Naming anything alien can be a pain, in my experience.
Does the Intelligence get to choose its own name, or is a name given to it? If the latter is the case (depending on context, of course) it might simply be referred to as 'AI' or 'computer' or even 'machine'. If it gets choice, it might not choose a name so much as reference some historic event or individual, or perhaps even name itself in binary or some other machine code.
I know I didn't answer with any suggestions as such, but I thought I'd share some ideas. That said, I'm struggling with names for my human AIs, much less the alien intelligences.