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removed extra comments, unnecessary variables, renaming variables and secondary functions

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This commit is contained in:
Margarita Lashina 2023-06-07 02:52:00 +03:00
parent cac5b513f3
commit 162e37cb2f
6 changed files with 165 additions and 223 deletions
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4
examples/src/main/kotlin/space/kscience/kmath/tensors/LevenbergMarquardt/StaticLm/staticDifficultTest.kt
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@ -49,9 +49,6 @@ fun main() {
p_min = p_min.div(1.0 / -50.0) p_min = p_min.div(1.0 / -50.0)
val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1))) val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / 50.0) p_min = p_min.div(1.0 / 50.0)
val consts = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.0)
).as2D()
val opts = doubleArrayOf(3.0, 10000.0, 1e-6, 1e-6, 1e-6, 1e-6, 1e-2, 11.0, 9.0, 1.0) val opts = doubleArrayOf(3.0, 10000.0, 1e-6, 1e-6, 1e-6, 1e-6, 1e-2, 11.0, 9.0, 1.0)
// val opts = doubleArrayOf(3.0, 10000.0, 1e-6, 1e-6, 1e-6, 1e-6, 1e-3, 11.0, 9.0, 1.0) // val opts = doubleArrayOf(3.0, 10000.0, 1e-6, 1e-6, 1e-6, 1e-6, 1e-3, 11.0, 9.0, 1.0)
@ -64,7 +61,6 @@ fun main() {
dp, dp,
p_min.as2D(), p_min.as2D(),
p_max.as2D(), p_max.as2D(),
consts,
opts, opts,
10, 10,
1 1

1
examples/src/main/kotlin/space/kscience/kmath/tensors/LevenbergMarquardt/StaticLm/staticEasyTest.kt
View File

@ -27,7 +27,6 @@ fun main() {
startedData.dp, startedData.dp,
startedData.p_min, startedData.p_min,
startedData.p_max, startedData.p_max,
startedData.consts,
startedData.opts, startedData.opts,
10, 10,
startedData.example_number startedData.example_number

4
examples/src/main/kotlin/space/kscience/kmath/tensors/LevenbergMarquardt/StaticLm/staticMiddleTest.kt
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@ -48,9 +48,6 @@ fun main() {
p_min = p_min.div(1.0 / -50.0) p_min = p_min.div(1.0 / -50.0)
val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1))) val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / 50.0) p_min = p_min.div(1.0 / 50.0)
val consts = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.0)
).as2D()
val opts = doubleArrayOf(3.0, 7000.0, 1e-5, 1e-5, 1e-5, 1e-5, 1e-5, 11.0, 9.0, 1.0) val opts = doubleArrayOf(3.0, 7000.0, 1e-5, 1e-5, 1e-5, 1e-5, 1e-5, 11.0, 9.0, 1.0)
val result = DoubleTensorAlgebra.lm( val result = DoubleTensorAlgebra.lm(
@ -62,7 +59,6 @@ fun main() {
dp, dp,
p_min.as2D(), p_min.as2D(),
p_max.as2D(), p_max.as2D(),
consts,
opts, opts,
10, 10,
1 1

2
examples/src/main/kotlin/space/kscience/kmath/tensors/LevenbergMarquardt/StreamingLm/streamLm.kt
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@ -26,7 +26,6 @@ fun streamLm(lm_func: KFunction3<MutableStructure2D<Double>, MutableStructure2D<
val dp = startData.dp val dp = startData.dp
val p_min = startData.p_min val p_min = startData.p_min
val p_max = startData.p_max val p_max = startData.p_max
val consts = startData.consts
val opts = startData.opts val opts = startData.opts
var steps = numberOfLaunches var steps = numberOfLaunches
@ -42,7 +41,6 @@ fun streamLm(lm_func: KFunction3<MutableStructure2D<Double>, MutableStructure2D<
dp, dp,
p_min, p_min,
p_max, p_max,
consts,
opts, opts,
10, 10,
example_number example_number

345
kmath-tensors/src/commonMain/kotlin/space/kscience/kmath/tensors/core/LevenbergMarquardtAlgorithm.kt
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@ -31,7 +31,7 @@ import kotlin.reflect.KFunction3
* InReducedChiSquare: chi-squared convergence achieved * InReducedChiSquare: chi-squared convergence achieved
* (chi squared value divided by (m - n + 1) < epsilon2 = opts[4], * (chi squared value divided by (m - n + 1) < epsilon2 = opts[4],
* where n - number of parameters, m - amount of points * where n - number of parameters, m - amount of points
* NoConvergence: the maximum number of iterations has been reached without reaching convergence * NoConvergence: the maximum number of iterations has been reached without reaching any convergence
*/ */
public enum class TypeOfConvergence{ public enum class TypeOfConvergence{
InGradient, InGradient,
@ -61,172 +61,141 @@ public data class LMResultInfo (
public fun DoubleTensorAlgebra.lm( public fun DoubleTensorAlgebra.lm(
func: KFunction3<MutableStructure2D<Double>, MutableStructure2D<Double>, Int, MutableStructure2D<Double>>, func: KFunction3<MutableStructure2D<Double>, MutableStructure2D<Double>, Int, MutableStructure2D<Double>>,
