Index

A

a_plus_b_times_c_minus_d() (pybnf.algorithms.optimizers.simplex.SimplexAlgorithm method) ab_plus_cd() (pybnf.algorithms.optimizers.simplex.SimplexAlgorithm method) Action (class in pybnf.pset) Adaptive_MCMC (class in pybnf.algorithms.samplers.adaptive_mcmc) AdaptiveMCMCConfig (class in pybnf.algorithms.samplers.adaptive_mcmc) add() (pybnf.pset.FreeParameter method) (pybnf.pset.Trajectory method) add_action() (pybnf.pset.BNGLModel method) add_iterations() (pybnf.algorithms.base.Algorithm method) (pybnf.algorithms.optimizers.cmaes.CMAESAlgorithm method) (pybnf.algorithms.optimizers.gradient_base.GradientOptimizer method) (pybnf.algorithms.optimizers.particle_swarm.ParticleSwarm method) (pybnf.algorithms.optimizers.powell.PowellAlgorithm method) (pybnf.algorithms.optimizers.simulated_annealing.SimulatedAnnealing method) (pybnf.algorithms.samplers.basic_mcmc.BasicBayesMCMCAlgorithm method) add_mutant() (pybnf.pset.Model method) add_rand() (pybnf.pset.FreeParameter method)

add_result() (pybnf.algorithms.core.Result method) add_to_trajectory() (pybnf.algorithms.base.Algorithm method) AdditiveNoiseScale (class in pybnf.noise.scale) aic (pybnf.objective.InformationCriteria attribute) aicc (pybnf.objective.InformationCriteria attribute) Algorithm (class in pybnf.algorithms.base) AlwaysConstraint (class in pybnf.constraint) apply() (pybnf.measurement.base.MeasurementLayer method) apply_routing() (in module pybnf.gradient.routing) assemble_constraint_gradient() (in module pybnf.gradient.assembly) assemble_gaussian_gradient() (in module pybnf.gradient.assembly) AsynchronousDifferentialEvolution (class in pybnf.algorithms.optimizers.differential_evolution) AtConstraint (class in pybnf.constraint) AveNormSumOfSquaresObjective (class in pybnf.objective) average() (pybnf.data.Data static method) average_results() (pybnf.algorithms.core.HybridJobGroup method) (pybnf.algorithms.core.JobGroup method) (pybnf.algorithms.core.MultimodelJobGroup method)

B

backup() (pybnf.algorithms.base.Algorithm method) BasicBayesMCMCAlgorithm (class in pybnf.algorithms.samplers.basic_mcmc) BasicMCMCConfig (class in pybnf.algorithms.samplers.basic_mcmc) BayesianAlgorithm (class in pybnf.algorithms.samplers.base) best_fit() (pybnf.pset.Trajectory method) best_fit_name() (pybnf.pset.Trajectory method) best_score() (pybnf.pset.Trajectory method) BetweenConstraint (class in pybnf.constraint) bic (pybnf.objective.InformationCriteria attribute) Bijector (class in pybnf.priors) (class in pybnf.priors.bijector) bijector_for_support() (in module pybnf.priors) (in module pybnf.priors.bijector)

bind_scale_param() (pybnf.constraint.Constraint method) bngl_body_to_petab_math() (in module pybnf.petab.formula) BnglModel (class in pybnf.petab.bngl_model) BNGLModel (class in pybnf.pset) BoxBijector (class in pybnf.priors.bijector) build() (pybnf.priors.base.NoPrior class method) (pybnf.priors.NoPrior class method) build_dose_response_conditions() (in module pybnf.petab.conditions) build_experiment_conditions() (in module pybnf.petab.conditions) build_named_objective() (in module pybnf.objective) build_preequilibration_conditions() (in module pybnf.petab.conditions) build_prior() (in module pybnf.priors) build_profile_objective() (in module pybnf.objective) build_whole_fit_noise_objective() (in module pybnf.objective)

C

calculate_new_pset() (pybnf.algorithms.samplers.dream.DreamAlgorithm method) (pybnf.algorithms.samplers.pdream.PDreamAlgorithm method) calculate_snooker_pset() (pybnf.algorithms.samplers.dream.DreamAlgorithm method) check_convergence() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) ChiSquareObjective (class in pybnf.objective) ChiSquareObjective_Dynamic (class in pybnf.objective) choose_new_pset() (pybnf.algorithms.optimizers.simulated_annealing.SimulatedAnnealing method) (pybnf.algorithms.samplers.basic_mcmc.BasicBayesMCMCAlgorithm method) classify_free_param() (in module pybnf.gradient.routing) clean_model_for_petab() (in module pybnf.petab.export) cleanup() (pybnf.algorithms.base.Algorithm method) (pybnf.algorithms.samplers.base.BayesianAlgorithm method) (pybnf.algorithms.samplers.basic_mcmc.BasicBayesMCMCAlgorithm method) clear_sim_registry() (in module pybnf.pset) Cluster (class in pybnf.cluster) CMAESAlgorithm (class in pybnf.algorithms.optimizers.cmaes) CMAESConfig (class in pybnf.algorithms.optimizers.cmaes) coerce_penalty_model() (pybnf.constraint.Constraint method) ColumnMeanSigma (class in pybnf.noise.source)

ColumnSummationObjective (class in pybnf.objective) compile_objective_expression() (in module pybnf.petab.formula) compile_petab_formula() (in module pybnf.petab.formula) compile_petab_formula_derivatives() (in module pybnf.petab.formula) compute_ess() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) compute_rhat() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) condition (pybnf.petab.import_.ImportedExperiment attribute) condition_factor() (in module pybnf.gradient.routing) CONDITION_ID_PREFIX (in module pybnf.petab.conditions) condition_name_from_id() (in module pybnf.petab.conditions) conditions_from_rows() (in module pybnf.petab.conditions) ConstantSigma (class in pybnf.noise.source) Constraint (class in pybnf.constraint) ConstraintCounter (class in pybnf.objective) ConstraintSet (class in pybnf.constraint) copy_with_param_set() (pybnf.pset.BNGLModel method) (pybnf.pset.Model method) (pybnf.pset.NetModel method) (pybnf.pset.SbmlModelNoTimeout method)

