Munkres’ Assignment Algorithm with RcppArmadillo

September 24, 2013
By

(This article was first published on Rcpp Gallery, and kindly contributed to R-bloggers)

Munkres’ Assignment Algorithm (Munkres (1957), also known as hungarian algorithm) is a well known algorithm in Operations Research solving the problem to optimally assign N jobs to N workers.

I needed to solve the Minimal Assignment Problem for a relabeling algorithm in MCMC sampling for finite mixture distributions, where I use a random permutation Gibbs sampler. For each sample an optimal labeling must be found, i.e. I have N parameter vectors and must assign each vector to one of the N components of the finite mixture under the restriction that each component gets a parameter vector. For the assignment of parameters to components Stephens (1997b) suggests an algorithm relying on the Minimal Assignment in regard to a loss matrix. The labeling with the smallest loss is then considered as optimal.

After an unsuccessful search for libraries implementing the algorithm easily for C++ or C, I made the decision to program it myself using RcppArmadillo for good performance. I found some guidance by the websites of Bob Pilgrim and TopCoder. These websites offer excellent tutorials to understand the algorithm and to convert it to code. The order of this implementation of Munkres’ algorithm is of an order N to the power of 4. There exists also a version of order N to the power of 3, but an order of N to the power of 4 works very good for me and coding time is as usual a critical factor for me.

In the following I walk through the different steps of Munkres’ algorithm and explain the main parts and their functionality.

Let’s begin. The first step in Munkres’ algorithm is to subtract the minimal element of each row from each element in this row.

#include<RcppArmadillo.h>
// [[Rcpp::depends(RcppArmadillo)]]

void step_one(unsigned int &step, arma::mat &cost, 
        const unsigned int &N) 
{    
    for (unsigned int r = 0; r < N; ++r) {
        cost.row(r) -= arma::min(cost.row(r));
    }
    step = 2;
}

Note, that we use references for all function arguments. As we have to switch between the steps of the algorithm continously, we always must be able to determine which step should be chosen next. Therefore we give a mutable unsigned integer step as an argument to each step function of the algorithm.

Inside the function we can easily access a whole row by Armadillo’s row() method for matrices. In the second step, we then search for a zero in the modified cost matrix of step one.

void step_two (unsigned int &step, const arma::mat &cost,
        arma::umat &indM, arma::ivec &rcov, 
        arma::ivec &ccov, const unsigned int &N)
{                      
    for (unsigned int r = 0; r < N; ++r) {
        for (unsigned int c = 0; c < N; ++c) {
            if (cost.at(r, c) == 0.0 && rcov.at(r) == 0 && ccov.at(c) == 0) {
                indM.at(r, c)  = 1;
                rcov.at(r)     = 1;
                ccov.at(c)     = 1;
                break;                                              // Only take the first
                                                                    // zero in a row and column
            }
        }
    }
    /* for later reuse */
    rcov.fill(0);
    ccov.fill(0);
    step = 3;
}

Only the first zero in a row is taken. Then, the indicator matrix indM indicates this zero by setting the corresponding element at (r, c) to 1. A unique zero - the only or first one in a column and row - is called starred zero. In step 2 we find such a starred zero.

Note, that we use here Armadillo’s element access via the method at(), which makes no bound checks and improves performance.

Note Bene: This code is thoroughly debugged - never do this for fresh written code!

In step 3 we cover each column with a starred zero. If already N columns are covered all starred zeros describe a complete assignment - so, go to step 7 and finish. Otherwise go to step 4.

void step_three(unsigned int &step, const arma::umat &indM,
        arma::ivec &ccov, const unsigned int &N) 
{
    unsigned int colcount = 0;
    for (unsigned int r = 0; r < N; ++r) {
        for (unsigned int c = 0; c < N; ++c) {
            if (indM.at(r, c) == 1) {
                ccov.at(c) = 1;
            }
        }
    }
    for (unsigned int c = 0; c < N; ++c) {
        if (ccov.at(c) == 1) {
            ++colcount;
        }
    }
    if (colcount == N) {
        step = 7;
    } else {
        step = 4;
    }
}

We cover a column by looking for 1s in the indicator matrix indM (See step 2 for assuring that these are indeed only starred zeros).

