Index

A

acqf_name (perfusio.bed.policies.BEDDecision attribute) acqf_value (perfusio.bed.policies.BEDDecision attribute) acquisition_surface() (in module perfusio.viz.interactive) alarm_file (perfusio.config.AlarmConfig attribute) AlarmConfig (class in perfusio.config) AlarmEvent (class in perfusio.twin.notifications) AlarmNotifier (class in perfusio.twin.notifications) allow_write (perfusio.config.RunConfig attribute) (perfusio.RunConfig attribute)

alpha_amm_gln (perfusio.mechanistic.kinetics.CHOKinetics attribute) Ambr250Emulator (class in perfusio.connectors.ambr250_emulator) AMM (perfusio.chemistry.species.SpeciesEnum attribute) ammonium_critical (perfusio.config.AlarmConfig attribute) ammonium_warning (perfusio.config.AlarmConfig attribute) apply() (perfusio.simulator.noise.NoiseModel method) AuditLogger (class in perfusio.twin.audit)

B

batch_size (perfusio.StateBatch property) (perfusio.states.StateBatch property) BEDDecision (class in perfusio.bed.policies) BEDPolicy (class in perfusio.bed.policies) BioreactorConnectorBase (class in perfusio.connectors.base)

bleed_trigger() (in module perfusio.chemistry.volumes) bounds_tensor (perfusio.config.DesignSpace property) (perfusio.DesignSpace property) box_behnken() (in module perfusio.simulator.doe) build_acquisition() (in module perfusio.bed.acquisitions)

C

cell_diameter() (perfusio.mechanistic.kinetics.CHOKinetics method) central_composite() (in module perfusio.simulator.doe) check_forecast() (perfusio.twin.notifications.AlarmNotifier method) CHOKinetics (class in perfusio.mechanistic.kinetics) CHOPerfusionModel (class in perfusio.mechanistic.models) CHOSimulator (class in perfusio.simulator.cho_perfusion) clone_id (perfusio.embedding.clones.CloneInfo attribute) (perfusio.State attribute) (perfusio.states.State attribute) (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute) clone_id() (perfusio.embedding.clones.CloneRegistry method) clone_ids (perfusio.StateBatch attribute) (perfusio.states.StateBatch attribute) CloneInfo (class in perfusio.embedding.clones) CloneRegistry (class in perfusio.embedding.clones) close() (perfusio.twin.audit.AuditLogger method) COLUMNS (perfusio.twin.audit.AuditLogger attribute) compute_flows() (perfusio.chemistry.balances.FlowRateCalculator method) compute_pareto_front() (in module perfusio.bed.pareto) constant_volume_harvest_rate() (in module perfusio.chemistry.volumes)

consumes_lactate (perfusio.embedding.clones.CloneInfo attribute) (perfusio.mechanistic.kinetics.CHOKinetics attribute) control_bounds (perfusio.config.DesignSpace attribute) (perfusio.DesignSpace attribute) control_names (perfusio.config.DesignSpace property) (perfusio.DesignSpace property) (perfusio.StateBatch attribute) (perfusio.states.StateBatch attribute) (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute) ControlBounds (class in perfusio.config) controls (perfusio.State attribute) (perfusio.StateBatch attribute) (perfusio.states.State attribute) (perfusio.states.StateBatch attribute) (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute) create_tables() (perfusio.connectors.sql_store.SQLStore method) crps() (in module perfusio.metrics.coverage) current_state (perfusio.bed.policies.BEDDecision attribute) cv_by_species (perfusio.simulator.noise.NoiseModel attribute)

