/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
* Copyright 2018-2022 Kathy Su, Kay Diederichs
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with this program. If not, see .
*/
/**
* Ported from https://doi.org/10.1107/S2059798317000699 by
* @AUTHOR MorellThomas
*/
package jalview.analysis;
import jalview.bin.Console;
import jalview.math.MatrixI;
import jalview.math.Matrix;
import jalview.math.MiscMath;
import java.lang.Math;
import java.lang.System;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Map.Entry;
import java.util.TreeMap;
import org.apache.commons.math3.analysis.MultivariateVectorFunction;
import org.apache.commons.math3.analysis.MultivariateMatrixFunction;
import org.apache.commons.math3.fitting.leastsquares.LeastSquaresOptimizer;
import org.apache.commons.math3.fitting.leastsquares.LeastSquaresProblem;
import org.apache.commons.math3.fitting.leastsquares.LeastSquaresBuilder;
import org.apache.commons.math3.fitting.leastsquares.LevenbergMarquardtOptimizer;
import org.apache.commons.math3.linear.ArrayRealVector;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.RealVector;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.SingularValueDecomposition;
/**
* A class to model rectangular matrices of double values and operations on them
*/
public class ccAnalysis
{
private byte dim = 0; //dimensions
private MatrixI scoresOld; //input scores
public ccAnalysis(MatrixI scores, byte dim)
{
//&! round matrix to .4f to be same as in pasimap
for (int i = 0; i < scores.height(); i++)
{
for (int j = 0; j < scores.width(); j++)
{
if (!Double.isNaN(scores.getValue(i,j)))
{
scores.setValue(i, j, (double) Math.round(scores.getValue(i,j) * (int) 10000) / 10000);
}
}
}
this.scoresOld = scores;
this.dim = dim;
}
/** TODO
* DOCUMENT ME
*
* @param hSigns ~ hypothesis signs (+/-) for each sequence
* @param scores ~ input score matrix
*
* @return distrustScores
*/
private int[] initialiseDistrusts(byte[] hSigns, MatrixI scores)
{
int[] distrustScores = new int[scores.width()];
// loop over symmetric matrix
for (int i = 0; i < scores.width(); i++)
{
byte hASign = hSigns[i];
int conHypNum = 0;
int proHypNum = 0;
for (int j = 0; j < scores.width(); j++)
{
double cell = scores.getRow(i)[j]; // value at [i][j] in scores
byte hBSign = hSigns[j];
if (!Double.isNaN(cell))
{
byte cellSign = (byte) Math.signum(cell); //check if sign of matrix value fits hyptohesis
if (cellSign == hASign * hBSign)
{
proHypNum++;
} else {
conHypNum++;
}
}
}
distrustScores[i] = conHypNum - proHypNum; //create distrust score for each sequence
}
return distrustScores;
}
/** TODO
* DOCUMENT ME
*
* @param hSigns ~ hypothesis signs (+/-)
* @param distrustScores
* @param scores ~ input score matrix
*
* @return hSigns
*/
private byte[] optimiseHypothesis(byte[] hSigns, int[] distrustScores, MatrixI scores)
{
// get maximum distrust score
int[] maxes = MiscMath.findMax(distrustScores);
int maxDistrustIndex = maxes[0];
int maxDistrust = maxes[1];
// if hypothesis is not optimal yet
if (maxDistrust > 0)
{
//toggle sign for hI with maximum distrust
hSigns[maxDistrustIndex] *= -1;
// update distrust at same position
distrustScores[maxDistrustIndex] *= -1;
// also update distrust scores for all hI that were not changed
byte hASign = hSigns[maxDistrustIndex];
for (int NOTmaxDistrustIndex = 0; NOTmaxDistrustIndex < distrustScores.length; NOTmaxDistrustIndex++)
{
if (NOTmaxDistrustIndex != maxDistrustIndex)
{
byte hBSign = hSigns[NOTmaxDistrustIndex];
double cell = scores.getRow(maxDistrustIndex)[NOTmaxDistrustIndex];
// distrust only changed if not NaN
if (!Double.isNaN(cell))
{
byte cellSign = (byte) Math.signum(cell);
// if sign of cell matches hypothesis decrease distrust by 2 because 1 more value supporting and 1 less contradicting
// else increase by 2
if (cellSign == hASign * hBSign)
{
distrustScores[NOTmaxDistrustIndex] -= 2;
} else {
distrustScores[NOTmaxDistrustIndex] += 2;
}
}
}
}
//further optimisation necessary
return optimiseHypothesis(hSigns, distrustScores, scores);
} else {
return hSigns;
}
}
/**
* takes the a symmetric MatrixI as input scores which may contain Double.NaN
* approximate the missing values using hypothesis optimisation
*
* runs analysis
*
* @param scores ~ score matrix
*
* @return
*/
public MatrixI run ()
{
MatrixI eigenMatrix = scoresOld.copy();
MatrixI repMatrix = scoresOld.copy();
try
{
/*
* Calculate correction factor for 2nd and higher eigenvalue(s).