D

d_data_fit_d_prediction() (pybnf.noise.base.NoiseModel method) (pybnf.noise.gaussian.Gaussian method) (pybnf.noise.laplace.Laplace method) (pybnf.noise.negative_binomial.NegBinomial method) (pybnf.noise.student_t.StudentT method) d_mean_offset_d_noise() (pybnf.noise.base.NoiseModel method) (pybnf.noise.gaussian.Gaussian method) (pybnf.noise.laplace.Laplace method) d_nll_d_noise_params() (pybnf.noise.base.NoiseModel method) (pybnf.noise.gaussian.Gaussian method) (pybnf.noise.laplace.Laplace method) (pybnf.noise.negative_binomial.NegBinomial method) (pybnf.noise.student_t.StudentT method) d_offset_d_noise() (pybnf.noise.location.LocationInterpretation method) d_residual_d_prediction() (pybnf.noise.base.NoiseModel method) (pybnf.noise.gaussian.Gaussian method) (pybnf.noise.laplace.Laplace method) (pybnf.noise.student_t.StudentT method) Data (class in pybnf.data) data_files (pybnf.petab.import_.ImportedExperiment attribute) data_fit() (pybnf.noise.base.NoiseModel method) (pybnf.noise.gaussian.Gaussian method) (pybnf.noise.laplace.Laplace method) (pybnf.noise.negative_binomial.NegBinomial method) (pybnf.noise.student_t.StudentT method)

data_fit_grad_point() (pybnf.objective.LikelihoodObjective method) (pybnf.objective.ObjectiveFunction method) data_from_measurement_rows() (in module pybnf.petab.measurements) DataColumnSigma (class in pybnf.noise.source) DEFamilyConfig (class in pybnf.algorithms.optimizers.differential_evolution) detect_and_reset_outliers() (pybnf.algorithms.samplers.dream.DreamAlgorithm method) dforward() (pybnf.noise.scale.AdditiveNoiseScale method) diff() (pybnf.pset.FreeParameter method) DifferentialEvolution (class in pybnf.algorithms.optimizers.differential_evolution) DifferentialEvolutionBase (class in pybnf.algorithms.optimizers.differential_evolution) DifferentialEvolutionConfig (class in pybnf.algorithms.optimizers.differential_evolution) DirectPassObjective (class in pybnf.objective) divergences (pybnf.algorithms.samplers.hmc.HMCSampler attribute) DONE (in module pybnf.algorithms.optimizers.gradient_base) dose_response_measurement_rows() (in module pybnf.petab.measurements) DreamAlgorithm (class in pybnf.algorithms.samplers.dream) DreamConfig (class in pybnf.algorithms.samplers.dream) DuplicateColumnError

E

ess() (in module pybnf.diagnostics) ess_from_chains() (in module pybnf.diagnostics) eval_column() (pybnf.objective.ColumnSummationObjective method) (pybnf.objective.KLLikelihood method) (pybnf.objective.WassersteinObjective method) eval_point() (pybnf.objective.AveNormSumOfSquaresObjective method) (pybnf.objective.LikelihoodObjective method) (pybnf.objective.NormSumOfSquaresObjective method) (pybnf.objective.SummationObjective method) (pybnf.objective.SumOfDiffsObjective method) (pybnf.objective.SumOfSquaresObjective method) evaluate() (pybnf.objective.AveNormSumOfSquaresObjective method) (pybnf.objective.ColumnSummationObjective method) (pybnf.objective.ConstraintCounter method) (pybnf.objective.DirectPassObjective method) (pybnf.objective.ObjectiveFunction method) (pybnf.objective.SummationObjective method)

evaluate_constraints() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) evaluate_multiple() (pybnf.objective.ConstraintCounter method) (pybnf.objective.DirectPassObjective method) (pybnf.objective.ObjectiveFunction method) evaluate_objective() (pybnf.objective.ObjectiveCalculator method) evaluate_pointwise() (pybnf.objective.LikelihoodObjective method) (pybnf.objective.ObjectiveFunction method) execute() (pybnf.pset.BNGLModel method) (pybnf.pset.Model method) (pybnf.pset.SbmlModel method) (pybnf.pset.SbmlModelNoTimeout method) exp10() (in module pybnf.algorithms.base) exp_column() (pybnf.noise.source.DataColumnSigma method) (pybnf.noise.source.SigmaSource method) ExperimentRouting (class in pybnf.gradient.routing) export_job() (in module pybnf.petab.export)

F

FailedSimulation (class in pybnf.algorithms.core) FailedSimulationError field_names (pybnf.priors.base.NoPrior attribute) (pybnf.priors.base.Prior attribute) (pybnf.priors.NoPrior attribute) (pybnf.priors.Prior attribute) find_keys() (pybnf.constraint.Constraint method) find_t_length() (pybnf.pset.BNGLModel method) fit_type (pybnf.algorithms.optimizers.lbfgs.LBFGSAlgorithm attribute) (pybnf.algorithms.optimizers.trf.TRFAlgorithm attribute) formula (pybnf.noise.source.FormulaSigma attribute) (pybnf.noise.source.PerMeasurementFormulaSigma attribute) formula_free_symbols() (in module pybnf.petab.formula) FormulaSigma (class in pybnf.noise.source) forward() (pybnf.noise.scale.AdditiveNoiseScale method) (pybnf.priors.Linear method) (pybnf.priors.Ln method) (pybnf.priors.Log10 method) (pybnf.priors.Scale method) (pybnf.priors.scale.Linear method) (pybnf.priors.scale.Ln method) (pybnf.priors.scale.Log10 method) (pybnf.priors.scale.Scale method)

