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Improved most recent edits by the OP to make them consistent with the notational suggestion in one of the anwers. In particular, the OP's main interest, namely $q(G)$, has been given a simpler notation, not emphasizing the `relativeness' of it (since this is what the OP is interested in anyway).
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We are given a graph $G=(V,E)$, which has clique number $k$. The graph invariant in question is given by

$$q(g)=\min_T \min_{A\subset T} |T|-|A|$$$$q_{\mathrm{a}}(G)=\min_T \min_{A\subset T} |T|-|A|$$

Wherewhere $T$ is a transversal of the maximum cliques;cliques of $G$; that is, a set with nonempty intersection with every $k$-clique, and $A$ a subset of $T$ that is an independent set in $G$. The question is this: how large can this quantity$q_{\mathrm{a}}(G)$ get compared to the number of vertices $|V|$, of the graph $G$? The key figure of merit is

$$q_k= \sup_{G, \, \omega(G)=k}q_r(G) ,$$$$q_k= \sup_{G, \, \omega(G)=k}q(G) ,$$ where $$q_r(G)=\frac{q(G)}{|G|}.$$$$q(G)=\frac{q_{\mathrm{a}}(G)}{|G|}.$$

Both upper and lower bounds are of great interest.

This problem is motivated by quantum foundations considerations, that I could elucidate if helpful.

We are given a graph $G=(V,E)$, which has clique number $k$. The graph invariant in question is given by

$$q(g)=\min_T \min_{A\subset T} |T|-|A|$$

Where $T$ is a transversal of the maximum cliques; that is, a set with nonempty intersection with every $k$-clique, and $A$ a subset of $T$ that is an independent set in $G$. The question is this: how large can this quantity get compared to the number of vertices $|V|$, of the graph $G$? The key figure of merit is

$$q_k= \sup_{G, \, \omega(G)=k}q_r(G) ,$$ where $$q_r(G)=\frac{q(G)}{|G|}.$$

Both upper and lower bounds are of great interest.

This problem is motivated by quantum foundations considerations, that I could elucidate if helpful.

We are given a graph $G=(V,E)$, which has clique number $k$. The graph invariant in question is given by

$$q_{\mathrm{a}}(G)=\min_T \min_{A\subset T} |T|-|A|$$

where $T$ is a transversal of the maximum cliques of $G$; that is, a set with nonempty intersection with every $k$-clique, and $A$ a subset of $T$ that is an independent set in $G$. The question is: how large can $q_{\mathrm{a}}(G)$ get compared to the number of vertices $|V|$? The key figure of merit is

$$q_k= \sup_{G, \, \omega(G)=k}q(G) ,$$ where $$q(G)=\frac{q_{\mathrm{a}}(G)}{|G|}.$$

Both upper and lower bounds are of great interest.

This problem is motivated by quantum foundations considerations, that I could elucidate if helpful.

edited body
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We are given a graph $G=(V,E)$, which has clique number $k$. The graph invariant in question is given by

$$q(g)=\min_T \min_{A\subset T} |T|-|A|$$

Where $T$ is a transversal of the maximum cliques; that is, a set with nonempty intersection with every $k$-clique, and $A$ a subset of $T$ that is an independent set in $G$. The question is this: how large can this quantity get compared to the number of vertices $|V|$, of the graph $G$? The key figure of merit is

$$q_k= \sup_{G, \, \omega(G)=k}q_r(G) .$$$$q_k= \sup_{G, \, \omega(G)=k}q_r(G) ,$$ where $$q_r(G)=\frac{q(G)}{|G|}.$$

Both upper and lower bounds are of great interest.

This problem is motivated by quantum foundations considerations, that I could elucidate if helpful.

We are given a graph $G=(V,E)$, which has clique number $k$. The graph invariant in question is given by

$$q(g)=\min_T \min_{A\subset T} |T|-|A|$$

Where $T$ is a transversal of the maximum cliques; that is, a set with nonempty intersection with every $k$-clique, and $A$ a subset of $T$ that is an independent set in $G$. The question is this: how large can this quantity get compared to the number of vertices $|V|$, of the graph $G$? The key figure of merit is

$$q_k= \sup_{G, \, \omega(G)=k}q_r(G) .$$ where $$q_r(G)=\frac{q(G)}{|G|}.$$

Both upper and lower bounds are of great interest.

This problem is motivated by quantum foundations considerations, that I could elucidate if helpful.

We are given a graph $G=(V,E)$, which has clique number $k$. The graph invariant in question is given by

$$q(g)=\min_T \min_{A\subset T} |T|-|A|$$

Where $T$ is a transversal of the maximum cliques; that is, a set with nonempty intersection with every $k$-clique, and $A$ a subset of $T$ that is an independent set in $G$. The question is this: how large can this quantity get compared to the number of vertices $|V|$, of the graph $G$? The key figure of merit is

$$q_k= \sup_{G, \, \omega(G)=k}q_r(G) ,$$ where $$q_r(G)=\frac{q(G)}{|G|}.$$

Both upper and lower bounds are of great interest.

This problem is motivated by quantum foundations considerations, that I could elucidate if helpful.

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We are given a graph $G=(V,E)$, which has clique number $k$. The graph invariant in question is given by

$$\min_T \min_{A\subset T} |T|-|A|$$$$q(g)=\min_T \min_{A\subset T} |T|-|A|$$

Where $T$ is a transversal of the maximum cliques; that is, a set with nonempty intersection with every $k$-clique, and $A$ a subset of $T$ that is an independent set in $G$. The question is this: how large can this quantity get compared to the number of vertices $|V|$, of the graph $G$? The key figure of merit is

In particular, I would also be interested in how this varies with the clique number $k$.$$q_k= \sup_{G, \, \omega(G)=k}q_r(G) .$$ where $$q_r(G)=\frac{q(G)}{|G|}.$$

Both upper and lower bounds are of great interest.

This problem is motivated by quantum foundations considerations, that I could elucidate if helpful.

We are given a graph $G=(V,E)$, which has clique number $k$. The graph invariant in question is given by

$$\min_T \min_{A\subset T} |T|-|A|$$

Where $T$ is a transversal of the maximum cliques; that is, a set with nonempty intersection with every $k$-clique, and $A$ a subset of $T$ that is an independent set in $G$. The question is this: how large can this quantity get compared to the number of vertices $|V|$, of the graph $G$?

In particular, I would also be interested in how this varies with the clique number $k$. Both upper and lower bounds are of great interest.

This problem is motivated by quantum foundations considerations, that I could elucidate if helpful.

We are given a graph $G=(V,E)$, which has clique number $k$. The graph invariant in question is given by

$$q(g)=\min_T \min_{A\subset T} |T|-|A|$$

Where $T$ is a transversal of the maximum cliques; that is, a set with nonempty intersection with every $k$-clique, and $A$ a subset of $T$ that is an independent set in $G$. The question is this: how large can this quantity get compared to the number of vertices $|V|$, of the graph $G$? The key figure of merit is

$$q_k= \sup_{G, \, \omega(G)=k}q_r(G) .$$ where $$q_r(G)=\frac{q(G)}{|G|}.$$

Both upper and lower bounds are of great interest.

This problem is motivated by quantum foundations considerations, that I could elucidate if helpful.

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