* This correction is NOT needed for the 1st eigenvalue, because the
* unknown (=NaN) values of the matrix are approximated by presuming
* 1-dimensional vectors as the basis of the matrix interpretation as dot
* products.
*/
//&! debug
System.out.println("input:");
eigenMatrix.print(System.out, "%1.4f ");
int matrixWidth = eigenMatrix.width(); // square matrix, so width == height
int matrixElementsTotal = (int) Math.pow(matrixWidth, 2); //total number of elemts
float correctionFactor = (float) (matrixElementsTotal - eigenMatrix.countNaN()) / (float) matrixElementsTotal;
/*
* Calculate hypothetical value (1-dimensional vector) h_i for each
* dataset by interpreting the given correlation coefficients as scalar
* products.
*/
/*
* Memory for current hypothesis concerning sign of each h_i.
* List of signs for all h_i in the encoding:
* * 1: positive
* * 0: zero
* * -1: negative
* Initial hypothesis: all signs are positive.
*/
byte[] hSigns = new byte[matrixWidth];
Arrays.fill(hSigns, (byte) 1);
//Estimate signs for each h_i by refining hypothesis on signs.
hSigns = optimiseHypothesis(hSigns, initialiseDistrusts(hSigns, eigenMatrix), eigenMatrix);
//Estimate absolute values for each h_i by determining sqrt of mean of
//non-NaN absolute values for every row.
//<++> hAbs = //np.sqrt(np.nanmean(np.absolute(eigenMatrix), axis=1))
MiscMath.print(eigenMatrix.absolute().meanRow(), "%1.8f");
double[] hAbs = MiscMath.sqrt(eigenMatrix.absolute().meanRow()); //np.sqrt(np.nanmean(np.absolute(eigenMatrix), axis=1))
//Combine estimated signs with absolute values in obtain total value for
//each h_i.
double[] hValues = MiscMath.elementwiseMultiply(hSigns, hAbs);
//<++>hValues.reshape((1,matrixWidth)); // doesnt it already look like this
/*Complement symmetric matrix by using the scalar products of estimated
*values of h_i to replace NaN-cells.
*Matrix positions that have estimated values
*(only for diagonal and upper off-diagonal values, due to the symmetry
*the positions of the lower-diagonal values can be inferred).
List of tuples (row_idx, column_idx).*/
ArrayList estimatedPositions = new ArrayList();
// for off-diagonal cells
for (int rowIndex = 0; rowIndex < matrixWidth - 1; rowIndex++)
{
for (int columnIndex = rowIndex + 1; columnIndex < matrixWidth; columnIndex++)
{
double cell = eigenMatrix.getValue(rowIndex, columnIndex);
if (Double.isNaN(cell))
{
//calculate scalar product as new cell value
cell = hValues[rowIndex] * hValues[columnIndex]; // something is wrong with hAbs andhValues and everything!!!!!!!!!!!!
//fill in new value in cell and symmetric partner
eigenMatrix.setValue(rowIndex, columnIndex, cell);
eigenMatrix.setValue(columnIndex, rowIndex, cell);
//save positions of estimated values
estimatedPositions.add(new int[]{rowIndex, columnIndex});
}
}
}
// for diagonal cells
for (int diagonalIndex = 0; diagonalIndex < matrixWidth; diagonalIndex++)
{
double cell = Math.pow(hValues[diagonalIndex], 2);
eigenMatrix.setValue(diagonalIndex, diagonalIndex, cell);
estimatedPositions.add(new int[]{diagonalIndex, diagonalIndex});
}
/*Refine total values of each h_i:
*Initialise h_values of the hypothetical non-existant previous iteration
*with the correct format but with impossible values.
