I am working on matrix multiplications in NumPy using np.dot(). As the data set is very large, I would like to reduce the overall run time as far as possible - ie perform as little as possible np.dot() products.
Specifically, I need to calculate the overall matrix product as well as the associated flow from each element of my values vector. Is there a way in NumPy to calculate all of this together in one or two np.dot() products? In the code below, is there a way to reduce the number of np.dot() products and still get the same output?
import pandas as pd
import numpy as np
vector = pd.DataFrame([1, 2, 3],
['A', 'B', 'C'], ["Values"])
matrix = pd.DataFrame([[0.5, 0.4, 0.1],
[0.2, 0.6, 0.2],
[0.1, 0.3, 0.6]],
index = ['A', 'B', 'C'], columns = ['A', 'B', 'C'])
# Can the number of matrix multiplications in this part be reduced?
overall = np.dot(vector.T, matrix)
from_A = np.dot(vector.T * [1,0,0], matrix)
from_B = np.dot(vector.T * [0,1,0], matrix)
from_C = np.dot(vector.T * [0,0,1], matrix)
print("Overall:", overall)
print("From A:", from_A)
print("From B:", from_B)
print("From C:", from_C)
If the vectors you use to select the row are indeed the unit vectors, you are much better off not doing matrix multiplication at all for from_A
, from_B
, from_C
. Matrix multiplication requires a lot more addition and multiplications than you need to just multiply each row of the matrix by it's corresponding entry in the vector:
from_ABC = matrix.values * vector.values
You will only need a single call to np.dot
to get overall
.
You could define a 3 x 3
shaped 2D
array of those scaling values and perform matrix-multiplication, like so -
scale = np.array([[1,0,0],[0,1,0],[0,0,1]])
from_ABC = np.dot(vector.values.ravel()*scale,matrix)
Sample run -
In [901]: from_A
Out[901]: array([[ 0.5, 0.4, 0.1]])
In [902]: from_B
Out[902]: array([[ 0.9, 1.6, 0.5]])
In [903]: from_C
Out[903]: array([[ 0.8, 1.3, 1.9]])
In [904]: from_ABC
Out[904]:
array([[ 0.5, 0.4, 0.1],
[ 0.9, 1.6, 0.5],
[ 0.8, 1.3, 1.9]])
Here's an alternative with np.einsum
to do all those in one step -
np.einsum('ij,ji,ik->jk',vector.values,scale,matrix)
Sample run -
In [915]: np.einsum('ij,ji,ik->jk',vector.values,scale,matrix)
Out[915]:
array([[ 0.5, 0.4, 0.1],
[ 0.9, 1.6, 0.5],
[ 0.8, 1.3, 1.9]])
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