Combination Safe

Congratulations, you're on your way to Honolulu. While searching the ship, you found a combination safe that looks important. It has a dial on it that you know needs three numbers for the combination. But what are the numbers?

While examining the safe, the girl you rescued—whose name you learned is Myia, named after one of Pythagoras' daughters—found the diagram below taped to the back of the safe. Could it have something to do with the combination that opens the safe? Would V.A.L.A. really be dumb enough to leave a puzzle taped to the safe that, if solved, would actually open it?