2022
Manifold Interpolating Optimal-Transport Flows for Trajectory Inference.
Huguet G, Magruder D, Tong A, Fasina O, Kuchroo M, Wolf G, Krishnaswamy S. Manifold Interpolating Optimal-Transport Flows for Trajectory Inference. Advances In Neural Information Processing Systems 2022, 35: 29705-29718. PMID: 37397786, PMCID: PMC10312391.Peer-Reviewed Original ResearchOptimal transportNeural ordinary differential equationsOrdinary differential equationsSchrödinger bridgesDifferential equationsData manifoldGeodesic distanceTrajectory inferenceDynamic modelManifold learningLatent spaceGenerative modelScRNA-seq dataPopulation snapshotsFlowEquationsManifoldSpace distanceBifurcationPopulation dynamicsGround distanceGeometryModelInferenceSpaceTransformer-based protein generation with regularized latent space optimization
Castro E, Godavarthi A, Rubinfien J, Givechian K, Bhaskar D, Krishnaswamy S. Transformer-based protein generation with regularized latent space optimization. Nature Machine Intelligence 2022, 4: 840-851. DOI: 10.1038/s42256-022-00532-1.Peer-Reviewed Original Research
2019
Modeling Global Dynamics from Local Snapshots with Deep Generative Neural Networks
Gigante S, van Dijk D, Moon K, Strzalkowski A, Wolf G, Krishnaswamy S. Modeling Global Dynamics from Local Snapshots with Deep Generative Neural Networks. 2019, 00: 1-4. DOI: 10.1109/sampta45681.2019.9030978.Peer-Reviewed Original ResearchStochastic dynamic systemsDeep generative neural networksProbability distributionDynamic systemsMarkov modelGlobal dynamicsLocal snapshotGenerative neural networksKalman filterSnapshot dataNeural networkNeural network frameworkRecurrent neural networkSuch systemsNext stateModeling networkNetwork frameworkDynamicsShallow modelsLocal transitionsHypothetical trajectoryModelBiological systemsNatural sciencesLongitudinal measurements