Couple questions...is it a hum/buzz or a bigger throb type sensation, where you can feel the braking cycle a little on a little off with the same lever pressure as the wheel rotates?
If it's the first, a light hum/buzz, try scuffing your pads a little as they may be glazed (This could be brought about by your braking habits or just a bad pad choice, by Ducati). If it goes away then you have found your culprit. Now if it comes back it might be as Chris pointed out, your pad compound. You could swap them out or if your on the cheap there is one more trick you can try. Here is the idea...Pull your pads out and file the leading edge of the pad at a slight angle, your beveling the edge of the pad. Not too far, just a little. Then reinstall them. Yamahas sometimes have buzzy brakes and this is one cure I've heard about and tried. It's worked great for me
Now, if it's the later and you feel a major pulse in the brakes, it's time for a warranty fix, or do what a lot of guys do and order up a set of cast iron full-floaters, slap some EBC HH pads in and have fun.
Good luck