{ "registry_schema": "nmd-vcell-model-opportunity-registry/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-16", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "record_count": 12, "status_vocabulary": [ "EXECUTED_LOCAL_LIMITED_PASS", "EXECUTED_LOCAL_GATE_FAIL", "EXECUTED_LOCAL_NO_GO", "EXECUTED_LOCAL_GATE_FAIL", "EXECUTED_8_LEGACY_CONFIGS_ALL_GATE_FAIL", "LOCAL_NVME_CORE_SMOKE_PASS_NO_COMPATIBLE_CHECKPOINT", "SOURCE_PINNED_INPUT_CONTRACT_FAIL", "NOT_ELIGIBLE_FOR_EXECUTION", "SOURCE_VERIFIED_NOT_RUN", "SOURCE_VERIFIED_REPRESENTATION_ONLY", "SOURCE_VERIFIED_CONTEXT_MISMATCH", "SOURCE_VERIFIED_EVALUATION_CANDIDATE" ], "records": [ { "model_id": "NMDVCELL-RIDGE-SAFE-2.3", "model_name": "Same-context ridge residual baseline", "provider": "NMD-VCell", "artifact_type": "MODEL", "model_class": "LINEAR_BASELINE", "task": "Same-context perturbation-response prediction", "context": "Processed HepG2 CRISPRi substrate", "status": "EXECUTED_LOCAL_LIMITED_PASS", "local_result": "Small mean-RMSE improvement over train mean; raw direction unsupported.", "recommended_role": "Permanent comparator on every compatible frozen task.", "next_gate": "Retain without expanding beyond the same-assay scope.", "dmd_claim_allowed": false, "source_url": "/resource/api/v1.1/model-runs/mrun-ridge-safe-2-3-g0-repeated-fold.json" }, { "model_id": "EXTERNAL-GEARS-0.1.2", "model_name": "GEARS", "provider": "External model · local NMD-VCell run", "artifact_type": "MODEL", "model_class": "GRAPH_PERTURBATION_MODEL", "task": "Genetic perturbation response", "context": "Five frozen HepG2 same-coverage splits", "status": "EXECUTED_LOCAL_GATE_FAIL", "local_result": "0/5 splits advanced; ridge won all five same-coverage comparisons.", "recommended_role": "Official negative control.", "next_gate": "No rerun without a new preregistration, data view or untouched test set.", "dmd_claim_allowed": false, "source_url": "/resource/api/v1.1/model-runs/mrun-gears-0-1-2-five-seed-20260713.json" }, { "model_id": "EXTERNAL-SCGPT-0.2.5", "model_name": "scGPT", "provider": "Bowang Lab · local NMD-VCell run", "artifact_type": "MODEL", "model_class": "SINGLE_CELL_FOUNDATION_MODEL", "task": "Checkpoint-supported genetic perturbation response", "context": "Restricted gene coverage on five frozen HepG2 splits", "status": "EXECUTED_LOCAL_GATE_FAIL", "local_result": "0/5 splits advanced; higher RMSE than same-coverage ridge.", "recommended_role": "Foundation-model negative control with coverage visible.", "next_gate": "Only reassess with a frozen adapter contract and untouched compatible task.", "dmd_claim_allowed": false, "source_url": "https://www.nature.com/articles/s41592-024-02201-0" }, { "model_id": "EXTERNAL-TXPERT-CONFIG-GAT", "model_name": "TxPert public-STRING config-gat", "provider": "Recursion / Valence Labs · local NMD-VCell run", "artifact_type": "MODEL", "model_class": "KNOWLEDGE_GRAPH_PERTURBATION_MODEL", "task": "Out-of-distribution transcriptomic perturbation response", "context": "Frozen HepG2 advancement gate", "status": "EXECUTED_LOCAL_GATE_FAIL", "local_result": "Median delta cosine 0.346196 was below train mean 0.373307.", "recommended_role": "Stopped advanced comparator.", "next_gate": "Remaining seeds stay locked unless a new prospective protocol is frozen.", "dmd_claim_allowed": false, "source_url": "https://www.nature.com/articles/s41587-026-03113-4" }, { "model_id": "EXTERNAL-MORPH-1AD06D4", "model_name": "MORPH DepMap validation pilot", "provider": "External model · local NMD-VCell run", "artifact_type": "MODEL", "model_class": "GENE_EMBEDDING_PERTURBATION_MODEL", "task": "Validation-only perturbation pilot", "context": "HepG2 with DepMap Public 25Q3 embeddings", "status": "EXECUTED_LOCAL_NO_GO", "local_result": "Engineering passed; the model did not beat train mean.", "recommended_role": "Sealed negative control.", "next_gate": "Keep the v27 test partition sealed; revisions need a fresh contract.", "dmd_claim_allowed": false, "source_url": "/resource/api/v1.1/model-runs/mrun-morph-depmap25q3-validation-20260722.json" }, { "model_id": "ARC-STATE-1.0", "model_name": "STATE 1.0", "provider": "Arc Institute", "artifact_type": "MODEL", "model_class": "SET_BASED_STATE_TRANSITION_MODEL", "task": "Population-level perturbation response across contexts", "context": "Large public observational and perturbational corpora", "status": "EXECUTED_8_LEGACY_CONFIGS_ALL_GATE_FAIL", "local_result": "Eight CPU/GPU and held-out/seen-perturbation receipts were migrated; none beat both zero and train mean on every split.", "recommended_role": "Stopped comparator unless a materially new preregistered task or untouched outcome exists.", "next_gate": "Do not rerun by reputation; require a corrected preregistration, untouched truth or materially different task-compatible checkpoint.", "dmd_claim_allowed": false, "source_url": "https://github.com/ArcInstitute/state" }, { "model_id": "ARC-STACK-2026", "model_name": "Stack", "provider": "Arc Institute", "artifact_type": "MODEL", "model_class": "IN_CONTEXT_SINGLE_CELL_FOUNDATION_MODEL", "task": "In-context