Needed for exit condition of otherwise endless loop.*/
System.out.print("initial values: [ ");
for (double h : hValues)
{
System.out.print(String.format("%1.4f, ", h));
}
System.out.println(" ]");
double[] hValuesOld = new double[matrixWidth];
int iterationCount = 0;
// repeat unitl values of h do not significantly change anymore
while (true)
{
for (int hIndex = 0; hIndex < matrixWidth; hIndex++)
{
//@python newH = np.sum(hValues * eigenMatrix[hIndex]) / np.sum(hValues ** 2)
double newH = Arrays.stream(MiscMath.elementwiseMultiply(hValues, eigenMatrix.getRow(hIndex))).sum() / Arrays.stream(MiscMath.elementwiseMultiply(hValues, hValues)).sum();
hValues[hIndex] = newH;
}
System.out.print(String.format("iteration %d: [ ", iterationCount));
for (double h : hValues)
{
System.out.print(String.format("%1.4f, ", h));
}
System.out.println(" ]");
//update values of estimated positions
for (int[] pair : estimatedPositions) // pair ~ row, col
{
double newVal = hValues[pair[0]] * hValues[pair[1]];
eigenMatrix.setValue(pair[0], pair[1], newVal);
eigenMatrix.setValue(pair[1], pair[0], newVal);
}
iterationCount++;
//exit loop as soon as new values are similar to the last iteration
if (MiscMath.allClose(hValues, hValuesOld, 0d, 1e-05d, false))
{
break;
}
//save hValues for comparison in the next iteration
System.arraycopy(hValues, 0, hValuesOld, 0, hValues.length);
}
//-----------------------------
//Use complemented symmetric matrix to calculate final representative
//vectors.
//&! debug
System.out.println("after estimating:");
eigenMatrix.print(System.out, "%1.8f ");
//Eigendecomposition.
eigenMatrix.tred();
System.out.println("tred");
eigenMatrix.print(System.out, "%8.2f");
eigenMatrix.tqli();
System.out.println("eigenvals");
eigenMatrix.printD(System.out, "%2.4f ");
System.out.println();
System.out.println("tqli");
eigenMatrix.print(System.out, "%8.2f");
double[] eigenVals = eigenMatrix.getD();
/*
TreeMap eigenPairs = new TreeMap<>(Comparator.reverseOrder());
for (int i = 0; i < eigenVals.length; i++)
{
eigenPairs.put(eigenVals[i], eigenMatrix.getColumn(i));
}
*/
TreeMap eigenPairs = new TreeMap<>(Comparator.reverseOrder());
for (int i = 0; i < eigenVals.length; i++)
{
eigenPairs.put(eigenVals[i], i);
}
// matrix of representative eigenvectors (each row is a vector)
double[][] _repMatrix = new double[eigenVals.length][dim]; //last ones were dim
double[][] _oldMatrix = new double[eigenVals.length][dim];
double[] correctedEigenValues = new double[dim];
//for (Entry pair : eigenPairs.entrySet())
int l = 0;
for (Entry pair : eigenPairs.entrySet())
{
double eigenValue = pair.getKey();
int column = pair.getValue();
double[] eigenVector = eigenMatrix.getColumn(column);
//for 2nd and higher eigenvalues
if (l >= 1)
{
eigenValue /= correctionFactor;
}
//l++;
//correctedEigenValues[dim - l] = eigenValue;
correctedEigenValues[l] = eigenValue;
for (int j = 0; j < eigenVector.length; j++)
{
//_repMatrix[j][dim - l] = (eigenValue < 0) ? 0.0 : Math.sqrt(eigenValue) * eigenVector[j];
_repMatrix[j][l] = (eigenValue < 0) ? 0.0 : - Math.sqrt(eigenValue) * eigenVector[j];
double tmpOldScore = scoresOld.getColumn(column)[j];
_oldMatrix[j][dim - l - 1] = (Double.isNaN(tmpOldScore)) ? 0.0 : tmpOldScore;
}
l++;
if (l >= dim)
{
break;
}
}
System.out.println("correctedEigenValues");
MiscMath.print(correctedEigenValues, "%2.4f ");
repMatrix = new Matrix(_repMatrix);
repMatrix.setD(correctedEigenValues);
MatrixI oldMatrix = new Matrix(_oldMatrix); //TODO do i even need it anymore?
System.out.println("old matrix");
oldMatrix.print(System.out, "%8.2f");
System.out.println("scoresOld");
scoresOld.print(System.out, "%1.4f ");
System.out.println("rep matrix");
repMatrix.print(System.out, "%1.8f ");
MatrixI dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
System.out.println("dot matrix");
dotMatrix.print(System.out, "%1.8f ");
double rmsd = scoresOld.rmsd(dotMatrix); //TODO do i need this here?