D

DailyScheduler (class in perfusio.twin.scheduler) day (perfusio.bed.policies.BEDDecision attribute) (perfusio.State attribute) (perfusio.StateBatch attribute) (perfusio.states.State attribute) (perfusio.states.StateBatch attribute) (perfusio.twin.notifications.AlarmEvent attribute) days (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute) DCD (perfusio.chemistry.species.SpeciesEnum attribute) decide() (perfusio.bed.policies.BEDPolicy method) DEFAULT (perfusio.chemistry.species.SpeciesRegistry attribute), [1] default() (perfusio.embedding.clones.CloneRegistry class method) default_cv (perfusio.simulator.noise.NoiseModel attribute) derived (perfusio.chemistry.species.SpeciesRegistry property)

description (perfusio.config.ControlBounds attribute) (perfusio.config.SpeciesBounds attribute) (perfusio.embedding.clones.CloneInfo attribute) DesignSpace (class in perfusio) (class in perfusio.config) device (perfusio.config.RunConfig attribute) (perfusio.RunConfig attribute) DIAM (perfusio.chemistry.species.SpeciesEnum attribute) diam_base (perfusio.mechanistic.kinetics.CHOKinetics attribute) diam_death_coeff (perfusio.mechanistic.kinetics.CHOKinetics attribute) DigitalTwin (class in perfusio.twin.digital_twin) direction (perfusio.twin.notifications.AlarmEvent attribute) disconnect() (perfusio.connectors.opcua_client.OPCUAConnector method) DiscreteMassBalance (class in perfusio.chemistry.balances) dtype (perfusio.config.RunConfig attribute) (perfusio.RunConfig attribute)

E

embed_and_concat() (perfusio.embedding.clones.EntityEmbedding method) EnsembleMember (class in perfusio.gp.ensemble) EntityEmbedding (class in perfusio.embedding.clones)

epsilon_indicator() (in module perfusio.metrics.multiobjective) evaluate() (perfusio.bed.objectives.MultiObjectiveOFV method) (perfusio.bed.objectives.TargetTrackingOFV method) evaluate_batch() (perfusio.bed.objectives.TargetTrackingOFV method)

F

fig4_training_trajectories() (in module perfusio.viz.static) fig6_model_predictions() (in module perfusio.viz.static) fig7_pareto_front() (in module perfusio.viz.static) fig8_closed_loop_performance() (in module perfusio.viz.static) FilesystemStore (class in perfusio.connectors.filesystem) fit() (perfusio.gp.ensemble.JackknifeEnsemble method) five_reactor_ensemble() (perfusio.connectors.ambr250_emulator.Ambr250Emulator class method) FlowRateCalculator (class in perfusio.chemistry.balances) forecast_figure() (in module perfusio.viz.interactive) forecast_mean (perfusio.bed.policies.BEDDecision attribute)

forecast_run() (in module perfusio.hybrid.forecast) forward() (perfusio.embedding.clones.EntityEmbedding method) (perfusio.gp.exact_gp.MultiTaskRateGP method) (perfusio.gp.kernels.PerfusionKernel method) (perfusio.gp.kernels.ResidualKernel method) (perfusio.gp.means.LinearMean method) (perfusio.gp.means.MechanisticPriorMean method) from_tensor() (perfusio.State class method) (perfusio.states.State class method) full_name (perfusio.chemistry.species.Species attribute)

G

generate_box_behnken_experiment() (perfusio.simulator.cho_perfusion.CHOSimulator method) get_species() (perfusio.states.Trajectory method) (perfusio.Trajectory method) GLC (perfusio.chemistry.species.SpeciesEnum attribute)

glc_switch (perfusio.mechanistic.kinetics.CHOKinetics attribute) GLN (perfusio.chemistry.species.SpeciesEnum attribute) GLU (perfusio.chemistry.species.SpeciesEnum attribute) glucose_critical (perfusio.config.AlarmConfig attribute) glucose_warning (perfusio.config.AlarmConfig attribute)

H

hard_lower (perfusio.config.ControlBounds attribute) hard_upper (perfusio.config.ControlBounds attribute) hi (perfusio.chemistry.species.Species attribute) (perfusio.config.ControlBounds attribute) (perfusio.config.SpeciesBounds attribute)

history (perfusio.bed.policies.BEDPolicy property) HybridStateSpaceModel (class in perfusio.hybrid.model) hypervolume() (in module perfusio.bed.pareto) hypervolume_indicator() (in module perfusio.metrics.multiobjective)

