A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins

Paul Horton and Kenta Nakai

We have defined a simple model of classification which combines human provided expert knowledge with probabilistic reasoning. We have developed software to implement this model and have applied it to the problem of classifying proteins into their various cellular localization sites based on their amino acid sequences. Since our system requires no hand tuning to learn training data, we can now evaluate the prediction accuracy of protein localization sites by a more objective cross-validation method than earlier studies using production rule type expert systems. 336 E.coli proteins were classified into 8 classes with an accuracy of 81 percent while 1484 yeast proteins were classified into 10 classes with an accuracy of 55 percent. Additionally we report empirical results using three different strategies for handling continuously valued variables in our probabilistic reasoning system.

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