feat: Phase W W2 charge-matched challenge schema (CMC-) -- documents pipeline AUROC vs charge-only baseline; VALID_CMC_VERDICTS (4), MEANINGFUL_GAP_THRESHOLD=0.05, auroc_gap auto-computed; blocks performance claims when charge explains the gap; 60 tests (#1004)

Co-authored-by: OpenCode <opencode@example.com>

Author: cschanhniem

docs/research/NEXT_100_PR_MAP.md

@@ -277,7 +277,7 @@ Make it machine-verifiable that the pipeline produces novel candidates that beat
 | ID | Task | Why it matters | Priority |
 |----|------|----------------|----------|
 | W1 | Add novelty challenge harness schema (NCH-) (complete). — src/openamp_foundry/evidence/novelty_challenge_harness.py: VALID_NCH_VERDICTS (4: novel_batch/mixed_novelty/near_neighbor_dominated/challenge_not_run), VALID_REFERENCE_DATABASES (6), NEAR_NEIGHBOR_IDENTITY_THRESHOLD=0.80, NOVEL_BATCH_CEILING=0.20, NEAR_NEIGHBOR_DOMINATED_FLOOR=0.60; NCHCandidateResult helper; build() auto-computes is_near_neighbor from identity vs threshold, fraction, verdict; dry_lab_only=True enforced; 63 tests in tests/evidence/test_novelty_challenge_harness.py. | Batch-level novelty challenge: documents the fraction of top candidates with ≥80% sequence identity to a known AMP in a reference database (APD3/DRAMP/etc.); blocks novel_batch claim when near-neighbor fraction exceeds 20%; prevents pipeline from advancing near-copies of known AMPs under a novelty label. | C |
-| W2 | Add charge-matched challenge schema (CMC-). | Formally documents the charge-matched challenge: compares pipeline AUROC vs a charge-only baseline on the same candidate set; verdict controlled vocabulary (gap_meaningful/gap_marginal/gap_absent/not_run); blocks performance claims when the charge-only baseline explains the gap. | C |
+| W2 | Add charge-matched challenge schema (CMC-) (complete). — src/openamp_foundry/evidence/charge_matched_challenge.py: VALID_CMC_VERDICTS (4: gap_meaningful/gap_marginal/gap_absent/challenge_not_run), VALID_CHARGE_BASELINE_METHODS (4), MEANINGFUL_GAP_THRESHOLD=0.05, MARGINAL_GAP_LOWER=0.02; auroc_gap auto-computed; verdict auto-derived; dry_lab_only=True enforced; 60 tests in tests/evidence/test_charge_matched_challenge.py. | Formally documents the charge-matched challenge: compares pipeline AUROC vs a charge-only baseline on the same candidate set; verdict controlled vocabulary (gap_meaningful/gap_marginal/gap_absent/not_run); blocks performance claims when the charge-only baseline explains the gap. | C |
 | W3 | Add similarity challenge harness schema (SCH-). | Documents whether pipeline-selected candidates are systematically more similar to known AMPs than random selection from the sequence space; flags selection bias from similarity clustering; prevents "novel panel" claim when selection is proximity-driven. | C |
 | W4 | Add benchmark challenge registry schema (BCR-). | Machine-readable registry of which benchmark challenges (NCH/CMC/SCH) have been run and passed for a given pipeline version; aggregates challenge verdicts; overall hardness grade (A: all passed, B: most passed, C: some passed, D: none passed). | C |
 | W5 | Add Phase W benchmark gate (WBG-). | Top-level gate asserting NCH + CMC + SCH + BCR all present; overall verdict: hardened/partially_hardened/not_hardened; closes Phase W; no batch-level performance claim is credible without passing this gate. | C |

