Context Transfer#
💡 Tip: Click the + in the first column to expand detailed method descriptions.
| Method | Year | Task | Model | Published | Code | |
|---|---|---|---|---|---|---|
| Biolord | 2024 | Multi-component DisentanglementUnseen Perturbation PredictionCombinatorial Effect PredictionContext Transfer |
ProbabilisticZINB likelihoodProtein-Count (totalVI) Likelihood |
✓ | GitHub | |
| CausCell | 2024 | Multi-component DisentanglementCausal StructureCombinatorial Effect PredictionContext TransferSeen Perturbation Prediction |
DiffusionAuxilary Classifiers |
✓ | GitHub | |
| CellBox | 2021 | Context TransferSeen Perturbation PredictionCombinatorial Effect Prediction |
ODE |
✓ | GitHub | |
| CellDISECT | 2025 | Nonlinear Gene ProgrammesContrastive DisentanglementContext Transfer |
VAEMixture of Experts |
✗ | GitHub | |
| cellFlow | 2025 | Trace Cell PopulationsContext TransferUnseen Perturbation PredictionCombinatorial Effect Prediction |
Conditional Flow MatchingOptimal Transport |
✗ | GitHub | |
| CellOT | 2023 | Trace Cell PopulationsPerturbation ResponsivenessContext Transfer |
Dual (min-max) Formulation OT |
✓ | GitHub | |
| CFGen | 2024 | Trace Cell PopulationsContext Transfer |
Optimal TransportMulti-modalConditional Flow Matching |
✓ | GitHub | |
| ChemCPA | 2022 | Unseen Perturbation PredictionContext TransferMulti-component Disentanglement |
AE framework inspired by CPAChemical representation embeddings |
✓ | GitHub | |
| CODEX | 2024 | Combinatorial Effect PredictionUnseen Perturbation PredictionContext Transfer |
DNN |
✓ | GitHub | |
| CondOT | 2022 | Trace Cell PopulationsUnseen Perturbation PredictionCombinatorial Effect PredictionContext Transfer |
Conditioned Dual (min-max) Formulation OT |
✓ | GitHub | |
| CPA | 2023 | Context TransferCombinatorial Effect PredictionMulti-component Disentanglement |
VAEDANN-based Adversary that attempts to eliminate treatment effects/ cellular context from latent representation |
✓ | 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 | |
| Dr.VAE | 2019 | Context TransferSeen Perturbation Prediction |
VAE |
✓ | GitHub | |
| FLeCS | 2025 | Context TransferGRN InferenceCausal Structure |
ODEOptimal Transport |
✗ | GitHub | |
| graphVCI | 2023 | Context Transfer |
Dual-branch variational bayes causal inference frameworkPK Representations |
✓ | GitHub | |
| GWOT | 2025 | Trace Cell PopulationsContext Transfer |
Optimal TransportMulti-modal |
✓ | GitHub | |
| MFM | 2024 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Flow MatchingOptimal TransportTime-resolved |
✓ | GitHub | |
| MMFM | 2024 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Flow MatchingOptimal TransportTime-resolved |
✓ | GitHub | |
| OmiCLIP | 2025 | Context Transfer |
ViTContrastive LearningMulti-modal |
✓ | GitHub | |
| PDGrapher | 2025 | Combinatorial Effect PredictionUnseen Perturbation PredictionContext Transfer |
GNN |
✓ | GitHub | |
| PrePR-CT | 2024 | Context Transfer |
Graph attentionRegression |
✗ | GitHub | |
| Prescient | 2021 | Trace Cell PopulationsSeen Perturbation PredictionContext Transfer |
Diffusion |
✓ | GitHub | |
| Prophet | 2024 | Unseen Perturbation PredictionContext Transfer |
TransformerMulti-modalKnowledge Informed |
✗ | GitHub | |
| RENGE | 2023 | Context TransferGRN InferenceCausal Structure |
Regression model |
✓ | GitHub | |
| RiTINI | 2024 | GRN InferenceCausal StructureContext Transfer |
Graph interventionsGraph-ODE |
✓ | GitHub | |
| scCausalVI | 2025 | Causal StructureUnsupervised DisentanglementSeen Perturbation PredictionContext TransferMulti-component DisentanglementPerturbation ResponsivenessDifferential Analysis |
Variational AutoencoderStructural Causal Model |
✓ | GitHub | |
| scDiffusion | 2024 | Context Transfer |
DiffusionVAE |
✓ | GitHub | |
| scGEN | 2019 | Context Transfer |
VAE |
✓ | GitHub | |
| scPRAM | 2024 | Context TransferTrace Cell Populations |
VAEOTAttention |
✓ | GitHub | |
| Squidiff | 2025 | Combinatorial Effect PredictionContext TransferUnseen Perturbation Prediction |
Diffusion Model |
✓ | GitHub | |
| State | 2025 | Combinatorial Effect PredictionContext Transfer |
DNNAttention |
✗ | GitHub | |
| SubCell | 2024 | Context TransferNonlinear Gene Programmes |
A collection of Vision Transformer ModelsContrastive loss |
✗ | GitHub | |
| svae-ligr | 2024 | Seen Perturbation PredictionContext TransferMulti-component DisentanglementCausal Structure |
VAENB likelihoodSparse Mechanism ShiftGenerative/Experience Replay |
✓ | GitHub | |
| TarDis | 2024 | Multi-component DisentanglementContext Transfer |
VAENB likelihoodMulti-modal |
✓ | 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 | |
| VirTues | 2025 | Context Transfer |
ViTMaked AutoencoderMulti-modal |
✓ | GitHub |