Covariance Mean subtraction in Principal Component Analysis

Discussion in 'MATLAB' started by fearry, Sep 15, 2005.

  1. fearry

    fearry Guest

    I was just wondering what is the advantage of subtracting the Mean from the covariance matrix when computing PCA. Is it valid to Perform PCA without previously subtracting the mean.

    I am working with dimension reduction of images.From my experiments I am finding that reconstructions of images are much more accurate when I don't subtract the mean from the covariance when performing PCA.

    Can anyone help explain this?
    fearry, Sep 15, 2005
    1. Advertisements

  2. It's my understanding in the Chemometrics (Analytical Spectroscopy)
    community, that it's not a "true" PCA calculation w/o mean centering.

    If you do not mean center, the first factor will be very closely related
    to the mean.

    In the "old" days, when we used to do this sort of calculation in
    Fortran and were limited to single precision, there were some numerical
    issues for wanting to remove the mean, but I doubt if that's still
    really an issue in double precision.

    Frederick Koehler
    Frederick W. Koehler, Sep 15, 2005
    1. Advertisements

  3. Yes, you can do PCA without subtracting the mean. Its
    entirely valid. But almost certainly the first component
    will be heavily biased towards the mean.

    (By the way, if you do not subtract the mean, its not
    called a covariance matrix. I've typically seen it called
    a second moment matrix in that case.)

    Your statement that you get much more accuracy when the
    mean is not subtracted makes no sense. Are you comparing
    the fraction of the total variance explained by a fixed
    number of components? If so, its an invalid comparison,
    since with the mean in there the total sum of squares
    is strongly inflated. In terms of absolute predictive
    value the PCA based on the covariance matrix must be a
    better predictor (unless the mean was zero) when compared
    to the PCA based on the second moment matrix. This should
    be a mathematically provable statement.

    My guess is that you have either made a mistake in your
    reconstructions or the problem is the one I suggest

    John D'Errico
    John D'Errico, Sep 16, 2005
  4. fearry

    Rune Allnor Guest

    The reason why your analysis works better without the mean subtracted,
    probably that images are non-negative in the first place.

    As for why the mean is subtracted in general PCA, consider two
    orthogonal sinusoidals s1 and s2 defined as, say,

    s1 = [sqrt(3)/2 1/2]'
    s2 = [-1/2 sqrt(3)/2]'

    A signal that comprises these sinusoidals will come out fine with
    to the eigenvectors of the covariance matrix, that is hermitian an thus

    have orthogonal eigenvectors.

    Now, if you add a non-zero mean m to these vectors, the vectors
    v1 = m + s1 and v2 = m + s2 are no longer orthigonal. And so
    the relation between the signal components and the eigenvectors
    of the covariance matrix is no longer "easy" to deal with.

    But again, these considerations work for the parameter estimation
    problem of sinusoidsals. They need not apply to other types
    of signals, like images.

    Rune Allnor, Sep 16, 2005

  5. This is an interesting point of view. But one can still
    find an orthogonal basis for the vectors [v1,v2]. It simply
    won't be the original trig functions. Its still just as
    valid, and will still reconstruct the data as well.

    In fact, since the eigenvalues for the original set will be
    equal to each other, even the original trig functions may
    not be recovered, since eigenvectors corresponding to
    multiple eigenvalues are not unique.

    John D'Errico, Sep 16, 2005
  6. fearry

    Rune Allnor Guest

    Sure. This si the Karhunen-Love Transform, if I am not mistaken.
    My point is merely that one usally imposes some significance
    on the eigenvecors, that holds in the zero-mean case.

    This significance, which usually is the basis for whatever
    elaborate analysis one is up to, is then lost in the case
    of a non-zero mean.
    There are several ways of getting from a set of eigenvectors
    to trig functions. MUSIC uses the NULL space of the covariance
    matrix of the noise-free signal, and searches for the sines
    that are orthogonal to the null space.

    The Kumaresan-Tufts Forward-Backward Linear prediction scheme
    sets up a set of equatons from the eigenvectors of the signal
    space of the covariance matrix, and solves for the frequency

    But all these methods provide ambiguous results, due to
    cos(-x) = cos(x), so you basically need restrictions on
    the solution to get a unique answer. In some applications
    it might be useful to convert the data from a real-valued
    representation to a complex-valued representation to avoid
    the ambiguity due to Euler's equations,

    2cos(x) = exp(jx) + exp(-jx)
    j2sin(x) = exp(jx) - exp(-jx)


    Rune Allnor, Sep 20, 2005
    1. Advertisements

Ask a Question

Want to reply to this thread or ask your own question?

You'll need to choose a username for the site, which only take a couple of moments (here). After that, you can post your question and our members will help you out.