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| Line 1: |
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| | == Objective == | | == Objective == |
| | | | |
| − | In this winter, Biostatistics 615/815 aims for providing students with a practical understanding of computational aspects in implementing statistical methods. Although C++ language will be used throughout the course, using Java programming language for homework and project will be acceptable. | + | In Fall 2011, Biostatistics 615/815 aims for providing students with a practical understanding of computational aspects in implementing statistical methods. Although C++ language will be used throughout the course, using Java programming language for homework and project will be acceptable. |
| | | | |
| | == Target Audience == | | == Target Audience == |
| Line 10: |
Line 10: |
| | | | |
| | == Textbook == | | == Textbook == |
| − | * Required Textbook : Cormen, Leiserson, Rivest, and Stein, "Introduction to Algorithms", Third Edition, The MIT Press, 2009 [http://mitpress.mit.edu/algorithms/ [Official Book Web Site]] | + | * Recommended Textbook : Cormen, Leiserson, Rivest, and Stein, "Introduction to Algorithms", Third Edition, The MIT Press, 2009 [http://mitpress.mit.edu/algorithms/ [Official Book Web Site]] |
| | * Optional Textbook : Press, Teukolsky, Vetterling, Flannery, "Numerical Recipes", 3rd Edition, Cambridge University Press, 2007 [http://www.nr.com/ [Official Book Web Site]] | | * Optional Textbook : Press, Teukolsky, Vetterling, Flannery, "Numerical Recipes", 3rd Edition, Cambridge University Press, 2007 [http://www.nr.com/ [Official Book Web Site]] |
| | | | |
| | == Class Schedule == | | == Class Schedule == |
| | | | |
| − | Classes are scheduled for Tuesday and Thursdays, 8:30 - 10:00 am at SPH II M4318 | + | Classes are scheduled for Tuesday and Thursdays, 8:30 - 10:00 am at SPH II M4332 |
| | | | |
| | == Topics == | | == Topics == |
| Line 21: |
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| | The following contents are planned to be covered. | | The following contents are planned to be covered. |
| | | | |
| − | === Part I : Algorithms 101 === | + | === Part I : C++ Basics and Introductory Algorithms === |
| − | * Understanding of Computational Time Complexity | + | * Computational Time Complexity |
| | * Sorting | | * Sorting |
| | * Divide and Conquer Algorithms | | * Divide and Conquer Algorithms |
| Line 28: |
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| | * Key Data Structure | | * Key Data Structure |
| | * Dynamic Programming | | * Dynamic Programming |
| | + | * Hidden Markov Models |
| | | | |
| − | === Part II : Matrix Operations and Numerical Optimizations === | + | === Part II : Numerical Methods and Randomized Algorithms === |
| − | * Matrix decomposition (LU, QR, SVD) | + | * Random Numbers |
| − | * Implementation of Linear Models | + | * Matrix Operations and Least Square Methods |
| − | * Numerical Optimizations
| + | * Importance Sampling |
| − | | |
| − | === Part III : Advanced Statistical Methods ===
| |
| − | * Hidden Markov Models | |
| | * Expectation Maximization | | * Expectation Maximization |
| | * Markov-Chain Monte Carlo Methods | | * Markov-Chain Monte Carlo Methods |
| | + | * Simulated Annealing |
| | + | * Gibbs Sampling |
| | | | |
| | == Class Notes == | | == Class Notes == |
| − | * Lecture 1 : Statistical Computing -- [[Media:Biostat615-lecture1-handout.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture1-presentation.pdf | (Presentation mode - PDF)]] | + | * Lecture 1 : Statistical Computing -- [[Media:Biostat615-Fall2011-lecture01.pdf | (PDF)]] |
| − | * Lecture 2 : C++ Basics and Precisions -- [[Media:Biostat615-lecture2-handout-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture2-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 3 : Implementing Fisher's Exact Test -- [[Media:Biostat615-lecture3-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture3.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 4 : Classes and STLs -- [[Media:Biostat615-lecture4-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture4-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 5 : Divide and Conquer Algorithms -- [[Media:Biostat615-lecture5-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture5.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 6 : Linear Sorting Algorithms and Elementary Data Structures -- [[Media:Biostat615-lecture6-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture6-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 7 : Data Structures -- [[Media:Biostat615-lecture7-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture7-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 8 : Hash Tables -- [[Media:Biostat615-lecture8-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture8-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 9 : Dyamic Programming -- [[Media:Biostat615-lecture9-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture9-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 10 : Boost Libraries and Graphical Algorithms -- [[Media:Biostat615-lecture10-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture10-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 11 : Hidden Markov Models -- [[Media:Biostat615-lecture11-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture11.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 12 : Hidden Markov Models -- [[Media:Biostat615-lecture12-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture12-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 13 : Matrix Computation -- [[Media:Biostat615-lecture13-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture13-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 14 : Implementing Linear Regression -- [[Media:Biostat615-lecture14-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture14-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 15 : Random Number Generation -- [[Media:Biostat615-lecture15-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture15-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 16 : Monte-Carlo methods and importance sampling -- [[Media:Biostat615-lecture16-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture16-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 17 : Numerical optimization -- [[Media:Biostat615-lecture17-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture17-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 18 : Numerical optimization II -- [[Media:Biostat615-lecture18-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture18-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Special Lecture : A practical session -- StatGen Library [[Media:StatGenLecture.pdf | (LectureNotes - PDF)]] [[Media:Debugging.pdf | (Debugging - PDF)]] Demo Code: [[Media:StatGenDemo.tar | StatGenDemo.tar]] Additional Notes: [[Media:GithubWithoutGit.pdf | GithubWithoutGit.pdf]], [[Debuggers]]