System.out.println(rmsd);
System.out.println("iteration, rmsd, maxDiff, rmsdDiff");
System.out.println(String.format("0, %8.5f, -, -", rmsd));
// Refine representative vectors by minimising sum-of-squared deviates between dotMatrix and original score matrix
for (int iteration = 1; iteration < 21; iteration++) // arbitrarily set to 20
{
MatrixI repMatrixOLD = repMatrix.copy();
MatrixI dotMatrixOLD = dotMatrix.copy();
// for all rows/hA in the original matrix
for (int hAIndex = 0; hAIndex < oldMatrix.height(); hAIndex++)
{
double[] row = oldMatrix.getRow(hAIndex);
double[] hA = repMatrix.getRow(hAIndex); // inverted
hAIndex = hAIndex;
//find least-squares-solution fo rdifferences between original scores and representative vectors
//--> originalToEquasionSystem(hA, hAIndex, repMatrix, row) --> double[]
System.out.println(String.format("||||||||||||||||||||||||||||||||||||||||||||\nIteration: %d", iteration));
//repMatrix = new Matrix( new double[][]{{ 0.92894902, -0.25013783, -0.0051076 }, { 0.91955135, -0.25024707, -0.00516568}, { 0.90957348, -0.21717002, -0.14259899}, { 0.90298063, -0.21678816, -0.14697814}, { 0.9157065, -0.04646437, 0.10105454}, { 0.9050301, -0.04689785, 0.18964432}, { 0.92498545, 0.03881933, 0.14771523}, { 0.88008842, 0.0142395, 0.11356242}, { 0.94276528, 0.25591474, -0.07190911}, { 0.93939976, 0.23375136, -0.07530558}, { 0.93550782, 0.24635804, -0.07317563}, { 0.92497731, 0.21729928, -0.02361162}});
//scoresOld = new Matrix( new double[][]{{ Double.NaN, 0.9914, 0.8879, 0.8803, 0.8528, 0.8481, 0.8434, 0.8174, 0.8174, 0.8232, 0.8148, 0.8114}, {0.9914, Double.NaN, 0.8792, 0.8717, 0.8441, 0.8395, 0.8347, 0.8087, 0.8085, 0.8143, 0.8059, 0.8024}, {0.8879, 0.8792, Double.NaN, 0.9578, 0.8289, 0.8075, 0.8268, 0.7815, 0.8165, 0.8168, 0.8084, 0.7974}, {0.8803, 0.8717, 0.9578, Double.NaN, 0.838, 0.7974, 0.8058, 0.7798, 0.8094, 0.8098, 0.8067, 0.7905}, {0.8528, 0.8441, 0.8289, 0.838, Double.NaN, 0.8954, 0.8412, 0.7879, 0.8418, 0.8384, 0.8389, 0.8556}, {0.8481, 0.8395, 0.8075, 0.7974, 0.8954, Double.NaN, 0.8699, 0.8106, 0.8267, 0.8234, 0.8222, 0.8241}, {0.8434, 0.8347, 0.8268, 0.8058, 0.8412, 0.8699, Double.NaN, 0.869, 0.8745, 0.8583, 0.8661, 0.8593}, {0.8174, 0.8087, 0.7815, 0.7798, 0.7879, 0.8106, 0.869, Double.NaN, 0.8273, 0.8331, 0.8137, 0.8029}, {0.8174, 0.8085, 0.8165, 0.8094, 0.8418, 0.8267, 0.8745, 0.8273, Double.NaN, 0.967, 0.978, 0.9373}, {0.8232, 0.8143, 0.8168, 0.8098, 0.8384, 0.8234, 0.8583, 0.8331, 0.967, Double.NaN, 0.9561, 0.9337}, {0.8148, 0.8059, 0.8084, 0.8067, 0.8389, 0.8222, 0.8661, 0.8137, 0.978, 0.9561, Double.NaN, 0.9263}, {0.8114, 0.8024, 0.7974, 0.7905, 0.8556, 0.8241, 0.8593, 0.8029, 0.9373, 0.9337, 0.9263, Double.NaN}});
double[] hAlsm = leastSquaresOptimisation(repMatrix, scoresOld, hAIndex);
// update repMatrix with new hAlsm
for (int j = 0; j < repMatrix.width(); j++)
{
repMatrix.setValue(hAIndex, j, hAlsm[j]);
}
break;
}
// dot product of representative vecotrs yields a matrix with values approximating the correlation matrix
dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
// calculate rmsd between approximation and correlation matrix
rmsd = scoresOld.rmsd(dotMatrix);
// calculate maximum change of representative vectors of current iteration
//repMatrix.subtract(repMatrixOLD).print(System.out, "%8.2f");
MatrixI diff = repMatrix.subtract(repMatrixOLD).absolute();
double maxDiff = 0.0;
for (int i = 0; i < diff.height(); i++)
{
for (int j = 0; j < diff.width(); j++)
