TEMPOBRIDGE: SOURCE-CONDITIONED FLOW MATCHINGWITHOPTIMALTRANSPORTCOUPLINGS FORSINGLE-CELLPOPULATIONTRANSITIONS

Destructivesingle-cellmeasurementsprovideunpairedpopulationsnapshotsrather thanobservationsofthesamecellsacrossconditions.Localcellstatesandtran sitionrequestsmayalsobeinsufficient todistinguishresponsesacrosssource populations.WeintroduceTempoBridge,acommonsource-conditionedtransport formulationfortemporal,genetic,andchemicalpopulationtransitions. Source cellsinitializelatenttransportandprovideafixedempiricalpopulationsummary. Thevelocityfieldreceivesthissummaryalongsidetheevolvingcellstate,flow time, andastructuredtransitiondescriptor. Minibatchoptimal transport (OT) suppliescouplingsonlyforconditionalflow-matchingtrainingpaths; inference requiresneithertargetexpressionnorOTcomputation.Onheld-outdonors,Tem poBridgeachievesanEnergydistanceof0.129versus0.144forscGen.Genetic mean-expressionL2erroris2.261versus3.156forscGPT-scratchunderSeen2/2. Onheld-outcompounds,condition-averageddrug-effectcorrelationis0.598versus 0.561fortheCellFlowadapter.Temporalablationsshowhighermeandistribu tionalerrorafterremovingsourcecontext,replacingoptimaltransportwithrandom pairing,orreplacingflowmatchingwithstaticresidualregression.Together,these resultsdemonstratethepredictiveutilityofacommonsource-conditionedtransport formulationacrossheld-outdonors,genecombinations,andcompounds.