representation and condition transfer", "context": "Reported pretraining on 149 million uniformly processed human cells", "status": "LOCAL_NVME_CORE_SMOKE_PASS_NO_COMPATIBLE_CHECKPOINT", "local_result": "After one 180-second dependency-path timeout, a bounded local-NVMe retry passed the official StateICLModelBase forward path on a V100 with finite outputs. No pretrained checkpoint or task benchmark was run.", "recommended_role": "Runtime- and checkpoint-gated context-model hypothesis generator.", "next_gate": "Identify a task-compatible pretrained genetic checkpoint and preregister an untouched benchmark before any model-performance claim.", "dmd_claim_allowed": false, "source_url": "https://arcinstitute.org/news/foundation-model-stack" }, { "model_id": "CZI-TRANSCRIPTFORMER-0.6.0", "model_name": "TranscriptFormer", "provider": "Chan Zuckerberg Initiative", "artifact_type": "MODEL", "model_class": "CROSS_SPECIES_GENERATIVE_FOUNDATION_MODEL", "task": "Cell embeddings, classification, disease-state and regulatory inference", "context": "Up to 112 million cells across 12 species", "status": "SOURCE_VERIFIED_REPRESENTATION_ONLY", "local_result": "No NMD-VCell execution; not registered as a perturbation-response model.", "recommended_role": "Cross-species and disease-context representation benchmark.", "next_gate": "Test whether embeddings improve a frozen donor- or disease-held-out task over PCA and scVI.", "dmd_claim_allowed": false, "source_url": "https://virtualcellmodels.cziscience.com/model/transcriptformer" }, { "model_id": "BIOHUB-SCLDM-CD4-0.1", "model_name": "scLDM.CD4", "provider": "CZ Biohub Chicago", "artifact_type": "MODEL", "model_class": "LATENT_FLOW_MATCHING_PERTURBATION_MODEL", "task": "Conditional perturbed profile generation", "context": "Primary human CD4+ T cells", "status": "SOURCE_VERIFIED_CONTEXT_MISMATCH", "local_result": "No NMD-VCell execution; CD4 context does not match muscle disease tasks.", "recommended_role": "Architecture reference, not a direct adapter priority.", "next_gate": "Require a compatible muscle perturbation corpus before adaptation is considered.", "dmd_claim_allowed": false, "source_url": "https://virtualcellmodels.cziscience.com/model/scldm-cd4" }, { "model_id": "CELLOT-2023", "model_name": "CellOT", "provider": "ETH Zurich and collaborators", "artifact_type": "MODEL", "model_class": "NEURAL_OPTIMAL_TRANSPORT", "task": "Distribution-to-distribution perturbation response", "context": "Unpaired treated and untreated single-cell populations", "status": "SOURCE_VERIFIED_NOT_RUN", "local_result": "No frozen NMD-VCell run.", "recommended_role": "Distribution-modeling comparator on compatible public drug/cytokine data.", "next_gate": "Compare against identity, mean-shift, linear and nearest-neighbour transport baselines on a sealed split.", "dmd_claim_allowed": false, "source_url": "https://www.nature.com/articles/s41592-023-01969-x" }, { "model_id": "CPA-2023", "model_name": "Compositional Perturbation Autoencoder", "provider": "Meta Research / scverse collaborators", "artifact_type": "MODEL", "model_class": "COMPOSITIONAL_GENERATIVE_MODEL", "task": "Dose, drug and combination response", "context": "High-throughput single-cell perturbation screens", "status": "SOURCE_VERIFIED_NOT_RUN", "local_result": "No frozen NMD-VCell run.", "recommended_role": "Permanent compositional baseline candidate for chemical tasks.", "next_gate": "Use only where dose, covariate and perturbation metadata are complete.", "dmd_claim_allowed": false, "source_url": "https://github.com/facebookresearch/CPA" }, { "model_id": "PERTURBENCH-2025", "model_name": "PerturBench", "provider": "Altos Labs and collaborators", "artifact_type": "BENCHMARK_FRAMEWORK", "model_class": "STANDARDIZED_EVALUATION", "task": "Cellular perturbation model benchmarking", "context": "Multiple datasets, model families and metric views", "status": "SOURCE_VERIFIED_EVALUATION_CANDIDATE", "local_result": "Not yet adopted as the NMD-VCell evaluation runtime.", "recommended_role": "Benchmark adapter and metric cross-check, not a predictor.", "next_gate": "Map NMD-VCell ModelRun inputs and outputs into PerturBench while preserving the existing metric firewall and simple baselines.", "dmd_claim_allowed": false, "source_url": "https://papers.nips.cc/paper_files/paper/2025/file/8aee537279a66ced96319dfca3c00002-Paper-Datasets_and_Benchmarks_Track.pdf" } ], "selection_rule": "Prefer task compatibility, complete metadata, reproducible code/checkpoints and baseline-comparable evaluation over novelty or parameter count.", "canonical_status_registry": "/resource/api/v1.1/model_execution_status_registry.json", "current_decision": "The first compatibility batch is executed without a DMD upgrade. Prioritize matched DMD intervention outcomes; rerun external models only after their explicit source, runtime, input and task gates pass.", "calibrated_dmd_model_count": 0, "claim_boundary": "Source verification means the publication, code or model card exists. It does not mean NMD-VCell reproduced the result or that the model transfers to DMD muscle." }