8.1.1.6. skimpy.sampling

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Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB), Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

8.1.1.6.1. Submodules

8.1.1.6.2. Package Contents

8.1.1.6.2.1. Classes

SaturationParameterFunction

A class used in the process of sampling to calculate Km's. Provided with a

FluxParameterFunction

ParameterSampler

Helper class that provides a standard way to create an ABC using

GaParameterSampler

A simple parameter sampler that samples stable model parameters

CMAESParameterSampler

A simple parameter sampler that samples stable model parameters

8.1.1.6.2.2. Functions

calc_max_eigenvalue(parameter_sample, compiled_model, concentration_dict, flux_dict)

Sample one set of staturations using theano complied functions

calc_parameters(saturations, compiled_model, concentration_dict, flux_dict, parameters_to_resample=None, fixed_parameters=None)

default_fitness(saturations, compiled_model=None, concentration_dict=dict(), flux_dict=dict(), max_eigenvalue=0)

run_ea(toolbox, stats=None, verbose=False)

init_parameters(low, up)

pareto_dominance(x, y)

calc_max_eigenvalue(parameter_sample, compiled_model, concentration_dict, flux_dict)

Sample one set of staturations using theano complied functions

calc_parameters(saturations, compiled_model, concentration_dict, flux_dict, parameters_to_resample=None, fixed_parameters=None)

run_ea(toolbox, stats=None, verbose=False)

init_parameters(low, up)

pareto_dominance(x, y)

8.1.1.6.2.3. Attributes

QSSA

TQSSA

MCA

ODE

ELEMENTARY

Jacobian Types

NUMERICAL

SYMBOLIC

MCA Types

NET

SPLIT

Item types

PARAMETER

VARIABLE

Units

KCAL

KJ

JOULE

OTHER

WATER_FORMULA

QSSA

TQSSA

MCA

ODE

ELEMENTARY

Jacobian Types

NUMERICAL

SYMBOLIC

MCA Types

NET

SPLIT

Item types

PARAMETER

VARIABLE

Units

KCAL

KJ

JOULE

OTHER

WATER_FORMULA

QSSA

TQSSA

MCA

ODE

ELEMENTARY

Jacobian Types

NUMERICAL

SYMBOLIC

MCA Types

NET

SPLIT

Item types

PARAMETER

VARIABLE

Units

KCAL

KJ

JOULE

OTHER

WATER_FORMULA

class skimpy.SaturationParameterFunction(model, parameters, concentrations)

A class used in the process of sampling to calculate Km’s. Provided with a model, creates self.__call__ function using Cython to calculate Km’s given (sampled) sigmas

Parameters

  • model –

  • parameters – the parameters of the model. Parameters with a .hook

field and an empty .value will be sampled :param concentrations:

__call__(self, saturations, parameters, concentrations, parameters_to_resample, fixed_parameters)
class skimpy.FluxParameterFunction(model, parameters, concentration_dict)
__call__(self, model, parameters, concentration_dict, flux_dict)
class skimpy.ParameterSampler(parameters=None)

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

property Parameters(self)

Parameter type specified for the parameters samples :return:

abstract sample(self)
Returns

skimpy.QSSA = qssa
skimpy.TQSSA = tqssa
skimpy.MCA = mca
skimpy.ODE = ode
skimpy.ELEMENTARY = elementary

Jacobian Types

skimpy.NUMERICAL = numerical
skimpy.SYMBOLIC = symbolic

MCA Types

skimpy.NET = net
skimpy.SPLIT = split

Item types

skimpy.PARAMETER = parameter
skimpy.VARIABLE = variable

Units

skimpy.KCAL = kcal
skimpy.KJ = kJ
skimpy.JOULE = JOULE

OTHER

skimpy.WATER_FORMULA = H2O
skimpy.calc_max_eigenvalue(parameter_sample, compiled_model, concentration_dict, flux_dict)

Sample one set of staturations using theano complied functions :param compiled_model: :param concentration_dict: :param flux_dict: :return:

skimpy.calc_parameters(saturations, compiled_model, concentration_dict, flux_dict, parameters_to_resample=None, fixed_parameters=None)
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

Parameters
__defaults__
sample(self, 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(self, 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)
skimpy.QSSA = qssa
skimpy.TQSSA = tqssa
skimpy.MCA = mca
skimpy.ODE = ode
skimpy.ELEMENTARY = elementary

Jacobian Types

skimpy.NUMERICAL = numerical
skimpy.SYMBOLIC = symbolic

MCA Types

skimpy.NET = net
skimpy.SPLIT = split

Item types

skimpy.PARAMETER = parameter
skimpy.VARIABLE = variable

Units

skimpy.KCAL = kcal
skimpy.KJ = kJ
skimpy.JOULE = JOULE

OTHER

skimpy.WATER_FORMULA = H2O
skimpy.calc_max_eigenvalue(parameter_sample, compiled_model, concentration_dict, flux_dict)

Sample one set of staturations using theano complied functions :param compiled_model: :param concentration_dict: :param flux_dict: :return:

skimpy.calc_parameters(saturations, compiled_model, concentration_dict, flux_dict, parameters_to_resample=None, fixed_parameters=None)
class skimpy.CMAESParameterSampler(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

Parameters
__defaults__
sample(self, compiled_model, flux_dict, concentration_dict, seed=123, max_generation=10, sigma=0.1, lambda_=1000, nhof=100, max_eigenvalue=0, min_km=0.001, max_km=1000.0)
Parameters

  • compiled_model –

  • flux_dict –

  • concentration_dict –

  • seed –

  • max_generation –

  • mutation_probability –

  • eta –

Returns

_compile_sampling_functions(self, model, concentrations, fluxes)

Compliles the function for sampling using theano :param model:

fitness(self, parameters)
update_parameters(self, parameters)
skimpy.run_ea(toolbox, ngen=None, stats=None, hof=None, verbose=False)
skimpy.init_parameters(low, up)
skimpy.pareto_dominance(x, y)
skimpy.QSSA = qssa
skimpy.TQSSA = tqssa
skimpy.MCA = mca
skimpy.ODE = ode
skimpy.ELEMENTARY = elementary

Jacobian Types

skimpy.NUMERICAL = numerical
skimpy.SYMBOLIC = symbolic

MCA Types

skimpy.NET = net
skimpy.SPLIT = split

Item types

skimpy.PARAMETER = parameter
skimpy.VARIABLE = variable

Units

skimpy.KCAL = kcal
skimpy.KJ = kJ
skimpy.JOULE = JOULE

OTHER

skimpy.WATER_FORMULA = H2O