source_id	title	source_type	evidence_grade	publication_year	url	supports	does_not_support	local_execution_state
SRC-SYSTEMA-2025	Systematic evaluation of perturbation-response predictors and simple matching baselines	PEER_REVIEWED_PRIMARY	A	2025	https://www.nature.com/articles/s41587-025-02777-8	mandatory perturbed/matching mean baselines | perturbation-specific evaluation | warning that common metrics reward systematic variation	a universal winning architecture | local NMD-VCell performance	METHOD_RULE_ABSORBED
SRC-NM-BENCHMARK-2025	Benchmarking 27 perturbation-response methods across 29 datasets	PEER_REVIEWED_PRIMARY	A	2025	https://www.nature.com/articles/s41592-025-02980-0	task- and context-dependent evaluation | multiple datasets and metrics | importance of cellular context	one method as best for every generalization axis	METHOD_RULE_ABSORBED
SRC-SIMPLE-BASELINES-2025	Deep learning perturbation models do not consistently beat deliberate simple baselines	PEER_REVIEWED_PRIMARY	A	2025	https://www.nature.com/articles/s41592-025-02772-6	permanent simple baselines | architecture-neutral benchmarking	that deep learning can never be useful	METHOD_RULE_ABSORBED
SRC-CZI-BENCHMARKS	CZI Virtual Cell Models benchmark ecosystem	OFFICIAL_DOC	B	2026	https://virtualcellmodels.cziscience.com/benchmarks	standardized task definitions | shared metrics | package, CLI and no-code entry points	NMD-VCell task compatibility or performance	PRODUCT_PATTERN_ABSORBED
SRC-ARC-STATE	Arc State virtual-cell architecture	OFFICIAL_PRODUCT_PREPRINT	B	2025	https://arcinstitute.org/news/virtual-cell-model-state	set-of-cells representation | separate state embedding and transition tasks | evaluation beyond mean expression	advancement beyond permanent baselines | validated DMD prediction	HISTORICAL_RECEIPTS_MIGRATED
SRC-ARC-STACK	Arc foundation model stack and in-context learning	OFFICIAL_PRODUCT_PREPRINT	B	2026	https://arcinstitute.org/news/foundation-model-stack	cell-set prompting as a model pattern | source-reported large-scale pretraining	checkpoint benchmark after runtime timeout | NMD-VCell performance inheritance	LOCAL_NVME_CORE_BASE_FORWARD_PASS_NO_CHECKPOINT
SRC-PERTPY-2025	Pertpy perturbation-analysis framework	PEER_REVIEWED_PRIMARY	A	2025	https://www.nature.com/articles/s41592-025-02909-7	end-to-end perturbation analysis | MMD, energy and Wasserstein distances | typed analysis modules	a disease-response prediction result	METHOD_REFERENCE
SRC-ANNDATA	AnnData annotated matrix and on-disk specification	OFFICIAL_DOC	A	2026	https://anndata.readthedocs.io/en/stable/generated/anndata.AnnData.html	X/obs/var/layers/obsm/uns data contract | typed annotated matrices	biological correctness of any uploaded object	DATA_CONTRACT_ABSORBED
SRC-CELLXGENE-SCHEMA	CELLxGENE schema 5.2.0	OFFICIAL_DOC	A	2026	https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.2.0/schema.md	ontology-backed biological and technical metadata | schema as a search and integration contract	automatic suitability for a perturbation task	ONTOLOGY_PATTERN_ABSORBED
SRC-GEARS-2023	GEARS graph neural network for perturbation prediction	PEER_REVIEWED_PRIMARY	A	2023	https://www.nature.com/articles/s41587-023-01905-6	graph-informed gene and perturbation embeddings | structured combination prediction task	success on the local frozen task | reliable combinations from single perturbations alone	LOCALLY_EXECUTED_FAILED_FIVE_SPLITS
SRC-CELLOT-2023	CellOT neural optimal transport	PEER_REVIEWED_PRIMARY	A	2023	https://www.nature.com/articles/s41592-023-01969-x	unpaired control-to-treated population mapping | distributional prediction	stable inference in sparse cell types | local DMD validation	SOURCE_VERIFIED_NOT_RUN
SRC-CPA-2023	Compositional perturbation autoencoder	PEER_REVIEWED_PRIMARY	A	2023	https://doi.org/10.15252/msb.202211517	factorized perturbation and covariate representations | dose/time/context composition	constant performance as unseen covariates accumulate | local NMD-VCell calibration	SOURCE_VERIFIED_NOT_RUN
SRC-GPERTURB-2025	GPerturb probabilistic perturbation-effect model	PEER_REVIEWED_PRIMARY	A	2025	https://www.nature.com/articles/s41467-025-61165-7	sparse interpretable effects | uncertainty estimates	treating cells as independent biological replicates | clinical prediction	SOURCE_VERIFIED_NOT_RUN
SRC-OPENPROBLEMS-PERTURBATION	Open Problems perturbation prediction benchmark	OFFICIAL_DOC	B	2024	https://openproblems.bio/benchmarks/perturbation_prediction/?version=v1.0.0	versioned task and metric metadata | automated score checking	generalization outside the declared competition task	BENCHMARK_PATTERN_ABSORBED