How should I state my MS degree in my CV when it was in practice a joint-program?
I would strongly recommend listing your degrees the same way they were awarded and (probably) printed on your diploma. You can add, of course, that your specialization was in the subfield of machine learning. This clearly separates the official title from your more specific description. 

You wouldn't want someone who needed to check items on your CV to find that you are claiming something that you didn't "earn" and the university doesn't even "award". 

This is true for nearly everyone, in fact. My degree is in Mathematics but my field was actually Real Analysis, so I can say PhD Mathematics (Real Analysis) honestly enough.