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You just have to define your polynomials as elements of the polynomial ring $\mathbb{F}_2[x]$ as follows:

sage: R.<x> = GF(2)[]
sage: x.parent()
Univariate Polynomial Ring in x over Finite Field of size 2 (using GF2X)
sage: A = matrix([[25*x^3+50*x^2+1],[18*x+11]])
sage: A
[x^3 + 1]
[      1]