BNMPy.simulation_evaluator

The simulation_evaluator module provides tools for evaluating PBN simulations against experimental data.

class BNMPy.simulation_evaluator.SimulationEvaluator(pbn, experiments, config=None, nodes_to_optimize=None)[source]

Bases: object

Evaluation engine for PBN parameter optimization Handles experiment simulation and SSE calculation

Methods

get_parameter_bounds()

Get bounds for optimization parameters Now returns bounds only for nodes being optimized

objective_function(cij_vector)

Calculate objective function (MSE) for given parameters
__init__(pbn, experiments, config=None, nodes_to_optimize=None)[source]

Initialize evaluator with PBN and experiments

objective_function(cij_vector: ndarray) → float[source]

Calculate objective function (MSE) for given parameters

get_parameter_bounds() → List[tuple][source]

Get bounds for optimization parameters Now returns bounds only for nodes being optimized

SimulationEvaluator Class

class BNMPy.simulation_evaluator.SimulationEvaluator(pbn, experiments, config=None, nodes_to_optimize=None)[source]

Bases: object

Evaluation engine for PBN parameter optimization Handles experiment simulation and SSE calculation

Methods

get_parameter_bounds()

Get bounds for optimization parameters Now returns bounds only for nodes being optimized

objective_function(cij_vector)

Calculate objective function (MSE) for given parameters
__init__(pbn, experiments, config=None, nodes_to_optimize=None)[source]

Initialize evaluator with PBN and experiments

objective_function(cij_vector: ndarray) → float[source]

Calculate objective function (MSE) for given parameters

get_parameter_bounds() → List[tuple][source]

Get bounds for optimization parameters Now returns bounds only for nodes being optimized

Overview

The SimulationEvaluator calculates the objective function for optimization by comparing PBN steady-state predictions with experimental measurements. It handles experimental conditions (stimuli/inhibitors) and computes mean squared error (MSE).

This module is automatically used by ParameterOptimizer.

See Also