{ "registry_schema": "nmd-vcell-model-registry/1.1", "interface_build": "EA-20260817-57", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "executed_object_count": 2, "frozen_model_run_count": 6, "calibrated_dmd_model_count": 0, "model_card_count": 5, "model_card_schema": "api/v1.1/model_card.schema.json", "model_card_audit_registry": "api/v1.1/model_card_audit_registry.json", "model_run_registry": "api/v1.1/model_run_registry.json", "model_capability_map_schema": "nmd-vcell-model-capability-map/1.0", "model_capability_map_url": "api/v1.1/model_capability_map.json", "model_capability_map": [ { "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/" ] } ], "records": [ { "model_id": "NMDVCELL-RIDGE-SAFE-2.3", "name": "Same-context perturbation baseline", "model_family": "ridge residual baseline", "lifecycle_state": "EXECUTED_LIMITED", "state": "limited", "status": "Executed · limited", "input": "Training folds of processed HepG2 perturbation-response deltas", "output": "Held-out 2,000-feature mean response vector", "training_context": "One processed HepG2 CRISPRi assay context", "held_out_task": "Repeated target-level balanced folds · G0", "permanent_baselines": "zero change · training-response mean · ridge residual", "primary_metrics": "RMSE · raw cosine · residual cosine", "current_result": "Small average-error improvement; response direction is not reliable.", "permitted_use": "Same-assay technical baseline and benchmark control only", "unlock_condition": "Beat simple baselines on harmonized external cell-level perturbation outcome before any transport claim.", "audit_card_slug": "nmdvcell-ridge-safe-2-3", "audit_card_url": "/resource/models/nmdvcell-ridge-safe-2-3/", "audit_card_json": "/resource/api/v1.1/model-cards/nmdvcell-ridge-safe-2-3.json" }, { "model_id": "NMDVCELL-TRANSFER-DIAGNOSTIC-1.0", "name": "External perturbation transfer diagnostic", "model_family": "evaluation adapter", "lifecycle_state": "EXECUTED_UNSUPPORTED", "state": "unsupported", "status": "Executed · unsupported", "input": "Frozen 55-target external aggregate diagnostic", "output": "Directional-transfer assessment", "training_context": "HepG2 response substrate", "held_out_task": "External aggregate target set · G1", "permanent_baselines": "zero change · training-response mean · ridge", "primary_metrics": "aggregate directional-agreement diagnostic", "current_result": "The current model did not transfer directionally.", "permitted_use": "Method diagnostic; not a cell-population or DMD benchmark", "unlock_condition": "Add harmonized cell-level outcome, exact feature alignment and a preregistered external estimator.", "audit_card_slug": "nmdvcell-transfer-diagnostic-1-0", "audit_card_url": "/resource/models/nmdvcell-transfer-diagnostic-1-0/", "audit_card_json": "/resource/api/v1.1/model-cards/nmdvcell-transfer-diagnostic-1-0.json" }, { "model_id": "NMDVCELL-DMD-TRANSITION-FUTURE", "name": "Disease-conditioned state-transition model", "model_family": "future conditional population model", "lifecycle_state": "LOCKED_NO_TRAINING_TRUTH", "state": "locked", "status": "Not trained", "input": "Required matched DMD/control myogenic perturbations with donor, state, time and function", "output": "Desired molecular response, state transition, functional effect, toxicity and calibrated uncertainty", "training_context": "No qualifying disease-relevant perturbation training set", "held_out_task": "Planned unseen donor · state · laboratory · disease line · G2–G6", "permanent_baselines": "zero change · train mean · ridge · nearest-neighbour transfer", "primary_metrics": "DES · PDS · MAE · calibration · AUPRC · hit rate · replication · abstention", "current_result": "No calibrated DMD state-transition prediction is emitted.", "permitted_use": "Architecture and evaluation contract only", "unlock_condition": "Return independent DMD perturbation outcomes through frozen Study, Prediction and Outcome objects.", "audit_card_slug": "nmdvcell-dmd-transition-future", "audit_card_url": "/resource/models/nmdvcell-dmd-transition-future/", "audit_card_json": "/resource/api/v1.1/model-cards/nmdvcell-dmd-transition-future.json" }, { "model_id": "NMDVCELL-GENE-CHEMICAL-BRIDGE-FUTURE", "name": "Gene–chemical bridge model", "model_family": "future multimodal perturbation model", "lifecycle_state": "LOCKED_NO_MATCHED_SCREENS", "state": "locked", "status": "Not trained", "input": "Required matched genetic and chemical screens in relevant muscle or DMD states", "output": "Desired cross-modality response, mechanism concordance and uncertainty", "training_context": "No