p_input: MutableStructure2D<Double>, t_input: MutableStructure2D<Double>, y_dat_input: MutableStructure2D<Double>, pInput: MutableStructure2D<Double>, tInput: MutableStructure2D<Double>, yDatInput: MutableStructure2D<Double>,
weight_input: MutableStructure2D<Double>, dp_input: MutableStructure2D<Double>, p_min_input: MutableStructure2D<Double>, p_max_input: MutableStructure2D<Double>, weightInput: MutableStructure2D<Double>, dpInput: MutableStructure2D<Double>, pMinInput: MutableStructure2D<Double>,
c_input: MutableStructure2D<Double>, opts_input: DoubleArray, nargin: Int, example_number: Int): LMResultInfo { pMaxInput: MutableStructure2D<Double>, optsInput: DoubleArray, nargin: Int, exampleNumber: Int): LMResultInfo {
val resultInfo = LMResultInfo(0, 0, 0.0, val resultInfo = LMResultInfo(0, 0, 0.0,
0.0, p_input, TypeOfConvergence.NoConvergence) 0.0, pInput, TypeOfConvergence.NoConvergence)
val eps:Double = 2.2204e-16 val eps = 2.2204e-16
val settings = LMSettings(0, 0, example_number) val settings = LMSettings(0, 0, exampleNumber)
settings.funcCalls = 0 // running count of function evaluations settings.funcCalls = 0 // running count of function evaluations
var p = p_input var p = pInput
val y_dat = y_dat_input val t = tInput
val t = t_input
val Npar = length(p) // number of parameters val Npar = length(p) // number of parameters
val Npnt = length(y_dat) // number of data points val Npnt = length(yDatInput) // number of data points
var p_old = zeros(ShapeND(intArrayOf(Npar, 1))).as2D() // previous set of parameters var pOld = zeros(ShapeND(intArrayOf(Npar, 1))).as2D() // previous set of parameters
var y_old = zeros(ShapeND(intArrayOf(Npnt, 1))).as2D() // previous model, y_old = y_hat(t;p_old) var yOld = zeros(ShapeND(intArrayOf(Npnt, 1))).as2D() // previous model, y_old = y_hat(t;p_old)
var X2 = 1e-3 / eps // a really big initial Chi-sq value var X2 = 1e-3 / eps // a really big initial Chi-sq value
var X2_old = 1e-3 / eps // a really big initial Chi-sq value var X2Old = 1e-3 / eps // a really big initial Chi-sq value
var J = zeros(ShapeND(intArrayOf(Npnt, Npar))).as2D() // Jacobian matrix var J = zeros(ShapeND(intArrayOf(Npnt, Npar))).as2D() // Jacobian matrix
val DoF = Npnt - Npar // statistical degrees of freedom val DoF = Npnt - Npar // statistical degrees of freedom
var corr_p = 0 var weight = weightInput
var sigma_p = 0
var sigma_y = 0
var R_sq = 0
var cvg_hist = 0
if (length(t) != length(y_dat)) {
// println("lm.m error: the length of t must equal the length of y_dat")
val length_t = length(t)
val length_y_dat = length(y_dat)
X2 = 0.0
corr_p = 0
sigma_p = 0
sigma_y = 0
R_sq = 0
cvg_hist = 0
}
var weight = weight_input
if (nargin < 5) { if (nargin < 5) {
weight = fromArray(ShapeND(intArrayOf(1, 1)), doubleArrayOf((y_dat.transpose().dot(y_dat)).as1D()[0])).as2D() weight = fromArray(ShapeND(intArrayOf(1, 1)), doubleArrayOf((yDatInput.transpose().dot(yDatInput)).as1D()[0])).as2D()
} }
var dp = dp_input var dp = dpInput
if (nargin < 6) { if (nargin < 6) {
dp = fromArray(ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.001)).as2D() dp = fromArray(ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.001)).as2D()
} }
var p_min = p_min_input var pMin = pMinInput
if (nargin < 7) { if (nargin < 7) {
p_min = p pMin = p
p_min.abs() pMin.abs()
p_min = p_min.div(-100.0).as2D() pMin = pMin.div(-100.0).as2D()
} }
var p_max = p_max_input var pMax = pMaxInput
if (nargin < 8) { if (nargin < 8) {
p_max = p pMax = p
p_max.abs() pMax.abs()
p_max = p_max.div(100.0).as2D() pMax = pMax.div(100.0).as2D()
} }
var c = c_input var opts = optsInput
if (nargin < 9) {
c = fromArray(ShapeND(intArrayOf(1, 1)), doubleArrayOf(1.0)).as2D()
}
var opts = opts_input
if (nargin < 10) { if (nargin < 10) {
opts = doubleArrayOf(3.0, 10.0 * Npar, 1e-3, 1e-3, 1e-1, 1e-1, 1e-2, 11.0, 9.0, 1.0) opts = doubleArrayOf(3.0, 10.0 * Npar, 1e-3, 1e-3, 1e-1, 1e-1, 1e-2, 11.0, 9.0, 1.0)
} }
val prnt = opts[0] // >1 intermediate results; >2 plots val prnt = opts[0] // >1 intermediate results; >2 plots
val MaxIter = opts[1].toInt() // maximum number of iterations val maxIterations = opts[1].toInt() // maximum number of iterations
val epsilon_1 = opts[2] // convergence tolerance for gradient val epsilon1 = opts[2] // convergence tolerance for gradient
val epsilon_2 = opts[3] // convergence tolerance for parameters val epsilon2 = opts[3] // convergence tolerance for parameters
