💡 Tip: Click the + in the first column to expand detailed method descriptions.
| Method | Year | Task | Model | Published | Code | |
|---|---|---|---|---|---|---|
| CausCell | 2024 | Multi-component DisentanglementCausal StructureCombinatorial Effect PredictionContext TransferSeen Perturbation Prediction |
DiffusionAuxilary Classifiers |
✓ | GitHub | |
| CellBox | 2021 | Context TransferSeen Perturbation PredictionCombinatorial Effect Prediction |
ODE |
✓ | GitHub | |
| CytoBridge | 2025 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Neural ODEFlow MatchingOptimal TransportTime-resolvedMean Field Model |
✓ | GitHub | |
| DeepRUOT | 2025 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Neural ODEFlow MatchingOptimal TransportTime-resolvedFisher-regularized Unbalanced Dynamics |
✓ | GitHub | |
| discrepancy-VAE | 2023 | Multi-component DisentanglementSeen Perturbation PredictionCombinatorial Effect PredictionCausal Structure |
VAEDisentanglement via Virtual Counterfactuals |
✓ | GitHub | |
| Dr.VAE | 2019 | Context TransferSeen Perturbation Prediction |
VAE |
✓ | GitHub | |
| FCR | 2024 | Multi-component DisentanglementSeen Perturbation Prediction |
VAEAdversarialPerturbation-covariate Interactions |
✓ | GitHub | |
| LEMUR | 2025 | Seen Perturbation PredictionDifferential Analysis |
Multi-condition PCA |
✓ | GitHub | |
| MFM | 2024 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Flow MatchingOptimal TransportTime-resolved |
✓ | GitHub | |
| MichiGAN | 2021 | Unsupervised DisentanglementSeen Perturbation PredictionCombinatorial Effect Prediction |
VAEconditioned GAN |
✓ | GitHub | |
| MMFM | 2024 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Flow MatchingOptimal TransportTime-resolved |
✓ | GitHub | |
| Prescient | 2021 | Trace Cell PopulationsSeen Perturbation PredictionContext Transfer |
Diffusion |
✓ | GitHub | |
| SAMS-VAE | 2023 | Multi-component DisentanglementCausal StructureSeen Perturbation PredictionCombinatorial Effect Prediction |
VAENB likelihoodConditional Latent EmbeddingsAddative ShiftSparse Mechanism Shift |
✓ | GitHub | |
| scCausalVI | 2025 | Causal StructureUnsupervised DisentanglementSeen Perturbation PredictionContext TransferMulti-component DisentanglementPerturbation ResponsivenessDifferential Analysis |
Variational AutoencoderStructural Causal Model |
✓ | GitHub | |
| scDisInFact | 2024 | Contrastive DisentanglementNonlinear Gene ProgrammesSeen Perturbation PredictionCombinatorial Effect Prediction |
VAENB likelihoodAdversarialGaussian Mixture Model |
✓ | GitHub | |
| scELMo | 2024 | Seen Perturbation Prediction |
Converts gene/cell metadata into text embeddingsIntegrates text and expression embeddingsFine-tunes embeddings via a lightweight neural adaptor |
✓ | GitHub | |
| scPreGan | 2022 | Seen Perturbation Prediction |
AEGAN |
✓ | GitHub | |
| SENA | 2024 | Causal StructureMulti-component DisentanglementSeen Perturbation PredictionCombinatorial Effect Prediction |
Discrepancy-VAE architectureVAEPK Representations |
✓ | GitHub | |
| svae-ligr | 2024 | Seen Perturbation PredictionContext TransferMulti-component DisentanglementCausal Structure |
VAENB likelihoodSparse Mechanism ShiftGenerative/Experience Replay |
✓ | GitHub | |
| sVAE+ | 2023 | Seen Perturbation PredictionMulti-component DisentanglementCausal StructureNonlinear Gene Programmes |
VAENB likelihoodSparse Mechanism Shift |
✓ | GitHub | |
| trVAE | 2020 | Context TransferSeen Perturbation PredictionMulti-component Disentanglement |
CVAE |
✓ | GitHub | |
| VCI | 2024 | Context TransferSeen Perturbation Prediction |
Dual-branch variational bayes causal inference framework |
✗ | GitHub |