I

igd_plus() (in module perfusio.metrics.multiobjective) index() (perfusio.chemistry.species.SpeciesRegistry method) integrate_run() (in module perfusio.mechanistic.integrators) is_alive() (perfusio.connectors.ambr250_emulator.Ambr250Emulator method) (perfusio.connectors.base.BioreactorConnectorBase method) (perfusio.connectors.filesystem.FilesystemStore method) (perfusio.connectors.opcua_client.OPCUAConnector method) (perfusio.connectors.sql_store.SQLStore method) (perfusio.simulator.cho_perfusion.CHOSimulator method)

is_control (perfusio.chemistry.species.Species attribute) is_measured (perfusio.chemistry.species.Species attribute) is_stationary (perfusio.gp.kernels.PerfusionKernel attribute) (perfusio.gp.kernels.ResidualKernel attribute)

J

JackknifeEnsemble (class in perfusio.gp.ensemble)

jitter_hours (perfusio.simulator.noise.NoiseModel attribute) joint_finetune() (perfusio.embedding.transfer.TransferLearner method)

K

K_d (perfusio.mechanistic.kinetics.CHOKinetics attribute) k_death() (perfusio.mechanistic.kinetics.CHOKinetics method) K_glc (perfusio.mechanistic.kinetics.CHOKinetics attribute)

K_gln (perfusio.mechanistic.kinetics.CHOKinetics attribute) k_pyr_amm (perfusio.mechanistic.kinetics.CHOKinetics attribute) K_T (perfusio.mechanistic.kinetics.CHOKinetics attribute)

L

LAC (perfusio.chemistry.species.SpeciesEnum attribute) lac_consump_rate (perfusio.mechanistic.kinetics.CHOKinetics attribute) latin_hypercube() (in module perfusio.simulator.doe) lead_days (perfusio.twin.notifications.AlarmEvent attribute) likelihood (perfusio.gp.ensemble.EnsembleMember attribute) LinearMean (class in perfusio.gp.means) lo (perfusio.chemistry.species.Species attribute) (perfusio.config.ControlBounds attribute) (perfusio.config.SpeciesBounds attribute)

load() (perfusio.embedding.transfer.TransferLearner method) log() (perfusio.twin.audit.AuditLogger method) log_audit_event() (perfusio.connectors.sql_store.SQLStore method) log_level (perfusio.config.RunConfig attribute) (perfusio.RunConfig attribute) LYS (perfusio.chemistry.species.SpeciesEnum attribute)

M

m_glc (perfusio.mechanistic.kinetics.CHOKinetics attribute) make_generator() (perfusio.config.RunConfig method) (perfusio.RunConfig method) measured (perfusio.chemistry.species.SpeciesRegistry property) MechanisticPriorMean (class in perfusio.gp.means) members (perfusio.gp.ensemble.JackknifeEnsemble attribute) metadata (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute) missing_prob (perfusio.simulator.noise.NoiseModel attribute) model (perfusio.gp.ensemble.EnsembleMember attribute) model_config (perfusio.config.AlarmConfig attribute) (perfusio.config.ControlBounds attribute) (perfusio.config.DesignSpace attribute) (perfusio.config.RunConfig attribute) (perfusio.config.SpeciesBounds attribute) (perfusio.DesignSpace attribute) (perfusio.RunConfig attribute) module perfusio perfusio.bed.acquisitions perfusio.bed.objectives perfusio.bed.pareto perfusio.bed.policies perfusio.bed.search perfusio.chemistry.balances perfusio.chemistry.species perfusio.chemistry.volumes perfusio.config perfusio.connectors.ambr250_emulator perfusio.connectors.base perfusio.connectors.filesystem perfusio.connectors.opcua_client perfusio.connectors.sql_store perfusio.embedding.clones perfusio.embedding.transfer perfusio.gp.ensemble perfusio.gp.exact_gp perfusio.gp.kernels perfusio.gp.means perfusio.gp.stepwise perfusio.hybrid.forecast perfusio.hybrid.model perfusio.hybrid.train perfusio.mechanistic.integrators perfusio.mechanistic.kinetics perfusio.mechanistic.models perfusio.metrics.coverage perfusio.metrics.multiobjective perfusio.metrics.rrmse perfusio.simulator.cho_perfusion perfusio.simulator.doe perfusio.simulator.noise perfusio.states perfusio.twin.audit perfusio.twin.digital_twin perfusio.twin.notifications perfusio.twin.scheduler perfusio.viz.interactive perfusio.viz.static

