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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -925,3 +925,8 @@ candidate-summary-card-check:
 	.venv/bin/openamp-foundry candidate-summary-card-check \
 		--entry-json '{"card_id":"CRD-001","candidate_id":"AMP-001","batch_id":"BATCH-001","pipeline_version":"0.8.6","sequence":"KWKLFKKIEK","sequence_length":10,"evidence_level":4,"predicted_activity":"high_activity","safety_flags":[],"selection_rationale_id":"SEL-001","reviewer":"alice","dry_lab_only":true}' \
 		--format text
+
+multi-candidate-comparison-check:
+	.venv/bin/openamp-foundry multi-candidate-comparison-check \
+		--entry-json '{"comparison_id":"CMP-001","batch_id":"BATCH-001","pipeline_version":"0.8.7","comparison_date":"2026-07-09","candidate_ids":["AMP-001","AMP-002","AMP-003"],"comparison_criteria":["predicted_mic","hemolysis_fraction","selectivity_index"],"top_candidate_id":"AMP-001","top_candidate_rationale":"Highest selectivity index with lowest hemolysis fraction.","evidence_level":4,"reviewer":"alice","dry_lab_only":true}' \
+		--format text
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:** 2026-07-09 (Phase L L3 — candidate summary card schema — v0.8.6)
+> **Last updated:** 2026-07-09 (Phase L L4 — multi-candidate comparison schema — v0.8.7)
+> **New in v0.8.7:** Multi-candidate comparison schema (L4 — Loop 126b) — docs/evidence/MULTI_CANDIDATE_COMPARISON_GUIDE.md with purpose, required field table (11 fields), minimum requirements (2 candidates, 2 criteria), warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/multi_candidate_comparison.py with MultiCandidateComparisonEntry dataclass (11 fields: comparison_id, batch_id, pipeline_version, comparison_date, candidate_ids, comparison_criteria, top_candidate_id, top_candidate_rationale, evidence_level, reviewer, dry_lab_only), MultiCandidateComparisonResult dataclass (5 fields: comparison_id, batch_id, candidate_count, passed, errors, warnings, dry_lab_only=True), MINIMUM_CANDIDATES (2), MINIMUM_CRITERIA (2), RECOMMENDED_CRITERIA (3), MAX_RATIONALE_LENGTH (500), LARGE_CANDIDATE_SET_THRESHOLD (10), VALID_EVIDENCE_LEVELS (6: 1-6), validate_multi_candidate_comparison() (11 checks: CMP- prefix, non-empty batch_id/pipeline_version/reviewer, YYYY-MM-DD comparison_date, candidate_ids>=2, comparison_criteria>=2, top_candidate_id in candidate_ids, non-empty rationale<=500 chars, valid evidence_level, dry_lab_only must be True; evidence_level<=2 warns, candidate_count>10 warns, criteria_count<3 warns), validate_multi_candidate_comparison_dict() (10 required fields guard). CLI (openamp-foundry multi-candidate-comparison-check) with --entry-json, --format text|json. make multi-candidate-comparison-check target. Phase L L4: side-by-side candidate comparisons are now machine-validated for publication-ready supplementary tables.
 > **New in v0.8.6:** Candidate summary card schema (L3 — Loop 126) — docs/evidence/CANDIDATE_SUMMARY_CARD_GUIDE.md with purpose, required field table (12 fields), valid activity labels (5), valid amino acid set (20 standard), warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/candidate_summary_card.py with CandidateSummaryCardEntry dataclass (12 fields: card_id, candidate_id, batch_id, pipeline_version, sequence, sequence_length, evidence_level, predicted_activity, safety_flags, selection_rationale_id, reviewer, dry_lab_only), CandidateSummaryCardResult dataclass (5 fields: card_id, candidate_id, sequence_length, passed, errors, warnings, dry_lab_only=True), VALID_ACTIVITY_LABELS (5: high_activity, inactive, low_activity, moderate_activity, uncertain), VALID_AMINO_ACIDS (20 standard one-letter codes), LONG_PEPTIDE_THRESHOLD (50), VALID_EVIDENCE_LEVELS (6: 1-6), validate_candidate_summary_card() (11 checks: CRD- prefix, non-empty candidate_id/batch_id/pipeline_version/reviewer, non-empty sequence with valid amino acids, sequence_length==len(sequence), valid evidence_level, valid predicted_activity, SEL- prefix on selection_rationale_id, dry_lab_only must be True; evidence_level<=2 warns, safety_flags non-empty warns, uncertain activity warns, length>50 warns), validate_candidate_summary_card_dict() (11 required fields guard). CLI (openamp-foundry candidate-summary-card-check) with --entry-json, --format text|json. make candidate-summary-card-check target. Phase L L3: every candidate now has a machine-validated publication-ready summary card.
 > **New in v0.8.5:** Reproducibility manifest schema (L2 — Loop 125) — docs/evidence/REPRODUCIBILITY_MANIFEST_GUIDE.md with purpose, required field table (11 fields), package checksums format, data checksums format, warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/reproducibility_manifest.py with ReproducibilityManifestEntry dataclass (11 fields: manifest_id, batch_id, pipeline_version, run_date, python_version, package_checksums, data_checksums, random_seeds, hardware_summary, reviewer, dry_lab_only), ReproducibilityManifestResult dataclass (6 fields: manifest_id, batch_id, package_count, data_file_count, passed, errors, warnings, dry_lab_only=True), MINIMUM_PACKAGES (3), MINIMUM_DATA_FILES (1), RECOMMENDED_PACKAGES (5), validate_reproducibility_manifest() (10 checks: RPM- prefix, non-empty batch_id/pipeline_version/python_version/hardware_summary/reviewer, YYYY-MM-DD run_date, package_checksums>=3, data_checksums>=1, dry_lab_only must be True; empty random_seeds warns, package_count<5 warns, hardware_summary contains 'unknown' warns), validate_reproducibility_manifest_dict() (10 required fields guard). CLI (openamp-foundry reproducibility-manifest-check) with --entry-json, --format text|json. make reproducibility-manifest-check target. Phase L L2: every pipeline run now has a machine-validated reproducibility record.
 > **New in v0.8.4:** Preprint evidence bundle schema (L1 — Loop 124) — docs/evidence/PREPRINT_BUNDLE_GUIDE.md with purpose, required field table (11 fields), minimum artifact count (3), evidence level guide, warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/preprint_bundle.py with PreprintBundleEntry dataclass (11 fields: bundle_id, batch_id, pipeline_version, submission_date, title, artifact_ids, evidence_level, preprint_doi, contact_email, release_approved, dry_lab_only), PreprintBundleResult dataclass (5 fields: bundle_id, batch_id, artifact_count, passed, errors, warnings, dry_lab_only=True), MINIMUM_ARTIFACTS (3), RECOMMENDED_ARTIFACT_COUNT (5), MAX_TITLE_LENGTH (300), VALID_EVIDENCE_LEVELS (6: 1-6), validate_preprint_bundle() (10 checks: BND- prefix, non-empty batch_id/pipeline_version/contact_email, YYYY-MM-DD submission_date, non-empty title<=300 chars, artifact_ids>=3, valid evidence_level 1-6, release_approved must be True, dry_lab_only must be True; evidence_level<=2 warns, empty preprint_doi warns, artifact_count<5 warns), validate_preprint_bundle_dict() (10 required fields guard). CLI (openamp-foundry preprint-bundle-check) with --entry-json, --format text|json. make preprint-bundle-check target. Phase L L1: scientific preprints now have a machine-validated evidence bundle structure.

