cschanhniem · Jul 9, 2026 · Jul 9, 2026
diff --git a/Makefile b/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 bench-strategy-compare 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 validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check advisory-review-check annual-review-check selection-rationale-check batch-priority-check pilot-package-check calibration-intake-check uncertainty-report-check preprint-bundle-check reproducibility-manifest-check candidate-summary-card-check multi-candidate-comparison-check pipeline-decision-audit-check claim-to-evidence-check score-decomposition-check reviewer-briefing-check audit-chain-check pre-registration-check hypothesis-outcome-check baseline-comparison-check dataset-release-check
+.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 bench-strategy-compare 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 validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check advisory-review-check annual-review-check selection-rationale-check batch-priority-check pilot-package-check calibration-intake-check uncertainty-report-check preprint-bundle-check reproducibility-manifest-check candidate-summary-card-check multi-candidate-comparison-check pipeline-decision-audit-check claim-to-evidence-check score-decomposition-check reviewer-briefing-check audit-chain-check pre-registration-check hypothesis-outcome-check baseline-comparison-check negative-result-check dataset-release-check
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -957,6 +957,9 @@ hypothesis-outcome-check:
 baseline-comparison-check:
 	openamp-foundry baseline-comparison-check --entry-json '{"manifest_id":"BCM-001","batch_id":"BATCH-001","pipeline_version":"0.9.6","comparison_date":"2026-07-10","metric_name":"hit_rate","pipeline_score":0.7,"baseline_scores":{"random_selection":0.1,"charge_matched":0.15},"pipeline_beats_all_baselines":true,"effect_size":0.55,"p_value":0.02,"comparison_direction":"higher_is_better","notes":"Pipeline beats random and charge-matched baselines.","reviewer":"test@example.com","dry_lab_only":true}' --format text
 
+negative-result-check:
+	openamp-foundry negative-result-check --entry-json '{"record_id":"NRR-001","batch_id":"BATCH-001","pipeline_version":"0.9.7","record_date":"2026-07-10","failure_category":"below_activity_threshold","failure_description":"Candidates did not meet MIC threshold in broth microdilution assay.","candidate_ids":["AMP-042"],"assay_type":"mic_assay","expected_outcome":"MIC <= 4 ug/mL","observed_outcome":"MIC = 128 ug/mL","hypothesis_impact":"Activity hypothesis refuted for these candidates. Pipeline review needed.","will_be_reported":true,"recorded_by":"test@example.com","dry_lab_only":true}' --format text
+
 dataset-release-check:
 	.venv/bin/openamp-foundry dataset-release-check \
 		--entry-json '{"release_id":"DSR-001","dataset_name":"OpenAMP Wave 0.5 Candidates","dataset_version":"1.0.0","release_date":"2026-07-09","license_identifier":"CC-BY-4.0","data_sources":["UniProt AMP database","APD3","in-house pipeline"],"contains_sequences":true,"contains_activity_data":false,"dual_use_assessed":true,"usage_policy_url":"https://openamp.example.org/data-policy","contact_email":"data@openamp.example.org","release_approved":true,"dry_lab_only":true}' \

diff --git a/docs/evidence/METRICS_CURRENT.md b/docs/evidence/METRICS_CURRENT.md
@@ -5,7 +5,8 @@ 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:** 2026-07-10 (Phase N N3 — baseline comparison manifest — v0.9.6)
+> **Last updated:** 2026-07-10 (Phase N N4 — negative result record — v0.9.7)
+> **New in v0.9.7:** Negative result record schema (N4 — Loop 136) — docs/evidence/NEGATIVE_RESULT_GUIDE.md with purpose, schema fields table (14 fields: record_id, batch_id, pipeline_version, record_date, failure_category, failure_description, candidate_ids, assay_type, expected_outcome, observed_outcome, hypothesis_impact, will_be_reported, recorded_by, dry_lab_only), 6 valid failure categories (assay_quality_failure, below_activity_threshold, excessive_toxicity, model_overprediction, pipeline_error, stability_failure), 5 valid assay types (cytotoxicity_assay, hemolysis_assay, membrane_disruption_assay, mic_assay, stability_assay), 9 validation rules, 3 warning conditions (not reported, large failure set, model overprediction without recalibration), honest-use boundary. NegativeResultEntry dataclass (14 fields), NegativeResultResult dataclass (7 fields), validate_negative_result() (9+ error checks: NRR- prefix, valid failure_category, non-empty failure_description<=500 chars, >=1 candidate_ids, valid assay_type, non-empty expected_outcome/observed_outcome, non-empty hypothesis_impact<=300 chars, non-empty recorded_by; 3 warnings: not reported contributes to publication bias, >10 candidates suggests systematic issue, model_overprediction without calibration mention triggers calibration review), validate_negative_result_dict() (13 required fields guard). CLI (openamp-foundry negative-result-check) with --entry-json, --format text|json. make negative-result-check target. 68 tests. Phase N N4: failed experiments are now documented, not discarded.
 > **New in v0.9.6:** Baseline comparison manifest schema (N3 — Loop 135) — docs/evidence/BASELINE_COMPARISON_GUIDE.md with purpose, schema fields table (14 fields: manifest_id, batch_id, pipeline_version, comparison_date, metric_name, pipeline_score, baseline_scores, pipeline_beats_all_baselines, effect_size, p_value, comparison_direction, notes, reviewer, dry_lab_only), 6 valid metric names (fold_change_mic, hemolysis_fraction, hit_rate, mic_value, novelty_score, selectivity_index), 2 valid comparison directions (higher_is_better, lower_is_better), 11 validation rules, 4 warning conditions (pipeline loses, inconsistent verdict, no p-value, large unchecked effect), honest-use boundary. BaselineComparisonEntry dataclass (14 fields), BaselineComparisonResult dataclass (7 fields), validate_baseline_comparison() (11+ error checks: BCM- prefix, valid metric_name, finite pipeline_score, >=1 baseline, finite baseline_scores, finite effect_size, p_value in [0.0,1.0] or -1.0, valid comparison_direction, notes<=300, non-empty reviewer, dry_lab_only must be True; 4 warning conditions: underperforms, inconsistent verdict, no p-value, large+unchecked), validate_baseline_comparison_dict() (13 required fields guard). CLI (openamp-foundry baseline-comparison-check) with --entry-json, --format text|json. make baseline-comparison-check target. 68 tests. Phase N N3: every performance claim against a baseline is now machine-verifiable.
 > **New in v0.9.5:** Pre-registration form schema (N1 — Loop 133) — docs/evidence/PRE_REGISTRATION_GUIDE.md with purpose, schema fields table (13 fields: registration_id, batch_id, pipeline_version, registration_date, primary_hypothesis, primary_outcome_metric, success_threshold, baseline_comparators, candidate_ids, assay_type, statistical_test, registered_by, dry_lab_only), 6 valid primary outcome metrics, 5 valid assay types, 10 validation rules, 4 warning conditions, honest-use boundary. PreRegistrationEntry dataclass (13 fields), PreRegistrationResult dataclass (6 fields), validate_pre_registration() (10+ error checks: PRE- prefix, non-empty hypothesis<=500 chars, valid outcome metric, finite success_threshold, >=1 baseline_comparators, >=1 candidate_ids, valid assay_type, non-empty statistical_test<=200 chars, non-empty registered_by, dry_lab_only must be True; 4 warning conditions: no random baseline, large candidate set >20, short hypothesis <50 chars, placeholder statistical test TBD/N/A/NA/none), validate_pre_registration_dict() (12 required fields guard). CLI (openamp-foundry pre-registration-check) with --entry-json, --format text|json. make pre-registration-check target. 62 tests. Phase N (Pre-registration & Baseline Honesty) started with N1.
 > > **New in v0.9.3:** Audit chain completeness checker (M5 — Loop 132) — docs/evidence/AUDIT_CHAIN_GUIDE.md with purpose, schema fields table (16 fields: chain_id, batch_id, pipeline_version, audit_date, 9 has_* bools, missing_links, auditor, dry_lab_only), 9 required chain links, validation rules (5), warning conditions (2: single auditor, future date), honest-use boundary. src/openamp_foundry/evidence/audit_chain_completeness.py with AuditChainEntry dataclass (16 fields: chain_id, batch_id, pipeline_version, audit_date, 9 has_* bools, missing_links list[str], auditor, dry_lab_only=True), AuditChainResult dataclass (7 fields: chain_id, batch_id, missing_link_count, passed, errors, warnings, dry_lab_only=True), CHAIN_LINK_FIELDS (9 entries), CHAIN_LINK_COUNT (9), AUDITOR_EMAIL_HINT ("@"), IMPLAUSIBLE_YEAR_THRESHOLD (2030), validate_audit_chain() (5+ error checks: ACH- prefix, non-empty auditor, dry_lab_only must be True, each false chain link errors, missing_links consistency; 2 warnings: no email, future date), validate_audit_chain_dict() (15 required fields guard). CLI (openamp-foundry audit-chain-check) with --entry-json, --format text|json. make audit-chain-check target. 39 tests. Phase M M5: the evidence chain is now machine-checkable end to end. Phase M (Audit Trail Infrastructure) is fully complete with M1-M5.

