For syntax clarity consider using @ matrix multiply instead of Numpy .dot(). The performance with either syntax is the same.

import numpy as np
X = np.random.random((5000,5000))
Y = np.random.random((5000,5000))

%timeit X @ Y

1 loop, best of 3: 1.65 s per loop

%timeit X.dot(Y)

1 loop, best of 3: 1.65 s per loop

%timeit np.dot(X,Y)

1 loop, best of 3: 1.65 s per loop