src/openamp_foundry/evidence/charge_matched_challenge.py

@@ -0,0 +1,154 @@
+"""CMC- charge-matched challenge schema.
+
+Documents the charge-matched challenge run for a batch: compares pipeline
+AUROC versus a charge-only baseline on the same candidate set with the same
+charge distribution. A meaningful gap is required to claim the pipeline adds
+value beyond simply preferring cationic sequences.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+
+VALID_CMC_VERDICTS: frozenset[str] = frozenset({
+    "gap_meaningful",
+    "gap_marginal",
+    "gap_absent",
+    "challenge_not_run",
+})
+
+VALID_CHARGE_BASELINE_METHODS: frozenset[str] = frozenset({
+    "charge_only_rank",
+    "charge_length_rank",
+    "charge_hydrophobicity_rank",
+    "logistic_charge_only",
+})
+
+MEANINGFUL_GAP_THRESHOLD: float = 0.05
+MARGINAL_GAP_LOWER: float = 0.02
+
+MIN_AUROC: float = 0.0
+MAX_AUROC: float = 1.0
+
+
+@dataclass
+class ChargeMatchedChallenge:
+    cmc_id: str
+    batch_id: str
+    pipeline_version: str
+    baseline_method: str
+    pipeline_auroc: float
+    baseline_auroc: float
+    auroc_gap: float
+    n_candidates: int
+    mean_charge_pipeline: float
+    mean_charge_baseline: float
+    charge_distribution_matched: bool
+    cmc_verdict: str
+    dry_lab_only: bool
+    limitations: list[str]
+    created_at: str
+
+
+def validate_charge_matched_challenge(cmc: ChargeMatchedChallenge) -> None:
+    if not cmc.cmc_id.startswith("CMC-"):
+        raise ValueError(f"cmc_id must start with 'CMC-': {cmc.cmc_id!r}")
+    if not cmc.batch_id:
+        raise ValueError("batch_id must be non-empty")
+    if not cmc.pipeline_version:
+        raise ValueError("pipeline_version must be non-empty")
+    if cmc.baseline_method not in VALID_CHARGE_BASELINE_METHODS:
+        raise ValueError(
+            f"baseline_method {cmc.baseline_method!r} not in VALID_CHARGE_BASELINE_METHODS"
+        )
+    if not (MIN_AUROC <= cmc.pipeline_auroc <= MAX_AUROC):
+        raise ValueError(
+            f"pipeline_auroc must be in [0, 1]: {cmc.pipeline_auroc}"
+        )
+    if not (MIN_AUROC <= cmc.baseline_auroc <= MAX_AUROC):
+        raise ValueError(
+            f"baseline_auroc must be in [0, 1]: {cmc.baseline_auroc}"
+        )
+    expected_gap = round(cmc.pipeline_auroc - cmc.baseline_auroc, 6)
+    if abs(cmc.auroc_gap - expected_gap) > 1e-4:
+        raise ValueError(
+            f"auroc_gap {cmc.auroc_gap} does not match computed "
+            f"{expected_gap} (pipeline_auroc - baseline_auroc)"
+        )
+    if cmc.n_candidates < 0:
+        raise ValueError("n_candidates must be non-negative")
+    if cmc.cmc_verdict not in VALID_CMC_VERDICTS:
+        raise ValueError(
+            f"cmc_verdict {cmc.cmc_verdict!r} not in VALID_CMC_VERDICTS"
+        )
+    if not cmc.dry_lab_only:
+        raise ValueError("dry_lab_only must be True")
+    if not cmc.limitations:
+        raise ValueError("limitations must be non-empty")
+    if not cmc.created_at:
+        raise ValueError("created_at must be non-empty")
+
+
+def _compute_verdict(n_candidates: int, auroc_gap: float) -> str:
+    if n_candidates == 0:
+        return "challenge_not_run"
+    if auroc_gap >= MEANINGFUL_GAP_THRESHOLD:
+        return "gap_meaningful"
+    if auroc_gap >= MARGINAL_GAP_LOWER:
+        return "gap_marginal"
+    return "gap_absent"
+
+
+def build_charge_matched_challenge(
+    *,
+    cmc_id: str,
+    batch_id: str,
+    pipeline_version: str,
+    baseline_method: str,
+    pipeline_auroc: float,
+    baseline_auroc: float,
+    n_candidates: int,
+    mean_charge_pipeline: float,
+    mean_charge_baseline: float,
+    charge_distribution_matched: bool,
+    limitations: list[str],
+    created_at: str,
+) -> ChargeMatchedChallenge:
+    auroc_gap = round(pipeline_auroc - baseline_auroc, 6)
+    verdict = _compute_verdict(n_candidates, auroc_gap)
+    cmc = ChargeMatchedChallenge(
+        cmc_id=cmc_id,
+        batch_id=batch_id,
+        pipeline_version=pipeline_version,
+        baseline_method=baseline_method,
+        pipeline_auroc=pipeline_auroc,
+        baseline_auroc=baseline_auroc,
+        auroc_gap=auroc_gap,
+        n_candidates=n_candidates,
+        mean_charge_pipeline=mean_charge_pipeline,
+        mean_charge_baseline=mean_charge_baseline,
+        charge_distribution_matched=charge_distribution_matched,
+        cmc_verdict=verdict,
+        dry_lab_only=True,
+        limitations=limitations,
+        created_at=created_at,
+    )
+    validate_charge_matched_challenge(cmc)
+    return cmc
+
+
+def format_charge_matched_challenge(cmc: ChargeMatchedChallenge) -> str:
+    lines = [
+        f"Charge-Matched Challenge — {cmc.cmc_id}",
+        f"Batch: {cmc.batch_id}  |  Pipeline: {cmc.pipeline_version}",
+        f"Baseline method: {cmc.baseline_method}",
+        f"Verdict: {cmc.cmc_verdict}",
+        f"Pipeline AUROC: {cmc.pipeline_auroc:.4f}  |  Baseline AUROC: {cmc.baseline_auroc:.4f}  |  Gap: {cmc.auroc_gap:+.4f}",
+        f"N candidates: {cmc.n_candidates}",
+        f"Mean charge — pipeline: {cmc.mean_charge_pipeline:.2f}  |  baseline: {cmc.mean_charge_baseline:.2f}",
+        f"Charge distribution matched: {cmc.charge_distribution_matched}",
+        f"Created: {cmc.created_at}",
+        f"Limitations: {'; '.join(cmc.limitations)}",
+        f"dry_lab_only: {cmc.dry_lab_only}",
+    ]
+    return "\n".join(lines)