Step 4 finds noncovered zeros and primes them. If there are zeros in a row and none of them is starred, prime them. For this task we program a helper function to keep the code more readable and reusable. The helper function searches for noncovered zeros.

void find_noncovered_zero(int &row, int &col,
        const arma::mat &cost, const arma::ivec &rcov, 
        const arma::ivec &ccov, const unsigned int &N)
{
    unsigned int r = 0;
    unsigned int c;
    bool done = false;
    row = -1;
    col = -1;
    while (!done) {
        c = 0;
        while (true) {
            if (cost.at(r, c) == 0.0 && rcov.at(r) == 0 && ccov.at(c) == 0) {
                row = r;
                col = c;
                done = true;
            }
            ++c;
            if (c == N || done) {
                break;
            }
        }
        ++r;
        if (r == N) {
            done = true;
        }
    }
}

We can detect noncovered zeros by checking if the cost matrix contains at row r and column c a zero and row and column are not covered yet, i.e. rcov(r) == 0, ccov(c) == 0. This loop breaks, if we have found our first uncovered zero or no uncovered zero at all.

In step 4, if no uncovered zero is found we go to step 6. If instead an uncovered zero has been found, we set the indicator matrix at its position to 2. We then have to search for a starred zero in the row with the uncovered zero, uncover the column with the starred zero and cover the row with the starred zero. To indicate a starred zero in a row and to find it we create again two helper functions.

bool star_in_row(int &row, const arma::umat &indM,
        const unsigned int &N) 
{
    bool tmp = false;
    for (unsigned int c = 0; c < N; ++c) {
        if (indM.at(row, c) == 1) {
            tmp = true;
            break;
        }
    }
    return tmp;
}

void find_star_in_row (const int &row, int &col, 
        const arma::umat &indM, const unsigned int &N) 
{
    col = -1;
    for (unsigned int c = 0; c < N; ++c) {
        if (indM.at(row, c) == 1) {
            col = c;
        }
    }
}

We know that starred zeros are indicated by the indicator matrix containing an element equal to 1. Now, step 4.

void step_four (unsigned int &step, const arma::mat &cost,
        arma::umat &indM, arma::ivec &rcov, arma::ivec &ccov,
        int &rpath_0, int &cpath_0, const unsigned int &N) 
{
    int row = -1;
    int col = -1;
    bool done = false;
    while(!done) {
        find_noncovered_zero(row, col, cost, rcov,
                ccov, N);                                 
                                                        
        if (row == -1) {                                
            done = true;
            step = 6;
        } else {
            /* uncovered zero */
            indM(row, col) = 2;                         
            if (star_in_row(row, indM, N)) {                            
                find_star_in_row(row, col, indM, N);    
                /* Cover the row with the starred zero
                 * and uncover the column with the starred
                 * zero. 
                 */
                rcov.at(row) = 1;                         
                ccov.at(col) = 0;                          
            } else {
                /* No starred zero in row with 
                 * uncovered zero 
                 */
                done = true;
                step = 5;
                rpath_0 = row;
                cpath_0 = col;
            }            
        }
    }
}

Notice the rpath_0 and cpath_0 variables. These integer variables store the first vertex for an augmenting path in step 5. If zeros could be primed we go further to step 5.

Step 5 constructs a path beginning at an uncovered primed zero (this is actually graph theory - alternating and augmenting paths) and alternating between starred and primed zeros. This path is continued until a primed zero with no starred zero in its column is found. Then, all starred zeros in this path are unstarred and all primed zeros are starred. All primes in the indicator matrix are erased and all rows are uncovered. Then return to step 3 to cover again columns.

