All Methods#
💡 Tip: Click the + in the first column to expand detailed method descriptions.
| Method | Year | Task | Model | Published | Code | |
|---|---|---|---|---|---|---|
| AMICI | 2025 | Linear Gene ProgrammesMulti-component Disentanglement |
Linear DecoderCross-attentionSpatially-informed |
✗ | GitHub | |
| ARTEMIS | 2025 | Trace Cell Populations |
VAESchrödinger Bridge |
✓ | GitHub | |
| AttentionPert | 2024 | Combinatorial Effect PredictionUnseen Perturbation Prediction |
Transformer ModelGNN |
✓ | GitHub | |
| AUGUR | 2020 | Perturbation ResponsivenessDifferential Analysis |
Random Forrest |
✓ | GitHub | |
| AVICI | 2022 | Causal Structure |
Amortized pre-trainingVariational Inference |
✓ | GitHub | |
| Bicycle | 2023 | Causal Structure |
Graph interventionsOrnstein-Uhlenbeck processSteady-State ODE |
✓ | GitHub | |
| Biolord | 2024 | Multi-component DisentanglementUnseen Perturbation PredictionCombinatorial Effect PredictionContext Transfer |
ProbabilisticZINB likelihoodProtein-Count (totalVI) Likelihood |
✓ | GitHub | |
| C2S-Scale | 2025 | Unseen Perturbation PredictionCombinatorial Effect Prediction |
Family of LLMs with to 27B parameters |
✗ | GitHub | |
| CausCell | 2024 | Multi-component DisentanglementCausal StructureCombinatorial Effect PredictionContext TransferSeen Perturbation Prediction |
DiffusionAuxilary Classifiers |
✓ | GitHub | |
| Celcomen | 2025 | Unsupervised DisentanglementFeature Relationships |
K-hop ConvolutionSpatially-informed |
✓ | GitHub | |
| CellBox | 2021 | Context TransferSeen Perturbation PredictionCombinatorial Effect Prediction |
ODE |
✓ | GitHub | |
| CellCap | 2024 | Multi-component DisentanglementLinear Gene Programmes |
VAEAttentionLinear Decoder |
✓ | GitHub | |
| CellDISECT | 2025 | Nonlinear Gene ProgrammesContrastive DisentanglementContext Transfer |
VAEMixture of Experts |
✗ | GitHub | |
| CellDrift | 2022 | Differential Analysis |
Generalised Linear ModelNB LikelihoodFunctional PCAFuzzy ClusteringTime-resolvedPerturbation-Covariate Interactions |
✓ | GitHub | |
| cellFlow | 2025 | Trace Cell PopulationsContext TransferUnseen Perturbation PredictionCombinatorial Effect Prediction |
Conditional Flow MatchingOptimal Transport |
✗ | GitHub | |
| CellOracle | 2023 | GRN Inference |
Multi-modalPrior Knowledge InformedRegularised (Linear) Regression |
✓ | 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 | |
| CINEMA-OT | 2023 | Trace Cell PopulationsPerturbation ResponsivenessUnsupervised Disentanglement |
Unbalanced OTEntropy-regularized SinkhornICA |
✓ | GitHub | |
| CIV | 2023 | Causal Structure |
Active LearningStructural Causal ModelDAG-Bayesian linear regression |
✓ | ✗ | |
| cLVM | 2019 | Linear Gene ProgrammesContrastive Disentanglement |
Factor ModelsContastive VAE |
✓ | 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 | |
| ContrastiveVI | 2023 | Nonlinear Gene ProgrammesContrastive Disentanglement |
ZINB LikelihoodProtein-Count (totalVI) LikelihoodContrastive VAEMulti-modal |
✓ | GitHub | |
| ContrastiveVI+ | 2024 | Perturbation ResponsivenessContrastive DisentanglementNonlinear Gene Programmes |
ZINB LikelihoodVAEContrastive |
✓ | GitHub | |
| CoSpar | 2022 | Trace Cell Populations |
Optimal TransportSparsity |
✓ | GitHub | |
| CPA | 2023 | Context TransferCombinatorial Effect PredictionMulti-component Disentanglement |
VAEDANN-based Adversary that attempts to eliminate treatment effects/ cellular context from latent representation |
✓ | GitHub | |