free_parameter_from_row() (in module pybnf.petab.parameters) free_parameters_from_file() (in module pybnf.petab.parameters) free_parameters_from_table() (in module pybnf.petab.parameters) FreeParameter (class in pybnf.pset) FreeParameterSigma (class in pybnf.noise.source) from_columns() (pybnf.data.Data class method) from_config() (pybnf.objective.ColumnSummationObjective class method) (pybnf.objective.LikelihoodObjective class method) (pybnf.objective.NegBinLikelihood class method) (pybnf.objective.ObjectiveFunction class method) (pybnf.objective.SummationObjective class method) from_file() (pybnf.petab.bngl_model.BnglModel static method) from_pybnf() (in module pybnf.inference_data) from_sampling_space() (pybnf.pset.FreeParameter method) from_sampling_space_jax() (pybnf.pset.FreeParameter method) frozen (pybnf.priors.base.NoPrior attribute) (pybnf.priors.base.Prior attribute) (pybnf.priors.NoPrior attribute) (pybnf.priors.Prior attribute) FrozenPrior (class in pybnf.priors) (class in pybnf.priors.base)

G

Gaussian (class in pybnf.noise.gaussian) gen_bootstrap_weights() (pybnf.data.Data method) get_backup_every() (pybnf.algorithms.base.Algorithm method) (pybnf.algorithms.optimizers.scatter_search.ScatterSearch method) get_difference() (pybnf.constraint.Constraint method) get_free_parameter_ids_with_values() (pybnf.petab.bngl_model.BnglModel method) get_key() (pybnf.constraint.Constraint method) get_log_likelihood() (pybnf.constraint.Constraint method) get_log_likelihood_logit() (pybnf.constraint.Constraint method) get_param() (pybnf.pset.PSet method) get_parameter_ids() (pybnf.petab.bngl_model.BnglModel method) get_parameter_value() (pybnf.petab.bngl_model.BnglModel method) get_penalty() (pybnf.constraint.Constraint method) get_penalty_gradient() (pybnf.constraint.Constraint method) get_row() (pybnf.data.Data method) get_static_penalty() (pybnf.constraint.Constraint method) get_suffixes() (pybnf.pset.BNGLModel method) (pybnf.pset.Model method) (pybnf.pset.SbmlModelNoTimeout method) get_sums() (pybnf.algorithms.optimizers.simplex.SimplexAlgorithm method) get_valid_ids_for_condition_table() (pybnf.petab.bngl_model.BnglModel method) get_valid_parameters_for_parameter_table() (pybnf.petab.bngl_model.BnglModel method)

got() (pybnf.algorithms.optimizers.gradient_base.GradientRunner method) got_result() (pybnf.algorithms.base.Algorithm method) (pybnf.algorithms.optimizers.cmaes.CMAESAlgorithm method) (pybnf.algorithms.optimizers.differential_evolution.AsynchronousDifferentialEvolution method) (pybnf.algorithms.optimizers.differential_evolution.DifferentialEvolution method) (pybnf.algorithms.optimizers.differential_evolution.DifferentialEvolutionBase method) (pybnf.algorithms.optimizers.gradient_base.GradientOptimizer method) (pybnf.algorithms.optimizers.particle_swarm.ParticleSwarm method) (pybnf.algorithms.optimizers.powell.PowellAlgorithm method) (pybnf.algorithms.optimizers.profile_likelihood.ProfileLikelihoodAlgorithm method) (pybnf.algorithms.optimizers.scatter_search.ScatterSearch method) (pybnf.algorithms.optimizers.simplex.SimplexAlgorithm method) (pybnf.algorithms.optimizers.simulated_annealing.SimulatedAnnealing method) (pybnf.algorithms.samplers.adaptive_mcmc.Adaptive_MCMC method) (pybnf.algorithms.samplers.base.BayesianAlgorithm method) (pybnf.algorithms.samplers.basic_mcmc.BasicBayesMCMCAlgorithm method) (pybnf.algorithms.samplers.dream.DreamAlgorithm method) (pybnf.algorithms.samplers.pdream.PDreamAlgorithm method) gradient_at() (pybnf.algorithms.optimizers.gradient_base.GradientOptimizer method) GradientNotSupported GradientOptimizer (class in pybnf.algorithms.optimizers.gradient_base) GradientResult (class in pybnf.gradient.assembly) GradientRunner (class in pybnf.algorithms.optimizers.gradient_base)

H

has_bounded_initialization (pybnf.pset.FreeParameter property) has_bounded_support (pybnf.priors.base.NoPrior attribute) (pybnf.priors.base.Prior attribute) (pybnf.priors.NoPrior attribute) (pybnf.priors.Prior attribute) (pybnf.priors.truncated.TruncatedPrior attribute) (pybnf.priors.TruncatedPrior attribute) (pybnf.pset.FreeParameter property) has_entity_with_id() (pybnf.petab.bngl_model.BnglModel method) has_least_squares_residual() (pybnf.objective.LikelihoodObjective method) (pybnf.objective.ObjectiveFunction method)

has_prior (pybnf.priors.base.NoPrior attribute) (pybnf.priors.base.Prior attribute) (pybnf.priors.NoPrior attribute) (pybnf.priors.Prior attribute) (pybnf.priors.truncated.TruncatedPrior attribute) (pybnf.priors.TruncatedPrior attribute) (pybnf.pset.FreeParameter property) HMCConfig (class in pybnf.algorithms.samplers.hmc) HMCSampler (class in pybnf.algorithms.samplers.hmc) HybridJobGroup (class in pybnf.algorithms.core)

