Given a (finite or infinite) subset $X$ of the free monoid $A^*$ over a finite alphabet $A$, the rank of $X$ is the minimal cardinality of a set $F$ such that $X \subseteq F^*$. A submonoid $M$ generated by $k$ elements of $A^*$ is $k$-maximal if there does not exist another submonoid generated by at most $k$ words containing $M$. We call a set $X \subseteq A^*$ primitive if it is the basis of a $|X|$-maximal submonoid. This extends the notion of primitive word: indeed, $\{w\}$ is a primitive set if and only if $w$ is a primitive word. By definition, for any set $X$, there exists a primitive set $Y$ such that $X \subseteq Y^*$. The set $Y$ is therefore called a primitive root of $X$. As a main result, we prove that if a set has rank $2$, then it has a unique primitive root. This result cannot be extended to sets of rank larger than 2. For a single word $w$, we say that the set $\{x,y\}$ is a {\em binary root} of $w$ if $w$ can be written as a concatenation of copies of $x$ and $y$ and $\{x,y\}$ is a primitive set. We prove that every primitive word $w$ has at most one binary root $\{x,y\}$ such that $|x|+|y|<\sqrt{|w|}$. That is, the binary root of a word is unique provided the length of the word is sufficiently large with respect to the size of the root. Our results are also compared to previous approaches that investigate pseudo-repetitions, where a morphic involutive function $θ$ is defined on $A^*$. In this setting, the notions of $θ$-power, $θ$-primitive and $θ$-root are defined, and it is shown that any word has a unique $θ$-primitive root. This result can be obtained with our approach by showing that a word $w$ is $θ$-primitive if and only if $\{w, θ(w)\}$ is a primitive set.