Andreas Löffler's Implementation of the Exact P-Values Calculations for the Mann-Whitney U Test


Mann-Whitney is one of the most popular non-parametric statistical tests. Unfortunately, most test implementations in statistical packages are far from perfect. The exact p-value calculation is time-consuming and can be impractical for large samples. Therefore, most implementations automatically switch to the asymptotic approximation, which can be quite inaccurate. Indeed, the classic normal approximation could produce enormous errors. Thanks to the Edgeworth expansion, the accuracy can be improved, but it is still not always satisfactory enough. I prefer using the exact p-value calculation whenever possible.

The computational complexity of the exact p-value calculation using the classic recurrent equation suggested by Mann and Whitney is $\mathcal{O}(n^2 m^2)$ in terms of time and memory. It’s not a problem for small samples, but for medium-size samples, it is slow, and it has an extremely huge memory footprint. This gives us an unpleasant dilemma: either we use the exact p-value calculation (which is extremely time and memory-consuming), or we use the asymptotic approximation (which gives poor accuracy).

Last week, I got acquainted with a brilliant algorithm for the exact p-value calculation suggested by Andreas Löffler in 1982. It’s much faster than the classic approach, and it requires only $\mathcal{O}(n+m)$ memory.

The algorithm idea

Let us say we compare two samples of sizes $n$ and $m$, and the Mann-Whitney U statistic value is $u$. To obtain the p-value, we need $p_{n,m}(u)$ (see [mann1947], page 51), which is typically defined using the following recurrent equation:

$$ p_{n,m}(u) = p_{n-1,m}(u - m) + p_{n,m-1}(u). $$

In [loeffler1982], Andreas Löffler derives an alternative recurrent equation:

$$ p_{n,m}(u) = \frac{1}{u} \sum_{i=0}^{u-1} p_{n,m}(i) \cdot \sigma_{n,m}(u - i), $$ $$ \sigma_{n,m}(u) = \sum_{u \operatorname{mod} d} \varepsilon_d d,\quad\textrm{where}\; \varepsilon_d = \begin{cases} 1, & \textrm{where}\; 1 \leq d \leq n, \\ 0, & \textrm{else}, \\ -1, & \textrm{where}\; m+1 \leq d \leq m+n. \end{cases} $$

The formula derivation uses a smart trick based on a generating function, and it takes only two pages. Here is a reference implementation in C# (the most straightforward one, further optimizations are possible; no big numbers support):

public long[] MannWhitneyLoeffler(int n, int m, int u)
{
    int[] sigma = new int[u + 1];
    for (int d = 1; d <= n; d++)
    for (int i = d; i <= u; i += d)
        sigma[i] += d;
    for (int d = m + 1; d <= m + n; d++)
    for (int i = d; i <= u; i += d)
        sigma[i] -= d;

    long[] p = new long[u + 1];
    p[0] = 1;
    for (int a = 1; a <= u; a++)
    {
        for (int i = 0; i < a; i++)
            p[a] += p[i] * sigma[a - i];
        p[a] /= a;
    }

    return p;
}

Further reading

For a better understanding of the suggested approach, I recommend reading the original papers: [mann1947] and [loeffler1982]. Also, it is worth reading the corresponding discussion about the adoption of this approach in R and SciPy: