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 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 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)
@@ -951,6 +951,9 @@ audit-chain-check:
 pre-registration-check:
 	openamp-foundry pre-registration-check --entry-json '{"registration_id":"PRE-001","batch_id":"BATCH-001","pipeline_version":"0.9.4","registration_date":"2026-07-10","primary_hypothesis":"Candidates selected by OpenAMP will show MIC values at least 2-fold lower than random length/charge-matched peptides in broth microdilution against E. coli ATCC 25922.","primary_outcome_metric":"mic_value","success_threshold":4.0,"baseline_comparators":["random_selection","charge_matched_random"],"candidate_ids":["AMP-001","AMP-002","AMP-003"],"assay_type":"mic_assay","statistical_test":"Mann-Whitney U test, two-sided, alpha=0.05","registered_by":"test@example.com","dry_lab_only":true}' --format text
 
+hypothesis-outcome-check:
+	openamp-foundry hypothesis-outcome-check --entry-json '{"outcome_id":"HOR-001","registration_id":"PRE-001","batch_id":"BATCH-001","pipeline_version":"0.9.5","outcome_date":"2026-07-15","outcome_verdict":"confirmed","observed_metric_value":2.5,"success_threshold_met":true,"interpretation":"Selected candidates showed median MIC of 2.5 ug/mL, meeting the threshold. Random baseline showed 32 ug/mL. Hypothesis confirmed with strong signal vs random.","deviation_from_plan":"","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/HYPOTHESIS_OUTCOME_GUIDE.md b/docs/evidence/HYPOTHESIS_OUTCOME_GUIDE.md
@@ -0,0 +1,59 @@
+# Hypothesis Outcome Record Guide
+
+## Purpose
+
+A hypothesis outcome record documents whether a pre-registered hypothesis was
+confirmed or refuted after experimental results are received. It links the
+outcome to the pre-registration form, records the observed metric value,
+and requires an explicit interpretation. This closes the HARKing-prevention
+loop: the pre-registration (N1) commits to what will be tested; the outcome
+record (N2) reports what was found, whether convenient or not.
+
+## Schema Fields
+
+| Field | Type | Description |
+|---|---|---|
+| outcome_id | str | Unique identifier (prefix "HOR-") |
+| registration_id | str | Matching PRE- registration this outcome closes |
+| batch_id | str | Batch that was tested |
+| pipeline_version | str | Pipeline version used |
+| outcome_date | str | ISO 8601 date results were recorded |
+| outcome_verdict | str | Whether hypothesis was confirmed or refuted (see valid verdicts) |
+| observed_metric_value | float | Actual observed value for the primary outcome metric |
+| success_threshold_met | bool | Whether the pre-specified threshold was met |
+| interpretation | str | Researcher's plain-language interpretation (max 500 chars) |
+| deviation_from_plan | str | Any deviation from pre-registered plan (empty string if none) |
+| recorded_by | str | Person or system that recorded this outcome |
+| dry_lab_only | bool | False if real lab data; True if computational simulation only |
+
+## Valid Outcome Verdicts
+
+- `confirmed` — hypothesis was supported by observations
+- `refuted` — hypothesis was not supported by observations
+- `inconclusive` — results were ambiguous or experiment had quality issues
+- `partially_confirmed` — hypothesis was supported for a subset of candidates
+
+## Validation Rules
+
+1. outcome_id must start with "HOR-"
+2. registration_id must start with "PRE-"
+3. outcome_verdict must be one of the valid verdicts
+4. observed_metric_value must be finite (not NaN or Inf)
+5. interpretation must not be empty and must not exceed 500 characters
+6. recorded_by must not be empty
+
+## Warning Conditions
+
+- Verdict/threshold mismatch: success_threshold_met=True but outcome_verdict="refuted" → warn about inconsistency
+- Verdict/threshold mismatch: success_threshold_met=False but outcome_verdict="confirmed" → warn about inconsistency
+- No deviation documented: outcome_verdict is "inconclusive" but deviation_from_plan is empty → warn that deviations should be documented when results are inconclusive
+- Short interpretation: interpretation < 50 chars → warn that interpretation may be underspecified
+
+## Honest Use Boundary
+
+A hypothesis outcome record is scientific evidence of what happened. A
+"refuted" verdict is not a failure — it is information. Do not suppress,
+reframe, or omit refuted outcomes. The value of pre-registration comes
+entirely from honest reporting of all outcomes including inconvenient ones.
+Selectively reporting confirmed outcomes while omitting refuted ones
+defeats the entire purpose and should be treated as a protocol violation.
diff --git a/docs/evidence/METRICS_CURRENT.md b/docs/evidence/METRICS_CURRENT.md
@@ -5,8 +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:** 2026-07-10 (Phase N N1 — pre-registration form — v0.9.4)
-> **New in v0.9.4:** 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.
+> **Last updated:** 2026-07-10 (Phase N N2 — hypothesis outcome record — v0.9.5)
+> **New in v0.9.5:** Hypothesis outcome record schema (N2 — Loop 134) — docs/evidence/HYPOTHESIS_OUTCOME_GUIDE.md with purpose, schema fields table (12 fields: outcome_id, registration_id, batch_id, pipeline_version, outcome_date, outcome_verdict, observed_metric_value, success_threshold_met, interpretation, deviation_from_plan, recorded_by, dry_lab_only), 4 valid outcome verdicts (confirmed, refuted, inconclusive, partially_confirmed), 6 validation rules, 4 warning conditions (threshold/verdict inconsistency, inconclusive no deviation, short interpretation), honest-use boundary. HypothesisOutcomeEntry dataclass (12 fields), HypothesisOutcomeResult dataclass (7 fields), validate_hypothesis_outcome() (6+ error checks: HOR- prefix, PRE- prefix, valid verdict, finite metric, non-empty interpretation<=500, non-empty recorded_by; 4 warning conditions: threshold/verdict mismatch, inconclusive no deviation, short interpretation), validate_hypothesis_outcome_dict() (11 required fields guard). CLI (openamp-foundry hypothesis-outcome-check) with --entry-json, --format text|json. make hypothesis-outcome-check target. 48 tests. Phase N N2: the pre-registration loop is now closed — outcomes are recorded and matched to their commitments.
+> > **New in v0.9.4:** 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.
 > **New in v0.9.1:** Score decomposition report schema (M3 — Loop 130) — docs/evidence/SCORE_DECOMPOSITION_GUIDE.md with purpose, schema fields table (12 fields), valid scoring methods (6), validation rules (9), warning conditions (4), honest-use boundary. src/openamp_foundry/evidence/score_decomposition_report.py with ScoreDecompositionEntry dataclass (12 fields: report_id, batch_id, candidate_id, pipeline_version, composite_score, component_scores, component_weights, scoring_method, score_range_min, score_range_max, reviewer, dry_lab_only=True), ScoreDecompositionResult dataclass (7 fields: report_id, batch_id, candidate_id, scoring_method, passed, errors, warnings, dry_lab_only=True), VALID_SCORING_METHODS (6: additive_weighted, geometric_mean, harmonic_mean, max_component, min_component, rank_aggregation), MINIMUM_COMPONENTS (2), WEIGHT_SUM_TOLERANCE (0.01), DOMINANT_WEIGHT_THRESHOLD (0.6), UNBALANCED_RATIO_THRESHOLD (5.0), MAX_COMPONENTS_WARNING (8), LOW_SCORE_FRACTION (0.2), validate_score_decomposition() (9 error checks: SDR- prefix, score_range_min<score_range_max, composite_score in range, >=2 components, weight keys match score keys, weights sum to ~1.0, valid scoring_method, non-empty reviewer, dry_lab_only must be True; 4 warning conditions: dominant component, unbalanced weights, many components, low composite score), validate_score_decomposition_dict() (11 required fields guard). CLI (openamp-foundry score-decomposition-check) with --entry-json, --format text|json. make score-decomposition-check target. Phase M M3: every composite score is now machine-decomposable into its named components for external audit.
 > **New in v0.9.0:** Claim-to-evidence mapper schema (M2 — Loop 129) — docs/evidence/CLAIM_TO_EVIDENCE_GUIDE.md with purpose, schema fields table (10 fields), valid claim types (7), validation rules (7), warning conditions (4), honest-use boundary, CLI usage. src/openamp_foundry/evidence/claim_to_evidence_mapper.py with ClaimToEvidenceEntry dataclass (10 fields: mapping_id, batch_id, pipeline_version, claim_text, claim_type, supporting_artifact_ids, evidence_level, pre_specified, reviewer, dry_lab_only=True), ClaimToEvidenceResult dataclass (7 fields: mapping_id, batch_id, claim_type, passed, errors, warnings, dry_lab_only=True), VALID_CLAIM_TYPES (7: activity_prediction, calibration_statement, novelty_claim, performance_comparison, reproducibility_claim, safety_assessment, selection_rationale), VALID_EVIDENCE_LEVELS (6: 1-6), MAX_CLAIM_TEXT_LENGTH (500), LONG_CLAIM_TEXT_THRESHOLD (300), WEAK_EVIDENCE_THRESHOLD (2), validate_claim_to_evidence() (7 error checks: CEM- prefix, non-empty claim_text<=500 chars, valid claim_type, non-empty supporting_artifact_ids, valid evidence_level 1-6, non-empty reviewer, dry_lab_only must be True; 4 warning conditions: post-hoc, weak evidence, single artifact, long claim text), validate_claim_to_evidence_dict() (9 required fields guard). CLI (openamp-foundry claim-to-evidence-check) with --entry-json, --format text|json. make claim-to-evidence-check target. Phase M M2: every scientific claim is now machine-mapped to its supporting artifacts for external audit.

