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Added arxiv:1905.02752 replication programs
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‎replication/org/cicirello/replication/arxiv2019may/CompareKendallTauSequenceDistAlgsDoubles.java‎

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/*
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* Copyright 2018-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
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*
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* This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
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*
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* JavaPermutationTools is free software: you can
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* redistribute it and/or modify it under the terms of the GNU
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* General Public License as published by the Free Software
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* Foundation, either version 3 of the License, or (at your
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* option) any later version.
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*
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* JavaPermutationTools is distributed in the hope
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* that it will be useful, but WITHOUT ANY WARRANTY; without even
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* the implied warranty of MERCHANTABILITY or FITNESS FOR A
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* PARTICULAR PURPOSE. See the GNU General Public License for more
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* details.
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*
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* You should have received a copy of the GNU General Public License
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* along with JavaPermutationTools. If not, see <http://www.gnu.org/licenses/>.
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*
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*/
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package org.cicirello.replication.arxiv2019may;
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import org.cicirello.sequences.distance.KendallTauSequenceDistance;
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import java.util.concurrent.ThreadLocalRandom;
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import java.lang.management.*;
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/**
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* <p>This program replicates the data for the paper:<br>
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* V.A. Cicirello, <a href="https://www.cicirello.org/publications/cicirello2019arXiv.html">"Kendall Tau
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* Sequence Distance: Extending Kendall Tau from Ranks to Sequences,"</a>
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* arXiv preprint arXiv:1905.02752 [cs.DM], May 2019.</p>
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*
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* @author <a href=https://www.cicirello.org/>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/>https://www.cicirello.org/</a>
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*/
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public class CompareKendallTauSequenceDistAlgsDoubles {
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public static void main(String[] args) {
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KendallTauSequenceDistance dHash = new KendallTauSequenceDistance();
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KendallTauSequenceDistance dSort = new KendallTauSequenceDistance(true);
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final int MIN_L = 256;
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final int MAX_L = 131072;
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final int N = 100;
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int[] alphabetSize = {1, 4, 16, 64, 256, 1024, 4096, 16384, 65536};
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ThreadMXBean bean = ManagementFactory.getThreadMXBean();
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System.out.printf("%8s\t%8s\t%8s\t%8s\n", "L", "Alphabet", "TimeHash", "TimeSort");
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for (int L = MIN_L; L <= MAX_L; L *= 2) {
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for (int j = 0; j < alphabetSize.length; j++) {
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int R = alphabetSize[j];
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//if (R < 1) R = 1;
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double[][] iArrays = new double[N][];
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double[][] iShuffled = new double[N][];
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for (int i = 0; i < N; i++) {
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iArrays[i] = randDoubleSequence(L, R);
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iShuffled[i] = shuffleCopy(iArrays[i]);
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}
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System.out.printf("%8d\t%8d", L, R);
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long start = bean.getCurrentThreadCpuTime();
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for (int i = 0; i < N; i++) {
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int d = dHash.distance(iArrays[i], iShuffled[i]);
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}
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long end = bean.getCurrentThreadCpuTime();
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double seconds = 1.0*(end-start)/1000000000/N;
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System.out.printf("\t%8.6f", seconds);
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start = bean.getCurrentThreadCpuTime();
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for (int i = 0; i < N; i++) {
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int d = dSort.distance(iArrays[i], iShuffled[i]);
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}
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end = bean.getCurrentThreadCpuTime();
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seconds = 1.0*(end-start)/1000000000/N;
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System.out.printf("\t%8.6f", seconds);
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System.out.println();
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}
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}
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}
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public static double[] shuffleCopy(double[] s) {
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double[] r = s.clone();
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for (int i = s.length-1; i > 0; i--) {
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int j = ThreadLocalRandom.current().nextInt(i+1);
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if (i==j) continue;
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double temp = r[i];
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r[i] = r[j];
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r[j] = temp;
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}
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return r;
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}
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public static double[] randDoubleSequence(int length, int range) {
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double[] s = new double[length];
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for (int i = 0; i < length; i++) {
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s[i] = 1.0*ThreadLocalRandom.current().nextInt(range);
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}
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return s;
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}
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}

