We don't know that yet.
I still have the nagging suspicion that Hank Pym, who is seen to be considerably older in the MCU, worked with Howard Stark to create artificial intelligeance.
And naturally (like he did with the Arc Reactor technology), Tony used his father and Pym's work to create J.A.R.V.I.S. and Ultron.
Or maybe, it was Howard who designed Ultron, betraying Hank in the process.
Either way, I very much believe that, while he doesn't create Ultron himself, Hank Pym does create the technology that makes him (and J.A.R.V.I.S.) possible.