diff --git a/docs/evidence/NEGATIVE_RESULT_GUIDE.md b/docs/evidence/NEGATIVE_RESULT_GUIDE.md
@@ -0,0 +1,73 @@
+# Negative Result Record Guide
+
+## Purpose
+
+A negative result record documents experiments or predictions that failed to
+meet expectations. Negative results are not failures of the pipeline — they
+are information. Recording them is mandatory for:
+
+1. Honest calibration (you cannot calibrate on cherry-picked successes)
+2. Preventing repeated experiments (institutional memory)
+3. Publication integrity (selective reporting is a form of bias)
+4. Future hypothesis generation (knowing what does NOT work narrows the space)
+
+## Schema Fields
+
+| Field | Type | Description |
+|---|---|---|
+| record_id | str | Unique identifier (prefix "NRR-") |
+| batch_id | str | Batch or experiment set this record covers |
+| pipeline_version | str | Pipeline version at time of experiment |
+| record_date | str | ISO 8601 date result was recorded |
+| failure_category | str | Category of failure (see valid categories) |
+| failure_description | str | Plain-language description of what failed (max 500 chars) |
+| candidate_ids | list[str] | IDs of candidates that failed (at least 1) |
+| assay_type | str | Assay in which failure was observed (see valid types) |
+| expected_outcome | str | What was predicted or expected |
+| observed_outcome | str | What was actually observed |
+| hypothesis_impact | str | How this result affects the working hypothesis (max 300 chars) |
+| will_be_reported | bool | Whether this result will be included in any publication or report |
+| recorded_by | str | Person or system recording this |
+| dry_lab_only | bool | False if real lab data; True if computational only |
+
+## Valid Failure Categories
+
+- `assay_quality_failure` — assay controls failed; results not interpretable
+- `below_activity_threshold` — predicted activity not confirmed
+- `excessive_toxicity` — candidate was too toxic (hemolysis/cytotoxicity)
+- `model_overprediction` — model was significantly more optimistic than results
+- `pipeline_error` — computational error or data quality issue
+- `stability_failure` — candidate degraded under assay conditions
+
+## Valid Assay Types
+
+- `cytotoxicity_assay`
+- `hemolysis_assay`
+- `membrane_disruption_assay`
+- `mic_assay`
+- `stability_assay`
+
+## Validation Rules
+
+1. record_id must start with "NRR-"
+2. failure_category must be one of the valid categories
+3. failure_description must not be empty and must not exceed 500 characters
+4. candidate_ids must contain at least 1 candidate
+5. assay_type must be one of the valid assay types
+6. expected_outcome must not be empty
+7. observed_outcome must not be empty
+8. hypothesis_impact must not be empty and must not exceed 300 characters
+9. recorded_by must not be empty
+
+## Warning Conditions
+
+- Not reported: will_be_reported=False → warn that suppressing negative results contributes to publication bias
+- Large failure set: len(candidate_ids) > 10 → warn about systematic failure; pipeline may need recalibration
+- Model overprediction without recalibration note: failure_category="model_overprediction" and "calibrat" not in hypothesis_impact.lower() → warn that recalibration should be considered
+
+## Honest Use Boundary
+
+A negative result record must be filed even when the result is inconvenient.
+The commitment to record negative results is not optional. A pipeline that only
+documents successes is not a scientific tool — it is a selection bias engine.
+Do not set will_be_reported=False without documenting why in hypothesis_impact.
diff --git a/docs/research/NEXT_100_PR_MAP.md b/docs/research/NEXT_100_PR_MAP.md
@@ -234,7 +234,7 @@ Make experiment predictions falsifiable before results are observed. Guard again
 | N1 | Add pre-registration form schema (complete — Loop 133). | Records what will be tested and how before experiments run. | B |
 | N2 | Add hypothesis outcome record schema (complete — Loop 134). | Documents whether pre-registered hypotheses were confirmed or refuted. | B/D |
 | N3 | Add baseline comparison manifest schema (complete — Loop 135). | Machine-verifiable proof the model beats cheap baselines. | B |
-| N4 | Add negative result record schema. | Ensures failed experiments are documented, not discarded. | B |
+| N4 | Add negative result record schema (complete — Loop 136). | Ensures failed experiments are documented, not discarded. | B | | Ensures failed experiments are documented, not discarded. | B |
 | N5 | Add experiment priority justification schema. | Documents why this batch was selected over alternatives. | B |
 
