Binary coded GA with NSGA-II in R - r

I have a multiobjective minimization function. I want to use NSGA-II in R. There are packages for this: nsga2R and mco. But these packages do not support binary coded chromosomes. In my fitness function I need binary chromosomes to achive best solution because of my problem's structure. Is there any way to use binary coded chromosome in nsga2 (or maybe with different algorithm) for R? Thanks.

I got the same problem so I decided to fix it on my own. But no guarentee if it's the right way.
The following part is for the package 'mco'
I copied parts out of the offical nsga2 implementation into the 'mco' package.
This workaround is only for binary (0-1) variables.
1. In /src/nsga2.c rewrite the functions as follows:
static void mutate_ind (nsga2_ctx *ctx, individual *ind) {
int j;
double prob;
GetRNGstate();
for (j = 0; j < ctx->input_dim; j++)
{
//for (k=0; k < ctx[j]->input_dim; k++)
//{
//prob = randomperc();
prob = unif_rand();
if (prob <= ctx->mutation_probability) {
if (ind->input[j] == 0)
{
ind->input[j] = 1;
}
else
{
ind->input[j] = 0;
}
ctx->input_mutations+=1;
}
//}
}
PutRNGstate();
then
static void crossover (nsga2_ctx *ctx,
individual *parent1, individual *parent2,
individual *child1, individual *child2) {
int i;
int nbits=1;
double rand;
int temp, site1, site2, temp2, temp3;
GetRNGstate();
rand=unif_rand();
if (rand <= ctx->crossing_probability)
{
ctx->input_crossings++;
//site1 = rnd(0,ctx->input_dim);
//site2 = rnd(0,ctx->input_dim);
if(unif_rand()<=0.5){
temp2=0;
}else{
temp2=1;
}
if(unif_rand()<=0.5){
temp3=0;
}else{
temp3=1;
}
site1=temp2;
site2=temp3;
if (site1 > site2)
{
temp = site1;
site1 = site2;
site2 = temp;
}
for (i=0; i<site1; i++)
{
child1->input[i] = parent1->input[i];
child2->input[i] = parent2->input[i];
}
for (i=site1; i<site2; i++)
{
child1->input[i] = parent2->input[i];
child2->input[i] = parent1->input[i];
}
for (i=site2; i<nbits; i++)
{
child1->input[i] = parent1->input[i];
child2->input[i] = parent2->input[i];
}
}
else
{
for (i=0; i<nbits; i++)
{
child1->input[i] = parent1->input[i];
child2->input[i] = parent2->input[i];
}
}
PutRNGstate();
}
and
static void population_initialize(nsga2_ctx *ctx, population *pop) {
GetRNGstate();
int i, j;
for (i = 0; i < pop->size; ++i) {
for (j=0; j<ctx->input_dim; ++j) {
/* Generate random value between lower and upper bound */
//double delta = ctx->upper_input_bound[j] - ctx->lower_input_bound[j];
//pop->ind[i].input[j] = ctx->lower_input_bound[j] + delta*unif_rand();
if(unif_rand() <= 0.5){
pop->ind[i].input[j] = 0;
}
else{
pop->ind[i].input[j] = 1;
}
}
}
PutRNGstate();
}
2. define the function randomperc() as follows
double seed;
double oldrand[55];
int jrand;
/* Create next batch of 55 random numbers */
void advance_random ()
{
int j1;
double new_random;
for(j1=0; j1<24; j1++)
{
new_random = oldrand[j1]-oldrand[j1+31];
if(new_random<0.0)
{
new_random = new_random+1.0;
}
oldrand[j1] = new_random;
}
for(j1=24; j1<55; j1++)
{
new_random = oldrand[j1]-oldrand[j1-24];
if(new_random<0.0)
{
new_random = new_random+1.0;
}
oldrand[j1] = new_random;
}
}
/* Fetch a single random number between 0.0 and 1.0 */
double randomperc()
{
jrand++;
if(jrand>=55)
{
jrand = 1;
advance_random();
}
return((double)oldrand[jrand]);
}
3. replace every unif_rand() with randomperc() in 'nsga2.c'
4. build the package in R

Related

How would this shell-sort algorithm be coded in recursive?

