/// <summary>
/// Runs the Newton-Raphson update for Cox's hazards learning until convergence.
/// </summary>
///
/// <param name="censor">The output (event) associated with each input vector.</param>
/// <param name="time">The time-to-event for the non-censored training samples.</param>
///
/// <returns>The maximum relative change in the parameters after the iteration.</returns>
///
public double Run(double[] time, SurvivalOutcome[] censor)
{
if (time.Length != censor.Length)
{
throw new DimensionMismatchException("time",
"The time and output vector must have the same length.");
}
// Sort data by time to accelerate performance
EmpiricalHazardDistribution.Sort(ref time, ref censor);
createBaseline(time, censor);
return(regression.GetPartialLogLikelihood(time, censor));
}
/// <summary>
/// Runs the Newton-Raphson update for Cox's hazards learning until convergence.
/// </summary>
///
/// <param name="inputs">The input data.</param>
/// <param name="censor">The output (event) associated with each input vector.</param>
/// <param name="time">The time-to-event for the non-censored training samples.</param>
///
/// <returns>The maximum relative change in the parameters after the iteration.</returns>
///
public double Run(double[][] inputs, double[] time, SurvivalOutcome[] censor)
{
if (inputs.Length != time.Length || time.Length != censor.Length)
{
throw new DimensionMismatchException("time",
"The inputs, time and output vector must have the same length.");
}
// Sort data by time to accelerate performance
EmpiricalHazardDistribution.Sort(ref time, ref censor, ref inputs);
double[] means = new double[parameterCount];
double[] sdev = new double[parameterCount];
for (int i = 0; i < sdev.Length; i++)
{
sdev[i] = 1;
}
if (normalize)
{
// Store means as regression centers
means = inputs.Mean();
for (int i = 0; i < means.Length; i++)
{
regression.Offsets[i] = means[i];
}
// Convert to unit scores for increased accuracy
sdev = BestCS.Statistics.Tools.StandardDeviation(inputs);
inputs = inputs.Subtract(means, 0).ElementwiseDivide(sdev, 0, inPlace: true);
for (int i = 0; i < regression.Coefficients.Length; i++)
{
regression.Coefficients[i] *= sdev[i];
}
}
// Compute actual outputs
double[] output = new double[inputs.Length];
for (int i = 0; i < output.Length; i++)
{
double sum = 0;
for (int j = 0; j < regression.Coefficients.Length; j++)
{
sum += regression.Coefficients[j] * inputs[i][j];
}
output[i] = Math.Exp(sum);
}
// Compute ties
int[] ties = new int[inputs.Length];
for (int i = 0; i < inputs.Length; i++)
{
for (int j = 0; j < time.Length; j++)
{
if (time[j] == time[i])
{
ties[i]++;
}
}
}
if (parameterCount == 0)
{
createBaseline(time, censor, output);
return(regression.GetPartialLogLikelihood(inputs, time, censor));
}
CurrentIteration = 0;
double smooth = Lambda;
do
{
// learning iterations until convergence
// or maximum number of iterations reached
CurrentIteration++;
// Reset Hessian matrix and gradient
Array.Clear(gradient, 0, gradient.Length);
Array.Clear(hessian, 0, hessian.Length);
// For each observation instance
for (int i = 0; i < inputs.Length; i++)
{
// Check if we should censor
if (censor[i] == SurvivalOutcome.Censored)
{
continue;
}
// Compute partials
double den = 0;
Array.Clear(partialGradient, 0, partialGradient.Length);
Array.Clear(partialHessian, 0, partialHessian.Length);
for (int j = 0; j < inputs.Length; j++)
{
if (time[j] >= time[i])
{
den += output[j];
}
}
for (int j = 0; j < inputs.Length; j++)
{
if (time[j] >= time[i])
{
// Compute partial gradient
for (int k = 0; k < partialGradient.Length; k++)
{
partialGradient[k] += inputs[j][k] * output[j] / den;
}
// Compute partial Hessian
for (int ii = 0; ii < inputs[j].Length; ii++)
{
for (int jj = 0; jj < inputs[j].Length; jj++)
{
partialHessian[ii, jj] += inputs[j][ii] * inputs[j][jj] * output[j] / den;
}
}
}
}
// Compute gradient vector
for (int j = 0; j < gradient.Length; j++)
{
gradient[j] += inputs[i][j] - partialGradient[j];
}
// Compute Hessian matrix
for (int j = 0; j < partialGradient.Length; j++)
{
for (int k = 0; k < partialGradient.Length; k++)
{
hessian[j, k] -= partialHessian[j, k] - partialGradient[j] * partialGradient[k];
}
}
}
// Decompose to solve the linear system. Usually the Hessian will
// be invertible and LU will succeed. However, sometimes the Hessian
// may be singular and a Singular Value Decomposition may be needed.
// The SVD is very stable, but is quite expensive, being on average
// about 10-15 times more expensive than LU decomposition. There are
// other ways to avoid a singular Hessian. For a very interesting
// reading on the subject, please see:
//
// - Jeff Gill & Gary King, "What to Do When Your Hessian Is Not Invertible",
// Sociological Methods & Research, Vol 33, No. 1, August 2004, 54-87.
// Available in: http://gking.harvard.edu/files/help.pdf
//
decomposition = new SingularValueDecomposition(hessian);
double[] deltas = decomposition.Solve(gradient);
if (convergence.Iterations > 0 || convergence.Tolerance > 0)
{
// Update coefficients using the calculated deltas
for (int i = 0; i < regression.Coefficients.Length; i++)
{
regression.Coefficients[i] -= smooth * deltas[i];
}
}
smooth += Lambda;
if (smooth > 1)
{
smooth = 1;
}
// Check relative maximum parameter change
convergence.NewValues = regression.Coefficients;
if (convergence.HasDiverged)
{
// Restore previous coefficients
for (int i = 0; i < regression.Coefficients.Length; i++)
{
regression.Coefficients[i] = convergence.OldValues[i];
}
}
// Recompute current outputs
for (int i = 0; i < output.Length; i++)
{
double sum = 0;
for (int j = 0; j < regression.Coefficients.Length; j++)
{
sum += regression.Coefficients[j] * inputs[i][j];
}
output[i] = Math.Exp(sum);
}
} while (!convergence.HasConverged);
for (int i = 0; i < regression.Coefficients.Length; i++)
{
regression.Coefficients[i] /= sdev[i];
}
if (computeStandardErrors)
{
// Grab the regression information matrix
double[,] inverse = decomposition.Inverse();
// Calculate coefficients' standard errors
double[] standardErrors = regression.StandardErrors;
for (int i = 0; i < standardErrors.Length; i++)
{
standardErrors[i] = Math.Sqrt(Math.Abs(inverse[i, i])) / sdev[i];
}
}
if (computeBaselineFunction)
{
createBaseline(time, censor, output);
}
return(regression.GetPartialLogLikelihood(inputs, time, censor));
}