diff --git a/docs/evidence/MULTI_CANDIDATE_COMPARISON_GUIDE.md b/docs/evidence/MULTI_CANDIDATE_COMPARISON_GUIDE.md
@@ -0,0 +1,59 @@
+# Multi-Candidate Comparison Guide
+
+A *multi-candidate comparison* is a structured record that compares the key predicted
+properties of two or more candidates from the same batch side-by-side. This enables
+publication-ready supplementary tables and supports consistent external review.
+
+## Purpose
+
+When nominating multiple candidates from a single batch, reviewers need to:
+- see how candidates differ across predicted properties,
+- confirm that comparison criteria are consistent across all candidates,
+- verify that the top-ranked candidate has a defensible advantage over runners-up.
+
+## Required fields
+
+| Field | Type | Constraint |
+|---|---|---|
+| `comparison_id` | str | Must start with `"CMP-"` |
+| `batch_id` | str | Non-empty |
+| `pipeline_version` | str | Non-empty |
+| `comparison_date` | str | ISO 8601 `YYYY-MM-DD` |
+| `candidate_ids` | list[str] | ≥ `MINIMUM_CANDIDATES` (2) entries |
+| `comparison_criteria` | list[str] | ≥ `MINIMUM_CRITERIA` (2) entries |
+| `top_candidate_id` | str | Must be in `candidate_ids` |
+| `top_candidate_rationale` | str | Non-empty, ≤ 500 characters |
+| `evidence_level` | int | 1 – 6 |
+| `reviewer` | str | Non-empty |
+| `dry_lab_only` | bool | Must be `True` |
+
+## Minimum requirements
+
+- At least 2 candidates must be compared (`MINIMUM_CANDIDATES = 2`).
+- At least 2 comparison criteria must be stated (`MINIMUM_CRITERIA = 2`).
+- The top candidate must appear in the `candidate_ids` list.
+
+## Valid evidence levels
+
+1 – 6 (from PROOF_LADDER.md)
+
+## Warnings
+
+- `evidence_level <= 2` — warning: low evidence; comparison may not be reliable.
+- `len(candidate_ids) > 10` — warning: large candidate set; consider splitting into sub-groups.
+- `len(comparison_criteria) < 3` — warning: fewer than 3 criteria; comparison may lack depth.
+
+## How to validate
+
+```bash
+make multi-candidate-comparison-check
+# or
+openamp-foundry multi-candidate-comparison-check \
+  --entry-json '{"comparison_id":"CMP-001","batch_id":"BATCH-001","pipeline_version":"0.8.7","comparison_date":"2026-07-09","candidate_ids":["AMP-001","AMP-002","AMP-003"],"comparison_criteria":["predicted_mic","hemolysis_fraction","selectivity_index"],"top_candidate_id":"AMP-001","top_candidate_rationale":"Highest selectivity index with lowest hemolysis fraction.","evidence_level":4,"reviewer":"alice","dry_lab_only":true}' \
+  --format text
+```
+
+## Honest-use boundary
+
+Multi-candidate comparisons are dry-lab outputs. Predicted property rankings do not
+imply experimental superiority. Wet-lab results may differ substantially from predictions.
diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,8 @@
 # Roadmap
 