‎replication/org/cicirello/replication/arxiv2019may/CompareKendallTauSequenceDistAlgsInts.java‎

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/*
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* Copyright 2018-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
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*
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* This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
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*
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* JavaPermutationTools is free software: you can
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* redistribute it and/or modify it under the terms of the GNU
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* General Public License as published by the Free Software
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* Foundation, either version 3 of the License, or (at your
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* option) any later version.
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*
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* JavaPermutationTools is distributed in the hope
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* that it will be useful, but WITHOUT ANY WARRANTY; without even
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* the implied warranty of MERCHANTABILITY or FITNESS FOR A
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* PARTICULAR PURPOSE. See the GNU General Public License for more
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* details.
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*
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* You should have received a copy of the GNU General Public License
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* along with JavaPermutationTools. If not, see <http://www.gnu.org/licenses/>.
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*
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*/
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package org.cicirello.replication.arxiv2019may;
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import org.cicirello.sequences.distance.KendallTauSequenceDistance;
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import java.util.concurrent.ThreadLocalRandom;
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import java.lang.management.*;
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/**
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* <p>This program replicates the data for the paper:<br>
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* V.A. Cicirello, <a href="https://www.cicirello.org/publications/cicirello2019arXiv.html">"Kendall Tau
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* Sequence Distance: Extending Kendall Tau from Ranks to Sequences,"</a>
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* arXiv preprint arXiv:1905.02752 [cs.DM], May 2019.</p>
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*
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* @author <a href=https://www.cicirello.org/>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/>https://www.cicirello.org/</a>
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*/
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public class CompareKendallTauSequenceDistAlgsInts {
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public static void main(String[] args) {
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KendallTauSequenceDistance dHash = new KendallTauSequenceDistance();
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KendallTauSequenceDistance dSort = new KendallTauSequenceDistance(true);
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final int MIN_L = 256;
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final int MAX_L = 131072;
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final int N = 100;
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int[] alphabetSize = {1, 4, 16, 64, 256, 1024, 4096, 16384, 65536};
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ThreadMXBean bean = ManagementFactory.getThreadMXBean();
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System.out.printf("%8s\t%8s\t%8s\t%8s\n", "L", "Alphabet", "TimeHash", "TimeSort");
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for (int L = MIN_L; L <= MAX_L; L *= 2) {
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for (int j = 0; j < alphabetSize.length; j++) {
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int R = alphabetSize[j];
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//if (R < 1) R = 1;
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int[][] iArrays = new int[N][];
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int[][] iShuffled = new int[N][];
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for (int i = 0; i < N; i++) {
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iArrays[i] = randIntSequence(L, R);
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iShuffled[i] = shuffleCopy(iArrays[i]);
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}
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System.out.printf("%8d\t%8d", L, R);
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long start = bean.getCurrentThreadCpuTime();
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for (int i = 0; i < N; i++) {
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int d = dHash.distance(iArrays[i], iShuffled[i]);
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}
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long end = bean.getCurrentThreadCpuTime();
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double seconds = 1.0*(end-start)/1000000000/N;
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System.out.printf("\t%8.6f", seconds);
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start = bean.getCurrentThreadCpuTime();
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for (int i = 0; i < N; i++) {
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int d = dSort.distance(iArrays[i], iShuffled[i]);
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}
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end = bean.getCurrentThreadCpuTime();
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seconds = 1.0*(end-start)/1000000000/N;
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System.out.printf("\t%8.6f", seconds);
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System.out.println();
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}
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}
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}
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public static int[] shuffleCopy(int[] s) {
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int[] r = s.clone();
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for (int i = s.length-1; i > 0; i--) {
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int j = ThreadLocalRandom.current().nextInt(i+1);
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if (i==j) continue;
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int temp = r[i];
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r[i] = r[j];
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r[j] = temp;
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}
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return r;
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}
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public static int[] randIntSequence(int length, int range) {
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int[] s = new int[length];
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for (int i = 0; i < length; i++) {
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s[i] = ThreadLocalRandom.current().nextInt(range);
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}
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return s;
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}
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}