Step 5 needs several helper functions. First, we need a function to find starred zeros in columns.

void find_star_in_col (const int &col, int &row,
        const arma::umat &indM, const unsigned int &N)
{
    row = -1;
    for (unsigned int r = 0; r < N; ++r) {
        if (indM.at(r, col) == 1) {
            row = r;
        }
    }
}

Then we need a function to find a primed zero in a row. Note, that these tasks are easily performed by searching the indicator matrix indM.

void find_prime_in_row (const int &row, int &col,
        const arma::umat &indM, const unsigned int &N)
{
    for (unsigned int c = 0; c < N; ++c) {
        if (indM.at(row, c) == 2) {
            col = c;
        }
    }
}

In addition we need a function to augment the path, one to clear the covers from rows and one to erase the primed zeros from the indicator matrix indM.

void augment_path (const int &path_count, arma::umat &indM,
        const arma::imat &path)
{
    for (unsigned int p = 0; p < path_count; ++p) {
        if (indM.at(path(p, 0), path(p, 1)) == 1) {
            indM.at(path(p, 0), path(p, 1)) = 0;
        } else {
            indM.at(path(p, 0), path(p, 1)) = 1;
        }
    }
}

void clear_covers (arma::ivec &rcov, arma::ivec &ccov)
{
    rcov.fill(0);
    ccov.fill(0);
}

void erase_primes(arma::umat &indM, const unsigned int &N)
{
    for (unsigned int r = 0; r < N; ++r) {
        for (unsigned int c = 0; c < N; ++c) {
            if (indM.at(r, c) == 2) {
                indM.at(r, c) = 0;
            }
        }
    }
}

The function to augment the path gets an integer matrix path of dimension 2 * N x 2. In it all vertices between rows and columns are stored row-wise. Now, we can set the complete step 5:

void step_five (unsigned int &step,
        arma::umat &indM, arma::ivec &rcov, 
        arma::ivec &ccov, arma::imat &path, 
        int &rpath_0, int &cpath_0, 
        const unsigned int &N)
{
    bool done = false;
    int row = -1;
    int col = -1;
    unsigned int path_count = 1;
    path.at(path_count - 1, 0) = rpath_0;
    path.at(path_count - 1, 1) = cpath_0;
    while (!done) {
        find_star_in_col(path.at(path_count - 1, 1), row, 
                indM, N);
        if (row > -1) {                                
            /* Starred zero in row 'row' */
            ++path_count;
            path.at(path_count - 1, 0) = row;
            path.at(path_count - 1, 1) = path.at(path_count - 2, 1);
        } else {
            done = true;
        }
        if (!done) {
            /* If there is a starred zero find a primed 
             * zero in this row; write index to 'col' */
            find_prime_in_row(path.at(path_count - 1, 0), col, 
                    indM, N);  
            ++path_count;
            path.at(path_count - 1, 0) = path.at(path_count - 2, 0);
            path.at(path_count - 1, 1) = col;
        }
    }
    augment_path(path_count, indM, path);
    clear_covers(rcov, ccov);
    erase_primes(indM, N);
    step = 3;
}

Recall, if step 4 was successfull in uncovering all columns and covering all rows with a primed zero, it then calls step 6. Step 6 takes the cover vectors rcov and ccov and looks in the uncovered region of the cost matrix for the smallest value. It then subtracts this value from each element in an uncovered column and adds it to each element in a covered row. After this transformation, the algorithm starts again at step 4. Our last helper function searches for the smallest value in the uncovered region of the cost matrix.

void find_smallest (double &minval, const arma::mat &cost, 
        const arma::ivec &rcov, const arma::ivec &ccov, 
        const unsigned int &N)
{
    for (unsigned int r = 0; r < N; ++r) {
        for (unsigned int c = 0; c < N; ++c) {
            if (rcov.at(r) == 0 && ccov.at(c) == 0) {                                                                    
                if (minval > cost.at(r, c)) {
                    minval = cost.at(r, c);
                }
            }
        }
    }
}

Step 6 looks as follows:

void step_six (unsigned int &step, arma::mat &cost,
        const arma::ivec &rcov, const arma::ivec &ccov, 
        const unsigned int &N) 
{
    double minval = DBL_MAX;
    find_smallest(minval, cost, rcov, ccov, N);
    for (unsigned int r = 0; r < N; ++r) {
        for (unsigned int c = 0; c < N; ++c) {
            if (rcov.at(r) == 1) {
                cost.at(r, c) += minval;
            }
            if (ccov.at(c) == 0) {
                cost.at(r, c) -= minval;
            }
        }
    }
    step = 4;
}

At last, we must create a function that enables us to jump around the different steps of the algorithm. The following code shows the main function of the algorithm. It defines also the important variables to be passed to the different steps.

