Computing SVD and pseudoinverse

In a nutshell, given the singular decomposition of a matrix A,

A = U \Sigma V^*

the Moore-Penrose pseudoinverse is given by

A^+ = V \Sigma^+ U^*.

This post will explain what the terms above mean, and how to compute them in Python and in Matheamtica.

Singular Value Decomposition (SVD)

The singular value decomposition of a matrix is a sort of change of coordinates that makes the matrix simple, a generalization of diagonalization.

Matrix diagonalization

If a square matrix A is diagonalizable, then there is a matrix P such that

A = P^{-1} D P

where the matrix D is diagonal. You could think of P as a change of coordinates that makes the action of A as simple as possible. The elements on the diagonal of D are the eigenvalues of A and the columns of P are the corresponding eigenvectors.

Unfortunately not all matrices can be diagonalized. Singular value decomposition is a way to do something like diagonalization for any matrix, even non-square matrices.

Generalization to SVD

Singular value decomposition generalizes diagonalization. The matrix Σ in SVD is analogous to D in diagonalization. Σ is diagonal, though it may not be square. The matrices on either side of Σ are analogous to the matrix P in diagonalization, though now there are two different matrices, and they are not necessarily inverses of each other. The matrices U and V are square, but not necessarily of the same dimension.

The elements along the diagonal of Σ are not necessarily eigenvalues but singular values, which are a generalization of eigenvalues. Similarly the columns of U and V are not necessarily eigenvectors but left singular vectors and right singular vectors respectively.

The star superscript indicates conjugate transpose. If a matrix has all real components, then the conjugate transpose is just the transpose. But if the matrix has complex entries, you take the conjugate and transpose each entry.

The matrices U and V are unitary. A matrix M is unitary if its inverse is its conjugate transpose, i.e. M* M = MM* = I.

Pseudoinverse and SVD

The (Moore-Penrose) pseudoinverse of a matrix generalizes the notion of an inverse, somewhat like the way SVD generalized diagonalization. Not every matrix has an inverse, but every matrix has a pseudoinverse, even non-square matrices.

Computing the pseudoinverse from the SVD is simple.


A = U \Sigma V^*


A^+ = V \Sigma^+ U^*

where Σ+ is formed from Σ by taking the reciprocal of all the non-zero elements, leaving all the zeros alone, and making the matrix the right shape: if Σ is an m by n matrix, then Σ+ must be an n by m matrix.

We’ll give examples below in Mathematica and Python.

Computing SVD in Mathematica

Let’s start with the matrix A below.

A = \begin{bmatrix} 2 & -1 & 0 \\ 4 & 3 & -2 \end{bmatrix}

We can find the SVD of A with the following Mathematica commands.

    A = {{2, -1, 0}, {4, 3, -2}}
    {U, S, V} = SingularValueDecomposition[A]

From this we learn that the singular value decomposition of A is

\begin{bmatrix} \frac{1}{\sqrt{26}} & -\frac{5}{\sqrt{26}} \\ \frac{5}{\sqrt{26}} & \frac{1}{\sqrt{26}} \\ \end{bmatrix} \begin{bmatrix} \sqrt{30} & 0 & 0 \\ 0 & 2 & 0 \end{bmatrix} \begin{bmatrix} \frac{11}{\sqrt{195}} & \frac{7}{\sqrt{195}} & -\sqrt{\frac{5}{39}} \\ -\frac{3}{\sqrt{26}} & 2 \sqrt{\frac{2}{13}} & -\frac{1}{\sqrt{26}} \\ \frac{1}{\sqrt{30}} & \sqrt{\frac{2}{15}} & \sqrt{\frac{5}{6}} \end{bmatrix}

Note that the last matrix is not V but the transpose of V. Mathematica returns V itself, not its transpose.

If we multiply the matrices back together we can verify that we get A back.

    U . S. Transpose[V]

This returns

    {{2, -1, 0}, {4, 3, -2}}

as we’d expect.

Computing pseudoinverse in Mathematica

The Mathematica command for computing the pseudoinverse is simply PseudoInverse. (The best thing about Mathematica is it’s consistent, predictable naming.)


This returns

    {{19/60, 1/12}, {-(11/30), 1/6}, {1/12, -(1/12)}}

And we can confirm that computing the pseudoinverse via the SVD

    Sp = {{1/Sqrt[30], 0}, {0, 1/2}, {0, 0}}
    V . Sp . Transpose[U]

gives the same result.

Computing SVD in Python

Next we compute the singular value decomposition in Python (NumPy).

    >>> a = np.matrix([[2, -1, 0],[4,3,-2]])
    >>> u, s, vt = np.linalg.svd(a, full_matrices=True)

Note that np.linalg.svd returns the transpose of V, not the V in the definition of singular value decomposition.

Also, the object s is not the diagonal matrix Σ but a vector containing only the diagonal elements, i.e. just the singular values. This can save a lot of space if the matrix is large. The NumPy method svd has other efficiency-related options that I won’t go into here.

We can verify that the SVD is correct by turning s back into a matrix and multiply the components together.

    >>> ss = np.matrix([[s[0], 0, 0], [0, s[1], 0]])
    >>> u*ss*vt

This returns the matrix A, within floating point accuracy. Since Python is doing floating point computations, not symbolic calculation like Mathematica, the zero in A turns into -3.8e-16.

Note that the singular value decompositions as computed by Mathematica and Python differ in a few signs here and there; the SVD is not unique.

Computing pseudoinverse in Python

The pseudoinverse can be computed in NumPy with np.linalg.pinv.

    >>> np.linalg.pinv(a)
    matrix([[ 0.31666667,  0.08333333],
            [-0.36666667,  0.16666667],
            [ 0.08333333, -0.08333333]])

This returns the same result as Mathematica above, up to floating point precision.

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