You can use the create_using= keyword to specify what kind of graph
you want like this:
In [1]: import numpy as np
In [2]: import networkx as nx
In [3]: A=np.matrix([[1,2],[3,0]])
In [4]: G=nx.from_numpy_matrix(A,create_using=nx.MultiDiGraph())
In [5]: G.edges(data=True)
Out[5]: [(0, 0, {'weight': 1}), (0, 1, {'weight': 2}), (1, 0, {'weight': 3})]
In [6]: A
Out[6]:
matrix([[1, 2],
[3, 0]])
Aric