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SpamAssassin's scores were assigned using a genetic algorithm in versions up to 3.0.0. A good intro on genetic algorithms can be found here:

Wiki MarkupVersions since 3.0.0 are now using a perceptron, written by Henry Stern, to perform the same task (but a lot faster); his program 'implements the "Stochastic Gradient Descent" method of training a neural network. It uses a single perceptron with a logsig activation function and maps the weights to [SpamAssassin] score space.' See the file "\[ masses/README.perceptron\]" for more details.

See RescoringProcess for further details.