val epsilon_3 = opts[4] // convergence tolerance for Chi-square val epsilon3 = opts[4] // convergence tolerance for Chi-square
val epsilon_4 = opts[5] // determines acceptance of a L-M step val epsilon4 = opts[5] // determines acceptance of a L-M step
val lambda_0 = opts[6] // initial value of damping paramter, lambda val lambda0 = opts[6] // initial value of damping paramter, lambda
val lambda_UP_fac = opts[7] // factor for increasing lambda val lambdaUpFac = opts[7] // factor for increasing lambda
val lambda_DN_fac = opts[8] // factor for decreasing lambda val lambdaDnFac = opts[8] // factor for decreasing lambda
val Update_Type = opts[9].toInt() // 1: Levenberg-Marquardt lambda update val updateType = opts[9].toInt() // 1: Levenberg-Marquardt lambda update
// 2: Quadratic update // 2: Quadratic update
// 3: Nielsen's lambda update equations // 3: Nielsen's lambda update equations
p_min = make_column(p_min) pMin = makeColumn(pMin)
p_max = make_column(p_max) pMax = makeColumn(pMax)
if (length(make_column(dp)) == 1) { if (length(makeColumn(dp)) == 1) {
dp = ones(ShapeND(intArrayOf(Npar, 1))).div(1 / dp[0, 0]).as2D() dp = ones(ShapeND(intArrayOf(Npar, 1))).div(1 / dp[0, 0]).as2D()
} }
val idx = get_zero_indices(dp) // indices of the parameters to be fit
val Nfit = idx?.shape?.component1() // number of parameters to fit
var stop = false // termination flag var stop = false // termination flag
val y_init = feval(func, t, p, example_number) // residual error using p_try
if (weight.shape.component1() == 1 || variance(weight) == 0.0) { // identical weights vector if (weight.shape.component1() == 1 || variance(weight) == 0.0) { // identical weights vector
weight = ones(ShapeND(intArrayOf(Npnt, 1))).div(1 / kotlin.math.abs(weight[0, 0])).as2D() weight = ones(ShapeND(intArrayOf(Npnt, 1))).div(1 / kotlin.math.abs(weight[0, 0])).as2D()
// println("using uniform weights for error analysis")
} }
else { else {
weight = make_column(weight) weight = makeColumn(weight)
weight.abs() weight.abs()
} }
// initialize Jacobian with finite difference calculation // initialize Jacobian with finite difference calculation
var lm_matx_ans = lm_matx(func, t, p_old, y_old,1, J, p, y_dat, weight, dp, settings) var lmMatxAns = lmMatx(func, t, pOld, yOld, 1, J, p, yDatInput, weight, dp, settings)
var JtWJ = lm_matx_ans[0] var JtWJ = lmMatxAns[0]
var JtWdy = lm_matx_ans[1] var JtWdy = lmMatxAns[1]
X2 = lm_matx_ans[2][0, 0] X2 = lmMatxAns[2][0, 0]
var y_hat = lm_matx_ans[3] var yHat = lmMatxAns[3]
J = lm_matx_ans[4] J = lmMatxAns[4]
if ( abs(JtWdy).max()!! < epsilon_1 ) { if ( abs(JtWdy).max() < epsilon1 ) {
// println(" *** Your Initial Guess is Extremely Close to Optimal ***\n")
// println(" *** epsilon_1 = %e\n$epsilon_1")
stop = true stop = true
} }
var lambda = 1.0 var lambda = 1.0
var nu = 1 var nu = 1
when (Update_Type) { when (updateType) {
1 -> lambda = lambda_0 // Marquardt: init'l lambda 1 -> lambda = lambda0 // Marquardt: init'l lambda
else -> { // Quadratic and Nielsen else -> { // Quadratic and Nielsen
lambda = lambda_0 * (diag(JtWJ)).max()!! lambda = lambda0 * (makeColumnFromDiagonal(JtWJ)).max()!!
nu = 2 nu = 2
} }
} }
X2_old = X2 // previous value of X2 X2Old = X2 // previous value of X2
var cvg_hst = ones(ShapeND(intArrayOf(MaxIter, Npar + 3))) // initialize convergence history
var h: DoubleTensor var h: DoubleTensor
var dX2 = X2
while (!stop && settings.iteration <= MaxIter) { //--- Start Main Loop while (!stop && settings.iteration <= maxIterations) { //--- Start Main Loop
settings.iteration += 1 settings.iteration += 1
// incremental change in parameters // incremental change in parameters
h = when (Update_Type) { h = when (updateType) {
1 -> { // Marquardt 1 -> { // Marquardt
val solve = solve(JtWJ.plus(make_matrx_with_diagonal(diag(JtWJ)).div(1 / lambda)).as2D(), JtWdy) val solve =
solve(JtWJ.plus(makeMatrixWithDiagonal(makeColumnFromDiagonal(JtWJ)).div(1 / lambda)).as2D(), JtWdy)
solve.asDoubleTensor() solve.asDoubleTensor()
} }
else -> { // Quadratic and Nielsen else -> { // Quadratic and Nielsen
val solve = solve(JtWJ.plus(lm_eye(Npar).div(1 / lambda)).as2D(), JtWdy) val solve = solve(JtWJ.plus(lmEye(Npar).div(1 / lambda)).as2D(), JtWdy)
solve.asDoubleTensor() solve.asDoubleTensor()
} }
} }
var p_try = (p + h).as2D() // update the [idx] elements var pTry = (p + h).as2D() // update the [idx] elements