I

IdentityBijector (class in pybnf.priors.bijector) import_job() (in module pybnf.petab.import_) ImportedExperiment (class in pybnf.petab.import_) index() (pybnf.constraint.Constraint method) information_criteria() (in module pybnf.objective) InformationCriteria (class in pybnf.objective) initial_value_from_quantile() (pybnf.pset.FreeParameter method) inline_assignment_rules() (in module pybnf.petab.formula) inline_constants() (in module pybnf.petab.formula) inverse() (pybnf.priors.Linear method) (pybnf.priors.Ln method) (pybnf.priors.Log10 method) (pybnf.priors.Scale method) (pybnf.priors.scale.Linear method) (pybnf.priors.scale.Ln method) (pybnf.priors.scale.Log10 method) (pybnf.priors.scale.Scale method)

inverse_jax() (pybnf.priors.Linear method) (pybnf.priors.Ln method) (pybnf.priors.Log10 method) (pybnf.priors.Scale method) (pybnf.priors.scale.Linear method) (pybnf.priors.scale.Ln method) (pybnf.priors.scale.Log10 method) (pybnf.priors.scale.Scale method) is_state_variable() (pybnf.petab.bngl_model.BnglModel method) is_valid() (pybnf.petab.bngl_model.BnglModel method)

J

Job (class in pybnf.algorithms.core) job_finished() (pybnf.algorithms.core.HybridJobGroup method) (pybnf.algorithms.core.JobGroup method)

JobGroup (class in pybnf.algorithms.core)

K

k (pybnf.objective.InformationCriteria attribute) keys() (pybnf.pset.PSet method)

keys_to_string() (pybnf.pset.PSet method) KLLikelihood (class in pybnf.objective)

L

Laplace (class in pybnf.noise.laplace) LaplaceObjective (class in pybnf.objective) latin_hypercube() (in module pybnf.algorithms.base) LBFGSAlgorithm (class in pybnf.algorithms.optimizers.lbfgs) LBFGSConfig (class in pybnf.algorithms.optimizers.lbfgs) likelihood_information_criteria() (in module pybnf.objective) LikelihoodObjective (class in pybnf.objective) Linear (class in pybnf.priors) (class in pybnf.priors.scale) Ln (class in pybnf.priors) (class in pybnf.priors.scale) ln_prior() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) load_constraint_file() (pybnf.constraint.ConstraintSet method) load_data() (pybnf.data.Data method) load_priors() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) load_rr_header() (pybnf.data.Data method) load_trajectory() (pybnf.pset.Trajectory static method) LocationInterpretation (class in pybnf.noise.location) Log10 (class in pybnf.priors) (class in pybnf.priors.scale) log_abs_dforward() (pybnf.noise.scale.AdditiveNoiseScale method) log_density() (pybnf.noise.base.NoiseModel method) log_likelihood (pybnf.objective.InformationCriteria attribute) log_normalizer() (pybnf.noise.base.NoiseModel method) (pybnf.noise.gaussian.Gaussian method) (pybnf.noise.laplace.Laplace method) logdet() (pybnf.priors.Bijector method) (pybnf.priors.bijector.Bijector method) (pybnf.priors.bijector.BoxBijector method) (pybnf.priors.bijector.IdentityBijector method) (pybnf.priors.bijector.LowerBoundedBijector method) (pybnf.priors.bijector.UpperBoundedBijector method)

logdet_jax() (pybnf.priors.Bijector method) (pybnf.priors.bijector.Bijector method) (pybnf.priors.bijector.BoxBijector method) (pybnf.priors.bijector.IdentityBijector method) (pybnf.priors.bijector.LowerBoundedBijector method) (pybnf.priors.bijector.UpperBoundedBijector method) LogNormalObjective (class in pybnf.objective) logpdf() (pybnf.priors.base.FrozenPrior method) (pybnf.priors.base.NoPrior method) (pybnf.priors.base.Prior method) (pybnf.priors.FrozenPrior method) (pybnf.priors.NoPrior method) (pybnf.priors.Prior method) (pybnf.priors.truncated.TruncatedPrior method) (pybnf.priors.TruncatedPrior method) logpdf_jax() (pybnf.priors.base.NoPrior method) (pybnf.priors.base.Prior method) (pybnf.priors.NoPrior method) (pybnf.priors.Prior method) (pybnf.priors.truncated.TruncatedPrior method) (pybnf.priors.TruncatedPrior method) LowerBoundedBijector (class in pybnf.priors.bijector)

