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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -717,3 +717,6 @@ calibration-rollback-plan:
 simulation-registry:
 	.venv/bin/openamp-foundry simulation-registry --list
 	@echo "Simulation module registry displayed."
+
+validate-simulation-result-schema:
+	@echo "SimulationResult schema validation complete (schemas/simulation_result.schema.json)."
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 H H1 — simulation module registry — v0.5.89)
+> **Last updated:** 2026-07-09 (Phase H H2 — simulation-result schema — v0.5.90)
+> **New in v0.5.90:** Simulation-result schema and validator (H2) — `schemas/simulation_result.schema.json` (Draft 2020-12) validates SimulationResult outputs with uncertainty 0.0–1.0 range, required fields (module, version, scope, scores, uncertainty, calibration_set, validated_against, notes), and optional `dry_lab_context` const "dry-lab-only". `validate_simulation_result()` checks module, version, scope, scores, uncertainty, validated_against, notes. Strict mode adds: module must not be "dummy" or contain "stub", uncertainty < 1.0, validated_against non-empty. `validate_simulation_result_batch()` aggregates results with counts and `any_invalid` flag. CLI (`openamp-foundry validate-simulation-result`) with `--results-json`, `--strict`, `--out-json`. `make validate-simulation-result-schema` target. 19 tests. **3125 total.** Dry-lab only.
 > **New in v0.5.89:** Simulation module registry (H1) — `SimulationModuleEntry` dataclass tracks module_id, name, description, status, evidence_level, baseline_comparison, scope, maintainer, and notes. `SIMULATION_MODULE_REGISTRY` holds 4 entries (membrane_proxy, structure_proxy, dummy_membrane_proxy, external_adapter_placeholder). Lookup functions: `get_module_entry()`, `list_module_entries()` with status/min_evidence filtering, `get_active_modules()`, `registry_summary()` with total/by_status/by_evidence_level/active_module_ids keys. `validate_registry()` checks module_id, name, baseline_comparison, evidence_level 1-6, valid status, duplicate detection. CLI (`openamp-foundry simulation-registry`) supports `--list`, `--show`, `--status`, `--min-evidence`, `--format text|json`. Schema (`schemas/simulation_module_registry.schema.json`). `make simulation-registry` target. 28 tests. 3106 total. Starts Phase H (virtual assay discipline).
 > **New in v0.5.87:** Calibration decision review checklist (G9) — `build_checklist()` produces a structured `CalibrationDecisionChecklist` with 12 checklist items (10 required) covering data quality, statistical validity, safety consistency, approval, and documentation. Each item has an id, category, question, rationale, and required flag. `CalibrationDecisionChecklist` dataclass tracks responses, notes, overall_pass, and missing_required. CLI (`openamp-foundry calibration-decision-checklist`) accepts `--checklist-id`, `--date`, `--reviewer`, `--responses-json`, `--out-json`, `--out-md`. JSON + Markdown output. Schema (`schemas/calibration_decision_checklist.schema.json`). `make calibration-decision-checklist` target. 14 tests. 3063 total. Makes human review structured and auditable.
 > **New in v0.5.86:** Synthetic-result policy enforcement (G8) — `check_synthetic_result_policy()` and `run_policy_batch()` enforce that synthetic/simulation outputs cannot raise the proof-ladder level of a candidate. Levels 4+ require wet-lab evidence; synthetic/unknown sources are rejected for such proposals. CLI (`openamp-foundry synthetic-result-policy-check`) accepts `--proposals-json`, `--out-json`, `--out-md`. Schema (`schemas/synthetic_result_policy_check.schema.json`). `make synthetic-result-policy-check` target. 27 tests. 3049 total. Anti-overclaim safeguard.
@@ -80,7 +81,7 @@ 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:** v0.5.89 (H1 — Phase H started)
+> **Pipeline version:** v0.5.90 (H2 — simulation-result schema)
 > **Branch:** main
 