| |
| − | * Lecture 19 : The Simplex Method [[Media:Biostat615-lecture19-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture19-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 20 : The E-M Algorithm [[Media:Biostat615-lecture20-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture20-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 21 : Simulated Annealing [[Media:Biostat615-lecture21-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture21-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 22 : Gibbs Sampler [[Media:Biostat615-lecture22-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture22-presentation.pdf | (Presentation mode - PDF)]]
| |
| − | * Lecture 23 : The Baum-Welch Algorithm [[Media:Biostat615-lecture23-nup.pdf | (Handout mode - PDF)]] [[Media:Biostat615-lecture23-presentation.pdf | (Presentation mode - PDF)]]
| |
| | | | |
| | == Problem Sets == | | == Problem Sets == |
| − | * Problem Set 1 : Due on January 20th, 2011 -- [[Media:Biostat615-homework1.pdf | (Problem Set 1 - PDF)]]
| |
| − | * Problem Set 2 : Due on February 8th, 2011 -- [[Media:Biostat615-homework2.pdf | (Problem Set 2 - PDF)]]
| |
| − | ** [[Media:Shuf-1M.txt.gz| (Example data - shuf-1M.txt.gz)]] 1,000,000 randomly shuffled data (gzipped)
| |
| − | ** [[Media:Rand-1M-3digits.txt.gz| (Example data - Rand-1M-3digits.txt.gz)]] 1,000,000 random data from 1 to 1,000]] (gzipped)
| |
| − | ** [[Media:Rand-50k.txt.gz | (Example data - Rand-50k.txt.gz)]] 50,000 random data from 1 to 1,000,000)]] (gzippd)
| |
| − | * Problem Set 3 : Due on February 17th, 2011 -- [[Media:Biostat615-homework3.pdf | (Problem Set 3 - PDF)]]
| |
| − | ** For problem 2 - For Visual C++ users : Refer to the [[Biostatistics 615/815: Main Page#Code_for_Problem_3_-_Problem_2 | (Code Example)]] for a better start
| |
| − | * Problem Set 4 : Due on March 8th, 2011 -- [[Media:Biostat615-homework4.pdf | (Problem Set 4 - PDF)]]
| |
| − | ** [[http://dl.dropbox.com/u/1850834/simulCoinInput.txt.gz Download sample input file (gzipped)]]
| |
| − | ** [[http://dl.dropbox.com/u/1850834/simulCoinOutput.txt.gz Download sample output file(gzipped)]]
| |
| − | ** See below if you want to copy and paste example code
| |
| − | * Problem Set 5 : Due on March 29th, 2011 -- [[Media:Biostat615-homework5.pdf | (Problem Set 5 - PDF)]]
| |
| − | * Problem Set 6 : Due on April 7th, 2011 -- [[Media:Biostat615-homework6.pdf | (Problem Set 6 - PDF)]]
| |
| − | * Problem Set 7 : Due on April 21th, 2011 -- [[Media:Biostat615-homework7.pdf | (Problem Set 7 - PDF)]]
| |
| − | ** [[http://www.sph.umich.edu/csg/abecasis/class/2006/ModelFittingData.txt Download The example data to use]]
| |
| − | ** [[http://dl.dropbox.com/u/1850834/mixData.txt Download Additional data for sanity check (same data used in the lecture slides)]]
| |
| − |
| |
| − |
| |
| − | === Source code for Homework 6 - simplex615.h ===
| |
| − | #ifndef __SIMPLEX_615_H
| |
| − | #define __SIMPLEX_615_H
| |
| − |
| |
| − | #include <vector>
| |
| − | #include <cmath>
| |
| − | #include <iostream>
| |
| − |
| |
| − | #define ZEPS 1e-10
| |
| − |
| |
| − | class optFunc {
| |
| − | public:
| |
| − | virtual double operator() (std::vector<double>& x) = 0;
| |
| − | };
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| − |
| |
| − | // Simplex contains (dim+1)*dim points
| |
| − | class simplex615 {
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| − | protected:
| |
| − | std::vector<std::vector<double> > X;
| |
| − | std::vector<double> Y;
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| − | std::vector<double> midPoint;
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| − | std::vector<double> thruLine;
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| − |
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| − | int dim, idxLo, idxHi, idxNextHi;
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| − |
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| − | void evaluateFunction(optFunc& foo);
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| − | void evaluateExtremes();
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| − | void prepareUpdate();
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| − | bool updateSimplex(optFunc& foo, double scale);
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| − | void contractSimplex(optFunc& foo);
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| − | static int check_tol(double fmax, double fmin, double ftol);
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| − |
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| − | public:
| |
| − | simplex615(double* p, int d);
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| − | void amoeba(optFunc& foo, double tol);
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| − | std::vector<double>& xmin();
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| − | double ymin();
| |
| − | };
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| − |
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| − | simplex615::simplex615(double* p, int d) : dim(d) {
| |
| − | X.resize(dim+1);
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| − | Y.resize(dim+1);
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| − | midPoint.resize(dim);