p_try = smallest_element_comparison(largest_element_comparison(p_min, p_try.as2D()), p_max) // apply constraints pTry = smallestElementComparison(largestElementComparison(pMin, pTry.as2D()), pMax) // apply constraints
var delta_y = y_dat.minus(feval(func, t, p_try, example_number)) // residual error using p_try var deltaY = yDatInput.minus(evaluateFunction(func, t, pTry, exampleNumber)) // residual error using p_try
for (i in 0 until delta_y.shape.component1()) { // floating point error; break for (i in 0 until deltaY.shape.component1()) { // floating point error; break
for (j in 0 until delta_y.shape.component2()) { for (j in 0 until deltaY.shape.component2()) {
if (delta_y[i, j] == Double.POSITIVE_INFINITY || delta_y[i, j] == Double.NEGATIVE_INFINITY) { if (deltaY[i, j] == Double.POSITIVE_INFINITY || deltaY[i, j] == Double.NEGATIVE_INFINITY) {
stop = true stop = true
break break
} }
@ -235,84 +204,87 @@ public fun DoubleTensorAlgebra.lm(
settings.funcCalls += 1 settings.funcCalls += 1
val tmp = delta_y.times(weight) val tmp = deltaY.times(weight)
var X2_try = delta_y.as2D().transpose().dot(tmp) // Chi-squared error criteria var X2Try = deltaY.as2D().transpose().dot(tmp) // Chi-squared error criteria
val alpha = 1.0 val alpha = 1.0
if (Update_Type == 2) { // Quadratic if (updateType == 2) { // Quadratic
// One step of quadratic line update in the h direction for minimum X2 // One step of quadratic line update in the h direction for minimum X2
val alpha = JtWdy.transpose().dot(h) / ( (X2_try.minus(X2)).div(2.0).plus(2 * JtWdy.transpose().dot(h)) ) val alpha = JtWdy.transpose().dot(h) / ((X2Try.minus(X2)).div(2.0).plus(2 * JtWdy.transpose().dot(h)))
h = h.dot(alpha) h = h.dot(alpha)
p_try = p.plus(h).as2D() // update only [idx] elements pTry = p.plus(h).as2D() // update only [idx] elements
p_try = smallest_element_comparison(largest_element_comparison(p_min, p_try), p_max) // apply constraints pTry = smallestElementComparison(largestElementComparison(pMin, pTry), pMax) // apply constraints
var delta_y = y_dat.minus(feval(func, t, p_try, example_number)) // residual error using p_try deltaY = yDatInput.minus(evaluateFunction(func, t, pTry, exampleNumber)) // residual error using p_try
settings.funcCalls += 1 settings.funcCalls += 1
val tmp = delta_y.times(weight) X2Try = deltaY.as2D().transpose().dot(deltaY.times(weight)) // Chi-squared error criteria
X2_try = delta_y.as2D().transpose().dot(tmp) // Chi-squared error criteria
} }
val rho = when (Update_Type) { // Nielsen val rho = when (updateType) { // Nielsen
1 -> { 1 -> {
val tmp = h.transposed().dot(make_matrx_with_diagonal(diag(JtWJ)).div(1 / lambda).dot(h).plus(JtWdy)) val tmp = h.transposed()
X2.minus(X2_try).as2D()[0, 0] / abs(tmp.as2D()).as2D()[0, 0] .dot(makeMatrixWithDiagonal(makeColumnFromDiagonal(JtWJ)).div(1 / lambda).dot(h).plus(JtWdy))
X2.minus(X2Try).as2D()[0, 0] / abs(tmp.as2D()).as2D()[0, 0]
} }
else -> { else -> {
val tmp = h.transposed().dot(h.div(1 / lambda).plus(JtWdy)) val tmp = h.transposed().dot(h.div(1 / lambda).plus(JtWdy))
X2.minus(X2_try).as2D()[0, 0] / abs(tmp.as2D()).as2D()[0, 0] X2.minus(X2Try).as2D()[0, 0] / abs(tmp.as2D()).as2D()[0, 0]
} }
} }
if (rho > epsilon_4) { // it IS significantly better if (rho > epsilon4) { // it IS significantly better
val dX2 = X2.minus(X2_old) val dX2 = X2.minus(X2Old)
X2_old = X2 X2Old = X2
p_old = p.copyToTensor().as2D() pOld = p.copyToTensor().as2D()
y_old = y_hat.copyToTensor().as2D() yOld = yHat.copyToTensor().as2D()
p = make_column(p_try) // accept p_try p = makeColumn(pTry) // accept p_try
lm_matx_ans = lm_matx(func, t, p_old, y_old, dX2.toInt(), J, p, y_dat, weight, dp, settings) lmMatxAns = lmMatx(func, t, pOld, yOld, dX2.toInt(), J, p, yDatInput, weight, dp, settings)
// decrease lambda ==> Gauss-Newton method // decrease lambda ==> Gauss-Newton method
JtWJ = lm_matx_ans[0] JtWJ = lmMatxAns[0]
JtWdy = lm_matx_ans[1] JtWdy = lmMatxAns[1]
X2 = lm_matx_ans[2][0, 0] X2 = lmMatxAns[2][0, 0]
y_hat = lm_matx_ans[3] yHat = lmMatxAns[3]
J = lm_matx_ans[4] J = lmMatxAns[4]
lambda = when (Update_Type) { lambda = when (updateType) {
1 -> { // Levenberg 1 -> { // Levenberg
max(lambda / lambda_DN_fac, 1e-7); max(lambda / lambdaDnFac, 1e-7);
} }
2 -> { // Quadratic 2 -> { // Quadratic
max(lambda / (1 + alpha), 1e-7); max(lambda / (1 + alpha), 1e-7);
} }
else -> { // Nielsen else -> { // Nielsen
nu = 2 nu = 2
lambda * max(1.0 / 3, 1 - (2 * rho - 1).pow(3)) lambda * max(1.0 / 3, 1 - (2 * rho - 1).pow(3))
} }
} }
