[SciPy-user] Calculating a lot of (squared) Mahalanobis distances

Robert Kern robert.kern@gmail....
Thu Nov 6 21:44:22 CST 2008

On Thu, Nov 6, 2008 at 21:36, David Warde-Farley <dwf@cs.toronto.edu> wrote:
> Hi folks,
> I'm trying to calculate a lot of Mahalanobis distances (in essence,
> applying a positive definite quadratic x.T * A * x to a lot of vectors
> x) and trying to think of the fastest way to do it with numpy.
> If I've got a single vector x and a 2D array sigmainv, then I've got
> something like this.
> import numpy as np
> ...
> xmmu = x - mu
> dist = np.dot(xmmu, np.dot(sigmainv, xmmu))
> However if I've got a DxN 2d array of N different vectors for which I
> want this quantity, it seems I can either use a loop or do something
> like
> xmmu = x - mu[:,np.newaxis]
> dist = np.diag(xmmu, np.dot(sigmainv, xmmu)))
> It seems like a lot of wasted computation to throw out the off-
> diagonals. One thought I've had would be to diagonalize sigmainv and
> then do something tricky with scalar products and broadcasting the
> diagonal, but I am not sure whether that would save me much.
> Does anyone have any other tricks up their sleeve?

(xmmu * np.dot(sigmainv, xmmu)).sum(axis=0)

Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
  -- Umberto Eco

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