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| − | thruLine.resize(dim);
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| − | for(int i=0; i < dim+1; ++i) {
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| − | X[i].resize(dim);
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| − | }
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| − |
| |
| − | // set every point the same
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| − | for(int i=0; i < dim+1; ++i) {
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| − | for(int j=0; j < dim; ++j) {
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| − | X[i][j] = p[j];
| |
| − | }
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| − | }
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| − |
| |
| − | // then increase each dimension by one except for the last point
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| − | for(int i=0; i < dim; ++i) {
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| − | X[i][i] += 1.;
| |
| − | }
| |
| − | }
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| − |
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| − | void simplex615::evaluateFunction(optFunc& foo) {
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| − | for(int i=0; i < dim+1; ++i) {
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| − | Y[i] = foo(X[i]);
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| − | }
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| − | }
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| − |
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| − | void simplex615::evaluateExtremes() {
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| − | if ( Y[0] > Y[1] ) {
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| − | idxHi = 0;
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| − | idxLo = idxNextHi = 1;
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| − | }
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| − | else {
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| − | idxHi = 1;
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| − | idxLo = idxNextHi = 0;
| |
| − | }
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| − |
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| − | for(int i=2; i < dim+1; ++i) {
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| − | if ( Y[i] <= Y[idxLo] ) {
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| − | idxLo = i;
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| − | }
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| − | else if ( Y[i] > Y[idxHi] ) {
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| − | idxNextHi = idxHi;
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| − | idxHi = i;
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| − | }
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| − | else if ( Y[i] > Y[idxNextHi] ) {
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| − | idxNextHi = i;
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| − | }
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| − | }
| |
| − | }
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| − |
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| − | void simplex615::prepareUpdate() {
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| − | for(int j=0; j < dim; ++j) {
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| − | midPoint[j] = 0;
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| − | }
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| − | for(int i=0; i < dim+1; ++i) {
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| − | if ( i != idxHi ) {
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| − | for(int j=0; j < dim; ++j) {
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| − | midPoint[j] += X[i][j];
| |
| − | }
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| − | }
| |
| − | }
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| − | for(int j=0; j < dim; ++j) {
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| − | midPoint[j] /= dim;
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| − | thruLine[j] = X[idxHi][j] - midPoint[j];
| |
| − | }
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| − | }
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| − |
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| − | bool simplex615::updateSimplex(optFunc& foo, double scale) {
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| − | std::vector<double> nextPoint;
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| − | nextPoint.resize(dim);
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| − | for(int i=0; i < dim; ++i) {
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| − | nextPoint[i] = midPoint[i] + scale * thruLine[i];
| |
| − | }
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| − | double fNext = foo(nextPoint);
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| − | if ( fNext < Y[idxHi] ) { // exchange with maximum
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| − | for(int i=0; i < dim; ++i) {
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| − | X[idxHi][i] = nextPoint[i];
| |
| − | }
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| − | Y[idxHi] = fNext;
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| − | return true;
| |
| − | }
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| − | else {
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| − | return false;
| |
| − | }
| |
| − | }
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| − |
| |
| − | void simplex615::contractSimplex(optFunc& foo) {
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| − | for(int i=0; i < dim+1; ++i) {
| |
| − | if ( i != idxLo ) {
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| − | for(int j=0; j < dim; ++j) {
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| − | X[i][j] = 0.5*( X[idxLo][j] + X[i][j] );
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| − | Y[i] = foo(X[i]);
| |
| − | }
| |
| − | }
| |
| − | }
| |
| − | }
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| − |