‎replication/org/cicirello/replication/arxiv2019may/CompareKendallTauSequenceDistAlgsString.java‎

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/*
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* Copyright 2018-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
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*
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* This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
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*
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* JavaPermutationTools is free software: you can
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* redistribute it and/or modify it under the terms of the GNU
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* General Public License as published by the Free Software
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* Foundation, either version 3 of the License, or (at your
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* option) any later version.
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*
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* JavaPermutationTools is distributed in the hope
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* that it will be useful, but WITHOUT ANY WARRANTY; without even
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* the implied warranty of MERCHANTABILITY or FITNESS FOR A
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* PARTICULAR PURPOSE. See the GNU General Public License for more
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* details.
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*
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* You should have received a copy of the GNU General Public License
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* along with JavaPermutationTools. If not, see <http://www.gnu.org/licenses/>.
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*
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*/
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package org.cicirello.replication.arxiv2019may;
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import org.cicirello.sequences.distance.KendallTauSequenceDistance;
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import java.util.concurrent.ThreadLocalRandom;
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import java.lang.management.*;
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/**
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* <p>This program replicates the data for the paper:<br>
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* V.A. Cicirello, <a href="https://www.cicirello.org/publications/cicirello2019arXiv.html">"Kendall Tau
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* Sequence Distance: Extending Kendall Tau from Ranks to Sequences,"</a>
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* arXiv preprint arXiv:1905.02752 [cs.DM], May 2019.</p>
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*
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* @author <a href=https://www.cicirello.org/>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/>https://www.cicirello.org/</a>
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*/
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public class CompareKendallTauSequenceDistAlgsString {
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public static void main(String[] args) {
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KendallTauSequenceDistance dHash = new KendallTauSequenceDistance();
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KendallTauSequenceDistance dSort = new KendallTauSequenceDistance(true);
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final int MIN_L = 256;
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final int MAX_L = 131072;
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final int N = 100;
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int[] alphabetSize = {1, 4, 16, 64, 256, 1024, 4096, 16384, 65536};
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ThreadMXBean bean = ManagementFactory.getThreadMXBean();
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System.out.printf("%8s\t%8s\t%8s\t%8s\n", "L", "Alphabet", "TimeHash", "TimeSort");
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for (int L = MIN_L; L <= MAX_L; L *= 2) {
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for (int j = 0; j < alphabetSize.length; j++) {
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int R = alphabetSize[j];
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//if (R < 1) R = 1;
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String[] sArray = new String[N];
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String[] sShuffled = new String[N];
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for (int i = 0; i < N; i++) {
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sArray[i] = randString(L, R);
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sShuffled[i] = shuffleCopy(sArray[i]);
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}
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System.out.printf("%8d\t%8d", L, R);
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long start = bean.getCurrentThreadCpuTime();
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for (int i = 0; i < N; i++) {
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int d = dHash.distance(sArray[i], sShuffled[i]);
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}
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long end = bean.getCurrentThreadCpuTime();
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double seconds = 1.0*(end-start)/1000000000/N;
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System.out.printf("\t%8.6f", seconds);
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start = bean.getCurrentThreadCpuTime();
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for (int i = 0; i < N; i++) {
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int d = dSort.distance(sArray[i], sShuffled[i]);
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}
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end = bean.getCurrentThreadCpuTime();
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seconds = 1.0*(end-start)/1000000000/N;
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System.out.printf("\t%8.6f", seconds);
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System.out.println();
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}
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}
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}
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public static String shuffleCopy(String s) {
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char[] c = s.toCharArray();
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for (int i = c.length-1; i > 0; i--) {
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int j = ThreadLocalRandom.current().nextInt(i+1);
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if (i==j) continue;
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char temp = c[i];
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c[i] = c[j];
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c[j] = temp;
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}
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return new String(c);
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}
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public static String randString(int length, int range) {
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char[] s = new char[length];
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for (int i = 0; i < length; i++) {
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s[i] = (char)ThreadLocalRandom.current().nextInt(range);
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}
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return new String(s);
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}
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}

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