💡 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 |