} } else { // it IS NOT better
else { // it IS NOT better X2 = X2Old // do not accept p_try
X2 = X2_old // do not accept p_try
if (settings.iteration % (2 * Npar) == 0) { // rank-1 update of Jacobian if (settings.iteration % (2 * Npar) == 0) { // rank-1 update of Jacobian
lm_matx_ans = lm_matx(func, t, p_old, y_old,-1, J, p, y_dat, weight, dp, settings) lmMatxAns = lmMatx(func, t, pOld, yOld, -1, J, p, yDatInput, weight, dp, settings)
JtWJ = lm_matx_ans[0] JtWJ = lmMatxAns[0]
JtWdy = lm_matx_ans[1] JtWdy = lmMatxAns[1]
dX2 = lm_matx_ans[2][0, 0] yHat = lmMatxAns[3]
y_hat = lm_matx_ans[3] J = lmMatxAns[4]
J = lm_matx_ans[4]
} }
// increase lambda ==> gradient descent method // increase lambda ==> gradient descent method
lambda = when (Update_Type) { lambda = when (updateType) {
1 -> { // Levenberg 1 -> { // Levenberg
min(lambda * lambda_UP_fac, 1e7) min(lambda * lambdaUpFac, 1e7)
} }
2 -> { // Quadratic 2 -> { // Quadratic
lambda + kotlin.math.abs(((X2_try.as2D()[0, 0] - X2) / 2) / alpha) lambda + kotlin.math.abs(((X2Try.as2D()[0, 0] - X2) / 2) / alpha)
} }
else -> { // Nielsen else -> { // Nielsen
nu *= 2 nu *= 2
lambda * (nu / 2) lambda * (nu / 2)
@ -321,30 +293,27 @@ public fun DoubleTensorAlgebra.lm(
} }
if (prnt > 1) { if (prnt > 1) {
val chi_sq = X2 / DoF val chiSq = X2 / DoF
resultInfo.iterations = settings.iteration resultInfo.iterations = settings.iteration
resultInfo.funcCalls = settings.funcCalls resultInfo.funcCalls = settings.funcCalls
resultInfo.resultChiSq = chi_sq resultInfo.resultChiSq = chiSq
resultInfo.resultLambda = lambda resultInfo.resultLambda = lambda
resultInfo.resultParameters = p resultInfo.resultParameters = p
} }
// update convergence history ... save _reduced_ Chi-square if (abs(JtWdy).max() < epsilon1 && settings.iteration > 2) {
// cvg_hst(iteration,:) = [ func_calls p' X2/DoF lambda ];
if (abs(JtWdy).max()!! < epsilon_1 && settings.iteration > 2) {
resultInfo.typeOfConvergence = TypeOfConvergence.InGradient resultInfo.typeOfConvergence = TypeOfConvergence.InGradient
stop = true stop = true
} }
if ((abs(h.as2D()).div(abs(p) + 1e-12)).max() < epsilon_2 && settings.iteration > 2) { if ((abs(h.as2D()).div(abs(p) + 1e-12)).max() < epsilon2 && settings.iteration > 2) {
resultInfo.typeOfConvergence = TypeOfConvergence.InParameters resultInfo.typeOfConvergence = TypeOfConvergence.InParameters
stop = true stop = true
} }
if (X2 / DoF < epsilon_3 && settings.iteration > 2) { if (X2 / DoF < epsilon3 && settings.iteration > 2) {
resultInfo.typeOfConvergence = TypeOfConvergence.InReducedChiSquare resultInfo.typeOfConvergence = TypeOfConvergence.InReducedChiSquare
stop = true stop = true
} }
if (settings.iteration == MaxIter) { if (settings.iteration == maxIterations) {
resultInfo.typeOfConvergence = TypeOfConvergence.NoConvergence resultInfo.typeOfConvergence = TypeOfConvergence.NoConvergence
stop = true stop = true
} }
@ -358,8 +327,8 @@ private data class LMSettings (
var exampleNumber:Int var exampleNumber:Int
) )
/* matrix -> column of all elemnets */ /* matrix -> column of all elements */
private fun make_column(tensor: MutableStructure2D<Double>) : MutableStructure2D<Double> { private fun makeColumn(tensor: MutableStructure2D<Double>): MutableStructure2D<Double> {
val shape = intArrayOf(tensor.shape.component1() * tensor.shape.component2(), 1) val shape = intArrayOf(tensor.shape.component1() * tensor.shape.component2(), 1)
val buffer = DoubleArray(tensor.shape.component1() * tensor.shape.component2()) val buffer = DoubleArray(tensor.shape.component1() * tensor.shape.component2())
for (i in 0 until tensor.shape.component1()) { for (i in 0 until tensor.shape.component1()) {
@ -367,8 +336,7 @@ private fun make_column(tensor: MutableStructure2D<Double>) : MutableStructure2D
buffer[i * tensor.shape.component2() + j] = tensor[i, j] buffer[i * tensor.shape.component2() + j] = tensor[i, j]
} }
} }
val column = BroadcastDoubleTensorAlgebra.fromArray(ShapeND(shape), buffer).as2D() return BroadcastDoubleTensorAlgebra.fromArray(ShapeND(shape), buffer).as2D()
return column
} }
/* column length */ /* column length */
@ -401,7 +369,7 @@ private fun abs(input: MutableStructure2D<Double>): MutableStructure2D<Double> {
return tensor return tensor
} }
private fun diag(input: MutableStructure2D<Double>): MutableStructure2D<Double> { private fun makeColumnFromDiagonal(input: MutableStructure2D<Double>): MutableStructure2D<Double> {
