PyBNF Module ReferencesΒΆ
Modules:
- PyBNF entry point (
pybnf.pybnf) - PyBNF algorithms (
pybnf.algorithms) - PyBNF cluster setup (
pybnf.cluster) - PyBNF configuration (
pybnf.config) - PyBNF constraint specification (
pybnf.constraint)AlwaysConstraintAtConstraintBetweenConstraintConstraintConstraint.bind_scale_param()Constraint.coerce_penalty_model()Constraint.find_keys()Constraint.get_difference()Constraint.get_key()Constraint.get_log_likelihood()Constraint.get_log_likelihood_logit()Constraint.get_penalty()Constraint.get_penalty_gradient()Constraint.get_static_penalty()Constraint.index()Constraint.penalty()Constraint.penalty_gradient()
ConstraintSetOnceConstraintSplitAtConstraint
- PyBNF data container (
pybnf.data) - PyBNF convergence diagnostics (
pybnf.diagnostics) - PyBNF gradient plumbing (
pybnf.gradient)- Errors
- Routing
- Assembly
- Convention pin (issue #449)
- Native -> sampling space (once, ADR-0029)
- Estimated noise scale (layer D, #451)
- Trajectory transforms + normalization (layer F, #453)
- Asymmetric / non-Gaussian families (layer G, #454; least-squares residual #459)
- Constraint / qualitative penalties (layer I, #456)
- Measurement-model layer (layer H, #455)
GradientResultassemble_constraint_gradient()assemble_gaussian_gradient()
- PyBNF ArviZ bridge (
pybnf.inference_data) - PyBNF measurement models (
pybnf.measurement) - PyBNF noise models (
pybnf.noise) - PyBNF objective functions (
pybnf.objective)AveNormSumOfSquaresObjectiveChiSquareObjectiveChiSquareObjective_DynamicColumnSummationObjectiveConstraintCounterDirectPassObjectiveInformationCriteriaKLLikelihoodLaplaceObjectiveLikelihoodObjectiveLikelihoodObjective.data_fit_grad_point()LikelihoodObjective.eval_point()LikelihoodObjective.evaluate_pointwise()LikelihoodObjective.from_config()LikelihoodObjective.has_least_squares_residual()LikelihoodObjective.noiseLikelihoodObjective.noise_grad_point()LikelihoodObjective.overridesLikelihoodObjective.required_free_noise_params()LikelihoodObjective.residual_point()LikelihoodObjective.set_default_location()LikelihoodObjective.supports_pointwise_log_likelihood
LogNormalObjectiveNegBinLikelihoodNegBinLikelihood_DynamicNormSumOfSquaresObjectiveObjectiveCalculatorObjectiveFunctionObjectiveFunction.data_fit_grad_point()ObjectiveFunction.evaluate()ObjectiveFunction.evaluate_multiple()ObjectiveFunction.evaluate_pointwise()ObjectiveFunction.from_config()ObjectiveFunction.has_least_squares_residual()ObjectiveFunction.measurementObjectiveFunction.noise_grad_point()ObjectiveFunction.required_free_noise_params()ObjectiveFunction.residual_point()ObjectiveFunction.supports_pointwise_log_likelihood
SumOfDiffsObjectiveSumOfSquaresObjectiveSummationObjectiveWassersteinObjectivebuild_named_objective()build_profile_objective()build_whole_fit_noise_objective()information_criteria()likelihood_information_criteria()
- PyBNF configuration parsing (
pybnf.parse) - PyBNF PEtab v2 interoperability (
pybnf.petab)- Parameters
- Observables and noise
- Measurements
PetabMeasurementRowdata_from_measurement_rows()dose_response_measurement_rows()measurement_param_bindings()measurement_rows_from_data()noise_parameter_ids_by_observable()observable_parameters_by_observable()read_measurement_table()reconstruct_dose_responses()row_varying_noise_ids()row_varying_observable_ids()write_measurement_table()
- Conditions and experiments
CONDITION_ID_PREFIXPetabConditionRowPetabExperimentRowREF_MARKERbuild_dose_response_conditions()build_experiment_conditions()build_preequilibration_conditions()condition_name_from_id()conditions_from_rows()mutation_target_value()read_condition_table()read_experiment_table()surrogate_name()write_condition_table()write_experiment_table()
- Measurement formulas
- BNGL model loader
- Importing a problem
- Exporting a job
- PyBNF printing functions (
pybnf.printing) - PyBNF priors (
pybnf.priors) - PyBNF model and parameter containers (
pybnf.pset)ActionBNGLModelFailedSimulationErrorFreeParameterFreeParameter.add()FreeParameter.add_rand()FreeParameter.diff()FreeParameter.from_sampling_space()FreeParameter.from_sampling_space_jax()FreeParameter.has_bounded_initializationFreeParameter.has_bounded_supportFreeParameter.has_priorFreeParameter.initial_value_from_quantile()FreeParameter.multiply()FreeParameter.prior_logpdf()FreeParameter.prior_logpdf_jax()FreeParameter.prior_support()FreeParameter.sample_initial_value()FreeParameter.sample_value()FreeParameter.set_value()FreeParameter.to_sampling_space()FreeParameter.value_from_quantile()
ModelModelErrorMutationSetNetModelOutOfBoundsExceptionPSetParamScanSbmlModelSbmlModelNoTimeoutTimeCourseTrajectoryclear_sim_registry()reap_active_sims()run_subprocess()set_sim_registry()