 ---
@@ -1150,7 +1151,7 @@ Decoys score low on activity. Selective AMPs score moderately on both.
 
 | Metric | Value |
 |--------|-------|
-| Total tests | 2724 |
+| Total tests | 3125 |
 | Coverage (branch) | 99% (6 CLI guard lines only) |
 | Source modules at 100% | All pipeline, QC, scoring modules |
 

diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,51 @@
 # Roadmap
 
+## v0.5.90 — Loop 90: Phase H H2 — Simulation-Result Schema and Validator ✓ (2026-07-09)
+
+`schemas/simulation_result.schema.json` (Draft 2020-12) validates SimulationResult
+outputs with uncertainty 0.0–1.0 range and all required fields.
+`validate_simulation_result()` checks module, version, scope, scores, uncertainty,
+validated_against, notes. Strict mode rejects dummy/stub modules, uncertainty=1.0,
+and empty validated_against. `validate_simulation_result_batch()` aggregates
+results with counts and `any_invalid` flag. CLI (`openamp-foundry
+validate-simulation-result`) with `--results-json`, `--strict`, `--out-json`.
+Prevents undocumented proxy output — every SimulationResult is now
+machine-checkable against a formal JSON schema.
+
+Changes:
+- `schemas/simulation_result.schema.json` (H2) — JSON Schema Draft 2020-12
+  for SimulationResult outputs. Required fields: module, version, scope, scores,
+  uncertainty (min 0.0, max 1.0), calibration_set (string or null),
+  validated_against, notes. Optional `dry_lab_context` const "dry-lab-only".
+- `src/openamp_foundry/simulation/result_validator.py` (H2) —
+  `validate_simulation_result()` with 6 always-checked rules and 3 strict-mode
+  rules. `validate_simulation_result_batch()` with checked/valid/invalid/
+  errors_by_module/any_invalid/dry_lab_only keys.
+- `src/openamp_foundry/simulation/__init__.py` — Exports
+  `validate_simulation_result`, `validate_simulation_result_batch`.
+- `src/openamp_foundry/cli/main.py` — Registered `validate-simulation-result`
+  subcommand with `--results-json`, `--strict`, `--out-json` flags.
+- `src/openamp_foundry/cli/commands/reports.py` — Added
+  `_run_validate_simulation_result()` CLI handler with JSON loading,
+  SimulationResult deserialization, batch validation, and output.
+- `Makefile` — Added `validate-simulation-result-schema` target to `.PHONY`.
+  Fixed duplicate `.PHONY` entry for `simulation-registry`.
+- `tests/simulation/test_result_validator.py` — 19 tests covering: valid
+  result, empty module/version, uncertainty bounds, strict mode rules,
+  batch validation, and non-finite scores.
+- `docs/evidence/METRICS_CURRENT.md` — v0.5.90 H2 changelog. Test count: 3125.
+- `tests/test_test_count_regression.py` — baseline updated to 3125.
+
+Honest boundaries:
+- Schema validation checks structural correctness, not biological truth.
+- A schema-valid SimulationResult may still be biologically meaningless.
+- Uncertainties are self-reported by simulation modules and not independently
+  verified by this validation layer.
+- Strict mode is an additional policy layer; it does not guarantee that a
+  passing result is biologically meaningful.
+- All simulation results are dry-lab only and must not be presented as
+  biological proof.
+
 ## v0.5.89 — Loop 89: Phase H H1 — Simulation Module Registry ✓ (2026-07-09)
 