matched DMD genetic–chemical screen", "held_out_task": "Planned unseen compound · gene · donor · disease state", "permanent_baselines": "nearest-neighbour · pathway mean · additive transfer", "primary_metrics": "retrieval · response similarity · calibration · prospective hit rate", "current_result": "No drug-response or gene-to-compound translation is emitted.", "permitted_use": "Future design contract only", "unlock_condition": "Import traceable dose, time, target-engagement and phenotype truth for both modalities.", "audit_card_slug": "nmdvcell-gene-chemical-bridge-future", "audit_card_url": "/resource/models/nmdvcell-gene-chemical-bridge-future/", "audit_card_json": "/resource/api/v1.1/model-cards/nmdvcell-gene-chemical-bridge-future.json" }, { "model_id": "NMDVCELL-PATIENT-TRAJECTORY-FUTURE", "name": "Patient trajectory model", "model_family": "future longitudinal disease model", "lifecycle_state": "LOCKED_NO_LONGITUDINAL_PATIENT_TRUTH", "state": "locked", "status": "Not available", "input": "Required longitudinal patient-linked cell state, intervention and outcome data", "output": "Desired patient-specific trajectory and intervention response with uncertainty", "training_context": "No patient-linked longitudinal perturbation trajectory", "held_out_task": "Required prospective patient and site holdout", "permanent_baselines": "natural-history and population-level reference models", "primary_metrics": "prospective calibration · safety · subgroup performance · clinical utility", "current_result": "No patient-specific trajectory or treatment simulation is permitted.", "permitted_use": "Research roadmap only; no clinical decision support", "unlock_condition": "Requires longitudinal data, prospective evaluation, privacy safeguards and clinical governance.", "audit_card_slug": "nmdvcell-patient-trajectory-future", "audit_card_url": "/resource/models/nmdvcell-patient-trajectory-future/", "audit_card_json": "/resource/api/v1.1/model-cards/nmdvcell-patient-trajectory-future.json" } ], "external_model_watch": [ { "name": "STATE v1", "source": "Arc Virtual Cell Initiative", "method_scope": "State embedding plus context-conditioned state transition", "reported_training_scope": "167M observational and more than 100M perturbational cells across 70 human contexts", "nmdvcell_state": "External architecture reference · not executed in this release", "url": "https://arcinstitute.org/virtual-cell-initiative" }, { "name": "scGPT", "source": "Nature Methods", "method_scope": "Generative pretraining for single-cell tasks including perturbation response", "reported_training_scope": "More than 33M cells", "nmdvcell_state": "Local five-seed benchmark completed · official negative control · no DMD claim", "url": "https://www.nature.com/articles/s41592-024-02201-0" }, { "name": "Geneformer", "source": "Nature", "method_scope": "Context-aware attention model for network biology", "reported_training_scope": "Approximately 30M single-cell transcriptomes", "nmdvcell_state": "External backbone candidate · no NMD-VCell benchmark run", "url": "https://www.nature.com/articles/s41586-023-06139-9" }, { "name": "SCALE", "source": "arXiv preprint · March 2026", "method_scope": "Conditional population transport for perturbation prediction", "reported_training_scope": "Preprint reports evaluation on Tahoe-100M", "nmdvcell_state": "External preprint watch · not independently reproduced here", "url": "https://arxiv.org/abs/2603.17380" }, { "name": "PRiMeFlow", "source": "arXiv preprint · April 2026", "method_scope": "End-to-end flow matching in gene-expression space for genetic and chemical perturbations", "reported_training_scope": "Preprint reports distribution-level evaluation and the method behind a 2025 VCC Generalist Prize entry", "nmdvcell_state": "External preprint watch · author-reported performance only · not reproduced here", "url": "https://arxiv.org/abs/2604.13986" }, { "name": "Lingshu-Cell", "source": "arXiv preprint · March 2026", "method_scope": "Masked discrete diffusion for perturbation-conditioned single-cell population generation", "reported_training_scope": "Preprint reports whole-transcriptome population generation and evaluation across perturbation datasets", "nmdvcell_state": "External preprint watch · author-reported performance only · not reproduced here", "url": "https://arxiv.org/abs/2603.25240" } ], "boundary": "Published performance is never inherited. A local ModelRun remains visible when it is negative, unsupported or stopped, but no current run supports a calibrated DMD prediction." }