mu() (perfusio.mechanistic.kinetics.CHOKinetics method) mu_max (perfusio.mechanistic.kinetics.CHOKinetics attribute) MultiObjectiveOFV (class in perfusio.bed.objectives) MultiTaskRateGP (class in perfusio.gp.exact_gp)

N

n_clones (perfusio.embedding.clones.CloneRegistry property) n_controls (perfusio.config.DesignSpace property) (perfusio.DesignSpace property) (perfusio.states.Trajectory property) (perfusio.Trajectory property) n_days (perfusio.states.Trajectory property) (perfusio.Trajectory property) n_mc_samples (perfusio.config.RunConfig attribute) (perfusio.RunConfig attribute)

n_restarts (perfusio.config.RunConfig attribute) (perfusio.RunConfig attribute) n_species (perfusio.states.Trajectory property) (perfusio.Trajectory property) name (perfusio.config.DesignSpace attribute) (perfusio.DesignSpace attribute) (perfusio.embedding.clones.CloneInfo attribute) names (perfusio.chemistry.species.SpeciesRegistry property) NoiseModel (class in perfusio.simulator.noise) notification_channel (perfusio.config.AlarmConfig attribute)

O

ode_rhs() (perfusio.mechanistic.kinetics.CHOKinetics method)

OPCUAConnector (class in perfusio.connectors.opcua_client) optimise_acquisition() (in module perfusio.bed.search)

P

pareto_scatter() (in module perfusio.viz.interactive) perfusio module perfusio.bed.acquisitions module perfusio.bed.objectives module perfusio.bed.pareto module perfusio.bed.policies module perfusio.bed.search module perfusio.chemistry.balances module perfusio.chemistry.species module perfusio.chemistry.volumes module perfusio.config module perfusio.connectors.ambr250_emulator module perfusio.connectors.base module perfusio.connectors.filesystem module perfusio.connectors.opcua_client module perfusio.connectors.sql_store module perfusio.embedding.clones module perfusio.embedding.transfer module perfusio.gp.ensemble module perfusio.gp.exact_gp module perfusio.gp.kernels module perfusio.gp.means module perfusio.gp.stepwise module perfusio.hybrid.forecast module

perfusio.hybrid.model module perfusio.hybrid.train module perfusio.mechanistic.integrators module perfusio.mechanistic.kinetics module perfusio.mechanistic.models module perfusio.metrics.coverage module perfusio.metrics.multiobjective module perfusio.metrics.rrmse module perfusio.simulator.cho_perfusion module perfusio.simulator.doe module perfusio.simulator.noise module perfusio.states module perfusio.twin.audit module perfusio.twin.digital_twin module perfusio.twin.notifications module perfusio.twin.scheduler module perfusio.viz.interactive module perfusio.viz.static module perfusion_volume_step() (in module perfusio.chemistry.volumes) PerfusionKernel (class in perfusio.gp.kernels) pi_coverage() (in module perfusio.metrics.coverage) predict() (perfusio.gp.ensemble.JackknifeEnsemble method) predict_next_state() (perfusio.hybrid.model.HybridStateSpaceModel method) predict_quantiles() (perfusio.gp.stepwise.StepwiseGP method) predict_rates() (perfusio.mechanistic.models.CHOPerfusionModel method) predict_rates_batch() (perfusio.mechanistic.models.CHOPerfusionModel method) predict_trajectory() (perfusio.hybrid.model.HybridStateSpaceModel method) predict_with_ci() (perfusio.gp.exact_gp.MultiTaskRateGP method) predicted_value (perfusio.twin.notifications.AlarmEvent attribute) PYR (perfusio.chemistry.species.SpeciesEnum attribute)

