💡 Tip: Click the + in the first column to expand detailed method descriptions.

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
CausCell	2024	Multi-component DisentanglementCausal StructureCombinatorial Effect PredictionContext TransferSeen Perturbation Prediction	DiffusionAuxilary Classifiers	✓	GitHub
CellBox	2021	Context TransferSeen Perturbation PredictionCombinatorial Effect Prediction	ODE	✓	GitHub
cellFlow	2025	Trace Cell PopulationsContext TransferUnseen Perturbation PredictionCombinatorial Effect Prediction	Conditional Flow MatchingOptimal Transport	✗	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
CPA	2023	Context TransferCombinatorial Effect PredictionMulti-component Disentanglement	VAEDANN-based Adversary that attempts to eliminate treatment effects/ cellular context from latent representation	✓	GitHub
discrepancy-VAE	2023	Multi-component DisentanglementSeen Perturbation PredictionCombinatorial Effect PredictionCausal Structure	VAEDisentanglement via Virtual Counterfactuals	✓	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
LPM	2025	Unseen Perturbation PredictionCombinatorial Effect Prediction	DNN Decoder	✗	✗
MichiGAN	2021	Unsupervised DisentanglementSeen Perturbation PredictionCombinatorial Effect Prediction	VAEconditioned GAN	✓	GitHub
MultiCPA	2022	Combinatorial Effect PredictionMulti-component Disentanglement	AE framework inspired by CPAtotalVI likelihood	✓	GitHub
PDGrapher	2025	Combinatorial Effect PredictionUnseen Perturbation PredictionContext Transfer	GNN	✓	GitHub
SALT&PEPER	2024	Combinatorial Effect Prediction	Additive ModelDNN	✓	✗
SAMS-VAE	2023	Multi-component DisentanglementCausal StructureSeen Perturbation PredictionCombinatorial Effect Prediction	VAENB likelihoodConditional Latent EmbeddingsAddative ShiftSparse Mechanism Shift	✓	GitHub
scDisInFact	2024	Contrastive DisentanglementNonlinear Gene ProgrammesSeen Perturbation PredictionCombinatorial Effect Prediction	VAENB likelihoodAdversarialGaussian Mixture Model	✓	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
SENA	2024	Causal StructureMulti-component DisentanglementSeen Perturbation PredictionCombinatorial Effect Prediction	Discrepancy-VAE architectureVAEPK Representations	✓	GitHub
Squidiff	2025	Combinatorial Effect PredictionContext TransferUnseen Perturbation Prediction	Diffusion Model	✓	GitHub
State	2025	Combinatorial Effect PredictionContext Transfer	DNNAttention	✗	GitHub