The theorem of Ahlbrandt and Ziegler says that two countable $\omega$-categorical structures $M$ and $N$ are bi-interpretable if and only if $Aut(M)\cong Aut(N)$ as topological groups.
Dropping the hypothesis of $\omega$-categoricity, the implication from left to right it is still true? I have read the original paper "Quasi finitely axiomatizable totally categorical theories" but there are a lot of details left to the reader.
So,in another word, my question is :
Let $M,N$ two countable structure. If they are bi-interpretable, then $Aut(M)\cong Aut(N)$ as topological groups?
Is there some references about it?
Yes, this is true even without the countability hypothesis. See Hodges Model Theory Section 5.4 Exercise 8(b) on p. 226.
This is a fairly straightforward exercise (though there are a lot of details to check). Here's an outline.