I understand that any iterative function can be written recursively, but I still don't quite understand how to write it as a recursive function.
This function receives an array (elements) and a int (number of elements), and sorts them from lower to higher, but I don't get how to make it recursive, any help would be appreciated!
void ShellSort(int *arr, int num){
for (int i = num / 2; i > 0; i = i / 2)
{
for (int j = i; j < num; j++)
{
for(int k = j - i; k >= 0; k = k - i)
{
if (arr[k+i] >= arr[k])
{
break;
}
else
{
arr[k]=arr[k] + arr[k+i];
arr[k+i]=arr[k] - arr[k+i];
arr[k]=arr[k] - arr[k+i];
}
}
}
}
return ;
}

Setting Base Cases for Recursive Function

class Solution {
//given a location on the matrix, this function recursively find the deepest possible depth, which is the length of a side of a found square
private int isSquare(int row_index, int col_index, int depth, char[][] matrix) {
int last_row = row_index + depth;
int last_col = col_index + depth;
if (row_index >= matrix.length || col_index >= matrix[0].length) {
return 0;
}
if (last_row >= matrix.length || last_col >= matrix[0].length) {
return 0;
}
for (int i = col_index; i < last_col; i++) {
if (matrix[row_index][i] != '1') {
return 0;
}
}
for (int i = row_index; i < last_row; i++ ) {
if (matrix[i][col_index] != '1') {
return 0;
}
}
return Math.max(depth, isSquare(row_index, col_index, depth + 1, matrix));
}
public int maximalSquare(char[][] matrix) {
int max = 0;
for (int row = 0; row < matrix.length; row ++) {
for (int col = 0; col <matrix[0].length; col ++) {
int curr_depth = isSquare(row, col, 1, matrix);
if (curr_depth > max) {
max = curr_depth;
}
}
};
return max * max;
}
}
Hi, I was working on LeetCode 221, and it seems like that my solution is not passing test cases with output 1, where the biggest square on the given matrix is just 1 x 1. To me it looks like those depth 1 cases are not passing the two for loops in function isSquare, which is supposed to catch 0s in the square.
I tried LC debugging tool but it did not help much, and my base cases seem fine to me. Please let me know what is going on here. For the problem, https://leetcode.com/problems/maximal-square/
One of the depth 1 test cases that I am failing is below.
Input:
[["0","1"],["1","0"]]
Output:
0
Expected:
1

How create an adjacency matrix of a Maze graph

I'm working on making a maze Generator using Prim's Algorithm. I understand i have to make an undirected weighted graph and represent it on an Adjacency Matrix or List. i created the boolean[][] adjacenyMatrix array to show which edges currently exist in the maze. But i have an issue trying to implement the algorithm i thought of. Here is my code:
import java.util.Scanner;
public class Main {
public static void main(String[] args) {
Scanner scanner = new Scanner (System.in);
System.out.println("Please enter the size of the maze");
int mazeHeight = scanner.nextInt();
int mazeWidth = scanner.nextInt();
int noOfNodes = mazeHeight * mazeWidth;
boolean[][] adjacencyMatrix = new boolean[noOfNodes][noOfNodes];
for (int i = 0; i < mazeHeight; i++) {
for (int j = 0; j < mazeWidth; j++ ) {
// Edges exist from left to right
adjacencyMatrix[i][j] = true;
adjacencyMatrix[j][i] = true;
}
}
for (int i = 0; i < mazeWidth; i++) {
for (int j = 0; j < noOfNodes; j + mazeWidth) { // <-----------I'm having an issue here; Not a statement
// Edges exist from top to bottom
adjacencyMatrix[i][j] = true;
adjacencyMatrix[j][i] = true;
}
}
}
}
After taking a break; i looked over it and realised that i forgot to include the "=" symbol >.<
so j += mazeWidth