{
maxDiff = (diff.getValue(i, j) > maxDiff) ? diff.getValue(i, j) : maxDiff;
}
}
System.out.println(String.format("maxDiff: %f", maxDiff));
// calculate rmsd between current and previous estimation
double rmsdDiff = dotMatrix.rmsd(dotMatrixOLD);
System.out.println(String.format("%d, %8.5f, %8.5f, %8.5f", iteration, rmsd, maxDiff, rmsdDiff));
if (!(Math.abs(maxDiff) > 1e-06))
{
repMatrix = repMatrixOLD.copy();
break;
}
break;
}
} catch (Exception q)
{
Console.error("Error computing cc_analysis: " + q.getMessage());
q.printStackTrace();
}
//repMatrix = repMatrix.transpose();
System.out.println("final repMatrix");
repMatrix.print(System.out, "%8.2f");
return repMatrix;
}
/**
* Create equations system using information on originally known
* pairwise correlation coefficients (parsed from infile) and the
* representative result vectors
*
* Each equation has the format:
* hA * hA - pairwiseCC = 0
* with:
* hA: unknown variable
* hB: known representative vector
* pairwiseCC: known pairwise correlation coefficien
*
* The resulting equations system is overdetermined, if there are more
* equations than unknown elements
*
* @param x ~ unknown n-dimensional column-vector
* (needed for generating equations system, NOT to be specified by user).
* @param hAIndex ~ index of currently optimised representative result vector.
* @param h ~ matrix with row-wise listing of representative result vectors.
* @param originalRow ~ matrix-row of originally parsed pairwise correlation coefficients.
*
* @return
*/
//private double[] originalToEquasionSystem(double[] x, int hAIndex, MatrixI h, MatrixI originalScores)
private double[] originalToEquasionSystem(double[] hA, MatrixI repMatrix, MatrixI scoresOld, int hAIndex)
{
double[] originalRow = scoresOld.getRow(hAIndex);
int nans = MiscMath.countNaN(originalRow);
double[] result = new double[originalRow.length - nans];
//for all pairwiseCC in originalRow
int resultIndex = 0;
for (int hBIndex = 0; hBIndex < originalRow.length; hBIndex++)
{
double pairwiseCC = originalRow[hBIndex];
// if not NaN -> create new equation and add it to the system
if (!Double.isNaN(pairwiseCC))
{
double[] hB = repMatrix.getRow(hBIndex);
result[resultIndex++] = MiscMath.sum(MiscMath.elementwiseMultiply(hA, hB)) - pairwiseCC;
} else {
}
}
return result;
}
/**
* returns the jacobian matrix
* @param repMatrix ~ matrix of representative vectors
* @param hAIndex ~ current row index
*
* @return
*/
private MatrixI approximateDerivative(MatrixI repMatrix, MatrixI scoresOld, int hAIndex)
{
//hA = x0
double[] hA = repMatrix.getRow(hAIndex);
double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld, hAIndex);
System.out.println("Approximate derivative with ");
System.out.print("hA (x): ");
MiscMath.print(hA, "%1.8f");
System.out.print("f0: ");
MiscMath.print(f0, "%1.8f");
double[] signX0 = new double[hA.length];
double[] xAbs = new double[hA.length];
for (int i = 0; i < hA.length; i++)
{
signX0[i] = (hA[i] >= 0) ? 1 : -1;
xAbs[i] = (Math.abs(hA[i]) >= 1.0) ? Math.abs(hA[i]) : 1.0;
}
double rstep = Math.pow(Math.ulp(1.0), 0.5);
double[] h = new double [hA.length];
for (int i = 0; i < hA.length; i++)
{
h[i] = rstep * signX0[i] * xAbs[i];
}
int m = f0.length;
int n = hA.length;
double[][] jTransposed = new double[n][m];
for (int i = 0; i < h.length; i++)
{
double[] x = new double[h.length];
System.arraycopy(hA, 0, x, 0, h.length);
x[i] += h[i];
double dx = x[i] - hA[i];
