💡 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 |