8.1.1.6.1.5. skimpy.sampling.ga_parameter_sampler

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8.1.1.6.1.5.1. Classes

GaParameterSampler

A simple parameter sampler that samples stable model parameters

8.1.1.6.1.5.2. Functions

default_fitness(saturations[, compiled_model, ...])

run_ea(toolbox[, stats, verbose])

init_parameters(low, up)

pareto_dominance(x, y)

8.1.1.6.1.5.3. Module Contents

skimpy.default_fitness(saturations, compiled_model=None, concentration_dict=dict(), flux_dict=dict(), max_eigenvalue=0)
class skimpy.GaParameterSampler(parameters=None)

Bases: skimpy.sampling.ParameterSampler

A simple parameter sampler that samples stable model parameters with respect to a steady state flux and concentration state

class Parameters

Bases: tuple

Parameter type specified for the parameters samples :return:

n_samples
sample(compiled_model, flux_dict, concentration_dict, seed=123, max_generation=10, mutation_probability=0.2, eta=20, fitness_fun=default_fitness, fitness_weights=(-1,), **kwargs)
Parameters:

  • compiled_model

  • flux_dict

  • concentration_dict

  • seed

  • max_generation

  • mutation_probability

  • eta

Returns:

_compile_sampling_functions(model, concentrations, fluxes)

Compliles the function for sampling using theano :param model:

skimpy.run_ea(toolbox, stats=None, verbose=False)
skimpy.init_parameters(low, up)
skimpy.pareto_dominance(x, y)