A Hybrid Levenberg–Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models

Abstract

We have studied the ability of three types of neural networks to predict the closeness of a given protein model to the native structure associated with its sequence. We show that a partial combination of the Levenberg–Marquardt algorithm and the back-propagation algorithm produced the best results, giving the lowest error and largest Pearson correlation coefficient. We also find, as previous studies, that adding associative memory to a neural network improves its performance. Additionally, we find that the hybrid method we propose was the most robust in the sense that other configurations of it experienced less decline in comparison to the other methods. We find that the hybrid networks also undergo more fluctuations on the path to convergence. We propose that these fluctuations allow for better sampling. Overall we find it may be beneficial to treat different parts of a neural network with varied computational approaches during optimization.