org.gersteinlab.regulation.model
Class RateModel

java.lang.Object
  org.gersteinlab.regulation.model.RateModel

Direct Known Subclasses:

LinearRateModel, MultiplicativeRateModel, SigmoidalRateModel

public abstract class RateModel
extends java.lang.Object

        Providing methods for a rate model based on differential equations. The
        goal is the estimate the expression levels of yj at different time
        points given its initial value at time 0 and the expression levels and
        rates of some potential regulators.
        

Version:

1.0 (September 1, 2008)

        Change History:
        1.0     - Initial version
        

Author:

Kevin Yuk-Lap Yip

Field Summary

protected double[]	a
protected double[][][]	dykdts
protected double	h
protected int	n
protected double[]	t
protected double	yj0
protected double[][][]	yks

Constructor Summary

RateModel(double[] tIn, double yj0In, double[][][] yksIn, double[][][] dykdtsIn)
Create the model with the given set of time points and target values and differentials.

Method Summary

abstract double[]	f() Return the estimated values at the specified time points.
abstract double[][]	gf() Return the estimated gradients at the specified time points with respect to the parameters.
abstract double[][][]	hf() Return the estimated Hessians at the specified time points with respect to the parameters.
void	setParam(double[] aIn) Set the parameter values.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

t

protected double[] t

yj0

protected double yj0

yks

protected double[][][] yks

dykdts

protected double[][][] dykdts

h

protected double h

n

protected int n

a

protected double[] a

Constructor Detail

RateModel

public RateModel(double[] tIn,
                 double yj0In,
                 double[][][] yksIn,
                 double[][][] dykdtsIn)

Create the model with the given set of time points and target values and differentials.

Parameters:

tIn - The set of time points

yj0In - The initial target value

yksIn - The values of the potential regulators First dimension: potential regulator Second dimension: time point

dykdtsIn - The differentials of the potential regulators First dimension: potential regulator Second dimension: time point

Method Detail

setParam

public void setParam(double[] aIn)

Set the parameter values.

Parameters:

aIn - The parameter values

f

public abstract double[] f()

Return the estimated values at the specified time points.

Returns:

The estimated values at the specified time points

gf

public abstract double[][] gf()

Return the estimated gradients at the specified time points with respect to the parameters.

Returns:

The estimated gradients at the specified time points First dimension: time point Second dimension: parameter

hf

public abstract double[][][] hf()

Return the estimated Hessians at the specified time points with respect to the parameters.

Returns:

The estimated Hessians at the specified time points First dimension: time point Second and third dimensions: parameter