public static double Calculate(ISymbolicDataAnalysisExpressionTreeInterpreter interpreter, ISymbolicExpressionTree tree, double lowerEstimationLimit, double upperEstimationLimit, IClassificationProblemData problemData,
IEnumerable <int> rows, bool applyLinearScaling, ISymbolicClassificationModelCreator modelCreator, double normalizedMeanSquaredErrorWeightingFactor, double falseNegativeRateWeightingFactor, double falsePositiveRateWeightingFactor)
{
var estimatedValues = interpreter.GetSymbolicExpressionTreeValues(tree, problemData.Dataset, rows);
var targetClassValues = problemData.Dataset.GetDoubleValues(problemData.TargetVariable, rows);
var boundedEstimatedValues = estimatedValues.LimitToRange(lowerEstimationLimit, upperEstimationLimit).ToArray();
OnlineCalculatorError errorState;
double nmse;
//calculate performance measures
string positiveClassName = problemData.PositiveClass;
double[] classValues, thresholds;
IEnumerable <double> estimatedClassValues = null;
ISymbolicDiscriminantFunctionClassificationModel m;
var model = modelCreator.CreateSymbolicClassificationModel(problemData.TargetVariable, tree, interpreter, lowerEstimationLimit, upperEstimationLimit);
if ((m = model as ISymbolicDiscriminantFunctionClassificationModel) != null)
{
m.ThresholdCalculator.Calculate(problemData, boundedEstimatedValues, targetClassValues, out classValues, out thresholds);
m.SetThresholdsAndClassValues(thresholds, classValues);
estimatedClassValues = m.GetEstimatedClassValues(boundedEstimatedValues);
}
else
{
model.RecalculateModelParameters(problemData, rows);
estimatedClassValues = model.GetEstimatedClassValues(problemData.Dataset, rows);
}
var performanceCalculator = new ClassificationPerformanceMeasuresCalculator(positiveClassName, problemData.GetClassValue(positiveClassName));
performanceCalculator.Calculate(targetClassValues, estimatedClassValues);
if (performanceCalculator.ErrorState != OnlineCalculatorError.None)
{
return(Double.NaN);
}
double falseNegativeRate = 1 - performanceCalculator.TruePositiveRate;
double falsePositiveRate = performanceCalculator.FalsePositiveRate;
if (applyLinearScaling)
{
throw new NotSupportedException("The Weighted Performance Measures Evaluator does not suppport linear scaling!");
}
nmse = OnlineNormalizedMeanSquaredErrorCalculator.Calculate(targetClassValues, boundedEstimatedValues, out errorState);
if (errorState != OnlineCalculatorError.None)
{
return(Double.NaN);
}
return(normalizedMeanSquaredErrorWeightingFactor * nmse + falseNegativeRateWeightingFactor * falseNegativeRate + falsePositiveRateWeightingFactor * falsePositiveRate);
}
/// <summary>
/// Elastic net with squared-error-loss for dense predictor matrix, runs the full path of all lambdas
/// </summary>
/// <param name="problemData">Predictor target matrix x and target vector y</param>
/// <param name="penalty">Penalty for balance between ridge (0.0) and lasso (1.0) regression</param>
/// <param name="nlam">Maximum number of lambda values (default 100)</param>
/// <param name="flmin">User control of lambda values (<1.0 => minimum lambda = flmin * (largest lambda value), >= 1.0 => use supplied lambda values</param>
/// <param name="ulam">User supplied lambda values</param>
/// <param name="lambda">Output lambda values</param>
/// <param name="trainNMSE">Vector of normalized mean of squared error (NMSE = Variance(res) / Variance(y)) values on the training set for each set of coefficients along the path</param>
/// <param name="testNMSE">Vector of normalized mean of squared error (NMSE = Variance(res) / Variance(y)) values on the test set for each set of coefficients along the path</param>
/// <param name="coeff">Vector of coefficient vectors for each solution along the path</param>
/// <param name="intercept">Vector of intercepts for each solution along the path</param>
/// <param name="coeffLowerBound">Optional lower bound for all coefficients</param>
/// <param name="coeffUpperBound">Optional upper bound for all coefficients</param>
/// <param name="maxVars">Maximum allowed number of variables in each solution along the path (-1 => all variables are allowed)</param>
private static void RunElasticNetLinearRegression(IRegressionProblemData problemData, double penalty,
int nlam, double flmin, double[] ulam, out double[] lambda, out double[] trainNMSE, out double[] testNMSE, out double[,] coeff, out double[] intercept,
double coeffLowerBound = double.NegativeInfinity, double coeffUpperBound = double.PositiveInfinity,
int maxVars = -1
)
{
if (penalty < 0.0 || penalty > 1.0)
{
throw new ArgumentException("0 <= penalty <= 1", "penalty");
}
double[,] trainX;
double[,] testX;
double[] trainY;
double[] testY;
PrepareData(problemData, out trainX, out trainY, out testX, out testY);
var numTrainObs = trainX.GetLength(1);
var numTestObs = testX.GetLength(1);
var numVars = trainX.GetLength(0);
int ka = 1; // => covariance updating algorithm
double parm = penalty;
double[] w = Enumerable.Repeat(1.0, numTrainObs).ToArray(); // all observations have the same weight