M

main() (in module pybnf.pybnf) make_job() (pybnf.algorithms.base.Algorithm method) materialize() (pybnf.measurement.base.MeasurementModel method) MCMCFamilyConfig (class in pybnf.algorithms.samplers.base) mean_offset() (pybnf.noise.base.NoiseModel method) (pybnf.noise.gaussian.Gaussian method) (pybnf.noise.laplace.Laplace method) (pybnf.noise.student_t.StudentT method) measparams_file (pybnf.petab.import_.ImportedExperiment attribute) measurement (pybnf.objective.ObjectiveFunction attribute) measurement_param_bindings() (in module pybnf.petab.measurements) measurement_rows_from_data() (in module pybnf.petab.measurements) MeasurementLayer (class in pybnf.measurement.base) MeasurementModel (class in pybnf.measurement.base) Model (class in pybnf.pset) model_config (pybnf.algorithms.optimizers.cmaes.CMAESConfig attribute) (pybnf.algorithms.optimizers.differential_evolution.DEFamilyConfig attribute) (pybnf.algorithms.optimizers.differential_evolution.DifferentialEvolutionConfig attribute) (pybnf.algorithms.optimizers.lbfgs.LBFGSConfig attribute) (pybnf.algorithms.optimizers.particle_swarm.PSOConfig attribute) (pybnf.algorithms.optimizers.powell.PowellConfig attribute) (pybnf.algorithms.optimizers.profile_likelihood.ProfileLikelihoodConfig attribute) (pybnf.algorithms.optimizers.scatter_search.ScatterSearchConfig attribute) (pybnf.algorithms.optimizers.simplex.SimplexConfig attribute) (pybnf.algorithms.optimizers.simulated_annealing.SimulatedAnnealingConfig attribute) (pybnf.algorithms.optimizers.trf.TRFConfig attribute) (pybnf.algorithms.samplers.adaptive_mcmc.AdaptiveMCMCConfig attribute) (pybnf.algorithms.samplers.base.MCMCFamilyConfig attribute) (pybnf.algorithms.samplers.basic_mcmc.BasicMCMCConfig attribute) (pybnf.algorithms.samplers.dream.DreamConfig attribute) (pybnf.algorithms.samplers.hmc.HMCConfig attribute) (pybnf.algorithms.samplers.pdream.PDreamConfig attribute) model_location (pybnf.petab.import_.ImportedExperiment attribute) model_text() (pybnf.pset.BNGLModel method) (pybnf.pset.SbmlModelNoTimeout method) MODEL_TYPE_BNGL (in module pybnf.petab.bngl_model) ModelCheck (class in pybnf.algorithms.model_check) ModelError module pybnf.algorithms.base pybnf.algorithms.core pybnf.algorithms.model_check pybnf.algorithms.optimizers.cmaes pybnf.algorithms.optimizers.differential_evolution pybnf.algorithms.optimizers.gradient_base pybnf.algorithms.optimizers.lbfgs pybnf.algorithms.optimizers.local_base pybnf.algorithms.optimizers.particle_swarm pybnf.algorithms.optimizers.powell pybnf.algorithms.optimizers.profile_likelihood pybnf.algorithms.optimizers.scatter_search pybnf.algorithms.optimizers.simplex pybnf.algorithms.optimizers.simulated_annealing pybnf.algorithms.optimizers.trf pybnf.algorithms.samplers.adaptive_mcmc pybnf.algorithms.samplers.base pybnf.algorithms.samplers.basic_mcmc pybnf.algorithms.samplers.dream pybnf.algorithms.samplers.hmc pybnf.algorithms.samplers.pdream pybnf.cluster pybnf.config pybnf.constraint pybnf.data pybnf.diagnostics pybnf.gradient.assembly pybnf.gradient.errors pybnf.gradient.routing pybnf.inference_data pybnf.measurement.base pybnf.noise.base pybnf.noise.gaussian pybnf.noise.laplace pybnf.noise.location pybnf.noise.negative_binomial pybnf.noise.scale pybnf.noise.source pybnf.noise.student_t pybnf.objective pybnf.parse pybnf.petab.bngl_model pybnf.petab.conditions pybnf.petab.export pybnf.petab.formula pybnf.petab.import_ pybnf.petab.measurements pybnf.petab.observables pybnf.petab.parameters pybnf.printing pybnf.priors pybnf.priors.base pybnf.priors.bijector pybnf.priors.scale pybnf.priors.truncated pybnf.pset pybnf.pybnf

MultimodelJobGroup (class in pybnf.algorithms.core) multiply() (pybnf.pset.FreeParameter method) mutation_target_value() (in module pybnf.petab.conditions) MutationSet (class in pybnf.pset)

N

n (pybnf.objective.InformationCriteria attribute) n_params (pybnf.priors.base.Prior attribute) (pybnf.priors.Prior attribute) name (pybnf.petab.import_.ImportedExperiment attribute) names (pybnf.noise.source.FormulaSigma attribute) (pybnf.noise.source.PerMeasurementFormulaSigma attribute) NegBinLikelihood (class in pybnf.objective) NegBinLikelihood_Dynamic (class in pybnf.objective) NegBinomial (class in pybnf.noise.negative_binomial) NetModel (class in pybnf.pset) new_individual() (pybnf.algorithms.optimizers.differential_evolution.DifferentialEvolutionBase method) nll() (pybnf.noise.base.NoiseModel method) noise (pybnf.objective.ChiSquareObjective attribute) (pybnf.objective.ChiSquareObjective_Dynamic attribute) (pybnf.objective.LaplaceObjective attribute) (pybnf.objective.LikelihoodObjective attribute) (pybnf.objective.LogNormalObjective attribute) (pybnf.objective.NegBinLikelihood attribute) (pybnf.objective.NegBinLikelihood_Dynamic attribute) noise_grad_point() (pybnf.objective.LikelihoodObjective method) (pybnf.objective.ObjectiveFunction method) noise_model_from_row() (in module pybnf.petab.observables) noise_models_from_file() (in module pybnf.petab.observables)

noise_models_from_table() (in module pybnf.petab.observables) noise_param_defaults (pybnf.noise.base.NoiseModel attribute) (pybnf.noise.student_t.StudentT attribute) noise_parameter_ids_by_observable() (in module pybnf.petab.measurements) noise_params (pybnf.noise.base.NoiseModel attribute) (pybnf.noise.gaussian.Gaussian attribute) (pybnf.noise.laplace.Laplace attribute) (pybnf.noise.negative_binomial.NegBinomial attribute) (pybnf.noise.student_t.StudentT attribute) NoiseModel (class in pybnf.noise.base) NoPrior (class in pybnf.priors) (class in pybnf.priors.base) NormalizationRecord (class in pybnf.data) normalize() (pybnf.algorithms.core.FailedSimulation method) (pybnf.algorithms.core.Result method) (pybnf.data.Data method) normalize_to_init() (pybnf.data.Data method) normalize_to_peak() (pybnf.data.Data method) normalize_to_unit_scale() (pybnf.data.Data method) normalize_to_zero() (pybnf.data.Data method) NormSumOfSquaresObjective (class in pybnf.objective) num_samples (pybnf.algorithms.samplers.hmc.HMCConfig attribute) num_warmup (pybnf.algorithms.samplers.hmc.HMCConfig attribute) number_failed() (pybnf.constraint.ConstraintSet method)

O

ObjectiveCalculator (class in pybnf.objective) ObjectiveFunction (class in pybnf.objective) observable_parameters_by_observable() (in module pybnf.petab.measurements) OnceConstraint (class in pybnf.constraint) OutOfBoundsException

output_itemized_eval() (pybnf.constraint.ConstraintSet method) output_length() (pybnf.pset.Action method) output_results() (pybnf.algorithms.base.Algorithm method) OutputSensitivities (class in pybnf.data) overrides (pybnf.objective.LikelihoodObjective attribute)