Q

q_amm() (perfusio.mechanistic.kinetics.CHOKinetics method) q_glc() (perfusio.mechanistic.kinetics.CHOKinetics method) q_glc_max (perfusio.mechanistic.kinetics.CHOKinetics attribute) q_gln() (perfusio.mechanistic.kinetics.CHOKinetics method)

q_gln_max (perfusio.mechanistic.kinetics.CHOKinetics attribute) q_lac() (perfusio.mechanistic.kinetics.CHOKinetics method) q_mab() (perfusio.mechanistic.kinetics.CHOKinetics method) q_mAb_growth (perfusio.mechanistic.kinetics.CHOKinetics attribute) q_mAb_nongrowth (perfusio.mechanistic.kinetics.CHOKinetics attribute)

R

rates_from_observations() (perfusio.chemistry.balances.DiscreteMassBalance method) rates_from_trajectory() (perfusio.chemistry.balances.DiscreteMassBalance method) raw_samples (perfusio.config.RunConfig attribute) (perfusio.RunConfig attribute) reactor_id (perfusio.State attribute) (perfusio.states.State attribute) (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute) reactor_ids (perfusio.StateBatch attribute) (perfusio.states.StateBatch attribute) read_sample() (perfusio.connectors.ambr250_emulator.Ambr250Emulator method) (perfusio.connectors.base.BioreactorConnectorBase method) (perfusio.connectors.filesystem.FilesystemStore method) (perfusio.connectors.opcua_client.OPCUAConnector method) (perfusio.connectors.sql_store.SQLStore method) (perfusio.simulator.cho_perfusion.CHOSimulator method)

recommended_controls (perfusio.bed.policies.BEDDecision attribute) ResidualKernel (class in perfusio.gp.kernels) retrain_online() (in module perfusio.hybrid.train) rrmse_horizon() (in module perfusio.metrics.rrmse) run() (perfusio.twin.digital_twin.DigitalTwin method) (perfusio.twin.scheduler.DailyScheduler method) run_id (perfusio.State attribute) (perfusio.states.State attribute) (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute) run_ids (perfusio.StateBatch attribute) (perfusio.states.StateBatch attribute) run_sync() (perfusio.twin.digital_twin.DigitalTwin method) RunConfig (class in perfusio) (class in perfusio.config)

S

save() (perfusio.embedding.transfer.TransferLearner method) scale_to_bounds() (in module perfusio.simulator.doe) score_trajectories() (perfusio.bed.objectives.TargetTrackingOFV method) seed (perfusio.config.RunConfig attribute) (perfusio.RunConfig attribute) (perfusio.simulator.noise.NoiseModel attribute) sharpness() (in module perfusio.metrics.coverage) short_name (perfusio.chemistry.species.Species attribute) simulate() (perfusio.mechanistic.models.CHOPerfusionModel method) simulate_run() (perfusio.connectors.ambr250_emulator.Ambr250Emulator method) (perfusio.simulator.cho_perfusion.CHOSimulator method) slice_days() (perfusio.states.Trajectory method) (perfusio.Trajectory method) Species (class in perfusio.chemistry.species) species (perfusio.chemistry.balances.DiscreteMassBalance property) (perfusio.State attribute) (perfusio.StateBatch attribute) (perfusio.states.State attribute) (perfusio.states.StateBatch attribute) (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute) (perfusio.twin.notifications.AlarmEvent attribute) species_bounds (perfusio.config.DesignSpace attribute) (perfusio.DesignSpace attribute)