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| − | void simplex615::amoeba(optFunc& foo, double tol) {
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| − | evaluateFunction(foo);
| |
| − | while(true) {
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| − | evaluateExtremes();
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| − | prepareUpdate();
| |
| − |
| |
| − | if ( check_tol(Y[idxHi],Y[idxLo],tol) ) break;
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| − |
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| − | updateSimplex(foo, -1.0); // reflection
| |
| − |
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| − | if ( Y[idxHi] < Y[idxLo] ) {
| |
| − | updateSimplex(foo, -2.0); // expansion
| |
| − | }
| |
| − | else if ( Y[idxHi] >= Y[idxNextHi] ) {
| |
| − | if ( !updateSimplex(foo, 0.5) ) {
| |
| − | contractSimplex(foo);
| |
| − | }
| |
| − | }
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | std::vector<double>& simplex615::xmin() {
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| − | return X[idxLo];
| |
| − | }
| |
| − |
| |
| − | double simplex615::ymin() {
| |
| − | return Y[idxLo];
| |
| − | }
| |
| − |
| |
| − | int simplex615::check_tol(double fmax, double fmin, double ftol) {
| |
| − | double delta = fabs(fmax - fmin); double accuracy = (fabs(fmax) + fabs(fmin)) * ftol;
| |
| − | return (delta < (accuracy + ZEPS));
| |
| − | }
| |
| − |
| |
| − | #endif // __SIMPLEX_615_H
| |
| − |
| |
| − |
| |
| − | === Source code for Homework 4 - Matrix615.h ===
| |
| − |
| |
| − | #ifndef __BIOSTAT615_MATRIX_H // avoid including the same header twice
| |
| − | #define __BIOSTAT615_MATRIX_H
| |
| − |
| |
| − | #include <iostream>
| |
| − | #include <fstream>
| |
| − | #include <boost/tokenizer.hpp>
| |
| − | #include <boost/lexical_cast.hpp>
| |
| − | #include <boost/foreach.hpp>
| |
| − |
| |
| − | #include <Eigen/Core>
| |
| − |
| |
| − | // a generic class for Matrix
| |
| − | template<class T>
| |
| − | class Matrix615 {
| |
| − | protected: // internal data
| |
| − | std::vector<T> data; // using std::vector - object copy is now possible
| |
| − | int nr, nc; // # rows and cols
| |
| − | bool hasMissing;
| |
| − | T valueMissing;
| |
| − | std::string strMissing;
| |
| − | public:
| |
| − | // default constructor
| |
| − | Matrix615() : nr(0), nc(0), hasMissing(false) {}
| |
| − | Matrix615(const char* filename) : nr(0), nc(0), hasMissing(false) {
| |
| − | readFromFile(filename);
| |
| − | }
| |
| − | Matrix615(const T value, const char* str) : nr(0), nc(0) {
| |
| − | enableMissingValue(value, str);
| |
| − | }
| |
| − |
| |
| − | // Allow missing value as a pair of actual value and string value
| |
| − | void enableMissingValue(const T value, const char* str) {
| |
| − | hasMissing = true;
| |
| − | valueMissing = value;
| |
| − | strMissing = str;
| |
| − | }
| |
| − |
| |
| − | // resize the dimension of the matrix
| |
| − | void resize(int nrows, int ncols) {
| |
| − | nr = nrows;
| |
| − | nc = ncols;
| |
| − | data.resize(nr*nc);
| |
| − | }
| |
| − |
| |
| − | // fill the content
| |
| − | void fill(T defaultValue) {
| |
| − | std::fill( data.begin(), data.end(), defaultValue );
| |
| − | }
| |
| − |
| |
| − | void copyTo(Eigen::Matrix<T,Eigen::Dynamic,Eigen::Dynamic>& m) {
| |
| − | m.resize(nr,nc);
| |
| − | for(int j=0; j < nc; ++j) {
| |
| − | for(int i=0; i < nr; ++i) {
| |
| − | m(i,j) = data[i*nc+j];
| |
| − | }
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | // access individual element
| |
| − | T& at(int r, int c) { return data[r*nc+c]; }
| |
| − |
| |
| − | int numRows() { return nr; }
| |
| − | int numCols() { return nc; }
| |
| − |
| |
| − | // print the content of the matrix
| |
| − | void print(std::ostream& o) {
| |
| − | for(int i=0; i < nr; ++i) {
| |
| − | for(int j=0; j < nc; ++j) {
| |
| − | if ( j > 0 ) o << "\t";
| |
| − | if ( hasMissing && ( valueMissing == at(i,j) ) )
| |
| − | o << strMissing;
| |
| − | else
| |
| − | o << at(i,j);
| |
| − | }
| |
| − | o << std::endl;
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | // opens a file to fill the matrix
| |
| − | void readFromFile(const char* file) {
| |
| − | std::ifstream ifs(file);
| |
| − | if ( ! ifs.is_open() ) {
| |
| − | std::cerr << "Cannot open file " << file << std::endl;
| |
| − | abort();
| |
| − | }
| |
| − |
| |
| − | std::string line;
| |
| − | boost::char_separator<char> sep(" \t");
| |
| − | typedef boost::tokenizer< boost::char_separator<char> > wsTokenizer;
| |
| − |
| |
| − | data.clear();
| |
| − | nr = nc = 0;
| |
| − | while( std::getline(ifs, line) ) {
| |
| − | wsTokenizer t(line,sep);
| |
| − | for(wsTokenizer::iterator i=t.begin(); i != t.end(); ++i) {
| |
| − | // if hasMissing is set, convert string "Missing" into special value for Missing
| |
| − | if ( hasMissing && ( i->compare(strMissing) == 0 ) )
| |
| − | data.push_back(valueMissing);
| |
| − | // Otherwise, convert the string to a particular type
| |
| − | else
| |
| − | data.push_back(boost::lexical_cast<T>(i->c_str()));
| |
| − | if ( nr == 0 ) ++nc; // count # of columns at the first row
| |
| − | }
| |
| − | ++nr;
| |
| − | // when reading each line, make sure that the # of columns match to expectation;
| |
| − | if ( (int)data.size() != nr*nc ) {
| |
| − | std::cerr << "The input file is not rectangle at line " << nr << std::endl;
| |
| − | abort();
| |
| − | }
| |
| − | }
| |
| − | }
| |
| − | };
| |
| − |
| |
| − | #endif
| |
| − |
| |
| − | === Source code for Homework 4 - Problem 1 ===
| |
| − | #include "Matrix615.h"
| |
| − |
| |
| − | #define NIL 999999
| |
| − |
| |
| − | int main(int argc, char** argv) {
| |
| − | if ( argc != 2 ) {
| |
| − | std::cerr << "Usage: floydWarshall [weight matrix]" << std::endl;
| |
| − | abort();
| |
| − | }
| |
| − |
| |
| − | Matrix615<int> W;
| |
| − | W.enableMissingValue(NIL,"NIL");
| |
| − | W.readFromFile(argv[1]);
| |
| − | if ( W.numRows() != W.numCols() ) {
| |
| − | std::cerr << "The input file is not exactly square" << std::endl;
| |
| − | abort();
| |
| − | }
| |
| − |
| |
| − | int n = W.numRows();
| |
| − | Matrix615<int> P;
| |