double[] df = originalToEquasionSystem(x, repMatrix, scoresOld, hAIndex);
for (int j = 0; j < df.length; j++)
{
df[j] -= f0[j];
jTransposed[i][j] = df[j] / dx;
}
}
MatrixI J = new Matrix(jTransposed).transpose(); // inverted
return J;
}
/**
* norm of regularized (by alpha) least-squares solution minus Delta
* @param alpha
* @param suf
* @param s
* @param Delta
*
* @return
*/
private double[] phiAndDerivative(double alpha, double[] suf, double[] s, double Delta)
{
double[] denom = MiscMath.elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha);
double pNorm = MiscMath.norm(MiscMath.elementwiseDivide(suf, denom));
double phi = pNorm - Delta;
// - sum ( suf**2 / denom**3) / pNorm
double phiPrime = - MiscMath.sum(MiscMath.elementwiseDivide(MiscMath.elementwiseMultiply(suf, suf), MiscMath.elementwiseMultiply(MiscMath.elementwiseMultiply(denom, denom), denom))) / pNorm;
return new double[]{phi, phiPrime};
}
/**
* class holding the result of solveLsqTrustRegion
*/
private class TrustRegion
{
private double[] step;
private double alpha;
private int iteration;
public TrustRegion(double[] step, double alpha, int iteration)
{
this.step = step;
this.alpha = alpha;
this.iteration = iteration;
}
public double[] getStep()
{
return this.step;
}
public double getAlpha()
{
return this.alpha;
}
public int getIteration()
{
return this.iteration;
}
}
/**
* solve a trust-region problem arising in least-squares optimisation
* @param n ~ number of variables
* @param m ~ number of residuals
* @param uf ~ <++>
* @param s ~ singular values of J
* @param V ~ transpose of VT
* @param Delta ~ radius of a trust region
* @param alpha ~ initial guess for alpha
*
* @return
*/
private TrustRegion solveLsqTrustRegion(int n, int m, double[] uf, double[] s, MatrixI V, double Delta, double alpha)
{
double[] suf = MiscMath.elementwiseMultiply(s, uf);
//check if J has full rank and tr Gauss-Newton step
boolean fullRank = false;
if (m >= n)
{
double threshold = s[0] * Math.ulp(1.0) * m;
fullRank = s[s.length - 1] > threshold;
}
if (fullRank)
{
double[] p = MiscMath.elementwiseMultiply(V.sumProduct(MiscMath.elementwiseDivide(uf, s)), -1); // inverted and roughly fine
if (MiscMath.norm(p) <= Delta)
{
TrustRegion result = new TrustRegion(p, 0.0, 0);
return result;
}
}
double alphaUpper = MiscMath.norm(suf) / Delta;
double alphaLower = 0.0;
if (fullRank)
{
double[] phiAndPrime = phiAndDerivative(0.0, suf, s, Delta);
alphaLower = - phiAndPrime[0] / phiAndPrime[1];
}
alpha = (!fullRank && alpha == 0.0) ? alpha = Math.max(0.001 * alphaUpper, Math.pow(alphaLower * alphaUpper, 0.5)) : alpha;
int iteration = 0;
while (iteration < 10) // 10 is default max_iter
{
alpha = (alpha < alphaLower || alpha > alphaUpper) ? alpha = Math.max(0.001 * alphaUpper, Math.pow(alphaLower * alphaUpper, 0.5)) : alpha;
double[] phiAndPrime = phiAndDerivative(alpha, suf, s, Delta);
double phi = phiAndPrime[0];
double phiPrime = phiAndPrime[1];
alphaUpper = (phi < 0) ? alpha : alphaUpper;
double ratio = phi / phiPrime;
alphaLower = Math.max(alphaLower, alpha - ratio);
alpha -= (phi + Delta) * ratio / Delta;
if (Math.abs(phi) < 0.01 * Delta) // default rtol set to 0.01
{
break;
}
iteration++;
}
// p = - V.dot( suf / (s**2 + alpha))
double[] tmp = MiscMath.elementwiseDivide(suf, MiscMath.elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha));
double[] p = MiscMath.elementwiseMultiply(V.sumProduct(tmp), -1);
// Make the norm of p equal to Delta, p is changed only slightly during this.
