LGANN - A PARALLEL SYSTEM COMBINING A LOCAL GENETIC ALGORITHM AND NEURAL NETWORKS FOR THE PREDICTION OF SECONDARY STRUCTURE OF PROTEINS

In this work we describe a parallel system consisting of feed-forward neural networks supervised by a local genetic algorithm. The system is implemented in a transputer architecture and is used to predict the s econdary structures of globular proteins. This method alloys a wide se arch in the parameter space of the neural networks and the determinati on of their optimal topology for the predictive task. Different neural network topologies are selected by the genetic algorithm on the basis of minimal values of mean square errors on the testing set. When the alpha-helix, beta-strand and random coil motifs of secondary structure s are discriminated, the maximal efficiency obtained is 0.62, with cor relation coefficients of 0.35, 0.31 and 0.37 respectively. This level of accuracy is similar to that previously attained by means of neural networks without hidden layers and using single protein sequences as i nput. The results validate the neural network topologies used for the prediction of protein secondary structures and highlight the relevance of the input information in determining the limit of their performanc e.