| − | P.enableMissingValue(NIL,"NIL");
| |
| − | P.resize(n,n);
| |
| − |
| |
| − | // Fill out the code in the part marked as *** [FILL HERE] ***
| |
| − |
| |
| − | // *** FILL HERE ** initialize P and W matrix as described in page 695-696 of the textbook
| |
| − |
| |
| − | Matrix615<int> D = W; // object copy is valid because no pointer is involved
| |
| − |
| |
| − | // print initial D and W matrix
| |
| − | std::cout << "---------- Initial D Matrix ---------------------------------" << std::endl;
| |
| − | D.print(std::cout);
| |
| − | std::cout << "---------- Initial PI Matrix ---------------------------------" << std::endl;
| |
| − | P.print(std::cout);
| |
| − |
| |
| − | for(int k=0; k < n; ++k) {
| |
| − | // *** FILL HERE *** Run floyd-Warshall algorithm for each k and
| |
| − |
| |
| − | // print out D and PI matrix for each iteration
| |
| − | std::cout << "---------- D Matrix after covering node " << k << "----------" << std::endl;
| |
| − | D.print(std::cout);
| |
| − | std::cout << "---------- PI Matrix after covering node " << k << "----------" << std::endl;
| |
| − | P.print(std::cout);
| |
| − | }
| |
| − |
| |
| − | // *** EXTRA POINTS *** Extra points (10\%) will be given if the optimal path
| |
| − | // for every pair of node is printed below
| |
| − |
| |
| − | return 0;
| |
| − | }
| |
| − |
| |
| − | === Source code for Homework 4 - Problem 2 ===
| |
| − | #include <cstdlib>
| |
| − | #include <iomanip>
| |
| − | #include <iostream>
| |
| − |
| |
| − | #include "Matrix615.h"
| |
| − |
| |
| − | #define N_STATES 2
| |
| − | #define N_DATA 2
| |
| − |
| |
| − | const char* stateLabels[N_STATES] = {"F","B"};
| |
| − | const char* dataLabels[N_DATA] = {"H","T"};
| |
| − |
| |
| − | class BiasedCoinHMM {
| |
| − | protected:
| |
| − | int T;
| |
| − | // HMM initial parameters
| |
| − | std::vector<double> pi; // N_STATES * 1 vector
| |
| − | Matrix615<double> A; // N_STATES * N_STATES matrix
| |
| − | // : A_{ij} is \Pr(q_t=i|q_{t-1}=j)
| |
| − | Matrix615<double> B; // N_OBS * N_STATES matrix
| |
| − | // : B_{ij} = b_j(o_i) = \Pr(o_t=i|q_t=j)
| |
| − |
| |
| − | // Data (observations)
| |
| − | std::vector<int> o; // vector observations
| |
| − |
| |
| − | // forward-backward probability
| |
| − | Matrix615<double> alphas; // T * N_STATES : alphas[i,j] = alpha_i(i)
| |
| − | Matrix615<double> betas; // T * N_STATES : betas[i,j] = beta_j(i)
| |
| − | Matrix615<double> gammas; // T * N_STATES : gammas[i,j] = gammas_j(i) = Pr(q_t=i|o_t=i)
| |
| − |
| |
| − | // viterbi probability and paths
| |
| − | Matrix615<double> deltas; // T * N_STATES
| |
| − | Matrix615<int> phis; // T * N_STATES
| |
| − | std::vector<int> mleStates; // vector of MLE states
| |
| − |
| |
| − | public:
| |
| − | BiasedCoinHMM(double priors[N_STATES], double trans[N_STATES][N_STATES], double emis[N_DATA][N_STATES]) {
| |
| − | for(int i=0; i < N_STATES; ++i) {
| |
| − | pi.push_back(priors[i]);
| |
| − | }
| |
| − |
| |
| − | A.resize(N_STATES,N_STATES);
| |
| − |
| |
| − | for(int i=0; i < N_STATES; ++i) {
| |
| − | for(int j=0; j < N_STATES; ++j) {
| |
| − | A.at(i,j) = trans[i][j];
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | B.resize(N_DATA,N_STATES);
| |
| − | for(int i=0; i < N_DATA; ++i) {
| |
| − | for(int j=0; j < N_STATES; ++j) {
| |
| − | B.at(i,j) = emis[i][j];
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | T = 0;
| |
| − | }
| |
| − |
| |
| − | void loadObservations(std::vector<int>& obs) {
| |
| − | o = obs;
| |
| − | T = o.size();
| |
| − |
| |
| − | alphas.resize(T,N_STATES);
| |
| − | betas.resize(T,N_STATES);
| |
| − | gammas.resize(T,N_STATES);
| |
| − | deltas.resize(T,N_STATES);
| |
| − | phis.resize(T,N_STATES);
| |
| − | mleStates.resize(T);
| |
| − | }
| |
| − |
| |
| − | void computeForwardBackward() {
| |
| − | // *** FILL OUT *** to compute
| |
| − | // forward and backward probabilities into alphas, betas, and gammas
| |
| − | }
| |
| − |
| |
| − | void computeViterbiPath() {
| |
| − | // *** FILL OUT *** to compute
| |
| − | // viterbi path and likelihood into deltas, phis, and mleStates,
| |
| − | }
| |
| − |
| |
| − | void outputResults(std::ostream& os, std::vector<int>& trueStates) {
| |
| − | if ( T != (int)trueStates.size() ) {
| |
| − | std::cerr << "True states are in different length with HMM" << std::endl;
| |
| − | abort();
| |
| − | }
| |
| − |
| |
| − | os << "#SEQ\tTRUE_S\tOBS\tP(q|o)\tMLE_S" << std::endl << std::fixed << std::setprecision(4);
| |
| − | for(int t = 0; t < T; ++t) {
| |
| − | os << t+1 << "\t"
| |
| − | << stateLabels[trueStates[t]] << "\t"
| |
| − | << dataLabels[o[t]] << "\t"
| |
| − | << gammas.at(t,1) << "\t" // prints Pr(q_t=1|o)
| |
| − | << stateLabels[mleStates[t]] << "\n";
| |
| − | }
| |
| − | }
| |
| − | };
| |
| − |
| |
| − | int main(int argc, char** argv) {
| |
| − | if ( argc != 2 ) {
| |
| − | std::cerr << "Usage: coinHMM [inputFile]" << std::endl;
| |
| − | return -1;
| |
| − | }
| |
| − |
| |
| − | std::vector<int> trueStates;
| |
| − | std::vector<int> observations;
| |
| − | std::ifstream ifs(argv[1]);
| |
| − |
| |
| − | if ( !ifs.is_open() ) {
| |
| − | std::cerr << "Cannot open file " << argv[1] << std::endl;
| |
| − | return -1;
| |
| − | }
| |
| − |
| |
| − | std::string tok;
| |
| − | for(int i=0; ifs >> tok; ++i) {
| |
| − | if ( i % 3 == 1 ) {
| |
| − | if ( tok.compare("F") == 0 ) {
| |
| − | trueStates.push_back(0);
| |
| − | }
| |
| − | else if ( tok.compare("B") == 0 ) {
| |
| − | trueStates.push_back(1);
| |
| − | }
| |
| − | else {
| |
| − | std::cerr << "Cannot recognize state " << tok << std::endl;
| |
| − | }
| |
| − | }
| |
| − | else if ( i % 3 == 2 ) {
| |
| − | if ( tok.compare("H") == 0 ) {
| |
| − | observations.push_back(0);
| |
| − | }
| |
| − | else if ( tok.compare("T") == 0 ) {
| |
| − | observations.push_back(1);
| |
| − | }
| |
| − | else {
| |
| − | std::cerr << "Cannot recognize observation " << tok << std::endl;
| |
| − | }
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | std::cout << "Finished reading " << trueStates.size() << " states and observations.." << std::endl;
| |
| − |
| |
