It's interesting to see the Machine progressing into figuring out friend versus foe.

In Season 1 - Nathan Ingram, Price of the Machine, at around 25 seconds in this video, the machine is determining who nathan is, and once weeks passes in front of him, the machine finally realizes who nathan is and puts the yellow box around him. however, more interestingly, once the machine recognizes alicia, the machine also puts a yellow box around her. also, the machine initially puts a yellow box around weeks, but as weeks talks and clearly is not happy with not having any other choice, the machine recognizes the tacit threat and changes weeks' box from yellow to red. once sentence by weeks, a sentence that on its face merely states frustration, and the machine figures him out.

like a child, everyone is a friend in the beginning. that one scene gives some insight into how the machine thinks.

Person Of Interest (1x11) - Nathan Ingram, Price of the Machine