Ellen and Link's Dad has a saying that he's been repeating to them since they were little kids:
Geeky is one of Dad's favorite words, and I listen with glee to my brother's imitation of our father: "Geeky people often have that which is most valuable in this life." Link pauses here for effect, so that James and I can join in, shouting Dad's favorite phrase, "A mind with its own heartbeat!"
He's trying to tell them, in his typically opaque way, that individuality and intellectual prowess are things that are highly valued. What's more interesting, though, is that his idea of individuality doesn't encompass all the different ways people can be different. His protestations over Link's possible gayness make him a bit of a hypocrite, do they not?
Either way, My Heartbeat is a very appropriate title because the story explores all the different ways Ellen, Link, and even James are struggling to establish what their mind's own heartbeat really means.