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I'm trying to implement the NEAT Algorithm using c#, based off of Kenneth O. Stanley's paper. On page 109 (12 in the pdf) it states "Matching genes are inherited randomly, whereas disjoint genes (those that do not match in the middle) and excess genes (those that do not match in the end) are inherited from the more fit parent."
Does this mean that the child will always have the exact structure that the more fit parent has? It seems like the only way the structure could differ from crossover was if the two parents were equally fit.

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Yes, if you follow the original implementation the children will inherit the topology from the most fit parent.

Keep in mind that the goal is to obtain a good population, maintaining the genetic diversity high but at the same time selecting the best individuals from the population; so, in theory you are allowed to give the topology you prefer to the children.

Here there is an example of an alternative topology inheritance in which a child gets the genes that lead to an excess node while another child gets only the genes that create a new connection.

enter image description here

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