Nonlinear Gene Programmes

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

	Method	Year	Task	Model	Published	Code
	CellDISECT	2025	Nonlinear Gene ProgrammesContrastive DisentanglementContext Transfer	VAEMixture of Experts	✗	GitHub
	ContrastiveVI	2023	Nonlinear Gene ProgrammesContrastive Disentanglement	ZINB LikelihoodProtein-Count (totalVI) LikelihoodContrastive VAEMulti-modal	✓	GitHub
	ContrastiveVI+	2024	Perturbation ResponsivenessContrastive DisentanglementNonlinear Gene Programmes	ZINB LikelihoodVAEContrastive	✓	GitHub
	DRVI	2024	Unsupervised DisentanglementNonlinear Gene Programmes	VAENB likelihoodAddative DecodersMulti-modal	✓	GitHub
	Expimap	2023	Nonlinear Gene Programmes	VAELinear DecoderNB likelihoodPK Representations	✓	GitHub
	GEASS	2023	Nonlinear Gene Programmes	Non-linear Granger CausalityStochastic Gate Layers (Feature Selectors)Time-resolved / Spatially-informed	✓	✗
	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
	Hotspot	2021	Nonlinear Gene ProgrammesFeature Relationships	AutocorrelationPairwise Local Correlations	✓	GitHub
	inVAE	2024	Multi-component DisentanglementNonlinear Gene Programmes	VAENB Likelihood	✗	GitHub
	MultiGroupVI	2022	Nonlinear Gene ProgrammesContrastive Disentanglement	ZINB LikelihoodVAEContrastive	✓	GitHub
	scDisInFact	2024	Contrastive DisentanglementNonlinear Gene ProgrammesSeen Perturbation PredictionCombinatorial Effect Prediction	VAENB likelihoodAdversarialGaussian Mixture Model	✓	GitHub
	scDSA	2023	Nonlinear Gene ProgrammesContrastive Disentanglement	NB likelihoodDomain-Adversarial NNsVAEAddative Shift	✓	✗
	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
	scPrint	2025	GRN InferenceMulti-component DisentanglementNonlinear Gene Programmes	Foundational Gene expression embeddings (from >50M human cells)BERT-like Bidirectional transformers (with flashattention2)Self-supervised masked regressionA classifier decoderZINB likelihood decoderPK Representations	✓	GitHub
	scVI	2018	Nonlinear Gene Programmes	VAEZINB likelihood	✓	GitHub
	SIMVI	2025	Nonlinear Gene ProgrammesUnsupervised Disentanglement	ZINB LikelihoodVAESpatially-informedMulti-modal	✓	GitHub
	SubCell	2024	Context TransferNonlinear Gene Programmes	A collection of Vision Transformer ModelsContrastive loss	✗	GitHub
	sVAE+	2023	Seen Perturbation PredictionMulti-component DisentanglementCausal StructureNonlinear Gene Programmes	VAENB likelihoodSparse Mechanism Shift	✓	GitHub