Beginner coder checking if input is part of a cycle?

public Graph (int nb){
this.nbNodes = nb;
this.adjacency = new boolean [nb][nb];
for (int i = 0; i < nb; i++){
for (int j = 0; j < nb; j++){
this.adjacency[i][j] = false;
}
}
}
public void addEdge (int i, int j){
if(!(i<0 || i>=this.nbNodes|| j<0 || j>=this.nbNodes))
{
this.adjacency[i][j] = true;
this.adjacency[j][i] = true;
}
}
public void removeEdge (int i, int j){
if(!(i<0 || i>=this.nbNodes|| j<0 || j>=this.nbNodes))
{
this.adjacency[i][j] = false;
this.adjacency[j][i] = false;
}
}
public int nbEdges(){
int c =0;
for(int i=0; i<this.nbNodes; i++)
{
for(int j= 0; j<this.nbNodes; j++)
{
if(this.adjacency[i][j]==true)
{
c++;
}
}
}
return c/2;
}
public boolean cycle(int start){
return false;
}
A Graph has a number of nodes nbNodes and is characterized by its adjacency matrix adjacency. adjacency[i][j] states whether or not there is an edge from the i-th node to the j-th node.
the graphs are undirected.
I am a beginner coder and am having trouble writing cycle(int start)
It takes as input an integer, g.cycle(i) returns true if the i-th node is part of a cycle (and false otherwise).
does anyone have any idea on how I should approach this?