diff --git a/docs/research/NEXT_100_PR_MAP.md b/docs/research/NEXT_100_PR_MAP.md
@@ -232,7 +232,7 @@ Make experiment predictions falsifiable before results are observed. Guard again
 | PR | Task | Why it matters | Review class |
 |---:|---|---|---|
 | 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. | Documents whether pre-registered hypotheses were confirmed or refuted. | B/D |
+| 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. | Machine-verifiable proof the model beats cheap baselines. | B |
 | N4 | Add negative result record schema. | Ensures failed experiments are documented, not discarded. | B |
 | N5 | Add experiment priority justification schema. | Documents why this batch was selected over alternatives. | B |

diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,13 @@
 # Roadmap
 
+### v0.9.5 — Phase N N2: Hypothesis Outcome Record
+- Added `HypothesisOutcomeEntry` schema linking pre-registration to actual experimental outcomes
+- Records confirmed/refuted/inconclusive/partially_confirmed verdicts with observed metric value
+- Warns on threshold/verdict inconsistency and undocumented inconclusive deviations
+- dry_lab_only=False supported (real lab data can be recorded)
+- CLI: `openamp-foundry hypothesis-outcome-check`
+- 48 tests; all passing
+
 ### v0.9.4 — Phase N N1: Pre-Registration Form (starts Phase N)
 - Added `PreRegistrationEntry` schema for machine-verifiable experiment pre-commitment
 - Records hypothesis, outcome metric, success threshold, and baseline comparators before results are observed