| cPCA | 2018 | Linear Gene ProgrammesContrastive Disentanglement |
Modified PCA |
✓ | GitHub | |
| CPLVMs | 2022 | Linear Gene ProgrammesContrastive Disentanglement |
NB likelihoodFactor Models |
✓ | GitHub | |
| CSMF | 2019 | Linear Gene ProgrammesContrastive Disentanglement |
NMF |
✓ | GitHub | |
| cVAE | 2019 | Contrastive Disentanglement |
Contrastive VAE |
✗ | GitHub | |
| cycleCDR | 2024 | Unseen Perturbation Prediction |
Autoencoder |
✓ | GitHub | |
| CytoBridge | 2025 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Neural ODEFlow MatchingOptimal TransportTime-resolvedMean Field Model |
✓ | GitHub | |
| DAG-GNN | 2019 | Causal Structure |
Continuous optimisation for acyclicityGNN |
✓ | GitHub | |
| DCD-FG | 2022 | Causal Structure |
Factor ModelDAGsLatent DAGs |
✓ | GitHub | |
| DCDI | 2020 | Causal Structure |
Graph interventionsDNNNormalizing-Flows |
✓ | GitHub | |
| DCI | 2021 | Causal Structure |
PC Algorithm |
✓ | GitHub | |
| Decipher | 2024 | Unsupervised DisentanglementLinear Gene Programmes |
VAELinear Decoder |
✗ | GitHub | |
| DeepRUOT | 2025 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Neural ODEFlow MatchingOptimal TransportTime-resolvedFisher-regularized Unbalanced Dynamics |
✓ | GitHub | |
| DIALOGUE | 2022 | Linear Gene Programmes |
Sparse CCAPartial CorrelationsMixed Linear Model |
✓ | GitHub | |
| Dictys | 2023 | GRN InferenceCausal Structure |
Ornstein–Uhlenbeck processSteady-State ODE |
✓ | 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 | |
| DRVI | 2024 | Unsupervised DisentanglementNonlinear Gene Programmes |
VAENB likelihoodAddative DecodersMulti-modal |
✓ | GitHub | |
| Expimap | 2023 | Nonlinear Gene Programmes |
VAELinear DecoderNB likelihoodPK Representations |
✓ | GitHub | |
| EXPORT | 2024 | Linear Gene Programmes |
VAELinear DecoderPK Representations |
✓ | GitHub | |
| FCR | 2024 | Multi-component DisentanglementSeen Perturbation Prediction |
VAEAdversarialPerturbation-covariate Interactions |
✓ | GitHub | |
| FLeCS | 2025 | Context TransferGRN InferenceCausal Structure |
ODEOptimal Transport |
✗ | GitHub | |
| GEARS | 2023 | Combinatorial Effect PredictionUnseen Perturbation Prediction |
GNNs for co-expression and GO relationshipsLabel embeddingsPK Representations |
✓ | GitHub | |
| GEASS | 2023 | Nonlinear Gene Programmes |
Non-linear Granger CausalityStochastic Gate Layers (Feature Selectors)Time-resolved / Spatially-informed |
✓ | ✗ | |
| GEDI | 2024 | Linear Gene Programmes |
ProbabilisticSample-specific DecodersPK Representations (optional)RNA Velocity (optional) |
✓ | 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 | |
| graphVCI | 2023 | Context Transfer |
Dual-branch variational bayes causal inference frameworkPK Representations |
✓ | GitHub | |
| GSFA | 2024 | Multi-component DisentanglementCausal StructureLinear Gene Programmes |
Factor AnalysisProbabilistic |
✓ | GitHub | |
| GWOT | 2025 | Trace Cell PopulationsContext Transfer |
Optimal TransportMulti-modal |
✓ | GitHub | |
| Hotspot | 2021 | Nonlinear Gene ProgrammesFeature Relationships |
AutocorrelationPairwise Local Correlations |
✓ | GitHub | |
| inVAE | 2024 | Multi-component DisentanglementNonlinear Gene Programmes |
VAENB Likelihood |
✗ | GitHub | |
| IterPert | 2024 | Unseen Perturbation PredictionCombinatorial Effect Prediction |
GEARSActive Learning |
✓ | GitHub | |
| Kasumi | 2025 | Feature Relationships |
Spatially-informedRandom Forrest (or other regression models)Convolution Operations |