| − | double trans[N_STATES][N_STATES] = { {0.95,0.2}, {0.05,0.8} };
| |
| − | double emis[N_DATA][N_STATES] = { {0.5,0.9}, {0.5,0.1} };
| |
| − | double pi[N_STATES] = {0.9,0.1};
| |
| − |
| |
| − | BiasedCoinHMM bcHMM(pi, trans, emis);
| |
| − |
| |
| − | bcHMM.loadObservations(observations);
| |
| − | bcHMM.computeForwardBackward();
| |
| − | bcHMM.computeViterbiPath();
| |
| − | bcHMM.outputResults(std::cout, trueStates);
| |
| − | return 0;
| |
| − | }
| |
| − |
| |
| − | === Additional example of containing negative weights ===
| |
| − | $ cat ./sampleInput2.txt
| |
| − | 0 3 8 NIL -4
| |
| − | NIL 0 NIL 1 7
| |
| − | NIL 4 0 NIL NIL
| |
| − | 2 NIL -5 0 NIL
| |
| − | NIL NIL NIL 6 0
| |
| − |
| |
| − | $ ./floydWarshall ./sampleInput2.txt
| |
| − | ---------- Initial D Matrix ---------------------------------
| |
| − | 0 3 8 NIL -4
| |
| − | NIL 0 NIL 1 7
| |
| − | NIL 4 0 NIL NIL
| |
| − | 2 NIL -5 0 NIL
| |
| − | NIL NIL NIL 6 0
| |
| − | ---------- Initial PI Matrix ---------------------------------
| |
| − | NIL 0 0 NIL 0
| |
| − | NIL NIL NIL 1 1
| |
| − | NIL 2 NIL NIL NIL
| |
| − | 3 NIL 3 NIL NIL
| |
| − | NIL NIL NIL 4 NIL
| |
| − | ---------- D Matrix after covering node 0----------
| |
| − | 0 3 8 NIL -4
| |
| − | NIL 0 NIL 1 7
| |
| − | NIL 4 0 NIL 999995
| |
| − | 2 5 -5 0 -2
| |
| − | NIL NIL NIL 6 0
| |
| − | ---------- PI Matrix after covering node 0----------
| |
| − | NIL 0 0 NIL 0
| |
| − | NIL NIL NIL 1 1
| |
| − | NIL 2 NIL NIL 0
| |
| − | 3 0 3 NIL 0
| |
| − | NIL NIL NIL 4 NIL
| |
| − | ---------- D Matrix after covering node 1----------
| |
| − | 0 3 8 4 -4
| |
| − | NIL 0 NIL 1 7
| |
| − | NIL 4 0 5 11
| |
| − | 2 5 -5 0 -2
| |
| − | NIL NIL NIL 6 0
| |
| − | ---------- PI Matrix after covering node 1----------
| |
| − | NIL 0 0 1 0
| |
| − | NIL NIL NIL 1 1
| |
| − | NIL 2 NIL 1 1
| |
| − | 3 0 3 NIL 0
| |
| − | NIL NIL NIL 4 NIL
| |
| − | ---------- D Matrix after covering node 2----------
| |
| − | 0 3 8 4 -4
| |
| − | NIL 0 NIL 1 7
| |
| − | NIL 4 0 5 11
| |
| − | 2 -1 -5 0 -2
| |
| − | NIL NIL NIL 6 0
| |
| − | ---------- PI Matrix after covering node 2----------
| |
| − | NIL 0 0 1 0
| |
| − | NIL NIL NIL 1 1
| |
| − | NIL 2 NIL 1 1
| |
| − | 3 2 3 NIL 0
| |
| − | NIL NIL NIL 4 NIL
| |
| − | ---------- D Matrix after covering node 3----------
| |
| − | 0 3 -1 4 -4
| |
| − | 3 0 -4 1 -1
| |
| − | 7 4 0 5 3
| |
| − | 2 -1 -5 0 -2
| |
| − | 8 5 1 6 0
| |
| − | ---------- PI Matrix after covering node 3----------
| |
| − | NIL 0 3 1 0
| |
| − | 3 NIL 3 1 0
| |
| − | 3 2 NIL 1 0
| |
| − | 3 2 3 NIL 0
| |
| − | 3 2 3 4 NIL
| |
| − | ---------- D Matrix after covering node 4----------
| |
| − | 0 1 -3 2 -4
| |
| − | 3 0 -4 1 -1
| |
| − | 7 4 0 5 3
| |
| − | 2 -1 -5 0 -2
| |
| − | 8 5 1 6 0
| |
| − | ---------- PI Matrix after covering node 4----------
| |
| − | NIL 2 3 4 0
| |
| − | 3 NIL 3 1 0
| |
| − | 3 2 NIL 1 0
| |
| − | 3 2 3 NIL 0
| |
| − | 3 2 3 4 NIL
| |
| − | Optimal path for 1 <- 0 (d = 1) : 1 <-(4)-- 2 <-(-5)-- 3 <-(6)-- 4 <-(-4)-- 0
| |
| − | Optimal path for 2 <- 0 (d = -3) : 2 <-(-5)-- 3 <-(6)-- 4 <-(-4)-- 0
| |
| − | Optimal path for 3 <- 0 (d = 2) : 3 <-(6)-- 4 <-(-4)-- 0
| |
| − | Optimal path for 4 <- 0 (d = -4) : 4 <-(-4)-- 0
| |
| − | Optimal path for 0 <- 1 (d = 3) : 0 <-(2)-- 3 <-(1)-- 1
| |
| − | Optimal path for 2 <- 1 (d = -4) : 2 <-(-5)-- 3 <-(1)-- 1
| |
| − | Optimal path for 3 <- 1 (d = 1) : 3 <-(1)-- 1
| |
| − | Optimal path for 4 <- 1 (d = -1) : 4 <-(-4)-- 0 <-(2)-- 3 <-(1)-- 1
| |
| − | Optimal path for 0 <- 2 (d = 7) : 0 <-(2)-- 3 <-(1)-- 1 <-(4)-- 2
| |
| − | Optimal path for 1 <- 2 (d = 4) : 1 <-(4)-- 2
| |
| − | Optimal path for 3 <- 2 (d = 5) : 3 <-(1)-- 1 <-(4)-- 2
| |
| − | Optimal path for 4 <- 2 (d = 3) : 4 <-(-4)-- 0 <-(2)-- 3 <-(1)-- 1 <-(4)-- 2
| |
| − | Optimal path for 0 <- 3 (d = 2) : 0 <-(2)-- 3
| |
| − | Optimal path for 1 <- 3 (d = -1) : 1 <-(4)-- 2 <-(-5)-- 3
| |
| − | Optimal path for 2 <- 3 (d = -5) : 2 <-(-5)-- 3
| |
| − | Optimal path for 4 <- 3 (d = -2) : 4 <-(-4)-- 0 <-(2)-- 3
| |
| − | Optimal path for 0 <- 4 (d = 8) : 0 <-(2)-- 3 <-(6)-- 4
| |
| − | Optimal path for 1 <- 4 (d = 5) : 1 <-(4)-- 2 <-(-5)-- 3 <-(6)-- 4
| |
| − | Optimal path for 2 <- 4 (d = 1) : 2 <-(-5)-- 3 <-(6)-- 4
| |
| − | Optimal path for 3 <- 4 (d = 6) : 3 <-(6)-- 4
| |
| − |
| |
| − | === Source code from Homework 2 - Problem 3 ===
| |
| − | #include <iostream>
| |
| − | #include <vector>
| |
| − | #include <ctime>
| |
| − | #include <fstream>
| |
| − | #include <set>
| |
| − | #include "mySortedArray.h"
| |
| − | #include "myTree.h"
| |
| − | #include "myList.h"
| |
| − |
| |
| − | int main(int argc, char** argv) {
| |
| − | int tok;
| |
| − | std::vector<int> v;
| |
| − | if ( argc > 1 ) {
| |
| − | std::ifstream fin(argv[1]);
| |
| − | while( fin >> tok ) { v.push_back(tok); }
| |
| − | fin.close();
| |
| − | }
| |
| − | else {
| |
| − | while( std::cin >> tok ) { v.push_back(tok); }
| |
| − | }
| |
| − | mySortedArray<int> c1;
| |
| − | myList<int> c2;
| |
| − | myTree<int> c3;
| |
| − | std::set<int> s;
| |
| − |
| |
| − | clock_t start = clock();
| |
| − | for(int i=0; i < (int)v.size(); ++i) {
| |
| − | c1.insert(v[i]);
| |
| − | }
| |
| − | clock_t finish = clock();
| |
| − | double duration = (double)(finish-start)/CLOCKS_PER_SEC;
| |
| − | std::cout << "Sorted Array (Insert) " << duration << std::endl;
| |
| − |
| |
| − | start = clock();
| |
| − | for(int i=0; i < (int)v.size(); ++i) {
| |
| − | c2.insert(v[i]);
| |
| − | }
| |
| − | finish = clock();
| |
| − | duration = (double)(finish-start)/CLOCKS_PER_SEC;
| |
| − | std::cout << "List (Insert) " << duration << std::endl;
| |
| − |
| |
| − | start = clock();
| |
| − | for(int i=0; i < (int)v.size(); ++i) {
| |
| − | c3.insert(v[i]);
| |
| − | }
| |
| − | finish = clock();
| |
| − | duration = (double)(finish-start)/CLOCKS_PER_SEC;
| |
| − | std::cout << "Tree (Insert) " << duration << std::endl;
| |
| − |
| |
| − | start = clock();
| |
| − | for(int i=0; i < (int)v.size(); ++i) {
| |
| − | s.insert(v[i]);
| |
| − | }
| |
| − | finish = clock();
| |
| − | duration = (double)(finish-start)/CLOCKS_PER_SEC;
| |
