org.gersteinlab.regulation.model
Class RateModel

java.lang.Object
  extended by 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