// It is done to prevent p lie outside of the trust region
p = MiscMath.elementwiseMultiply(p, Delta / MiscMath.norm(p));
TrustRegion result = new TrustRegion(p, alpha, iteration + 1);
return result;
}
/**
* compute values of a quadratic function arising in least squares
* function: 0.5 * s.T * (J.T * J + diag) * s + g.T * s
*
* @param J ~ jacobian matrix
* @param g ~ gradient
* @param s ~ steps and rows
*
* @return
*/
private double evaluateQuadratic(MatrixI J, double[] g, double[] s)
{
//TODO s (-> stepH) is slightly different
double[] Js = J.sumProduct(s); //TODO completely wromg
double q = MiscMath.dot(Js, Js);
double l = MiscMath.dot(s, g);
/*
System.out.println("doing evaluateQuadratic");
System.out.println("inputs");
System.out.print("J");
J.print(System.out, "%f ");
System.out.print("g");
MiscMath.print(g, "%f");
System.out.print("s");
MiscMath.print(s, "%f");
System.out.print("\nJs");
MiscMath.print(Js, "%f");
System.out.println(String.format("0.5 * %f + %f", q, l));
*/
return 0.5 * q + l;
}
/**
* update the radius of a trust region based on the cost reduction
*
* @param Delta
* @param actualReduction
* @param predictedReduction
* @param stepNorm
* @param boundHit
*
* @return
*/
private double[] updateTrustRegionRadius(double Delta, double actualReduction, double predictedReduction, double stepNorm, boolean boundHit)
{
double ratio = 0;
if (predictedReduction > 0)
{
ratio = actualReduction / predictedReduction;
} else if (predictedReduction == 0 && actualReduction == 0) {
ratio = 1;
} else {
ratio = 0;
}
if (ratio < 0.25)
{
Delta = 0.25 * stepNorm;
} else if (ratio > 0.75 && boundHit) {
Delta *= 2.0;
}
return new double[]{Delta, ratio};
}
/**
* check the termination condition for nonlinear least squares
* TODO can be removed and added just as one line in trf (: terminationStatus = (ftolSatisfied condition || xtolSatisfied condition) ? 1 : 0;) doesnt matter as long as distinguished between 0 and rest
*
* @param actualReduction
* @param cost
* @param stepNorm
* @param xNorm
* @param ratio
*
* @return
*/
private byte checkTermination(double actualReduction, double cost, double stepNorm, double xNorm, double ratio)
{
// default ftol and xtol = 1e-8
boolean ftolSatisfied = actualReduction < (1e-8 * cost) && ratio > 0.25;
boolean xtolSatisfied = stepNorm < (1e-8 * (1e-8 + xNorm));
if (ftolSatisfied && xtolSatisfied)
{
return (byte) 4;
} else if (ftolSatisfied) {
return (byte) 2;
} else if (xtolSatisfied) {
return (byte) 3;
} else {
return (byte) 0;
}
}
/**
* TODO DOCUMENT ME!
* @param repMatrix ~ Matrix containing representative vectors
* @param scoresOld ~ Matrix containing initial observations
* @param index ~ current row index
* @param J ~ jacobian matrix
*
* @return
*/
private double[] trf(MatrixI repMatrix, MatrixI scoresOld, int index, MatrixI J)
{
System.out.println("-----------------\nStart of trf");
//hA = x0
double[] hA = repMatrix.getRow(index); //inverted
double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld, index);
int nfev = 1; // ??
int njev = 1; // ??
int m = J.height();
int n = J.width();
double cost = 0.5 * MiscMath.dot(f0, f0);
double[] g = J.transpose().sumProduct(f0); // inverted
double[] scale = new double[hA.length];
Arrays.fill(scale, 1); // ??
double Delta = MiscMath.norm(hA);
int maxNfev = hA.length * 100; // ??
double alpha = 0.0; // ?? "Levenberg-Marquardt" parameter
System.out.println("Checking initial values:");
System.out.print("hA (x): ");
MiscMath.print(hA, "%1.8f");
System.out.print("f0: ");
MiscMath.print(f0, "%1.8f");
//System.out.println(String.format("nfev: %d, njev: %d, maxNfev: %d", nfev, njev, maxNfev));
//System.out.println(String.format("m: %d, n: %d", m, n));
System.out.println(String.format("cost: %1.8f, Delta: %1.8f, alpha: %1.8f", cost, Delta, alpha));
System.out.print("g: ");
MiscMath.print(g, "%1.8f");
double gNorm = 0;
byte terminationStatus = 0;
int iteration = 0;
System.out.println("outer while loop starts");
while (true)
{
System.out.println(String.format("iteration: %d", iteration));
gNorm = MiscMath.norm(g);
if (terminationStatus != 0 || nfev == maxNfev)
{
System.out.println(String.format("outer loop broken with terminationStatus: %d and nfev: %d", terminationStatus, nfev));
break;
}
// d = scale
SingularValueDecomposition svd = new SingularValueDecomposition(new Array2DRowRealMatrix(J.asArray()));
// svd not 100% correct -> origin of problems
MatrixI U = new Matrix(svd.getU().getData()); // inverted
double[] s = svd.getSingularValues(); // ??