✓ | GitHub | |
| LEMUR | 2025 | Seen Perturbation PredictionDifferential Analysis |
Multi-condition PCA |
✓ | GitHub | |
| LINGER | 2024 | GRN Inference |
Multi-modalPrior Knowledge InformedShapley valuesDNN |
✓ | GitHub | |
| LLM+GP | 2024 | Unseen Perturbation Prediction |
Gaussian Process ModelLanguage embeddings |
✓ | ✗ | |
| LPM | 2025 | Unseen Perturbation PredictionCombinatorial Effect Prediction |
DNN Decoder |
✗ | ✗ | |
| MEFISTO | 2022 | Linear Gene ProgrammesUnsupervised Disentanglement |
Group Factor ModelMulti-modalSpatially-informedTime-resolved |
✓ | GitHub | |
| MELD(-VCF) | 2021 | Perturbation Responsiveness |
Manifold LearningVertex-frequency analysisGraph Diffusion |
✓ | GitHub | |
| Memento | 2024 | Differential AnalysisLinear Gene ProgrammesFeature Relationships |
Hypergeometric testProbabilistic |
✓ | 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 | |
| MiloDE | 2024 | Differential Analysis |
Generalised Linear ModelNB Likelihood |
✓ | GitHub | |
| MioFlow | 2022 | Trace Cell Populations |
Neural ODEGeodasic Autoencoder |
✓ | GitHub | |
| MISTy | 2022 | Feature Relationships |
Spatially-informedRandom Forrest (or other regression models) |
✓ | GitHub | |
| Mixscale | 2025 | Differential AnalysisPerturbation Responsiveness |
Gaussian Mixture ModelWeighted multivariate regression |
✓ | GitHub | |
| Mixscape | 2021 | Perturbation ResponsivenessLinear Gene Programmes |
Gaussian Mixture ModelLDA |
✓ | GitHub | |
| MMFM | 2024 | Trace Cell PopulationsContext TransferSeen Perturbation Prediction |
Flow MatchingOptimal TransportTime-resolved |
✓ | GitHub | |
| mmVAE | 2022 | Contrastive Disentanglement |
Contrastive VAE |
✓ | GitHub | |
| MOFA-FLEX | 2025 | Linear Gene ProgrammesUnsupervised DisentanglementMulti-component Disentanglement |
Group Factor ModelMulti-modalPK RepresentationsSpatially-informedTime-resolvedGaussian Process priorsStochastic Variational Inference |
✗ | GitHub | |
| MOFA+ | 2020 | Linear Gene ProgrammesUnsupervised Disentanglement |
Group Factor ModelMulti-modal |
✓ | GitHub | |
| MOFAcell | 2023 | Linear Gene Programmes |
Group Factor Analysis (MOFA+) |
✓ | GitHub | |
| moscot | 2025 | Trace Cell Populations |
Unbalanced OTEntropy-regularised SinkhornLow-rank OTSparse Map OT |
✓ | GitHub | |
| MultiCPA | 2022 | Combinatorial Effect PredictionMulti-component Disentanglement |
AE framework inspired by CPAtotalVI likelihood |
✓ | GitHub | |
| MultiGroupVI | 2022 | Nonlinear Gene ProgrammesContrastive Disentanglement |
ZINB LikelihoodVAEContrastive |
✓ | GitHub | |
| MUSIC | 2019 | Perturbation ResponsivenessLinear Gene Programmes |
Topic Model |
✓ | GitHub | |
| MuVi | 2023 | Linear Gene ProgrammesUnsupervised Disentanglement |
Group Factor ModelPK RepresentationsMulti-modal |
✓ | GitHub | |
| NicheCompass | 2024 | Linear Gene Programmes |
Graph VAELinear DecoderNB LikelihoodSpatially-informedPK RepresentationsMulti-modal |
✓ | GitHub | |
| NODAGS-Flow | 2023 | Causal Structure |
Graph interventionsDNNResidual Flow\nSteady-State ODE |
✓ | GitHub | |
| NOTEARS-MLP | 2020 | Causal Structure |
Continuous optimisation for acyclicityDNN |
✓ | GitHub | |
| NOTEARS | 2018 | Causal Structure |
Continuous optimisation for acyclicity |
✓ | GitHub | |
| OmiCLIP | 2025 | Context Transfer |
ViTContrastive LearningMulti-modal |
✓ | GitHub | |
| ontoVAE | 2023 | Linear Gene Programmes |
VAELinear DecoderPK Representations |
✓ | GitHub | |
| OT-CFM | 2024 | Trace Cell Populations |
