v0.5.29:** Expanded benchmark to 500 AMPs + 500 composition-matched decoys (n=1000). AUROC 0.7792 (CI₉₅: 0.7505–0.8065) confirms signal generalizes. Cluster-aware CI: 0.746–0.8102. Representative AUROC: 0.778. Standard benchmark (n=191) retained for backward comparison.
-> **Pipeline version:** v0.5.76
+> **Pipeline version:** v0.5.77
 > **Branch:** main
 
 ---