+### v0.8.7
+- Phase L L4: multi-candidate comparison schema — validates structured side-by-side comparisons of two or more candidates for publication-ready supplementary tables. MultiCandidateComparisonEntry dataclass, validate_multi_candidate_comparison(), CLI multi-candidate-comparison-check.
+
 ### v0.8.6
 - Phase L L3: candidate summary card schema — validates publication-ready per-candidate structured summaries with sequence, evidence level, activity prediction, and safety flags. CandidateSummaryCardEntry dataclass, validate_candidate_summary_card(), CLI candidate-summary-card-check.
 

diff --git a/src/openamp_foundry/cli/commands/reports.py b/src/openamp_foundry/cli/commands/reports.py
@@ -3090,3 +3090,37 @@ def _run_candidate_summary_card_check(args: argparse.Namespace) -> int:
             print("  Candidate summary card validated. Ready for reviewer packet.")
 
     return 0 if result.passed else 3
+
+
+def _run_multi_candidate_comparison_check(args: argparse.Namespace) -> int:
+    """Validate a multi-candidate comparison entry."""
+    import json as _json
+    from openamp_foundry.evidence.multi_candidate_comparison import validate_multi_candidate_comparison_dict
+
+    try:
+        d = _json.loads(args.entry_json)
+    except _json.JSONDecodeError as exc:
+        print(_json.dumps({"status": "error", "error": f"Invalid JSON: {exc}"}))
+        return 2
+
+    if not isinstance(d, dict):
+        print(_json.dumps({"status": "error", "error": "--entry-json must be a JSON object"}))
+        return 2
+
+    result = validate_multi_candidate_comparison_dict(d)
+    output_format = getattr(args, "format", "text")
+
+    if output_format == "json":
+        import dataclasses
+        print(_json.dumps(dataclasses.asdict(result), indent=2))
+    else:
+        status = "PASS" if result.passed else "FAIL"
+        print(f"Multi-candidate comparison {result.comparison_id} (batch {result.batch_id}, {result.candidate_count} candidates): {status}")
+        for e in result.errors:
+            print(f"  ERROR: {e}")
+        for w in result.warnings:
+            print(f"  WARN:  {w}")
+        if result.passed:
+            print("  Multi-candidate comparison validated. Ready for supplementary table.")
+
+    return 0 if result.passed else 3
diff --git a/src/openamp_foundry/cli/main.py b/src/openamp_foundry/cli/main.py
@@ -15,7 +15,7 @@
 from openamp_foundry.cli.commands.reports import _run_security_report_check
 from openamp_foundry.cli.commands.reports import _run_citation_check
 from openamp_foundry.cli.commands.reports import _run_roadmap_sync_check
-from openamp_foundry.cli.commands.reports import _run_advisory_review_check, _run_annual_review_check, _run_selection_rationale_check, _run_batch_priority_check, _run_pilot_package_check, _run_calibration_intake_check, _run_uncertainty_report_check, _run_preprint_bundle_check, _run_reproducibility_manifest_check, _run_candidate_summary_card_check
+from openamp_foundry.cli.commands.reports import _run_advisory_review_check, _run_annual_review_check, _run_selection_rationale_check, _run_batch_priority_check, _run_pilot_package_check, _run_calibration_intake_check, _run_uncertainty_report_check, _run_preprint_bundle_check, _run_reproducibility_manifest_check, _run_candidate_summary_card_check, _run_multi_candidate_comparison_check
 
 import argparse
 import json
@@ -2125,6 +2125,24 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Multi-candidate comparison check (Phase L L4) ─────────────────
+    mccc = sub.add_parser(
+        "multi-candidate-comparison-check",
+        help=(
+            "Validate a multi-candidate comparison. Confirms candidate list, "
+            "criteria, top-candidate rationale, and evidence level. Dry-lab only."
+        ),
+    )
+    mccc.add_argument(
+        "--entry-json", type=str, required=True,
+        help="JSON string of a MultiCandidateComparisonEntry dict (required).",
+    )
+    mccc.add_argument(
+        "--format", type=str, default="text",
+        choices=["text", "json"],
+        help="Output format (default: text).",
+    )
+
     # ── Selection rationale check (Phase K K1) ───────────────────────
     src2 = sub.add_parser(
         "selection-rationale-check",
@@ -2454,6 +2472,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "candidate-summary-card-check":
         return _run_candidate_summary_card_check(args)
 
+    if args.command == "multi-candidate-comparison-check":
+        return _run_multi_candidate_comparison_check(args)
+
     parser.error("unknown command")
     return 2