Flow MatchingSchrödinger Bridge |
✓ | GitHub | |
| PCPCA | 2024 | Linear Gene ProgrammesContrastive Disentanglement |
modified PCA |
✓ | GitHub | |
| PDGrapher | 2025 | Combinatorial Effect PredictionUnseen Perturbation PredictionContext Transfer |
GNN |
✓ | GitHub | |
| Perturbation Score | 2025 | Perturbation ResponsivenessDifferential Analysis |
Robust Rank AggregateRidge RegressionRegularised Linear Models |
✓ | GitHub | |
| pmVAE | 2021 | Linear Gene Programmes |
Multiple VAEsPK Representations |
✓ | GitHub | |
| PrePR-CT | 2024 | Context Transfer |
Graph attentionRegression |
✗ | GitHub | |
| PRESAGE | 2025 | Unseen Perturbation Prediction |
MLPAttention-based pooling of embedding sourcesPK Representations |
✗ | GitHub | |
| Prescient | 2021 | Trace Cell PopulationsSeen Perturbation PredictionContext Transfer |
Diffusion |
✓ | GitHub | |
| PRNet | 2024 | Unseen Perturbation Prediction |
DNN |
✓ | 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 | |
| River | 2024 | Differential Analysis |
Non-linear ClassifierFeature AttributionSpatially-informed |
✗ | GitHub | |
| SALT&PEPER | 2024 | Combinatorial Effect Prediction |
Additive ModelDNN |
✓ | ✗ | |
| SAMS-VAE | 2023 | Multi-component DisentanglementCausal StructureSeen Perturbation PredictionCombinatorial Effect Prediction |
VAENB likelihoodConditional Latent EmbeddingsAddative ShiftSparse Mechanism Shift |
✓ | GitHub | |
| SBALIGN | 2023 | Trace Cell Populations |
Schrödinger Bridge |
✓ | GitHub | |
| SC-VAE | 2024 | Contrastive DisentanglementPerturbation Responsiveness |
VAENB likelihood |
✓ | ✗ | |
| scCausalVI | 2025 | Causal StructureUnsupervised DisentanglementSeen Perturbation PredictionContext TransferMulti-component DisentanglementPerturbation ResponsivenessDifferential Analysis |
Variational AutoencoderStructural Causal Model |
✓ | GitHub | |
| SCCVAE | 2025 | Unseen Perturbation PredictionCausal Structure |
VAEVariational InferenceLatent Causal Structure |
✗ | GitHub | |
| scDiffusion | 2024 | Context Transfer |
DiffusionVAE |
✓ | GitHub | |
| scDisInFact | 2024 | Contrastive DisentanglementNonlinear Gene ProgrammesSeen Perturbation PredictionCombinatorial Effect Prediction |
VAENB likelihoodAdversarialGaussian Mixture Model |
✓ | GitHub | |
| scDIST | 2024 | Perturbation ResponsivenessDifferential Analysis |
Generalised Linear Model |
✓ | GitHub | |
| scDoRI | 2025 | GRN Inference |
Multi-modalPrior Knowledge InformedAutoencoderTopic Modelling |
✗ | GitHub | |
| scDSA | 2023 | Nonlinear Gene ProgrammesContrastive Disentanglement |
NB likelihoodDomain-Adversarial NNsVAEAddative Shift |
✓ | ✗ | |
| scELMo | 2024 | Seen Perturbation Prediction |
Converts gene/cell metadata into text embeddingsIntegrates text and expression embeddingsFine-tunes embeddings via a lightweight neural adaptor |
✓ | GitHub | |
| SCENIC+ | 2022 | GRN Inference |
Multi-modalPrior Knowledge InformedGradient Boosting |
✓ | GitHub | |
| SCEPTRE | 2021 | Differential AnalysisPerturbation Responsiveness |
Conditional ResamplingGeneralised Linear ModelNB Likelihood |
✓ | GitHub | |
| scETM | 2021 | Linear Gene Programmes |
VAEEmbedding Topic ModelLinear DecoderPK Representations |
✓ | GitHub | |
| 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 | |
| scGEN | 2019 | Context Transfer |
VAE |
✓ | 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 | |
| scINSIGHT | 2022 | Contrastive DisentanglementLinear Gene Programmes |
NMF |
✓ | GitHub | |
| scITD | 2024 | Linear Gene Programmes |