val tensor = BroadcastDoubleTensorAlgebra.ones(ShapeND(intArrayOf(input.shape.component1(), 1))).as2D() val tensor = BroadcastDoubleTensorAlgebra.ones(ShapeND(intArrayOf(input.shape.component1(), 1))).as2D()
for (i in 0 until tensor.shape.component1()) { for (i in 0 until tensor.shape.component1()) {
tensor[i, 0] = input[i, i] tensor[i, 0] = input[i, i]
@ -409,7 +377,7 @@ private fun diag(input: MutableStructure2D<Double>): MutableStructure2D<Double>
return tensor return tensor
} }
private fun make_matrx_with_diagonal(column: MutableStructure2D<Double>): MutableStructure2D<Double> { private fun makeMatrixWithDiagonal(column: MutableStructure2D<Double>): MutableStructure2D<Double> {
val size = column.shape.component1() val size = column.shape.component1()
val tensor = BroadcastDoubleTensorAlgebra.zeros(ShapeND(intArrayOf(size, size))).as2D() val tensor = BroadcastDoubleTensorAlgebra.zeros(ShapeND(intArrayOf(size, size))).as2D()
for (i in 0 until size) { for (i in 0 until size) {
@ -418,23 +386,23 @@ private fun make_matrx_with_diagonal(column: MutableStructure2D<Double>): Mutabl
return tensor return tensor
} }
private fun lm_eye(size: Int): MutableStructure2D<Double> { private fun lmEye(size: Int): MutableStructure2D<Double> {
val column = BroadcastDoubleTensorAlgebra.ones(ShapeND(intArrayOf(size, 1))).as2D() val column = BroadcastDoubleTensorAlgebra.ones(ShapeND(intArrayOf(size, 1))).as2D()
return make_matrx_with_diagonal(column) return makeMatrixWithDiagonal(column)
} }
private fun largest_element_comparison(a: MutableStructure2D<Double>, b: MutableStructure2D<Double>): MutableStructure2D<Double> { private fun largestElementComparison(a: MutableStructure2D<Double>, b: MutableStructure2D<Double>): MutableStructure2D<Double> {
val a_sizeX = a.shape.component1() val aSizeX = a.shape.component1()
val a_sizeY = a.shape.component2() val aSizeY = a.shape.component2()
val b_sizeX = b.shape.component1() val bSizeX = b.shape.component1()
val b_sizeY = b.shape.component2() val bSizeY = b.shape.component2()
val tensor = BroadcastDoubleTensorAlgebra.zeros(ShapeND(intArrayOf(max(a_sizeX, b_sizeX), max(a_sizeY, b_sizeY)))).as2D() val tensor = BroadcastDoubleTensorAlgebra.zeros(ShapeND(intArrayOf(max(aSizeX, bSizeX), max(aSizeY, bSizeY)))).as2D()
for (i in 0 until tensor.shape.component1()) { for (i in 0 until tensor.shape.component1()) {
for (j in 0 until tensor.shape.component2()) { for (j in 0 until tensor.shape.component2()) {
if (i < a_sizeX && i < b_sizeX && j < a_sizeY && j < b_sizeY) { if (i < aSizeX && i < bSizeX && j < aSizeY && j < bSizeY) {
tensor[i, j] = max(a[i, j], b[i, j]) tensor[i, j] = max(a[i, j], b[i, j])
} }
else if (i < a_sizeX && j < a_sizeY) { else if (i < aSizeX && j < aSizeY) {
tensor[i, j] = a[i, j] tensor[i, j] = a[i, j]
} }
else { else {
@ -445,18 +413,18 @@ private fun largest_element_comparison(a: MutableStructure2D<Double>, b: Mutable
return tensor return tensor
} }
private fun smallest_element_comparison(a: MutableStructure2D<Double>, b: MutableStructure2D<Double>): MutableStructure2D<Double> { private fun smallestElementComparison(a: MutableStructure2D<Double>, b: MutableStructure2D<Double>): MutableStructure2D<Double> {
val a_sizeX = a.shape.component1() val aSizeX = a.shape.component1()
val a_sizeY = a.shape.component2() val aSizeY = a.shape.component2()
val b_sizeX = b.shape.component1() val bSizeX = b.shape.component1()
val b_sizeY = b.shape.component2() val bSizeY = b.shape.component2()
val tensor = BroadcastDoubleTensorAlgebra.zeros(ShapeND(intArrayOf(max(a_sizeX, b_sizeX), max(a_sizeY, b_sizeY)))).as2D() val tensor = BroadcastDoubleTensorAlgebra.zeros(ShapeND(intArrayOf(max(aSizeX, bSizeX), max(aSizeY, bSizeY)))).as2D()
for (i in 0 until tensor.shape.component1()) { for (i in 0 until tensor.shape.component1()) {
for (j in 0 until tensor.shape.component2()) { for (j in 0 until tensor.shape.component2()) {
if (i < a_sizeX && i < b_sizeX && j < a_sizeY && j < b_sizeY) { if (i < aSizeX && i < bSizeX && j < aSizeY && j < bSizeY) {
tensor[i, j] = min(a[i, j], b[i, j]) tensor[i, j] = min(a[i, j], b[i, j])
} }
else if (i < a_sizeX && j < a_sizeY) { else if (i < aSizeX && j < aSizeY) {
tensor[i, j] = a[i, j] tensor[i, j] = a[i, j]
} }
else { else {
@ -467,69 +435,67 @@ private fun smallest_element_comparison(a: MutableStructure2D<Double>, b: Mutabl
return tensor return tensor
} }