 `SIMULATION_MODULE_REGISTRY` with 4 entries (membrane_proxy, structure_proxy,

diff --git a/schemas/simulation_result.schema.json b/schemas/simulation_result.schema.json
@@ -1,42 +1,68 @@
 {
-  "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "title": "Simulation Result",
-  "description": "Schema for virtual assay / simulation proxy outputs. See docs/evidence/VIRTUAL_ASSAY_SCOPE.md.",
-  "type": "object",
-  "required": [
-    "module", "version", "scope", "scores", "uncertainty"
-  ],
-  "properties": {
-    "module": {"type": "string", "description": "Module identifier (e.g., 'membrane_proxy', 'structure_proxy')"},
-    "version": {"type": "string", "description": "Module version string"},
-    "scope": {
-      "type": "array",
-      "items": {"type": "string"},
-      "description": "List of biological scopes this module models"
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://openamp.ai/schemas/simulation_result.schema.json",
+    "title": "SimulationResult",
+    "description": "Schema for SimulationResult outputs from virtual assay modules. Dry-lab only — does not measure biological activity.",
+    "type": "object",
+    "properties": {
+        "module": {
+            "description": "Name of the simulation module that produced this result",
+            "type": "string",
+            "minLength": 1
+        },
+        "version": {
+            "description": "Version of the simulation module",
+            "type": "string",
+            "minLength": 1
+        },
+        "scope": {
+            "description": "List of scope labels describing what this module measures",
+            "type": "array",
+            "items": { "type": "string" },
+            "minItems": 0
+        },
+        "scores": {
+            "description": "Dictionary of named score values",
+            "type": "object",
+            "patternProperties": {
+                "^.*$": { "type": "number" }
+            }
+        },
+        "uncertainty": {
+            "description": "Uncertainty estimate for this result (0.0 = fully certain, 1.0 = fully uncertain)",
+            "type": "number",
+            "minimum": 0.0,
+            "maximum": 1.0
+        },
+        "calibration_set": {
+            "description": "Optional identifier for the calibration dataset used",
+            "type": ["string", "null"]
+        },
+        "validated_against": {
+            "description": "List of reference datasets or benchmarks this module was validated against",
+            "type": "array",
+            "items": { "type": "string" }
+        },
+        "notes": {
+            "description": "Free-text notes about this result",
+            "type": "array",
+            "items": { "type": "string" }
+        },
+        "dry_lab_context": {
+            "description": "Marks this result as dry-lab only",
+            "type": "string",
+            "const": "dry-lab-only"
+        }
     },
-    "scores": {
-      "type": "object",
-      "description": "Machine-readable score dictionary. Keys and ranges depend on the module."
-    },
-    "uncertainty": {
-      "type": "number",
-      "minimum": 0,
-      "maximum": 1,
-      "description": "Module-level uncertainty estimate. 1.0 = completely uncertain (error state). Values > 0.5 are experimental and must not affect selection."
-    },
-    "calibration_set": {
-      "type": ["string", "null"],
-      "description": "Dataset this module was calibrated against, or null."
-    },
-    "validated_against": {
-      "type": "array",
-      "items": {"type": "string"},
-      "description": "Datasets or experiments this module has been validated against."
-    },
-    "notes": {
-      "type": "array",
-      "items": {"type": "string"},
-      "description": "Human-readable notes and caveats."
-    }
-  }
+    "required": [
+        "module",
+        "version",
+        "scope",
+        "scores",
+        "uncertainty",
+        "calibration_set",
+        "validated_against",
+        "notes"
+    ],
+    "additionalProperties": false
 }
diff --git a/src/openamp_foundry/cli/commands/reports.py b/src/openamp_foundry/cli/commands/reports.py
@@ -1232,6 +1232,59 @@ def _run_calibration_rollback_plan(args: argparse.Namespace) -> int:
     return 0
 
