parpe.hierarchical_optimization

Functions related to hierarchical optimization

https://doi.org/10.1093/bioinformatics/btz581

Functions

get_analytical_parameter_table(...)

Generate (scalingIdx, conditionIdx, observableIdx) table for all occurrences of the given parameter names.

get_candidates_for_hierarchical(...)

Based on PEtab files, check which parameters are suitable for hierarchical optimization.

parameter_is_offset_parameter(parameter, formula)

Check if is offset parameter.

parameter_is_scaling_parameter(parameter, ...)

Check if is scaling parameter.

Functions

parpe.hierarchical_optimization.get_analytical_parameter_table(hierarchical_candidate_ids, parameter_type, condition_id_to_index, observable_df, measurement_df, observable_ids, condition_map, no_preeq_condition_idx)[source]

Generate (scalingIdx, conditionIdx, observableIdx) table for all occurrences of the given parameter names.

Parameters:

  • hierarchical_candidate_ids (list) – Ids of optimization parameters for hierarchical optimization. This table depends on ordering of this list.

  • parameter_type (str) – ‘observable’ or ‘noise’

Return type:

List[Tuple[int, int, int]]

Returns:

list of (scalingIdx, conditionIdx, observableIdx) tuples

parpe.hierarchical_optimization.get_candidates_for_hierarchical(observable_df, measurement_df, parameter_df)[source]

Based on PEtab files, check which parameters are suitable for hierarchical optimization.

Parameters:

  • observable_df (DataFrame) – PEtab observable table

  • measurement_df (DataFrame) – PEtab measurement table

  • parameter_df (DataFrame) – PEtab measurement table

Returns:

parpe.hierarchical_optimization.parameter_is_offset_parameter(parameter, formula)[source]

Check if is offset parameter.

Parameters:

  • parameter (str) – Some identifier.

  • formula (str) – Some sympy-compatible formula.

Return type:

bool

Returns:

True if parameter parameter is an offset parameter with positive sign in formula formula.

parpe.hierarchical_optimization.parameter_is_scaling_parameter(parameter, formula)[source]

Check if is scaling parameter.

Parameters:

  • parameter (str) – Some identifier.

  • formula (str) – Some sympy-compatible formula.

Return type:

bool

Returns:

True if parameter parameter is a scaling parameter in formula

formula.