| − | std::cout << "std::set (Insert) " << duration << std::endl;
| |
| − |
| |
| − | start = clock();
| |
| − | for(int i=0; i < (int)v.size(); ++i) {
| |
| − | c1.search(v[i]);
| |
| − | }
| |
| − | finish = clock();
| |
| − | duration = (double)(finish-start)/CLOCKS_PER_SEC;
| |
| − | std::cout << "Sorted Array (Search) " << duration << std::endl;
| |
| − |
| |
| − | start = clock();
| |
| − | for(int i=0; i < (int)v.size(); ++i) {
| |
| − | c2.search(v[i]);
| |
| − | }
| |
| − | finish = clock();
| |
| − | duration = (double)(finish-start)/CLOCKS_PER_SEC;
| |
| − | std::cout << "List (Search) " << duration << std::endl;
| |
| − |
| |
| − | start = clock();
| |
| − | for(int i=0; i < (int)v.size(); ++i) {
| |
| − | c3.search(v[i]);
| |
| − | }
| |
| − | finish = clock();
| |
| − | duration = (double)(finish-start)/CLOCKS_PER_SEC;
| |
| − | std::cout << "Tree (Search) " << duration << std::endl;
| |
| − |
| |
| − | start = clock();
| |
| − | for(int i=0; i < (int)v.size(); ++i) {
| |
| − | s.find(v[i]);
| |
| − | }
| |
| − | finish = clock();
| |
| − | duration = (double)(finish-start)/CLOCKS_PER_SEC;
| |
| − | std::cout << "std::set (Search) " << duration << std::endl;
| |
| − | }
| |
| − |
| |
| − | === The header file of mySortedArray.h (For Homework 2 Problem 3)===
| |
| − |
| |
| − | #include <iostream>
| |
| − | #define DEFAULT_ALLOC 1024
| |
| − | template <class T> // template supporting a generic type
| |
| − | class mySortedArray {
| |
| − | protected: // member variables hidden from outside
| |
| − | T *data; // array of the genetic type
| |
| − | int size; // number of elements in the container
| |
| − | int nalloc; // # of objects allocated in the memory
| |
| − | mySortedArray(mySortedArray& a) {};
| |
| − | int search(const T& x, int begin, int end);
| |
| − | public: // abstract interface visible to outside
| |
| − | mySortedArray(); // default constructor
| |
| − | ~mySortedArray(); // desctructor
| |
| − | void insert(const T& x); // insert an element x
| |
| − | int search(const T& x); // search for an element x and return its location
| |
| − | bool remove(const T& x); // delete a particular element
| |
| − | };
| |
| − |
| |
| − | template <class T>
| |
| − | mySortedArray<T>::mySortedArray() { // default constructor
| |
| − | size = 0; // array do not have element initially
| |
| − | nalloc = DEFAULT_ALLOC;
| |
| − | data = new T[nalloc]; // allocate default # of objects in memory
| |
| − | }
| |
| − |
| |
| − | template <class T>
| |
| − | mySortedArray<T>::~mySortedArray() { // destructor
| |
| − | if ( data != NULL ) {
| |
| − | delete [] data; // delete the allocated memory before destorying
| |
| − | } // the object. otherwise, memory leak happens
| |
| − | }
| |
| − |
| |
| − | template <class T>
| |
| − | void mySortedArray<T>::insert(const T& x) {
| |
| − | if ( size >= nalloc ) { // if container has more elements than allocated
| |
| − | T* newdata = new T[nalloc*2]; // make an array at doubled size
| |
| − | for(int i=0; i < nalloc; ++i) {
| |
| − | newdata[i] = data[i]; // copy the contents of array
| |
| − | }
| |
| − | delete [] data; // delete the original array
| |
| − | data = newdata; // and reassign data ptr
| |
| − | }
| |
| − |
| |
| − | int i;
| |
| − | for(i=size-1; (i >= 0) && (data[i] > x); --i) {
| |
| − | data[i+1] = data[i]; // insert the list into right position
| |
| − | }
| |
| − | data[i+1] = x;
| |
| − | ++size; // increase the size
| |
| − | }
| |
| − |
| |
| − | template <class T>
| |
| − | int mySortedArray<T>::search(const T& x) {
| |
| − | return search(x, 0, size-1);
| |
| − | }
| |
| − |
| |
| − | template <class T>
| |
| − | int mySortedArray<T>::search(const T& x, int begin, int end) {
| |
| − | if ( begin > end ) {
| |
| − | return -1;
| |
| − | }
| |
| − | else {
| |
| − | int mid = (begin+end)/2;
| |
| − | if ( data[mid] == x ) {
| |
| − | return mid;
| |
| − | }
| |
| − | else if ( data[mid] < x ) {
| |
| − | return search(x, mid+1, end);
| |
| − | }
| |
| − | else {
| |
| − | return search(x, begin, mid);
| |
| − | }
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | template <class T>
| |
| − | bool mySortedArray<T>::remove(const T& x) {
| |
| − | int i = search(x); // try to find the element
| |
| − | if ( i >= 0 ) { // if found
| |
| − | for(int j=i; j < size-1; ++j) {
| |
| − | data[i] = data[i+1]; // shift all the elements by one
| |
| − | }
| |
| − | --size; // and reduce the array size
| |
| − | return true; // successfully removed the value
| |
| − | }
| |
| − | else {
| |
| − | return false; // cannot find the value to remove
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | === Example code to generare all possible permutations ===
| |
| − |
| |
| − | Note that http://www.cplusplus.com/reference/algorithm/next_permutation/ provides much simpler solution for generating permutation. (Thanks to Matthew Snyder)
| |
| − |
| |
| − | // Code to generate permutations from 1..n
| |
| − | // These code was adopted from
| |
| − | // http://geeksforgeeks.org/?p=767 by Hyun Min Kang
| |
| − | #include <iostream>
| |
| − | #include <vector>
| |
| − |
| |
| − | // swaps two elements
| |
| − | void swap(std::vector<int>& v, int i, int j) {
| |
| − | int tmp = v[i];
| |
| − | v[i] = v[j];
| |
| − | v[j] = tmp;
| |
| − | return;
| |
| − | }
| |
| − |
| |
| − | // actual engine - recursively calls permutation
| |
| − | void permute(std::vector<int>& v, int from, int to) {
| |
| − | if ( from == to ) { // print the permutation
| |
| − | for(int i=0; i < v.size(); ++i) {
| |
| − | std::cout << " " << v[i];
| |
| − | }
| |
| − | std::cout << std::endl;
| |
| − | }
| |
| − | else {
| |
| − | for(int i = from; i <= to; ++i) {
| |
| − | swap(v,from,i); // swaps two elements
| |
| − | permute(v, from+1, to); // permute the rest
| |
| − | swap(v,from,i); // recover the vector to the original state
| |
| − | }
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | // Permutation Example
| |
| − | int main(int argc, char** argv) {
| |
| − | if ( argc != 2 ) {
| |
| − | std::cerr << "Usage: " << argv[0] << " " << "[# of samples]" << std::endl;
| |
| − | return -1;
| |
| − | }
| |
| − |
| |