arma::umat hungarian(const arma::mat &input_cost)
{
    const unsigned int N = input_cost.n_rows;
    unsigned int step = 1;
    int cpath_0 = 0;
    int rpath_0 = 0;
    arma::mat cost(input_cost);
    arma::umat indM(N, N);
    arma::ivec rcov(N);
    arma::ivec ccov(N);
    arma::imat path(2 * N, 2);

    indM = arma::zeros<arma::umat>(N, N);
    bool done = false;
    while (!done) {
        switch (step) {
            case 1:
                step_one(step, cost, N);
                break;
            case 2:
                step_two(step, cost, indM, rcov, ccov, N);
                break;
            case 3:
                step_three(step, indM, ccov, N);
                break;
            case 4:
                step_four(step, cost, indM, rcov, ccov,
                        rpath_0, cpath_0, N);
                break;
            case 5: 
                step_five(step, indM, rcov, ccov,
                        path, rpath_0, cpath_0, N);
                break;
            case 6:
                step_six(step, cost, rcov, ccov, N);
                break;
            case 7:            
                done = true;
                break;
        }
    }
    return indM;
}

Note, this function takes the numeric cost matrix as an argument and returns the integer indicator matrix indM.

I chose to set the argument input_cost constant and copy it for reasons of reusability of the cost matrix in other C++ code. When working with rather huge cost matrices, it makes sense to make the argument mutable. Though, I used pass-by-reference for all the arguments in functions to avoid useless copying inside the functions.

To call the main function hungarian from R and to use our algorithm we construct an Rcpp Attribute:

// [[Rcpp::export]]

arma::imat hungarian_cc(Rcpp::NumericMatrix cost)
{
    // Reuse memory from R
    unsigned int N = cost.rows();
    arma::mat arma_cost(cost.begin(), N, N, false, true);
    // Call the C++-function 'hungarian'
    arma::umat indM = hungarian(arma_cost);
    //Convert the result to an Armadillo integer
    //matrix - R does not know unsigned integers.
    return arma::conv_to<arma::imat>::from(indM);
}

If we want to provide this function also to other users we should probably ensure, that the matrix is square (There exists also an extension to rectangular matrices, see Burgeois and Lasalle (1971)). This can be done easily with the exceptions provided by Rcpp passed over to R:

// [[Rcpp::export]]
arma::imat hungariansafe_cc(Rcpp::NumericMatrix cost)
{
    unsigned int N = cost.rows();
    unsigned int K = cost.cols();
    if (N != K) {
        throw Rcpp::exception("Matrix is not square.");
    }
    // Reuse memory from R
    arma::mat arma_cost(cost.begin(), N, K, false, true);
    // Call the C++-function 'hungarian'
    arma::umat indM = hungarian(arma_cost);
    //convert the result to an Armadillo integer
    //matrix - R does not know unsigned integers.
    return arma::conv_to<arma::imat>::from(indM);
}

Note, that it is also possible to use for the attribute directly an Armadillo matrix, but following the recent discussion on the Rcpp-devel list, a pass-by-reference of arguments is not yet possible. Romain Francois’ proposals seem promising, so maybe we can expect in some of the next releases shallow copies allowing pass-by-reference in Rcpp Attributes.

Let us begin now with a very easy example that makes clear what is going on.

# Check exception:
cost <- matrix(c(1:6), nrow = 3, ncol = 2, byrow = TRUE)
tryCatch(indM <- hungariansafe_cc(cost), error = function(e) {print(e)})
<Rcpp::exception: Matrix is not square.>
cost <- matrix(c(1, 2, 2, 4), nrow = 2, ncol = 2, byrow = TRUE)
cost
     [,1] [,2]
[1,]    1    2
[2,]    2    4
indM <- hungarian_cc(cost)
indM
     [,1] [,2]
[1,]    0    1
[2,]    1    0
min.cost <- sum(indM * cost)
min.cost
[1] 4

We can also compute a maximal assignment over a revenue matrix by simply considering the difference between a big value and this matrix as a cost matrix.

