Instead of simply "programming" a smart AI, their matrix is created by scanning and replicating the neural pathways of a human brain.This process destroys the original brain tissue, and so the brain being used is typically obtained after the host is dead.This process is still inefficient, however, as neural linkages are "wasted" in the process of the budding AI generating its own system of more efficient neural linkages to replace those of the seed brain, in turn eroding the AI's limited lifespan.
Because of the nature of this process the smart AI often retains residual thoughts, memories and/or feelings from the brain donor.These residuals can be anything from the "feeling" of a hair brush being pulled through hair (in the case of Sif),to an effect on the mannerisms and characteristics that make up the personality of an AI, in the case of Cortana and her likeness to Dr. Catherine Halsey as well as her possessing many of Halsey's memories, which surfaced during her descent into rampancy.When the Weapon is created from another one of Dr. Halsey's cloned brains, she is described as an exact copy of Cortana with the same routines and systems, but without all of her knowledge and history. While talking to John-117 about the Weapon, Halsey refers to her as "a blank slate."
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