Trace Cell Populations#
đź’ˇ Tip: Click the + in the first column to expand detailed method descriptions.
| Method | Year | Task | Model | Published | Code | |
|---|---|---|---|---|---|---|
| ARTEMIS | 2025 | Trace Cell Populations |
VAESchrödinger Bridge |
âś“ | GitHub | |
| cellFlow | 2025 | Trace Cell PopulationsContext TransferUnseen Perturbation PredictionCombinatorial Effect Prediction |
Conditional Flow MatchingOptimal Transport |
âś— | GitHub | |
| CellOT | 2023 | Trace Cell PopulationsPerturbation ResponsivenessContext Transfer |
Dual (min-max) Formulation OT |
âś“ | GitHub | |
| CFGen | 2024 | Trace Cell PopulationsContext Transfer |
Optimal TransportMulti-modalConditional Flow Matching |
âś“ | GitHub | |
| CINEMA-OT | 2023 | Trace Cell PopulationsPerturbation ResponsivenessUnsupervised Disentanglement |
Unbalanced OTEntropy-regularized SinkhornICA |
âś“ | GitHub | |
| CondOT | 2022 | Trace Cell PopulationsUnseen Perturbation PredictionCombinatorial Effect PredictionContext Transfer |
Conditioned Dual (min-max) Formulation OT |
âś“ | GitHub | |
| CoSpar | 2022 | Trace Cell Populations |
Optimal TransportSparsity |
âś“ | GitHub | |
| CytoBridge | 2025 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Neural ODEFlow MatchingOptimal TransportTime-resolvedMean Field Model |
âś“ | GitHub | |
| DeepRUOT | 2025 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Neural ODEFlow MatchingOptimal TransportTime-resolvedFisher-regularized Unbalanced Dynamics |
âś“ | GitHub | |
| GWOT | 2025 | Trace Cell PopulationsContext Transfer |
Optimal TransportMulti-modal |
âś“ | GitHub | |
| MFM | 2024 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Flow MatchingOptimal TransportTime-resolved |
âś“ | GitHub | |
| MioFlow | 2022 | Trace Cell Populations |
Neural ODEGeodasic Autoencoder |
âś“ | GitHub | |
| MMFM | 2024 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Flow MatchingOptimal TransportTime-resolved |
âś“ | GitHub | |
| moscot | 2025 | Trace Cell Populations |
Unbalanced OTEntropy-regularised SinkhornLow-rank OTSparse Map OT |
âś“ | GitHub | |
| OT-CFM | 2024 | Trace Cell Populations |
Flow MatchingSchrödinger Bridge |
âś“ | GitHub | |
| Prescient | 2021 | Trace Cell PopulationsSeen Perturbation PredictionContext Transfer |
Diffusion |
âś“ | GitHub | |
| SBALIGN | 2023 | Trace Cell Populations |
Schrödinger Bridge |
âś“ | GitHub | |
| scPRAM | 2024 | Context TransferTrace Cell Populations |
VAEOTAttention |
âś“ | GitHub | |
| Waddington-OT | 2019 | Trace Cell PopulationsLinear Gene Programmes |
Unbalanced OTEntropy-regularized Sinkhorn |
âś“ | GitHub |