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Misha comments on Prisoner's Dilemma Tournament Results - Less Wrong
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Trouble is, when your bot plays itself it gets stuck in a loop, runs out of time and gets 0. This will make it very unlikely to ever rise to dominance in an evolutionary tournament.
Depending on how much time is allowed the following might be a viable solution: with a 1% chance cooperate, otherwise run the other bot's source code. If the bot plays itself, or for that matter any other bot that tries to run its source code, after 100 (on average) iterations it will return cooperate, and then working backwards will (usually) converge to the right thing.
Obviously, the value of 1% should be as small as possible; the average time used is proportional to the reciprocal of the probability.