 ## Prioritization rule

diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,12 @@
 # Roadmap
 
+### v0.9.7 — Phase N N4: Negative Result Record
+- Added `NegativeResultEntry` schema ensuring failed experiments are documented, not discarded
+- 6 failure categories, 5 assay types; warns on suppressed reporting, systematic failures, uncalibrated overprediction
+- dry_lab_only=False supported for real lab data
+- CLI: `openamp-foundry negative-result-check`
+- 68 tests; all passing
+
 ### v0.9.6 — Phase N N3: Baseline Comparison Manifest
 - Added `BaselineComparisonEntry` schema for machine-verifiable proof the pipeline beats cheap baselines
 - 6 metric names, 2 comparison directions, p_value sentinel for uncomputed significance

diff --git a/src/openamp_foundry/cli/commands/reports.py b/src/openamp_foundry/cli/commands/reports.py
@@ -3368,3 +3368,23 @@ def _run_baseline_comparison_check(args: argparse.Namespace) -> None:
             print(f"  ERROR: {e}")
         for w in result.warnings:
             print(f"  WARN:  {w}")
+
+
+def _run_negative_result_check(args: argparse.Namespace) -> None:
+    import json
+    from openamp_foundry.evidence.negative_result_record import validate_negative_result_dict
+
+    entry_dict = json.loads(args.entry_json)
+    result = validate_negative_result_dict(entry_dict)
+
+    if args.format == "json":
+        import dataclasses
+        print(json.dumps(dataclasses.asdict(result), indent=2))
+    else:
+        status = "PASS" if result.passed else "FAIL"
+        reported = "will be reported" if result.will_be_reported else "NOT REPORTED"
+        print(f"[{status}] Negative Result: {result.record_id} ({result.failure_category}, {result.candidate_count} candidates, {reported})")
+        for e in result.errors:
+            print(f"  ERROR: {e}")
+        for w in result.warnings:
+            print(f"  WARN:  {w}")