P

param_normalizers() (pybnf.noise.base.NoiseModel method) (pybnf.noise.student_t.StudentT method) ParamRoute (class in pybnf.gradient.routing) ParamScan (class in pybnf.pset) parse_normalization_def() (in module pybnf.parse) ParticleSwarm (class in pybnf.algorithms.optimizers.particle_swarm) PDreamAlgorithm (class in pybnf.algorithms.samplers.pdream) PDreamConfig (class in pybnf.algorithms.samplers.pdream) penalty() (pybnf.constraint.Constraint method) penalty_gradient() (pybnf.constraint.Constraint method) PerMeasurementFormulaSigma (class in pybnf.noise.source) PerMeasurementModel (class in pybnf.measurement.base) petab_observable_row() (in module pybnf.petab.observables) petab_parameter_row() (in module pybnf.petab.parameters) PetabConditionRow (class in pybnf.petab.conditions) PetabExperimentRow (class in pybnf.petab.conditions) PetabMeasurementRow (class in pybnf.petab.measurements) PetabObservableRow (class in pybnf.petab.observables) PetabParameterRow (class in pybnf.petab.parameters) pick_new_pset() (pybnf.algorithms.samplers.adaptive_mcmc.Adaptive_MCMC method) postprocess() (pybnf.algorithms.samplers.base.MCMCFamilyConfig class method) (pybnf.algorithms.samplers.dream.DreamConfig class method) postprocess_data() (pybnf.algorithms.core.FailedSimulation method) (pybnf.algorithms.core.Result method) PowellAlgorithm (class in pybnf.algorithms.optimizers.powell) PowellConfig (class in pybnf.algorithms.optimizers.powell) ppf() (pybnf.priors.base.FrozenPrior method) (pybnf.priors.base.NoPrior method) (pybnf.priors.base.Prior method) (pybnf.priors.FrozenPrior method) (pybnf.priors.NoPrior method) (pybnf.priors.Prior method) (pybnf.priors.truncated.TruncatedPrior method) (pybnf.priors.TruncatedPrior method) prediction_sensitivity() (pybnf.measurement.base.MeasurementModel method) (pybnf.measurement.base.PerMeasurementModel method) (pybnf.objective.SummationObjective method) preequilibrate (pybnf.petab.import_.ImportedExperiment attribute) print0() (in module pybnf.printing) print1() (in module pybnf.printing) print2() (in module pybnf.printing) Prior (class in pybnf.priors) (class in pybnf.priors.base) prior_logpdf() (pybnf.pset.FreeParameter method) prior_logpdf_jax() (pybnf.pset.FreeParameter method) prior_support() (pybnf.pset.FreeParameter method) ProfileLikelihoodAlgorithm (class in pybnf.algorithms.optimizers.profile_likelihood) ProfileLikelihoodConfig (class in pybnf.algorithms.optimizers.profile_likelihood) progress_detail() (pybnf.algorithms.optimizers.gradient_base.GradientRunner method) PSet (class in pybnf.pset) PSOConfig (class in pybnf.algorithms.optimizers.particle_swarm) pybnf.algorithms.base module pybnf.algorithms.core module pybnf.algorithms.model_check module pybnf.algorithms.optimizers.cmaes module pybnf.algorithms.optimizers.differential_evolution module pybnf.algorithms.optimizers.gradient_base module pybnf.algorithms.optimizers.lbfgs module pybnf.algorithms.optimizers.local_base module pybnf.algorithms.optimizers.particle_swarm module pybnf.algorithms.optimizers.powell module pybnf.algorithms.optimizers.profile_likelihood module pybnf.algorithms.optimizers.scatter_search module pybnf.algorithms.optimizers.simplex module pybnf.algorithms.optimizers.simulated_annealing module pybnf.algorithms.optimizers.trf module pybnf.algorithms.samplers.adaptive_mcmc module

pybnf.algorithms.samplers.base module pybnf.algorithms.samplers.basic_mcmc module pybnf.algorithms.samplers.dream module pybnf.algorithms.samplers.hmc module pybnf.algorithms.samplers.pdream module pybnf.cluster module pybnf.config module pybnf.constraint module pybnf.data module pybnf.diagnostics module pybnf.gradient.assembly module pybnf.gradient.errors module pybnf.gradient.routing module pybnf.inference_data module pybnf.measurement.base module pybnf.noise.base module pybnf.noise.gaussian module pybnf.noise.laplace module pybnf.noise.location module pybnf.noise.negative_binomial module pybnf.noise.scale module pybnf.noise.source module pybnf.noise.student_t module pybnf.objective module pybnf.parse module pybnf.petab.bngl_model module pybnf.petab.conditions module pybnf.petab.export module pybnf.petab.formula module pybnf.petab.import_ module pybnf.petab.measurements module pybnf.petab.observables module pybnf.petab.parameters module pybnf.printing module pybnf.priors module pybnf.priors.base module pybnf.priors.bijector module pybnf.priors.scale module pybnf.priors.truncated module pybnf.pset module pybnf.pybnf module PybnfError