Tensor Decomposition (Tucker) |
✓ | GitHub | |
| scLAMBDA | 2024 | Unseen Perturbation PredictionCombinatorial Effect PredictionMulti-component Disentanglement |
VAELLM Gene EmbeddingsAdditive ShiftMutual information (MINE) disentanglementAdversarial perturbation embeddings |
✗ | GitHub | |
| scLDM | 2025 | Unseen Perturbation PredictionContext Transfer |
Transformer VAEMulti-head Cross-Attention poolingNB likelihoodLatent DiffusionConditional Flow MatchingClassifier-free Guidance |
✗ | GitHub | |
| scMAGeCK | 2020 | Differential Analysis |
Robust Rank AggregateRidge Regression |
✓ | GitHub | |
| scPCA | 2020 | Linear Gene ProgrammesContrastive Disentanglement |
Modified PCA |
✓ | GitHub | |
| scPRAM | 2024 | Context TransferTrace Cell Populations |
VAEOTAttention |
✓ | GitHub | |
| scPreGan | 2022 | Seen Perturbation Prediction |
AEGAN |
✓ | 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 | |
| scVI | 2018 | Nonlinear Gene Programmes |
VAEZINB likelihood |
✓ | GitHub | |
| SEA | 2024 | Causal Structure |
Amortized pre-trainingTransfomerGraph Attention |
✓ | GitHub | |
| SENA | 2024 | Causal StructureMulti-component DisentanglementSeen Perturbation PredictionCombinatorial Effect Prediction |
Discrepancy-VAE architectureVAEPK Representations |
✓ | GitHub | |
| SIMVI | 2025 | Nonlinear Gene ProgrammesUnsupervised Disentanglement |
ZINB LikelihoodVAESpatially-informedMulti-modal |
✓ | GitHub | |
| SOFA | 2024 | Multi-component Disentanglement |
Group Factor Analysis |
✗ | GitHub | |
| SpaCeNet | 2024 | Feature Relationships |
Generalised Gaussian Graphical ModelSpatially-informed |
✓ | GitHub | |
| sparseVAE | 2022 | Unsupervised Disentanglement |
VAE |
✓ | GitHub | |
| SpatialDIVA | 2025 | Multi-component Disentanglement |
VAESpatially-informedNB LikelihoodMulti-modal |
✗ | GitHub | |
| Spectra | 2023 | Linear Gene ProgrammesMulti-component Disentanglement |
Poisson LikelihoodFactor AnalysisPK Representations |
✓ | GitHub | |
| Squidiff | 2025 | Combinatorial Effect PredictionContext TransferUnseen Perturbation Prediction |
Diffusion Model |
✓ | GitHub | |
| STAMP | 2024 | Linear Gene ProgrammesUnsupervised Disentanglement |
Spatially-informedTime-resolvedGraph encoderFactor Analysis |
✓ | 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 | |
| sVAE+ | 2023 | Seen Perturbation PredictionMulti-component DisentanglementCausal StructureNonlinear Gene Programmes |
VAENB likelihoodSparse Mechanism Shift |
✓ | GitHub | |
| Taichi | 2024 | Perturbation ResponsivenessDifferential Analysis |
Graph DiffusionK-meansLogistic RegressionSpatially-informed |
✗ | 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 | |
| VEGA | 2023 | Linear Gene Programmes |
VAELinear DecoderPK Representations |
✓ | GitHub | |
| Vespucci | 2024 | Perturbation ResponsivenessDifferential Analysis |
Random ForrestSpatially-Informed |
✗ | GitHub | |
| VirTues | 2025 | Context Transfer |
ViTMaked AutoencoderMulti-modal |
✓ | GitHub | |
| Waddington-OT | 2019 | Trace Cell PopulationsLinear Gene Programmes |
Unbalanced OTEntropy-regularized Sinkhorn |
✓ | GitHub |
- Causal Structure
- Combinatorial Effect Prediction
- Context Transfer
- Contrastive Disentanglement
- Differential Analysis
- Feature Relationships
- GRN Inference
- Linear Gene Programmes
- Multi-component Disentanglement
- Nonlinear Gene Programmes
- Perturbation Responsiveness
- Seen Perturbation Prediction
- Trace Cell Populations
- Unseen Perturbation Prediction
- Unsupervised Disentanglement