Finding squared distances beteen n points to m points in numpy

Question

I have 2 numpy arrays (say X and Y) which each row represents a point vector.
I would like to find the squared euclidean distances (will call this ‘dist’) between each point in X to each point in Y.
I would like the output to be a matrix D where D(i,j) is dist(X(i) , Y(j)).

I have the following python code based on : http://nonconditional.com/2014/04/on-the-trick-for-computing-the-squared-euclidian-distances-between-two-sets-of-vectors/

def get_sq_distances(X, Y):
    a = np.sum(np.square(X),axis=1,keepdims=1)
    b = np.ones((1,Y.shape[0]))
    c = a.dot(b)
    a = np.ones((X.shape[0],1))
    b = np.sum(np.square(Y),axis=1,keepdims=1).T
    c += a.dot(b)
    c -= 2*X.dot(Y.T)
    return c

I’m trying to avoid loops (should I?) and to use matrix multiplication in order to do a fast computation.

But I have the problem with "Memory Error" on large arrays. Maybe there is a better way to do this?

Asked By: member555

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Source

Answer 1

Scipy has the cdist function that does exactly what you want:

from scipy.spatial import distance
distance.cdist(X, Y, 'sqeuclidean')

The docs linked above have some good examples.

Answered By: Mad Physicist

Answer 2

subtract lists, then square the list, then do sum.

import numpy as np
def get_sq_distances(a,b):
    return np.sum(np.square(np.subtract(a,b)))
print(get_sq_distances([5,7,9],[4,5,6]))

Answered By: ben_stays_anonymous

Finding squared distances beteen n points to m points in numpy

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