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Let $G=Z_2^n$ and $S\subset G$. Is there any relation for number of distinct eigenvalues of $\Gamma=Cayley(G,S)$ graph depending on $n$ and $|S|$, or at least diameter of $\Gamma$? If you have any hints or references would be appreciated?

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I don't think there any deep relations. The eigenvalues are integers, whence the number of distinct eigenvalues is at most $2|C|+1$ (and you can apply trhis to the complement). If the diameter is $d$, then the number of distinct eigenvalues is at least $d+1$. (Since a shortest path between two vertices must use each element of $C$ at most once, $d\le|C|$.)

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