Fit the parameters in a model of a genetic switch. More...

#include <GeneticSwitch.hpp>

Inheritance diagram for Unfit::Examples::GeneticSwitch:

Public Member Functions
	GeneticSwitch (const std::vector< double > &z_a, double dt)

std::vector< double >	operator() (const std::vector< double > &param)

Public Member Functions inherited from Unfit::GenericCostFunction
virtual	~GenericCostFunction ()

Private Attributes
const std::vector< double >	z_a_data_

const double	dt_

Detailed Description

Fit the parameters in a model of a genetic switch.

An example two ordinary differential equations (ODE) data fitting problem. The equations describe genetic switch between two genes, z_a and z_b, for protein regulation. They depend on four constants, u, n, v1 and v2. Here the goal is to fit these constants given experimental data for z_a. The two ODEs are:

dz_a/dt = u/(1 + z_b^n) - z_a - v1 dz_b/dt = u/(1 + z_b^n) - z_b - v2

The initial conditions are z_a(0) = 10, and z_b(0) = 10, and the goal is to find the values of u, n, v1 & v2 that best fit the data. In terms of the model, u = param[0], n = param[1], v1 = param[2] and v2 = param[3].

Constructor & Destructor Documentation

◆ GeneticSwitch()

Unfit::Examples::GeneticSwitch::GeneticSwitch	(	const std::vector< double > &	z_a,
		double	dt
	)

inline

Create the cost function. Here the experimental data must be passed in, and cannot be changed (if you want to, just create another cost function object). Here the experimental data is a vector containing the value of z_a, and the time step used in the data collection.

Intended use : GeneticSwitch cost_func(z_a, t);

Parameters

z_a	A vector of experimental z_a values
dt	The experimental time step

Member Function Documentation

◆ operator()()

std::vector<double> Unfit::Examples::GeneticSwitch::operator() ( const std::vector< double > & param )

inlinevirtual

Calculate the linear distance (residuals) between our model and the data. This method encapsulates the model, and expects the current estimates of the unknown parameters as an input. See the class documentation for details about the model.

Intended use : residuals = cost_func(param)

Parameters

param A vector containing the current estimates of the parameters we are trying to fit

Returns: A vector containing the residuals

Implements Unfit::GenericCostFunction.

Member Data Documentation

◆ dt_

const double Unfit::Examples::GeneticSwitch::dt_

private

A vector to store the time step, dt

◆ z_a_data_

const std::vector<double> Unfit::Examples::GeneticSwitch::z_a_data_

private

A vector to store the experimental data, Z_A

The documentation for this class was generated from the following file:

examples/GeneticSwitch.hpp

Public Member Functions

Private Attributes