GRN Inference

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

	Method	Year	Task	Model	Published	Code
	CellOracle	2023	GRN Inference	Multi-modalPrior Knowledge InformedRegularised (Linear) Regression	✓	GitHub
	Dictys	2023	GRN InferenceCausal Structure	Ornstein–Uhlenbeck processSteady-State ODE	✓	GitHub
	FLeCS	2025	Context TransferGRN InferenceCausal Structure	ODEOptimal Transport	✗	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
	Geneformer	2023	GRN Inference	Foundational Gene expression embeddings (from ~30M human cells)Self-supervised masked regressionStandard transformer attention	✓	GitHub
	LINGER	2024	GRN Inference	Multi-modalPrior Knowledge InformedShapley valuesDNN	✓	GitHub
	RENGE	2023	Context TransferGRN InferenceCausal Structure	Regression model	✓	GitHub
	RiTINI	2024	GRN InferenceCausal StructureContext Transfer	Graph interventionsGraph-ODE	✓	GitHub
	scDoRI	2025	GRN Inference	Multi-modalPrior Knowledge InformedAutoencoderTopic Modelling	✗	GitHub
	SCENIC+	2022	GRN Inference	Multi-modalPrior Knowledge InformedGradient Boosting	✓	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
	scRANK	2024	Linear Gene ProgrammesPerturbation ResponsivenessGRN Inference	PC RegressionTensor Decomposition (PARAFAC)Network Diffusion	✓	GitHub