Python: convert matrix to positive semi-definite

Question

I'm currently working on kernel methods, and at some point I needed to make a non positive semi-definite matrix (i.e. similarity matrix) into one PSD matrix. I tried this approach:

def makePSD(mat):
    #make symmetric
    k = (mat+mat.T)/2
    #make PSD
    min_eig = np.min(np.real(linalg.eigvals(mat)))
    e = np.max([0, -min_eig + 1e-4])
    mat = k + e*np.eye(mat.shape[0]);
    return mat

but it fails if I test the resulting matrix with the following function:

def isPSD(A, tol=1e-8):
    E,V = linalg.eigh(A)
    return np.all(E >= -tol)

I also tried the approach suggested in other related question (How can I calculate the nearest positive semi-definite matrix?), but the resulting matrix also failed to pass the isPSD test.

Do you have any suggestions on how to correctly make such transformation correctly?

Answer 1

First thing I’d say is don’t use eigh for testing positive-definiteness, since eigh assumes the input is Hermitian. That’s probably why you think the answer you reference isn’t working.

I didn’t like that answer because it had an iteration (and, I couldn’t understand its example), nor the other answer there it doesn’t promise to give you the best positive-definite matrix, i.e., the one closest to the input in terms of the Frobenius norm (squared-sum of elements). (I have absolutely no idea what your code in your question is supposed to do.)

I do like this Matlab implementation of Higham’s 1988 paper: https://www.mathworks.com/matlabcentral/fileexchange/42885-nearestspd so I ported it to Python (edit updated for Python 3):

from numpy import linalg as la
import numpy as np


def nearestPD(A):
    """Find the nearest positive-definite matrix to input

    A Python/Numpy port of John D'Errico's `nearestSPD` MATLAB code [1], which
    credits [2].

    [1] https://www.mathworks.com/matlabcentral/fileexchange/42885-nearestspd

    [2] N.J. Higham, "Computing a nearest symmetric positive semidefinite
    matrix" (1988): https://doi.org/10.1016/0024-3795(88)90223-6
    """

    B = (A + A.T) / 2
    _, s, V = la.svd(B)

    H = np.dot(V.T, np.dot(np.diag(s), V))

    A2 = (B + H) / 2

    A3 = (A2 + A2.T) / 2

    if isPD(A3):
        return A3

    spacing = np.spacing(la.norm(A))
    # The above is different from [1]. It appears that MATLAB's `chol` Cholesky
    # decomposition will accept matrixes with exactly 0-eigenvalue, whereas
    # Numpy's will not. So where [1] uses `eps(mineig)` (where `eps` is Matlab
    # for `np.spacing`), we use the above definition. CAVEAT: our `spacing`
    # will be much larger than [1]'s `eps(mineig)`, since `mineig` is usually on
    # the order of 1e-16, and `eps(1e-16)` is on the order of 1e-34, whereas
    # `spacing` will, for Gaussian random matrixes of small dimension, be on
    # othe order of 1e-16. In practice, both ways converge, as the unit test
    # below suggests.
    I = np.eye(A.shape[0])
    k = 1
    while not isPD(A3):
        mineig = np.min(np.real(la.eigvals(A3)))
        A3 += I * (-mineig * k**2 + spacing)
        k += 1

    return A3


def isPD(B):
    """Returns true when input is positive-definite, via Cholesky"""
    try:
        _ = la.cholesky(B)
        return True
    except la.LinAlgError:
        return False


if __name__ == '__main__':
    import numpy as np
    for i in range(10):
        for j in range(2, 100):
            A = np.random.randn(j, j)
            B = nearestPD(A)
            assert (isPD(B))
    print('unit test passed!')

In addition to just finding the nearest positive-definite matrix, the above library includes isPD which uses the Cholesky decomposition to determine whether a matrix is positive-definite. This way, you don’t need any tolerances—any function that wants a positive-definite will run Cholesky on it, so it’s the absolute best way to determine positive-definiteness.

It also has a Monte Carlo-based unit test at the end. If you put this in posdef.py and run python posdef.py, it’ll run a unit-test that passes in ~a second on my laptop. Then in your code you can import posdef and call posdef.nearestPD or posdef.isPD.

The code is also in a Gist if you do that.