{ "map_schema": "nmd-vcell-model-capability-map/1.0", "interface_build": "EA-20260817-57", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "capability_count": 4, "purpose": "Translate the model and ModelRun registry into answerable questions, unsupported questions, required datasets and required outcomes.", "use_rule": "Capability is granted by local evidence objects and returned outcomes, not by model-family reputation.", "records": [ { "capability_schema": "nmd-vcell-model-capability-map/1.0", "capability_id": "CAP-MODEL-SAME-ASSAY-RESPONSE", "lane": "Same-assay response baseline", "current_state": "Available as a bounded technical comparator", "current_model_ids": [ "NMDVCELL-RIDGE-SAFE-2.3" ], "current_model_run_ids": [ "MRUN-RIDGE-SAFE-2.3-G0-REPEATED-FOLD" ], "can_answer_now": [ "Whether the released HepG2 CRISPRi ridge baseline improves mean response error within its own processed assay context.", "Which permanent controls a future perturbation model must beat before it earns a stronger local claim." ], "cannot_answer_yet": [ "DMD muscle response, pathway reversal, patient response or treatment simulation.", "Directionally reliable biology outside the same processed HepG2 task." ], "required_dataset_to_unlock": [ "A compatible same-assay holdout for continued technical benchmarking.", "A harmonized external cell-level perturbation outcome before any transfer claim." ], "required_outcome_to_unlock": [ "Task-bound response vectors with the same frozen feature space, split rule and leakage controls.", "For DMD relevance, matched disease-context perturbation outcomes must be registered separately." ], "next_decision": "Retain as the permanent comparator every new architecture must clear.", "handoff_route": "/resource/model-run/mrun-ridge-safe-2-3-g0-repeated-fold/", "evidence_objects": [ "/resource/model-run/mrun-ridge-safe-2-3-g0-repeated-fold/", "/resource/api/v1.1/model-runs/mrun-ridge-safe-2-3-g0-repeated-fold.json", "/resource/models/nmdvcell-ridge-safe-2-3/", "/resource/dataset/nmdvcell-hepg2-crispri/" ] }, { "capability_schema": "nmd-vcell-model-capability-map/1.0", "capability_id": "CAP-MODEL-EXTERNAL-TRANSFER-COMPARATOR", "lane": "External transfer and advanced comparators", "current_state": "Executed evidence shows where complex models did not advance", "current_model_ids": [ "NMDVCELL-TRANSFER-DIAGNOSTIC-1.0" ], "current_model_run_ids": [ "MRUN-TRANSFER-DIAGNOSTIC-1.0-G1", "MRUN-GEARS-0.1.2-FIVE-SEED-20260713", "MRUN-SCGPT-0.2.5-FIVE-SEED-20260714", "MRUN-TXPERT-CONFIG-GAT-SEED-20260712", "MRUN-MORPH-DEPMAP25Q3-VALIDATION-20260722" ], "can_answer_now": [ "Which frozen advanced-comparator runs failed, stopped or remained negative against the released baselines.", "Which provenance, seed and feature-coverage gaps prevent a model-family reputation from becoming local evidence." ], "cannot_answer_yet": [ "General superiority of GEARS, scGPT, TxPert, MORPH or any watched external model inside NMD-VCell.", "A valid DMD or muscle-context transfer claim from aggregate HepG2-only evidence." ], "required_dataset_to_unlock": [ "Harmonized cell-level perturbation outcomes with exact gene-feature alignment and reusable adapters.", "External holdouts with preregistered task, split, baseline stack and failure-preserving ModelRun receipts." ], "required_outcome_to_unlock": [ "Prospective transfer outcomes returned under the same evaluator and permanent baseline policy.", "Feature-coverage, seed, code, container and data-digest receipts that make reruns auditable." ], "next_decision": "Use these runs as a value-producing negative-control library, then bind any new comparator to a fresh frozen task.", "handoff_route": "/resource/benchmarks/", "evidence_objects": [ "/resource/benchmarks/", "/resource/api/v1.1/model_run_registry.json", "/resource/model-run/mrun-transfer-diagnostic-1-0-g1/", "/resource/model-run/mrun-gears-0-1-2-five-seed-20260713/", "/resource/model-run/mrun-scgpt-0-2-5-five-seed-20260714/", "/resource/model-run/mrun-txpert-config-gat-seed-20260712/", "/resource/model-run/mrun-morph-depmap25q3-validation-20260722/" ] }, { "capability_schema": "nmd-vcell-model-capability-map/1.0", "capability_id": "CAP-MODEL-DMD-PERTURBATION-RESPONSE", "lane": "DMD perturbation response", "current_state": "Ready as an evaluation contract; awaiting disease-context truth", "current_model_ids": [ "NMDVCELL-DMD-TRANSITION-FUTURE", "NMDVCELL-GENE-CHEMICAL-BRIDGE-FUTURE" ], "current_model_run_ids": [], "can_answer_now": [ "Which exact evidence object is missing before NMD-VCell can train or release a disease-conditioned response model.", "How a candidate should move from Evidence Card to Study Card to registered Prediction and returned Outcome." ], "cannot_answer_yet": [ "Candidate-conditioned DMD molecular response, myogenic functional effect, toxicity or calibrated uncertainty.", "Gene-to-drug translation in DMD without matched genetic and chemical perturbation screens." ], "required_dataset_to_unlock": [ "Matched DMD and control myogenic perturbation dataset with donor, state, time, perturbation modality and target-engagement fields.", "For the gene–chemical bridge, paired genetic and compound screens in the same relevant muscle-state space." ], "required_outcome_to_unlock": [ "Replicated molecular plus fusion or viability endpoint returned through Study → Prediction → Outcome objects.", "Donor- and context-disjoint holdouts with calibration, abstention and toxicity-miss audits." ], "next_decision": "Convert the strongest candidate handoffs into a small registered DMD outcome pilot instead of emitting a premature prediction.", "handoff_route": "/resource/dmd-outcome-pilot/", "evidence_objects": [ "/resource/models/nmdvcell-dmd-transition-future/", "/resource/models/nmdvcell-gene-chemical-bridge-future/", "/resource/dmd-outcome-pilot/", "/resource/study-card/ZNF133.html", "/resource/study-card/MON1A.html" ] }, { "capability_schema": "nmd-vcell-model-capability-map/1.0", "capability_id": "CAP-MODEL-PATIENT-FUNCTIONAL-GENERALIZATION", "lane": "Patient and functional generalization", "current_state": "Research roadmap with governance requirements", "current_model_ids": [ "NMDVCELL-PATIENT-TRAJECTORY-FUTURE" ], "current_model_run_ids": [], "can_answer_now": [ "What patient-linked validation, privacy and prospective evaluation would require before trajectory modeling becomes meaningful.", "Which current artifacts can prepare the path: dataset registry, outcome pilot, distribution contract and ModelRun ledger." ], "cannot_answer_yet": [ "Patient-specific progression, individual treatment response, clinical decision support or therapeutic utility.", "Functional recovery claims without longitudinal patient-linked outcomes and independent clinical governance." ], "required_dataset_to_unlock": [ "Longitudinal patient-linked cell-state, intervention and phenotype datasets with auditable consent and privacy boundaries.", "Site-, donor- and time-disjoint cohorts connected to molecular and functional readouts." ], "required_outcome_to_unlock": [ "Prospective functional outcomes that can test calibration, safety, subgroup performance and clinical utility.", "A governance-approved endpoint definition before any patient-facing interpretation is exposed." ], "next_decision": "Keep this lane as the north-star validation program while near-term work focuses on DMD perturbation truth.", "handoff_route": "/resource/research-program/", "evidence_objects": [ "/resource/models/nmdvcell-patient-trajectory-future/", "/resource/research-program/", "/resource/trajectory/", "/resource/distribution-modeling/" ] } ] }