Numpy: Vectorize Sum Of Distances To A Set Of Points

I'm trying to implementing a k-medoids clustering algorithm in Python/NumPy. As part of this algo, I have to compute the sum of distances from objects to their 'medoids' (cluster r

Solution 1:

How about:

In [17]: D[np.arange(n_samples),medoids[cl]].sum()
Out[17]: 10.777269629999999