private fun get_zero_indices(column: MutableStructure2D<Double>, epsilon: Double = 0.000001): MutableStructure2D<Double>? { private fun getZeroIndices(column: MutableStructure2D<Double>, epsilon: Double = 0.000001): MutableStructure2D<Double>? {
var idx = emptyArray<Double>() var idx = emptyArray<Double>()
for (i in 0 until column.shape.component1()) { for (i in 0 until column.shape.component1()) {
if (kotlin.math.abs(column[i, 0]) > epsilon) { if (kotlin.math.abs(column[i, 0]) > epsilon) {
idx += (i + 1.0) idx += (i + 1.0)
} }
} }
if (idx.size > 0) { if (idx.isNotEmpty()) {
return BroadcastDoubleTensorAlgebra.fromArray(ShapeND(intArrayOf(idx.size, 1)), idx.toDoubleArray()).as2D() return BroadcastDoubleTensorAlgebra.fromArray(ShapeND(intArrayOf(idx.size, 1)), idx.toDoubleArray()).as2D()
} }
return null return null
} }
private fun feval(func: (MutableStructure2D<Double>, MutableStructure2D<Double>, Int) -> MutableStructure2D<Double>, private fun evaluateFunction(func: (MutableStructure2D<Double>, MutableStructure2D<Double>, Int) -> MutableStructure2D<Double>,
t: MutableStructure2D<Double>, p: MutableStructure2D<Double>, exampleNumber: Int) t: MutableStructure2D<Double>, p: MutableStructure2D<Double>, exampleNumber: Int)
: MutableStructure2D<Double> : MutableStructure2D<Double>
{ {
return func(t, p, exampleNumber) return func(t, p, exampleNumber)
} }
private fun lm_matx(func: (MutableStructure2D<Double>, MutableStructure2D<Double>, Int) -> MutableStructure2D<Double>, private fun lmMatx(func: (MutableStructure2D<Double>, MutableStructure2D<Double>, Int) -> MutableStructure2D<Double>,
t: MutableStructure2D<Double>, p_old: MutableStructure2D<Double>, y_old: MutableStructure2D<Double>, t: MutableStructure2D<Double>, pOld: MutableStructure2D<Double>, yOld: MutableStructure2D<Double>,
dX2: Int, J_input: MutableStructure2D<Double>, p: MutableStructure2D<Double>, dX2: Int, JInput: MutableStructure2D<Double>, p: MutableStructure2D<Double>,
y_dat: MutableStructure2D<Double>, weight: MutableStructure2D<Double>, dp:MutableStructure2D<Double>, settings:LMSettings) : Array<MutableStructure2D<Double>> yDat: MutableStructure2D<Double>, weight: MutableStructure2D<Double>, dp:MutableStructure2D<Double>, settings:LMSettings) : Array<MutableStructure2D<Double>>
{ {
// default: dp = 0.001 // default: dp = 0.001
val Npnt = length(y_dat) // number of data points
val Npar = length(p) // number of parameters val Npar = length(p) // number of parameters
val y_hat = feval(func, t, p, settings.exampleNumber) // evaluate model using parameters 'p' val yHat = evaluateFunction(func, t, p, settings.exampleNumber) // evaluate model using parameters 'p'
settings.funcCalls += 1 settings.funcCalls += 1
var J = J_input var J = JInput
if (settings.iteration % (2 * Npar) == 0 || dX2 > 0) { J = if (settings.iteration % (2 * Npar) == 0 || dX2 > 0) {
J = lm_FD_J(func, t, p, y_hat, dp, settings).as2D() // finite difference lmFdJ(func, t, p, yHat, dp, settings).as2D() // finite difference
} }
else { else {
J = lm_Broyden_J(p_old, y_old, J, p, y_hat).as2D() // rank-1 update lmBroydenJ(pOld, yOld, J, p, yHat).as2D() // rank-1 update
} }
val delta_y = y_dat.minus(y_hat) val deltaY = yDat.minus(yHat)
val Chi_sq = delta_y.transposed().dot( delta_y.times(weight) ).as2D() val chiSq = deltaY.transposed().dot( deltaY.times(weight) ).as2D()
val JtWJ = J.transposed().dot ( J.times( weight.dot(BroadcastDoubleTensorAlgebra.ones(ShapeND(intArrayOf(1, Npar)))) ) ).as2D() val JtWJ = J.transposed().dot ( J.times( weight.dot(BroadcastDoubleTensorAlgebra.ones(ShapeND(intArrayOf(1, Npar)))) ) ).as2D()
val JtWdy = J.transposed().dot( weight.times(delta_y) ).as2D() val JtWdy = J.transposed().dot( weight.times(deltaY) ).as2D()
return arrayOf(JtWJ,JtWdy,Chi_sq,y_hat,J) return arrayOf(JtWJ,JtWdy,chiSq,yHat,J)
} }
private fun lm_Broyden_J(p_old: MutableStructure2D<Double>, y_old: MutableStructure2D<Double>, J_input: MutableStructure2D<Double>, private fun lmBroydenJ(pOld: MutableStructure2D<Double>, yOld: MutableStructure2D<Double>, JInput: MutableStructure2D<Double>,
p: MutableStructure2D<Double>, y: MutableStructure2D<Double>): MutableStructure2D<Double> { p: MutableStructure2D<Double>, y: MutableStructure2D<Double>): MutableStructure2D<Double> {
var J = J_input.copyToTensor() var J = JInput.copyToTensor()
val h = p.minus(p_old) val h = p.minus(pOld)
val increase = y.minus(y_old).minus( J.dot(h) ).dot(h.transposed()).div( (h.transposed().dot(h)).as2D()[0, 0] ) val increase = y.minus(yOld).minus( J.dot(h) ).dot(h.transposed()).div( (h.transposed().dot(h)).as2D()[0, 0] )
