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I created a CSR matrix X and then copied it to another variable X1 by X1=X. Now when I change any value in X, the changes are reflected in X1 too. How can I keep the value of X1 unchanged because I need the original value in each iterations?

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X1 and X are both pointers. When you use X1=X, you assign the address of X to X1 and hence any change in X is reflected in X1. It will happen with array, list, dictionary data structures too. There are a couple of ways you can try.

Approach 1: Use copy module

>>> import numpy as np

>>> from scipy.sparse import csr_matrix

>>> from copy import deepcopy

>>> row = np.array([0, 0, 1, 2, 2, 2,3,4,4])

>>> col = np.array([0, 2, 2, 0, 1, 2,2,0,2])

>>> data = np.array([1]*len(row))

>>> X=csr_matrix((data, (row, col)), shape=(5, 3))

>>> X

<5x3 sparse matrix of type '<type 'numpy.int32'>'

        with 9 stored elements in Compressed Sparse Row format>

>>> X.toarray()

array([[1, 0, 1],

       [0, 0, 1],

       [1, 1, 1],

       [0, 0, 1],

       [1, 0, 1]])

>>> X1=deepcopy(X)

>>> X1.toarray()

array([[1, 0, 1],

       [0, 0, 1],

       [1, 1, 1],

       [0, 0, 1],

       [1, 0, 1]])

>>> X[1]=[1,2,3]

>>> X.toarray()

array([[1, 0, 1],

       [1, 2, 3],

       [1, 1, 1],

       [0, 0, 1],

       [1, 0, 1]])

>>> X1.toarray()

array([[1, 0, 1],

       [0, 0, 1],

       [1, 1, 1],

       [0, 0, 1],

       [1, 0, 1]])

Approach 2: Using ':' 

>>> import numpy as np

>>> from scipy.sparse import csr_matrix

>>> row = np.array([0, 0, 1, 2, 2, 2,3,4,4])

>>> col = np.array([0, 2, 2, 0, 1, 2,2,0,2])

>>> data = np.array([1]*len(row))

>>> X=csr_matrix((data, (row, col)), shape=(5, 3))

>>> X.toarray()

array([[1, 0, 1],

       [0, 0, 1],

       [1, 1, 1],

       [0, 0, 1],

       [1, 0, 1]])

>>> X1=X[:]

>>> X1.toarray()

array([[1, 0, 1],

       [0, 0, 1],

       [1, 1, 1],

       [0, 0, 1],

       [1, 0, 1]])

>>> X[1]=[1,2,3]

>>> X.toarray()

array([[1, 0, 1],

       [1, 2, 3],

       [1, 1, 1],

       [0, 0, 1],

       [1, 0, 1]])

>>> X1.toarray()

array([[1, 0, 1],

       [0, 0, 1],

       [1, 1, 1],

       [0, 0, 1],

       [1, 0, 1]])

...