revenues <- matrix(seq(1, 4)) %*% seq(1, 4)
revenues
     [,1] [,2] [,3] [,4]
[1,]    1    2    3    4
[2,]    2    4    6    8
[3,]    3    6    9   12
[4,]    4    8   12   16
cost <- 100 - revenues
indM <- hungarian_cc(cost)
indM
     [,1] [,2] [,3] [,4]
[1,]    1    0    0    0
[2,]    0    1    0    0
[3,]    0    0    1    0
[4,]    0    0    0    1
max.revenue <- sum(indM * revenues)
max.revenue
[1] 30

CoCost matrices containing negative values work as well:

cost <- matrix(rnorm(100), ncol = 10, nrow = 10)
cost
          [,1]    [,2]    [,3]     [,4]     [,5]     [,6]    [,7]
 [1,] -0.23018  0.3598 -0.2180 -0.29507 -0.20792 -0.02855 -0.5023
 [2,]  1.55871  0.4008 -1.0260  0.89513 -1.26540 -0.04287 -0.3332
 [3,]  0.07051  0.1107 -0.7289  0.87813  2.16896  1.36860 -1.0186
 [4,]  0.12929 -0.5558 -0.6250  0.82158  1.20796 -0.22577 -1.0718
 [5,]  1.71506  1.7869 -1.6867  0.68864 -1.12311  1.51647  0.3035
 [6,]  0.46092  0.4979  0.8378  0.55392 -0.40288 -1.54875  0.4482
 [7,] -1.26506 -1.9666  0.1534 -0.06191 -0.46666  0.58461  0.0530
 [8,] -0.68685  0.7014 -1.1381 -0.30596  0.77997  0.12385  0.9223
 [9,] -0.44566 -0.4728  1.2538 -0.38047 -0.08337  0.21594  2.0501
[10,]  1.22408 -1.0678  0.4265 -0.69471  0.25332  0.37964 -0.4910
           [,8]    [,9]   [,10]
 [1,] -2.309169  0.3853  0.5484
 [2,]  1.005739 -0.3707  0.2387
 [3,] -0.709201  0.6444 -0.6279
 [4,] -0.688009 -0.2205  1.3607
 [5,]  1.025571  0.3318 -0.6003
 [6,] -0.284773  1.0968  2.1873
 [7,] -1.220718  0.4352  1.5326
 [8,]  0.181303 -0.3259 -0.2357
 [9,] -0.138891  1.1488 -1.0264
[10,]  0.005764  0.9935 -0.7104
indM <- hungarian_cc(cost)
indM
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    0    0    0    0    0    0    0    1    0     0
 [2,]    0    0    0    0    1    0    0    0    0     0
 [3,]    0    0    0    0    0    0    1    0    0     0
 [4,]    0    0    0    0    0    0    0    0    1     0
 [5,]    0    0    1    0    0    0    0    0    0     0
 [6,]    0    0    0    0    0    1    0    0    0     0
 [7,]    0    1    0    0    0    0    0    0    0     0
 [8,]    1    0    0    0    0    0    0    0    0     0
 [9,]    0    0    0    0    0    0    0    0    0     1
[10,]    0    0    0    1    0    0    0    0    0     0
min.cost <- sum(indM * cost)
min.cost
[1] -12.42

Finally let us make some benchmarking. We load the rbenchmark package and take now a more realistic cost matrix.

library(rbenchmark)
cost <- matrix(rpois(10000, 312), ncol = 100, nrow = 100)
benchmark(indM <- hungarian_cc(cost), columns=c('test','replications','elapsed','user.self','sys.self'), replications=1000)
                        test replications elapsed user.self sys.self
1 indM <- hungarian_cc(cost)         1000   10.53      10.5    0.004

But we also see, where the limitations of this algorithm lie - huge matrices:

cost <- matrix(rpois(250000, 312), ncol = 500, nrow = 500)
system.time(indM <- hungarian_cc(cost))
   user  system elapsed 
  3.656   0.008   3.674 

Some last notes on the structure of the code. I prefer to put the code of the algorithm in an header file, e.g. hungarian.h. And use an attributes.cpp (attributes.cc) file to program the Rcpp Attributes. With this, I can easily reuse the algorithm in C++ code by simple inclusion (#include "hungarian.h") and have a complete overview on all the C++ functions I export to R.

To leave a comment for the author, please follow the link and comment on his blog: Rcpp Gallery.

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