J = J.plus(increase) J = J.plus(increase)
return J.as2D() return J.as2D()
} }
private fun lm_FD_J(func: (MutableStructure2D<Double>, MutableStructure2D<Double>, exampleNumber: Int) -> MutableStructure2D<Double>, private fun lmFdJ(func: (MutableStructure2D<Double>, MutableStructure2D<Double>, exampleNumber: Int) -> MutableStructure2D<Double>,
t: MutableStructure2D<Double>, p: MutableStructure2D<Double>, y: MutableStructure2D<Double>, t: MutableStructure2D<Double>, p: MutableStructure2D<Double>, y: MutableStructure2D<Double>,
dp: MutableStructure2D<Double>, settings: LMSettings): MutableStructure2D<Double> { dp: MutableStructure2D<Double>, settings: LMSettings): MutableStructure2D<Double> {
// default: dp = 0.001 * ones(1,n) // default: dp = 0.001 * ones(1,n)
@ -548,7 +514,7 @@ private fun lm_FD_J(func: (MutableStructure2D<Double>, MutableStructure2D<Double
val epsilon = 0.0000001 val epsilon = 0.0000001
if (kotlin.math.abs(del[j, 0]) > epsilon) { if (kotlin.math.abs(del[j, 0]) > epsilon) {
val y1 = feval(func, t, p, settings.exampleNumber) val y1 = evaluateFunction(func, t, p, settings.exampleNumber)
settings.funcCalls += 1 settings.funcCalls += 1
if (dp[j, 0] < 0) { // backwards difference if (dp[j, 0] < 0) { // backwards difference
@ -558,10 +524,9 @@ private fun lm_FD_J(func: (MutableStructure2D<Double>, MutableStructure2D<Double
} }
else { else {
// Do tests for it // Do tests for it
println("Potential mistake")
p[j, 0] = ps[j, 0] - del[j, 0] // central difference, additional func call p[j, 0] = ps[j, 0] - del[j, 0] // central difference, additional func call
for (i in 0 until J.shape.component1()) { for (i in 0 until J.shape.component1()) {
J[i, j] = (y1.as2D().minus(feval(func, t, p, settings.exampleNumber)).as2D())[i, 0] / (2 * del[j, 0]) J[i, j] = (y1.as2D().minus(evaluateFunction(func, t, p, settings.exampleNumber)).as2D())[i, 0] / (2 * del[j, 0])
} }
settings.funcCalls += 1 settings.funcCalls += 1
} }

14
kmath-tensors/src/commonTest/kotlin/space/kscience/kmath/tensors/core/TestLmAlgorithm.kt
View File

@ -121,13 +121,9 @@ class TestLmAlgorithm {
ShapeND(intArrayOf(4, 1)), doubleArrayOf(50.0, 20.0, 2.0, 100.0) ShapeND(intArrayOf(4, 1)), doubleArrayOf(50.0, 20.0, 2.0, 100.0)
).as2D() ).as2D()
val consts = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.0)
).as2D()
val opts = doubleArrayOf(3.0, 100.0, 1e-3, 1e-3, 1e-1, 1e-1, 1e-2, 11.0, 9.0, 1.0) val opts = doubleArrayOf(3.0, 100.0, 1e-3, 1e-3, 1e-1, 1e-1, 1e-2, 11.0, 9.0, 1.0)
val result = lm(::funcEasyForLm, p_init, t, y_dat, weight, dp, p_min, p_max, consts, opts, 10, example_number) val result = lm(::funcEasyForLm, p_init, t, y_dat, weight, dp, p_min, p_max, opts, 10, example_number)
assertEquals(13, result.iterations) assertEquals(13, result.iterations)
assertEquals(31, result.funcCalls) assertEquals(31, result.funcCalls)
assertEquals(0.9131368192633, (result.resultChiSq * 1e13).roundToLong() / 1e13) assertEquals(0.9131368192633, (result.resultChiSq * 1e13).roundToLong() / 1e13)
@ -182,9 +178,6 @@ class TestLmAlgorithm {
p_min = p_min.div(1.0 / -50.0) p_min = p_min.div(1.0 / -50.0)
val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1))) val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / 50.0) p_min = p_min.div(1.0 / 50.0)
val consts = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.0)
).as2D()
val opts = doubleArrayOf(3.0, 7000.0, 1e-5, 1e-5, 1e-5, 1e-5, 1e-5, 11.0, 9.0, 1.0) val opts = doubleArrayOf(3.0, 7000.0, 1e-5, 1e-5, 1e-5, 1e-5, 1e-5, 11.0, 9.0, 1.0)
val result = DoubleTensorAlgebra.lm( val result = DoubleTensorAlgebra.lm(
@ -196,7 +189,6 @@ class TestLmAlgorithm {
dp, dp,
p_min.as2D(), p_min.as2D(),
p_max.as2D(), p_max.as2D(),
consts,
opts, opts,
10, 10,
1 1
@ -238,9 +230,6 @@ class TestLmAlgorithm {
p_min = p_min.div(1.0 / -50.0) p_min = p_min.div(1.0 / -50.0)
val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1))) val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / 50.0) p_min = p_min.div(1.0 / 50.0)
val consts = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.0)
).as2D()
val opts = doubleArrayOf(3.0, 7000.0, 1e-2, 1e-3, 1e-2, 1e-2, 1e-2, 11.0, 9.0, 1.0) val opts = doubleArrayOf(3.0, 7000.0, 1e-2, 1e-3, 1e-2, 1e-2, 1e-2, 11.0, 9.0, 1.0)
val result = DoubleTensorAlgebra.lm( val result = DoubleTensorAlgebra.lm(
@ -252,7 +241,6 @@ class TestLmAlgorithm {
dp, dp,
p_min.as2D(), p_min.as2D(),
p_max.as2D(), p_max.as2D(),
consts,
opts, opts,
10, 10,
1 1