R

random_latin_hypercube_psets() (pybnf.algorithms.base.Algorithm method) random_pset() (pybnf.algorithms.base.Algorithm method) read_condition_table() (in module pybnf.petab.conditions) read_experiment_table() (in module pybnf.petab.conditions) read_measurement_table() (in module pybnf.petab.measurements) read_node_names() (pybnf.cluster.Cluster static method) read_observable_table() (in module pybnf.petab.observables) read_parameter_table() (in module pybnf.petab.parameters) read_problem_yaml() (in module pybnf.petab.import_) reap_active_sims() (in module pybnf.pset) reconstruct_dose_responses() (in module pybnf.petab.measurements) record_pointwise_loglik() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) REF_MARKER (in module pybnf.petab.conditions) register_bngl() (in module pybnf.petab.bngl_model) reinit_logging() (in module pybnf.config) RelativeSigma (class in pybnf.noise.source) rename_column() (pybnf.data.Data method) replica_exchange() (pybnf.algorithms.samplers.basic_mcmc.BasicBayesMCMCAlgorithm method) report_constraint_satisfaction() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) report_convergence_diagnostics() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) required_free_noise_params() (pybnf.objective.LikelihoodObjective method) (pybnf.objective.ObjectiveFunction method) required_free_param() (pybnf.noise.source.FreeParameterSigma method) (pybnf.noise.source.SigmaSource method) required_free_params() (pybnf.noise.source.FormulaSigma method) (pybnf.noise.source.PerMeasurementFormulaSigma method) (pybnf.noise.source.SigmaSource method) requires_master_scoring (pybnf.algorithms.optimizers.gradient_base.GradientOptimizer attribute) reset() (pybnf.algorithms.base.Algorithm method) (pybnf.algorithms.optimizers.cmaes.CMAESAlgorithm method) (pybnf.algorithms.optimizers.differential_evolution.AsynchronousDifferentialEvolution method) (pybnf.algorithms.optimizers.differential_evolution.DifferentialEvolution method) (pybnf.algorithms.optimizers.gradient_base.GradientOptimizer method) (pybnf.algorithms.optimizers.particle_swarm.ParticleSwarm method) (pybnf.algorithms.optimizers.powell.PowellAlgorithm method) (pybnf.algorithms.optimizers.profile_likelihood.ProfileLikelihoodAlgorithm method) (pybnf.algorithms.optimizers.scatter_search.ScatterSearch method) (pybnf.algorithms.optimizers.simplex.SimplexAlgorithm method) (pybnf.algorithms.optimizers.simulated_annealing.SimulatedAnnealing method) (pybnf.algorithms.samplers.adaptive_mcmc.Adaptive_MCMC method) (pybnf.algorithms.samplers.basic_mcmc.BasicBayesMCMCAlgorithm method)

residual() (pybnf.noise.base.NoiseModel method) (pybnf.noise.gaussian.Gaussian method) (pybnf.noise.laplace.Laplace method) (pybnf.noise.student_t.StudentT method) residual_point() (pybnf.objective.LikelihoodObjective method) (pybnf.objective.ObjectiveFunction method) Result (class in pybnf.algorithms.core) result_from_completed() (in module pybnf.algorithms.core) rhat() (in module pybnf.diagnostics) route_experiment() (in module pybnf.gradient.routing) route_for_model() (in module pybnf.gradient.routing) row_varying_noise_ids() (in module pybnf.petab.measurements) row_varying_observable_ids() (in module pybnf.petab.measurements) run() (pybnf.algorithms.base.Algorithm method) (pybnf.algorithms.samplers.hmc.HMCSampler method) run_check() (pybnf.algorithms.model_check.ModelCheck method) run_job() (in module pybnf.algorithms.core) run_simulation() (pybnf.algorithms.core.Job method) run_subprocess() (in module pybnf.pset) rvs() (pybnf.priors.base.FrozenPrior method) (pybnf.priors.base.NoPrior method) (pybnf.priors.base.Prior method) (pybnf.priors.FrozenPrior method) (pybnf.priors.NoPrior method) (pybnf.priors.Prior method) (pybnf.priors.truncated.TruncatedPrior method) (pybnf.priors.TruncatedPrior method)

S

sample_initial_value() (pybnf.pset.FreeParameter method) sample_pset() (pybnf.algorithms.samplers.base.BayesianAlgorithm method) sample_value() (pybnf.pset.FreeParameter method) save() (pybnf.pset.BNGLModel method) (pybnf.pset.Model method) (pybnf.pset.NetModel method) (pybnf.pset.SbmlModelNoTimeout method) save_all() (pybnf.pset.BNGLModel method) SbmlModel (class in pybnf.pset) SbmlModelNoTimeout (class in pybnf.pset) Scale (class in pybnf.priors) (class in pybnf.priors.scale) ScatterSearch (class in pybnf.algorithms.optimizers.scatter_search) ScatterSearchConfig (class in pybnf.algorithms.optimizers.scatter_search) sensitivity_ic (pybnf.gradient.routing.ExperimentRouting property) sensitivity_params (pybnf.gradient.routing.ExperimentRouting property) set_default_location() (pybnf.objective.LikelihoodObjective method) set_preequilibration() (pybnf.pset.TimeCourse method) set_sim_registry() (in module pybnf.pset) set_value() (pybnf.pset.FreeParameter method) setup_cluster() (pybnf.cluster.Cluster static method) should_pickle() (pybnf.algorithms.base.Algorithm static method) should_sample() (pybnf.algorithms.samplers.basic_mcmc.BasicBayesMCMCAlgorithm method) SigmaSource (class in pybnf.noise.source) SimplexAlgorithm (class in pybnf.algorithms.optimizers.simplex) SimplexConfig (class in pybnf.algorithms.optimizers.simplex) SimulatedAnnealing (class in pybnf.algorithms.optimizers.simulated_annealing) SimulatedAnnealingConfig (class in pybnf.algorithms.optimizers.simulated_annealing) slice_for() (pybnf.data.OutputSensitivities method) spawn_chain_rngs() (pybnf.algorithms.base.Algorithm method) split_chain_rhat() (in module pybnf.diagnostics) split_chains() (in module pybnf.diagnostics) SplitAtConstraint (class in pybnf.constraint) start() (pybnf.algorithms.optimizers.gradient_base.GradientRunner method) START_POINT_KEY (pybnf.algorithms.optimizers.cmaes.CMAESAlgorithm attribute) (pybnf.algorithms.optimizers.lbfgs.LBFGSAlgorithm attribute) (pybnf.algorithms.optimizers.local_base.StartPointOptimizer attribute) (pybnf.algorithms.optimizers.powell.PowellAlgorithm attribute) (pybnf.algorithms.optimizers.simplex.SimplexAlgorithm attribute) (pybnf.algorithms.optimizers.trf.TRFAlgorithm attribute)

