Unseen Perturbation Prediction

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	Method	Year	Task	Model	Published	Code
	AttentionPert	2024	Combinatorial Effect PredictionUnseen Perturbation Prediction	Transformer ModelGNN	✓	GitHub
	Biolord	2024	Multi-component DisentanglementUnseen Perturbation PredictionCombinatorial Effect PredictionContext Transfer	ProbabilisticZINB likelihoodProtein-Count (totalVI) Likelihood	✓	GitHub
	C2S-Scale	2025	Unseen Perturbation PredictionCombinatorial Effect Prediction	Family of LLMs with to 27B parameters	✗	GitHub
	cellFlow	2025	Trace Cell PopulationsContext TransferUnseen Perturbation PredictionCombinatorial Effect Prediction	Conditional Flow MatchingOptimal Transport	✗	GitHub
	ChemCPA	2022	Unseen Perturbation PredictionContext TransferMulti-component Disentanglement	AE framework inspired by CPAChemical representation embeddings	✓	GitHub
	CODEX	2024	Combinatorial Effect PredictionUnseen Perturbation PredictionContext Transfer	DNN	✓	GitHub
	CondOT	2022	Trace Cell PopulationsUnseen Perturbation PredictionCombinatorial Effect PredictionContext Transfer	Conditioned Dual (min-max) Formulation OT	✓	GitHub
	cycleCDR	2024	Unseen Perturbation Prediction	Autoencoder	✓	GitHub
	GEARS	2023	Combinatorial Effect PredictionUnseen Perturbation Prediction	GNNs for co-expression and GO relationshipsLabel embeddingsPK Representations	✓	GitHub
	GeneCompass	2024	Unseen Perturbation PredictionCombinatorial Effect PredictionGRN InferenceNonlinear Gene Programmes	Foundational Gene expression embeddings (from >50M human cells)Self-supervised masked regression with down-samplingSparse transformer encoderPerformer-style attention decoderPK-informed	✓	GitHub
	IterPert	2024	Unseen Perturbation PredictionCombinatorial Effect Prediction	GEARSActive Learning	✓	GitHub
	LLM+GP	2024	Unseen Perturbation Prediction	Gaussian Process ModelLanguage embeddings	✓	✗
	LPM	2025	Unseen Perturbation PredictionCombinatorial Effect Prediction	DNN Decoder	✗	✗
	PDGrapher	2025	Combinatorial Effect PredictionUnseen Perturbation PredictionContext Transfer	GNN	✓	GitHub
	PRNet	2024	Unseen Perturbation Prediction	DNN	✓	GitHub
	Prophet	2024	Unseen Perturbation PredictionContext Transfer	TransformerMulti-modalKnowledge Informed	✗	GitHub
	SCCVAE	2025	Unseen Perturbation PredictionCausal Structure	VAEVariational InferenceLatent Causal Structure	✗	GitHub
	scFoundation	2024	Nonlinear Gene ProgrammesUnseen Perturbation PredictionCombinatorial Effect Prediction	Foundational Gene expression embeddings (from >50M human cells)Self-supervised masked regression with down-samplingSparse transformer encoderPerformer-style attention decoder	✓	GitHub
	scGenePT	2025	Unseen Perturbation PredictionCombinatorial Effect PredictionGRN InferenceNonlinear Gene Programmes	scGPTChatGPT prompts	✗	✗
	scGPT	2024	Unseen Perturbation PredictionCombinatorial Effect PredictionGRN InferenceNonlinear Gene Programmes	Foundational Gene expression embeddings (from >33M human cells)Self-supervised masked expression predictionCustomised non-sequential (flash) attention	✓	GitHub
	Squidiff	2025	Combinatorial Effect PredictionContext TransferUnseen Perturbation Prediction	Diffusion Model	✓	GitHub