| − | // takes input from 1..n
| |
| − | int n = atoi(argv[1]);
| |
| − | std::vector<int> input;
| |
| − | for(int i=1; i <= n; ++i) {
| |
| − | input.push_back(i);
| |
| − | }
| |
| − | permute(input, 0, n-1); // print all possible permutations
| |
| − | return 0;
| |
| − | }
| |
| − |
| |
| − | #include <iostream> // for input/output
| |
| − | #include <boost/graph/adjacency_list.hpp> // for using graph type
| |
| − | #include <boost/graph/dijkstra_shortest_paths.hpp> // for dijkstra algorithm
| |
| − | using namespace std; // allow to omit prefix 'std::'
| |
| − | using namespace boost; // allow to omit prefix 'boost::'
| |
| − |
| |
| − | int getNodeID(int node) {
| |
| − | return ((node/5)+1)*10+(node%5+1);
| |
| − | }
| |
| − |
| |
| − | === Code for Problem 3 - Problem 2 ===
| |
| − |
| |
| − | #include <iostream> // for input/output
| |
| − | #include <boost/graph/adjacency_list.hpp> // for using graph type
| |
| − | #include <boost/graph/dijkstra_shortest_paths.hpp> // for dijkstra algorithm
| |
| − | using namespace std; // allow to omit prefix 'std::'
| |
| − | using namespace boost; // allow to omit prefix 'boost::'
| |
| − |
| |
| − | int getNodeID(int node) {
| |
| − | return ((node/5)+1)*10+(node%5+1);
| |
| − | }
| |
| − |
| |
| − | int main(int argc, char** argv) {
| |
| − | // defining a graph type
| |
| − | // 1. edges are stored as std::list internally
| |
| − | // 2. verticies are stored as std::vector internally
| |
| − | // 3. the graph is directed (undirectedS, bidirectionalS can be used)
| |
| − | // 4. vertices do not carry particular properties
| |
| − | // 5. edges contains weight property as integer value
| |
| − | typedef adjacency_list< listS, vecS, directedS, no_property, property< edge_weight_t, int> > graph_t;
| |
| − |
| |
| − | // vertex_descriptor is a type for representing vertices
| |
| − | typedef graph_traits< graph_t >::vertex_descriptor vertex_descriptor;
| |
| − | // a nodes is represented as an integer, and an edge is a pair of integers
| |
| − | typedef std::pair<int, int> E;
| |
| − |
| |
| − | // Connect between verticies as in the Manhattan Tourist Problem
| |
| − | // Each node is numbered as a two-digit integer of [#row] and [#col]
| |
| − | enum { N11, N12, N13, N14, N15,
| |
| − | N21, N22, N23, N24, N25,
| |
| − | N31, N32, N33, N34, N35,
| |
| − | N41, N42, N43, N44, N45,
| |
| − | N51, N52, N53, N54, N55 };
| |
| − |
| |
| − | E edges [] = { E(N11,N12), E(N12,N13), E(N13,N14), E(N14,N15),
| |
| − | E(N21,N22), E(N22,N23), E(N23,N24), E(N24,N25),
| |
| − | E(N31,N32), E(N32,N33), E(N33,N34), E(N34,N35),
| |
| − | E(N41,N42), E(N42,N43), E(N43,N44), E(N44,N45),
| |
| − | E(N51,N52), E(N52,N53), E(N53,N54), E(N54,N55),
| |
| − | E(N11,N21), E(N12,N22), E(N13,N23), E(N14,N24), E(N15,N25),
| |
| − | E(N21,N31), E(N22,N32), E(N23,N33), E(N24,N34), E(N25,N35),
| |
| − | E(N31,N41), E(N32,N42), E(N33,N43), E(N34,N44), E(N35,N45),
| |
| − | E(N41,N51), E(N42,N52), E(N43,N53), E(N44,N54), E(N45,N55) };
| |
| − | // Assign weights for each edge
| |
| − | int weight [] = { 4, 2, 0, 7, // horizontal weights
| |
| − | 7, 4, 5, 9,
| |
| − | 6, 8, 1, 0,
| |
| − | 1, 6, 4, 7,
| |
| − | 1, 5, 8, 5,
| |
| − | 0, 6, 6, 2, 4, // vertical weights
| |
| − | 9, 7, 1, 0, 6,
| |
| − | 1, 8, 4, 8, 9,
| |
| − | 3, 6, 6, 0, 7 };
| |
| − |
| |
| − | // define a graph as an array of edges and weights
| |
| − | #if defined(BOOST_MSVC) && BOOST_MSVC <= 1300 // special routine for MS VC++
| |
| − | typedef graph_traits < graph_t >::edge_descriptor edge_descriptor;
| |
| − | graph_t g(25);
| |
| − | property_map<graph_t, edge_weight_t>::type weightmap = get(edge_weight, g);
| |
| − | for (std::size_t j = 0; j < sizeof(edges)/sizeof(E); ++j) {
| |
| − | edge_descriptor e;
| |
| − | bool inserted;
| |
| − | boost::tie(e, inserted) = add_edge(edge_array[j].first, edge_array[j].second, g);
| |
| − | weightmap[e] = weights[j];
| |
| − | }
| |
| − | #else // for regulat compilers
| |
| − | graph_t g(edges, edges + sizeof(edges) / sizeof(E), weight, 25);
| |
| − | #endif
| |
| − |
| |
| − | std::vector<vertex_descriptor> p(num_vertices(g));
| |
| − | std::vector<int> d(num_vertices(g));
| |
| − | vertex_descriptor s = vertex(N11, g);
| |
| − |
| |
| − | #if defined(BOOST_MSVC) && BOOST_MSVC <= 1300 // for VC++
| |
| − | property_map<graph_t, vertex_index_t>::type indexmap = get(vertex_index, g);
| |
| − | dijkstra_shortest_paths(g, s, &p[0], &d[0], weightmap, indexmap,
| |
| − | std::less<int>(), closed_plus<int>(),
| |
| − | (std::numeric_limits<int>::max)(), 0,
| |
| − | default_dijkstra_visitor());
| |
| − | #else // for regular compilers
| |
| − | dijkstra_shortest_paths(g, s, predecessor_map(&p[0]).distance_map(&d[0]));
| |
| − | #endif
| |
| − | graph_traits < graph_t >::vertex_iterator vi, vend;
| |
| − |
| |
| − | std::cout << "Backtracking the optimal path from the destination to source" << std::endl;
| |
| − | for(int node = N55; node != N11; node = p[node]) {
| |
| − | std::cout << "Path: N" << getNodeID(p[node]) << " -> N" << getNodeID(node) << ", Distance from origin is " << d[node] << std::endl;
| |
| − | }
| |
| − | return 0;
| |
| − | }
| |
| | | | |
| | == Office Hours == | | == Office Hours == |
| − | * Friday 9:30AM-12:30PM | + | * Friday 9:00AM-10:30PM |
| − | | |
| − | == Information on Biostatistics Cluster ==
| |
| − | * You may want to request an account to the biostatistics cluster. Refer to https://webservices.itcs.umich.edu/mediawiki/Biostatistics/index.php/Cluster for further information.
| |
| | | | |
| | == Standards of Academic Conduct == | | == Standards of Academic Conduct == |
| Line 1,036: |
Line 56: |
| | | | |
| | == Course History == | | == Course History == |
| − | | + | * Winter 2011 Course Web Site [[Biostatistics_615/815_Winter_2011]] |
| − | Goncalo Abecasis taught it in several academic years previously. For previous course notes, see [[http://www.sph.umich.edu/csg/abecasis/class Goncalo's older class notes]]. | + | * Goncalo Abecasis taught it in several academic years previously. For previous course notes, see [[http://www.sph.umich.edu/csg/abecasis/class Goncalo's older class notes]]. |