start_run() (pybnf.algorithms.base.Algorithm method) (pybnf.algorithms.optimizers.cmaes.CMAESAlgorithm method) (pybnf.algorithms.optimizers.differential_evolution.AsynchronousDifferentialEvolution method) (pybnf.algorithms.optimizers.differential_evolution.DifferentialEvolution method) (pybnf.algorithms.optimizers.differential_evolution.DifferentialEvolutionBase method) (pybnf.algorithms.optimizers.gradient_base.GradientOptimizer method) (pybnf.algorithms.optimizers.particle_swarm.ParticleSwarm method) (pybnf.algorithms.optimizers.powell.PowellAlgorithm method) (pybnf.algorithms.optimizers.profile_likelihood.ProfileLikelihoodAlgorithm method) (pybnf.algorithms.optimizers.scatter_search.ScatterSearch method) (pybnf.algorithms.optimizers.simplex.SimplexAlgorithm method) (pybnf.algorithms.optimizers.simulated_annealing.SimulatedAnnealing method) (pybnf.algorithms.samplers.adaptive_mcmc.Adaptive_MCMC method) (pybnf.algorithms.samplers.base.BayesianAlgorithm method) (pybnf.algorithms.samplers.basic_mcmc.BasicBayesMCMCAlgorithm method) (pybnf.algorithms.samplers.dream.DreamAlgorithm method) StartPointOptimizer (class in pybnf.algorithms.optimizers.local_base) StudentT (class in pybnf.noise.student_t) substitute_placeholders() (in module pybnf.petab.formula) SummationObjective (class in pybnf.objective) SumOfDiffsObjective (class in pybnf.objective) SumOfSquaresObjective (class in pybnf.objective) support() (pybnf.priors.base.FrozenPrior method) (pybnf.priors.base.NoPrior method) (pybnf.priors.base.Prior method) (pybnf.priors.FrozenPrior method) (pybnf.priors.NoPrior method) (pybnf.priors.Prior method) (pybnf.priors.truncated.TruncatedPrior method) (pybnf.priors.TruncatedPrior method) support_lo_u (pybnf.priors.base.Prior attribute) (pybnf.priors.Prior attribute) supports_pointwise_log_likelihood (pybnf.objective.LikelihoodObjective attribute) (pybnf.objective.ObjectiveFunction attribute) surrogate_name() (in module pybnf.petab.conditions) symbol_allowed_in_observable_formula() (pybnf.petab.bngl_model.BnglModel method)

T

t_end (pybnf.petab.import_.ImportedExperiment attribute) target_accept (pybnf.algorithms.samplers.hmc.HMCConfig attribute) teardown() (pybnf.cluster.Cluster method) TimeCourse (class in pybnf.pset) to_constrained() (pybnf.priors.Bijector method) (pybnf.priors.bijector.Bijector method) (pybnf.priors.bijector.BoxBijector method) (pybnf.priors.bijector.IdentityBijector method) (pybnf.priors.bijector.LowerBoundedBijector method) (pybnf.priors.bijector.UpperBoundedBijector method) to_constrained_jax() (pybnf.priors.Bijector method) (pybnf.priors.bijector.Bijector method) (pybnf.priors.bijector.BoxBijector method) (pybnf.priors.bijector.IdentityBijector method) (pybnf.priors.bijector.LowerBoundedBijector method) (pybnf.priors.bijector.UpperBoundedBijector method)

to_file() (pybnf.petab.bngl_model.BnglModel method) to_sampling_space() (pybnf.pset.FreeParameter method) to_unconstrained() (pybnf.priors.Bijector method) (pybnf.priors.bijector.Bijector method) (pybnf.priors.bijector.BoxBijector method) (pybnf.priors.bijector.IdentityBijector method) (pybnf.priors.bijector.LowerBoundedBijector method) (pybnf.priors.bijector.UpperBoundedBijector method) total_penalty() (pybnf.constraint.ConstraintSet method) Trajectory (class in pybnf.pset) TRFAlgorithm (class in pybnf.algorithms.optimizers.trf) TRFConfig (class in pybnf.algorithms.optimizers.trf) TruncatedPrior (class in pybnf.priors) (class in pybnf.priors.truncated) try_to_choose_new_pset() (pybnf.algorithms.samplers.basic_mcmc.BasicBayesMCMCAlgorithm method)

U

UnknownObjectiveFunctionError UnmatchedExperimentalDataError UnspecifiedConfigurationKeyError

update_histograms() (pybnf.algorithms.samplers.adaptive_mcmc.Adaptive_MCMC method) (pybnf.algorithms.samplers.base.BayesianAlgorithm method) UpperBoundedBijector (class in pybnf.priors.bijector)

V

value() (pybnf.measurement.base.PerMeasurementModel method) (pybnf.noise.source.ColumnMeanSigma method) (pybnf.noise.source.ConstantSigma method) (pybnf.noise.source.DataColumnSigma method) (pybnf.noise.source.FormulaSigma method) (pybnf.noise.source.FreeParameterSigma method) (pybnf.noise.source.PerMeasurementFormulaSigma method) (pybnf.noise.source.RelativeSigma method) (pybnf.noise.source.SigmaSource method)

value_from_quantile() (pybnf.pset.FreeParameter method) values_to_string() (pybnf.pset.PSet method) var_keyword_grammar() (in module pybnf.priors)

W

WassersteinObjective (class in pybnf.objective) with_location() (pybnf.noise.base.NoiseModel method) (pybnf.noise.gaussian.Gaussian method) (pybnf.noise.laplace.Laplace method) (pybnf.noise.negative_binomial.NegBinomial method) (pybnf.noise.student_t.StudentT method)

write_condition_table() (in module pybnf.petab.conditions) write_experiment_table() (in module pybnf.petab.conditions) write_measurement_table() (in module pybnf.petab.measurements) write_observable_table() (in module pybnf.petab.observables) write_parameter_table() (in module pybnf.petab.parameters) write_problem_yaml() (in module pybnf.petab.export) write_to_file() (pybnf.pset.Trajectory method)