[Numpy-discussion] inversion of large matrices

David Warde-Farley dwf@cs.toronto....
Tue Aug 31 15:31:52 CDT 2010

On 2010-08-30, at 10:19 PM, Dan Elliott wrote:

> You don't think this will choke on a large (e.g. 10K x 10K) covariance matrix?  

That depends. Is it very close to being rank deficient?That would be my main concern. NumPy/LAPACK will have no trouble Cholesky-decomposing a matrix this big, presuming the matrix is well-behaved/full rank. Depending on your hardware it will be slow, but the Cholesky decomposition will be faster (I think usually by about a factor of 2) than other methods that do not assume positive-definiteness.

At any rate, inverting the matrix explicitly will take longer and be quite a bit worse in terms of the eventual accuracy of your result.

> Given what you know about how it computes the log determinant and how the 
> Cholesky decomposition, do you suppose I would be better off using eigen-
> decomposition to do this since I will also get the determinant from the sum of 
> the logs of the eigenvalues?

You could do it this way, though I am not certain of the stability concerns (and I'm in the middle of a move so my copy of Golub and Van Loan is packed up somewhere). I know that the SVD is used in numpy.leastsq, so it can't be that bad. I've never used covariance matrices quite so big that computing the determinant was a significant cost.

One thing to note is that you should definitely not be solving the system for every single RHS vector separately. scipy.linalg.solve supports matrix RHSes, and will only do the matrix factorization (be it LU or Cholesky) once, requiring only the O(n^2) forward/backsubstitution to be done repeatedly. This will result in significant savings:

In [5]: X = randn(10000,20000)

In [6]: Y = dot(X, X.T)

In [7]: timeit scipy.linalg.solve(Y, randn(10000), sym_pos=True)
10 loops, best of 3: 78.6 s per loop

In [8]: timeit scipy.linalg.solve(Y, randn(10000, 50), sym_pos=True)
10 loops, best of 3: 81.6 s per loop


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