int[] jd = new int[1]; // do not force to use any of the variables
double[] vp = Enumerable.Repeat(1.0, numVars).ToArray(); // all predictor variables are unpenalized
double[,] cl = new double[numVars, 2]; // use the same bounds for all coefficients
for (int i = 0; i < numVars; i++)
{
cl[i, 0] = coeffLowerBound;
cl[i, 1] = coeffUpperBound;
}
int ne = maxVars > 0 ? maxVars : numVars;
int nx = numVars;
double thr = 1.0e-5; // default value as recommended in glmnet
int isd = 1; // => regression on standardized predictor variables
int intr = 1; // => do include intercept in model
int maxit = 100000; // default value as recommended in glmnet
// outputs
int lmu = -1;
double[,] ca;
int[] ia;
int[] nin;
int nlp = -99;
int jerr = -99;
double[] trainR2;
Glmnet.elnet(ka, parm, numTrainObs, numVars, trainX, trainY, w, jd, vp, cl, ne, nx, nlam, flmin, ulam, thr, isd, intr, maxit, out lmu, out intercept, out ca, out ia, out nin, out trainR2, out lambda, out nlp, out jerr);
trainNMSE = new double[lmu]; // elnet returns R**2 as 1 - NMSE
testNMSE = new double[lmu];
coeff = new double[lmu, numVars];
for (int solIdx = 0; solIdx < lmu; solIdx++)
{
trainNMSE[solIdx] = 1.0 - trainR2[solIdx];
// uncompress coefficients of solution
int selectedNin = nin[solIdx];
double[] coefficients;
double[] selectedCa = new double[nx];
for (int i = 0; i < nx; i++)
{
selectedCa[i] = ca[solIdx, i];
}
// apply to test set to calculate test NMSE values for each lambda step
double[] fn;
Glmnet.modval(intercept[solIdx], selectedCa, ia, selectedNin, numTestObs, testX, out fn);
OnlineCalculatorError error;
var nmse = OnlineNormalizedMeanSquaredErrorCalculator.Calculate(testY, fn, out error);
if (error != OnlineCalculatorError.None)
{
nmse = double.NaN;
}
testNMSE[solIdx] = nmse;
// uncompress coefficients
Glmnet.uncomp(numVars, selectedCa, ia, selectedNin, out coefficients);
for (int i = 0; i < coefficients.Length; i++)
{
coeff[solIdx, i] = coefficients[i];
}
}
}
public override IOperation Apply()
{
var operation = base.Apply();
var paretoFront = TrainingBestSolutionsParameter.ActualValue;
IResult result;
ScatterPlot qualityToTreeSize;
if (!ResultCollection.TryGetValue("Pareto Front Analysis", out result))
{
qualityToTreeSize = new ScatterPlot("Quality vs Tree Size", "");
qualityToTreeSize.VisualProperties.XAxisMinimumAuto = false;
qualityToTreeSize.VisualProperties.XAxisMaximumAuto = false;
qualityToTreeSize.VisualProperties.YAxisMinimumAuto = false;
qualityToTreeSize.VisualProperties.YAxisMaximumAuto = false;
qualityToTreeSize.VisualProperties.XAxisMinimumFixedValue = 0;
qualityToTreeSize.VisualProperties.XAxisMaximumFixedValue = MaximumSymbolicExpressionTreeLengthParameter.ActualValue.Value;
qualityToTreeSize.VisualProperties.YAxisMinimumFixedValue = 0;
qualityToTreeSize.VisualProperties.YAxisMaximumFixedValue = 2;
ResultCollection.Add(new Result("Pareto Front Analysis", qualityToTreeSize));
}
else
{
qualityToTreeSize = (ScatterPlot)result.Value;
}
int previousTreeLength = -1;
var sizeParetoFront = new LinkedList <ISymbolicRegressionSolution>();
foreach (var solution in paretoFront.OrderBy(s => s.Model.SymbolicExpressionTree.Length))
{
int treeLength = solution.Model.SymbolicExpressionTree.Length;
if (!sizeParetoFront.Any())
{
sizeParetoFront.AddLast(solution);
}
if (solution.TrainingNormalizedMeanSquaredError < sizeParetoFront.Last.Value.TrainingNormalizedMeanSquaredError)
{
if (treeLength == previousTreeLength)
{
sizeParetoFront.RemoveLast();
}
sizeParetoFront.AddLast(solution);
}
previousTreeLength = treeLength;
}
qualityToTreeSize.Rows.Clear();
var trainingRow = new ScatterPlotDataRow("Training NMSE", "", sizeParetoFront.Select(x => new Point2D <double>(x.Model.SymbolicExpressionTree.Length, x.TrainingNormalizedMeanSquaredError, x)));
trainingRow.VisualProperties.PointSize = 8;
qualityToTreeSize.Rows.Add(trainingRow);
if (AnalyzeTestError)
{
var testRow = new ScatterPlotDataRow("Test NMSE", "",
sizeParetoFront.Select(x => new Point2D <double>(x.Model.SymbolicExpressionTree.Length, x.TestNormalizedMeanSquaredError, x)));
testRow.VisualProperties.PointSize = 8;
qualityToTreeSize.Rows.Add(testRow);
}
var validationPartition = ValidationPartitionParameter.ActualValue;
if (validationPartition.Size != 0)
{
var problemData = ProblemDataParameter.ActualValue;
var validationIndizes = Enumerable.Range(validationPartition.Start, validationPartition.Size).ToList();
var targetValues = problemData.Dataset.GetDoubleValues(problemData.TargetVariable, validationIndizes).ToList();
OnlineCalculatorError error;
var validationRow = new ScatterPlotDataRow("Validation NMSE", "",
sizeParetoFront.Select(x => new Point2D <double>(x.Model.SymbolicExpressionTree.Length,
OnlineNormalizedMeanSquaredErrorCalculator.Calculate(targetValues, x.GetEstimatedValues(validationIndizes), out error))));
validationRow.VisualProperties.PointSize = 7;
qualityToTreeSize.Rows.Add(validationRow);
}
return(operation);
}