parpe.hierarchical_optimization¶

Functions related to hierarchical optimization

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz581/5538985

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, 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: Ids of optimization parameters for: hierarchical optimization. This table depends on ordering of this list.
parameter_type:: ‘observable’ or ‘noise’

Returns:

list of (scalingIdx, conditionIdx, observableIdx) tuples

Return type: List[Tuple[int, int, int]]

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.

Arguments:: observable_df: PEtab observable table measurement_df: PEtab measurement table parameter_df: PEtab measurement table

Returns:

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

Check if is offset parameter.

Arguments:: parameter: Some identifier. formula: Some sympy-compatible formula.
Returns:: True if parameter parameter is an offset parameter with positive sign in formula formula.

Return type: bool

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

Check if is scaling parameter.

Arguments:

parameter: Some identifier. formula: Some sympy-compatible formula.

Returns:

True if parameter parameter is a scaling parameter in formula: formula.

Return type: bool