That depends.
Miracle is obviously a female, the way she lets you think you've won, then suddenly plays a miracle and crushes all your hopes and dreams...yep, she's a female.
I always imagined Siesem as a kind of stupid ogre/troll/rock thing. Since he lacks any subtlety in the way he continually kills you, It's safe to assume he is a male.
Dark Matter? Mets not go into that area. If you've ever studied Dark matter, you probbalbly don't want to know whether it is male or female, or just a mixture of the two. It's best left unknown, like dark matter.