I struggled to understand where "denote" is better than "be". For example:
Let A denote a vertex cover of the graph.
or
Let A be a vertex cover of the graph.
I struggled to understand where "denote" is better than "be". For example:
Let A denote a vertex cover of the graph.
or
Let A be a vertex cover of the graph.
Your example should use be.
We generally use the verb "denote" only if we're introducing a notation for an existing unique entity; hence "Let <notation> denote <entity>" nearly always involves an entity introduced with the, not a. For example:
So in your example, "denote" isn't appropriate, because any non-empty graph has multiple vertex covers, and we're choosing one of them arbitrarily; we can't just start "denoting" it without deciding which one it is. (If you really wanted to use the verb "denote" here, I suppose you could separate the "choose a vertex cover" step from the "define a notation" step — something like "We choose some vertex cover of the graph, and denote it by A" — but there's just no reason to do that.) By contrast, the formula "Let <symbol> be <characterization>" is a very standard way to combine selecting an entity with assigning it a name.
Note that even when "denote" is appropriate, "be" is still fine, and often preferable; for example, I'd expect to see "Let x be the greatest element of S", rather than "Let x denote the greatest element of S", even though there's nothing really wrong with the latter.
In the context of scientific work, "denote" means that you are introducing notation. For example:
A circumflex denotes the unit vector in the direction of a vector: $ \hat{x} = \frac{\vec{x}}{\left|\vec{x}\right|} $
Notice that you absolutely cannot say "A circumflex is the unit vector...", which makes no sense. When you are giving the complete name or symbol of the thing you want to denote, you can (and probably should) use the simpler word "is". For example:
$\hat{x}$ is the unit vector in the direction of $\vec{x}$.