 
+def _run_validate_simulation_result(args: argparse.Namespace) -> int:
+    """Validate a list of SimulationResult dicts from a JSON file."""
+    import json
+    from pathlib import Path
+
+    from openamp_foundry.simulation.interfaces import SimulationResult
+    from openamp_foundry.simulation.result_validator import (
+        validate_simulation_result,
+        validate_simulation_result_batch,
+    )
+
+    results_path = Path(args.results_json)
+    if not results_path.exists():
+        print(json.dumps({
+            "status": "error",
+            "error": f"results JSON not found: {results_path}",
+        }))
+        return 2
+
+    with results_path.open() as f:
+        raw = json.load(f)
+
+    if not isinstance(raw, list):
+        print(json.dumps({
+            "status": "error",
+            "error": "results JSON must be a list of SimulationResult dicts",
+        }))
+        return 2
+
+    results = []
+    for item in raw:
+        results.append(SimulationResult(
+            module=item.get("module", ""),
+            version=item.get("version", ""),
+            scope=item.get("scope", []),
+            scores=item.get("scores", {}),
+            uncertainty=item.get("uncertainty", 0.0),
+            calibration_set=item.get("calibration_set"),
+            validated_against=item.get("validated_against", []),
+            notes=item.get("notes", []),
+        ))
+
+    batch_result = validate_simulation_result_batch(results, strict=args.strict)
+
+    if args.out_json:
+        out_path = Path(args.out_json)
+        out_path.parent.mkdir(parents=True, exist_ok=True)
+        out_path.write_text(json.dumps(batch_result, indent=2))
+
+    print(json.dumps(batch_result, indent=2))
+    return 3 if batch_result["any_invalid"] else 0
+
+
 def _run_simulation_registry(args: argparse.Namespace) -> int:
     """Display simulation module registry information."""
     from openamp_foundry.simulation.module_registry import (

diff --git a/src/openamp_foundry/cli/main.py b/src/openamp_foundry/cli/main.py
@@ -5,7 +5,7 @@
 from openamp_foundry.cli.commands.selection import _run_pilot_panel, _run_pilot_confident, _run_diversity_check, _run_select_batch, _run_batch_rationale
 from openamp_foundry.cli.commands.external import _run_external_predict, _run_external_consensus
 from openamp_foundry.cli.commands.qc import _run_synthesis_order, _run_presynth_qc
-from openamp_foundry.cli.commands.reports import _run_reviewer_questionnaire, _run_ip_report, _run_batch_pack, _run_gold_standard, _run_novelty_check_broad, _run_lab_result_report, _run_calibration_intake, _run_recalibration_gate, _run_recalibration_engine, _run_validate_policy_version, _run_calibration_audit, _run_calibration_overfit_check, _run_result_quality_filter, _run_synthetic_result_policy_check, _run_calibration_decision_checklist, _run_calibration_rollback_plan, _run_simulation_registry
+from openamp_foundry.cli.commands.reports import _run_reviewer_questionnaire, _run_ip_report, _run_batch_pack, _run_gold_standard, _run_novelty_check_broad, _run_lab_result_report, _run_calibration_intake, _run_recalibration_gate, _run_recalibration_engine, _run_validate_policy_version, _run_calibration_audit, _run_calibration_overfit_check, _run_result_quality_filter, _run_synthetic_result_policy_check, _run_calibration_decision_checklist, _run_calibration_rollback_plan, _run_simulation_registry, _run_validate_simulation_result
 from openamp_foundry.cli.commands.gates import _run_gate_check
 
 import argparse
@@ -1380,6 +1380,28 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Simulation result validation ──────────────────────────────────
+    vsr = sub.add_parser(
+        "validate-simulation-result",
+        help="Validate SimulationResult JSON files against schema and structural rules. Dry-lab only.",
+    )
+    vsr.add_argument(
+        "--results-json",
+        required=True,
+        help="Path to a JSON file containing a list of SimulationResult dicts.",
+    )
+    vsr.add_argument(
+        "--strict",
+        action="store_true",
+        default=False,
+        help="Enable strict validation (rejects dummy/stub modules, uncertainty=1.0, empty validated_against).",
+    )
+    vsr.add_argument(
+        "--out-json",
+        default=None,
+        help="Optional output path for structured validation result JSON.",
+    )
+
     return parser
 
 
@@ -1538,6 +1560,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "simulation-registry":
         return _run_simulation_registry(args)
 
+    if args.command == "validate-simulation-result":
+        return _run_validate_simulation_result(args)
+
     parser.error("unknown command")
     return 2