MatrixI V = new Matrix(svd.getV().getData()).transpose(); //TODO inverted origin of probelm
double[] uf = U.transpose().sumProduct(f0);
System.out.println("After SVD");
System.out.println(String.format("gNorm: %1.8f", gNorm));
System.out.print("U: ");
U.print(System.out, "%1.8f ");
System.out.print("s: ");
MiscMath.print(s, "%1.8f");
System.out.print("V: ");
V.print(System.out, "%1.8f ");
System.out.print("uf: ");
MiscMath.print(uf, "%1.8f");
double actualReduction = -1;
double[] xNew = new double[hA.length];
double[] fNew = new double[f0.length];
double costNew = 0;
double stepHnorm = 0;
System.out.println("Inner while loop starts");
while (actualReduction <= 0 && nfev < maxNfev)
{
TrustRegion trustRegion = solveLsqTrustRegion(n, m, uf, s, V, Delta, alpha);
double[] stepH = trustRegion.getStep();
alpha = trustRegion.getAlpha();
int nIterations = trustRegion.getIteration();
double predictedReduction = - (evaluateQuadratic(J, g, stepH));
xNew = MiscMath.elementwiseAdd(hA, stepH);
fNew = originalToEquasionSystem(xNew, repMatrix, scoresOld, index);
nfev++;
stepHnorm = MiscMath.norm(stepH);
System.out.println("After TrustRegion");
System.out.print("stepH: ");
MiscMath.print(stepH, "%1.8f ");
System.out.println(String.format("alpha: %1.8f, nIterations: %d, predictedReduction: %1.8f, nfev: %d, stepHnorm: %1.8f", alpha, nIterations, predictedReduction, nfev, stepHnorm));
System.out.print("xNew: ");
MiscMath.print(xNew, "%1.8f ");
System.out.print("fNew: ");
MiscMath.print(fNew, "%1.8f ");
if (MiscMath.countNaN(fNew) > 0)
{
Delta = 0.25 * stepHnorm;
System.out.println(String.format("Loop continued with %d NaNs and Delta: %1.8f", MiscMath.countNaN(fNew), Delta));
continue;
}
// usual trust-region step quality estimation
costNew = 0.5 * MiscMath.dot(fNew, fNew);
actualReduction = cost - costNew;
double[] updatedTrustRegion = updateTrustRegionRadius(Delta, actualReduction, predictedReduction, stepHnorm, stepHnorm > (0.95 * Delta));
double DeltaNew = updatedTrustRegion[0];
double ratio = updatedTrustRegion[1];
terminationStatus = checkTermination(actualReduction, cost, stepHnorm, MiscMath.norm(hA), ratio);
if (terminationStatus != 0)
{
break;
}
alpha *= Delta / DeltaNew;
Delta = DeltaNew;
System.out.println(String.format("actualReduction: %1.8f, alpha: %1.8f, Delta: %1.8f, termination_status: %d, cost_new: %1.8f", actualReduction, alpha, Delta, terminationStatus, costNew));
//break;
}
System.out.println(String.format("actualReduction before check: %1.8f", actualReduction));
if (actualReduction > 0)
{
hA = xNew;
f0 = fNew;
cost = costNew;
J = approximateDerivative(repMatrix, scoresOld, index);
System.out.println("J in the end");
J.print(System.out, "%1.8f ");
njev++;
g = J.transpose().sumProduct(f0);
} else {
stepHnorm = 0;
actualReduction = 0;
}
iteration++;
}
System.out.println("into OptimizeResult");
System.out.println("x (hA)");
MiscMath.print(hA, "%1.8f");
System.out.println(String.format("cost: %1.8f", cost));
System.out.println("f0");
MiscMath.print(f0, "%1.8f");
System.out.println("J");
J.print(System.out, "%1.8f ");
System.out.println("g");
MiscMath.print(g, "%1.8f");
System.out.println(String.format("gNorm: %1.8f", gNorm));
System.out.println(String.format("nfev: %d", nfev));
System.out.println(String.format("njev: %d", njev));
System.out.println(String.format("terminationStatus: %d", terminationStatus));
// OptimizeResult(x, cost, f0, J, g, gNorm, 0 in shape x, nfev, njev, terminationStatus)
return hA;
}
/**
* TODO DOCUMENT ME!
* @param repMatrix ~ Matrix containing representative vectors
* @param scoresOld ~ Matrix containing initial observations
* @param index ~ current row index
*
* @return
*/
private double[] leastSquaresOptimisation(MatrixI repMatrix, MatrixI scoresOld, int index)
{
System.out.println("lsq starts!!!");
MatrixI J = approximateDerivative(repMatrix, scoresOld, index);
System.out.println("J");
J.print(System.out, "%1.8f ");
double[] result = trf(repMatrix, scoresOld, index, J);
return result;
}
}