species_index (perfusio.bed.objectives.TargetSpec attribute) species_index() (perfusio.states.Trajectory method) (perfusio.Trajectory method) species_names (perfusio.config.DesignSpace property) (perfusio.DesignSpace property) (perfusio.StateBatch attribute) (perfusio.states.StateBatch attribute) (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute) SpeciesBounds (class in perfusio.config) SpeciesEnum (class in perfusio.chemistry.species) SpeciesRegistry (class in perfusio.chemistry.species) SQLStore (class in perfusio.connectors.sql_store) State (class in perfusio) (class in perfusio.states) STATE_ORDER (perfusio.mechanistic.kinetics.CHOKinetics attribute) STATE_SPECIES (perfusio.mechanistic.models.CHOPerfusionModel attribute) (perfusio.simulator.cho_perfusion.CHOSimulator attribute) StateBatch (class in perfusio) (class in perfusio.states) step() (perfusio.chemistry.balances.DiscreteMassBalance method) (perfusio.twin.digital_twin.DigitalTwin method) StepwiseGP (class in perfusio.gp.stepwise) stop() (perfusio.twin.scheduler.DailyScheduler method) subset() (perfusio.chemistry.species.SpeciesRegistry method)

T

T_ref (perfusio.mechanistic.kinetics.CHOKinetics attribute) target (perfusio.bed.objectives.TargetSpec attribute) TargetSpec (class in perfusio.bed.objectives) TargetTrackingOFV (class in perfusio.bed.objectives) threshold (perfusio.twin.notifications.AlarmEvent attribute) time_jitter() (perfusio.simulator.noise.NoiseModel method) timestamp (perfusio.bed.policies.BEDDecision attribute) TITER (perfusio.chemistry.species.SpeciesEnum attribute) titer_target (perfusio.config.DesignSpace attribute) (perfusio.DesignSpace attribute) to() (perfusio.states.Trajectory method) (perfusio.Trajectory method) to_input_tensor() (perfusio.StateBatch method) (perfusio.states.StateBatch method) (perfusio.states.Trajectory method) (perfusio.Trajectory method)

to_tensor() (perfusio.State method) (perfusio.states.State method) torch_device (perfusio.config.RunConfig property) (perfusio.RunConfig property) torch_dtype (perfusio.config.RunConfig property) (perfusio.RunConfig property) train_hybrid() (in module perfusio.hybrid.train) train_idx (perfusio.gp.ensemble.EnsembleMember attribute) Trajectory (class in perfusio) (class in perfusio.states) trajectory_figure() (in module perfusio.viz.interactive) TransferLearner (class in perfusio.embedding.transfer)

U

unit (perfusio.chemistry.species.Species attribute) (perfusio.config.ControlBounds attribute) (perfusio.config.SpeciesBounds attribute)

V

valid_mask() (perfusio.states.Trajectory method) (perfusio.Trajectory method) VCD (perfusio.chemistry.species.SpeciesEnum attribute) VCV (perfusio.chemistry.species.SpeciesEnum attribute) vcv_target (perfusio.config.DesignSpace attribute) (perfusio.DesignSpace attribute) VIA (perfusio.chemistry.species.SpeciesEnum attribute) viability_critical (perfusio.config.AlarmConfig attribute)

viability_min (perfusio.config.DesignSpace attribute) (perfusio.DesignSpace attribute) viability_warning (perfusio.config.AlarmConfig attribute) volume_L (perfusio.State attribute) (perfusio.StateBatch attribute) (perfusio.states.State attribute) (perfusio.states.StateBatch attribute) (perfusio.states.Trajectory attribute) (perfusio.Trajectory attribute)

W

warm_start() (perfusio.embedding.transfer.TransferLearner method) weight (perfusio.bed.objectives.TargetSpec attribute) write_sample() (perfusio.connectors.sql_store.SQLStore method) write_setpoints() (perfusio.connectors.ambr250_emulator.Ambr250Emulator method) (perfusio.connectors.base.BioreactorConnectorBase method) (perfusio.connectors.filesystem.FilesystemStore method) (perfusio.connectors.opcua_client.OPCUAConnector method) (perfusio.connectors.sql_store.SQLStore method) (perfusio.simulator.cho_perfusion.CHOSimulator method)

Y

Y_lac_glc (perfusio.mechanistic.kinetics.CHOKinetics attribute)

Z

ZeroMeanMultiTask (class in perfusio.gp.means)