Perlin Noise Assistance

Ok so I found this article and I am confused by some parts of it. If anyone can explain this process in more depth to me I would greatly appreciate it because I have been trying to code this for 2 months now and still have not gotten a correct version working yet. I am specifically confused about the Persistence part of the article because I mostly do not understand what the author is trying to explain about it and at the bottom of the article he talks about a 2D pseudo code implementation of this but the PerlinNoise_2D function does not make sense to me because after the random value is smoothed and interpolated, it is an integer value but the function takes float values? Underneath the persistence portion there is the octaves part. I do not quite understand because he "adds" the smoothed functions together to get the Perlin function. What does he mean by"adds" because you obviously do not add the values together. So if anyone can explain these parts to me I would be very happy. Thanks.
Here is my code:
import java.awt.Color;
import java.awt.Graphics;
import java.util.Random;
import javax.swing.JFrame;
import javax.swing.JPanel;
#SuppressWarnings("serial")
public class TerrainGen extends JPanel {
public static int layers = 3;
public static float[][][][] noise = new float[16][16][81][layers];
public static int[][][][] octaves = new int[16][16][81][layers];
public static int[][][][] perlin = new int[16][16][81][layers];
public static int[][][] perlinnoise = new int[16][16][81];
public static int SmoothAmount = 3;
public static int interpolate1 = 0;
public static int interpolate2 = 10;
public static double persistence = 0.25;
//generate noise
//smooth noise
//interpolate noise
//perlin equation
public TerrainGen() {
for(int t = 0; t < layers; t++) {
for(int z = 0; z < 81; z++) {
for(int y = 0; y < 16; y++) {
for(int x = 0; x < 16; x++) {
noise[x][y][z][t] = GenerateNoise();
}
}
}
}
for(int t = 0; t < layers; t++) {
SmoothNoise(t);
}
for(int t = 0; t < layers; t++) {
for(int z = 0; z < 81; z++) {
for(int y = 0; y < 16; y++) {
for(int x = 0; x < 16; x++) {
octaves[x][y][z][t] = InterpolateNoise(interpolate1, interpolate2, noise[x][y][z][t]);
}
}
}
}
for(int t = 0; t < layers; t++) {
PerlinNoise(t);
}
}
public static Random generation = new Random(5);
public float GenerateNoise() {
float i = generation.nextFloat();
return i;
}
public void SmoothNoise(int t) {
//Huge smoothing algorithm
}
//Cosine interpolation
public int InterpolateNoise(int base, int top, float input) {
return (int) ((1 - ((1 - Math.cos(input * 3.1415927)) * 0.5)) + top * ((1 - Math.cos(input * 3.1415927)) * 0.5));
}
public void PerlinNoise(int t) {
double f = Math.pow(2.0, new Double(t));
double a = Math.pow(persistence, new Double(t));
for(int z = 0; z < 81; z++) {
for(int y = 0; y < 16; y++) {
for(int x = 0; x < 16; x++) {
perlin[x][y][z][t] = (int) ((octaves[x][y][z][t] * f) * a);
}
}
}
}
public static void main(String [] args) {
JFrame frame = new JFrame();
frame.setSize(180, 180);
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
TerrainGen test = new TerrainGen();
frame.add(test);
frame.setVisible(true);
}
public static int size = 5;
public void paintComponent(Graphics g) {
super.paintComponent(g);
int i = 0;
for(int t = 0; t < 9; t++) {
for(int z = 0; z < 9; z++) {
for(int y = 0; y < 16; y++) {
for(int x = 0; x < 16; x++) {
g.setColor(new Color(perlin[x][y][i][0] * 10, perlin[x][y][i][0] * 10, perlin[x][y][i][0] * 10));
g.fillRect((z * (16 * size)) + (x * size), (t * (16 * size)) + (y * size), size, size);
}
}
i++;
}
}
repaint();
}
}
And I did not include the smoothing part because that was about 400 lines of code to smooth between chunks.
What the article calls persistence is how the amplitude of the higher frequency noises "falls off" when they are combined.
"octaves" are just what the article calls the noise functions at different frequencies.
You take 1.0 and repeatedly multiply by the persistence to get the list of amplitudes to multiply each octave by - e.g. a persistence of 0.8 gives factors 1.0, 0.8, 0.64, 0.512.
The noise is not an integer, his function Noise1 produces noise in the range 0..1 - i.e. variable n is an Int32 bit it returns a float.
The input paramters are integers i.e. The Noise1 function is only evaluated at (1, 0) or (2, 2).
After smoothing/smearing the noise a bit in SmoothNoise_1 the values get interpolated to produce the values inbetween.
Hope that helped!!
this loop makes octaves from 2d noise. same loop would work for 3d perlin...
function octaves( vtx: Vector3 ): float
{
var total = 0.0;
for (var i:int = 1; i < 7; i ++)//num octaves
{
total+= PerlinNoise(Vector3 (vtx.x*(i*i),0.0,vtx.z*(i*i)))/(i*i);
}
return total;//added multiple perlins into noise with 1/2/4/8 etc ratios
}
the best thing i have seen for learning perlin is the following code. instead of hash tables, it uses sin based semi random function. using 2-3 octaves it becomes high quality perlin... the amazing thing is that i ran 30 octave of this on a realtime landscape and it didnt slow down, whereas i used 1 voronoi once and it was slowing. so... amazing code to learn from.
#ifndef __noise_hlsl_
#define __noise_hlsl_
// hash based 3d value noise
// function taken from https://www.shadertoy.com/view/XslGRr
// Created by inigo quilez - iq/2013
// License Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
// ported from GLSL to HLSL
float hash( float n )
{
return frac(sin(n)*43758.5453);
}
float noise( float3 x )
{
// The noise function returns a value in the range -1.0f -> 1.0f
float3 p = floor(x);
float3 f = frac(x);
f = f*f*(3.0-2.0*f);
float n = p.x + p.y*57.0 + 113.0*p.z;
return lerp(lerp(lerp( hash(n+0.0), hash(n+1.0),f.x),
lerp( hash(n+57.0), hash(n+58.0),f.x),f.y),
lerp(lerp( hash(n+113.0), hash(n+114.0),f.x),
lerp( hash(n+170.0), hash(n+171.0),f.x),f.y),f.z);
}
note that sin is expensive on CPU, instead you would use:
function hash ( n: float ): float
{//random -1, 1
var e = ( n *73.9543)%1;
return (e*e*142.05432)%2-1;// fast cpu random by me :) uses e*e rather than sin
}

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