Co-DeepNet: A Cooperative Convolutional Neural Network for DNA Methylation-Based Age Prediction

Prediction of the age of each individual is possible using the changing pattern of DNA methylation with age. In this paper an age prediction approach to work out multivariate regression problems using DNA methylation data is developed. In this research study a convolutional neural network (CNN)-based model optimised by the genetic algorithm (GA) is addressed. This paper contributes to enhancing age prediction as a regression problem using a union of two CNNs and exchanging knowledge between them. This specifically re-starts the training process from a possibly higher-quality point in different iterations and, consequently, causes potentially yeilds better results at each iteration. The method proposed, which is called cooperative deep neural network (Co-DeepNet), is tested on two types of age prediction problems. Sixteen datasets containing 1899 healthy blood samples and nine datasets containing 2395 diseased blood samples are employed to examine the method's efficiency. As a result, the mean absolute deviation (MAD) is 1.49 and 3.61 years for training and testing data, respectively, when the healthy data is tested. The diseased blood data show MAD results of 3.81 and 5.43 years for training and testing data, respectively. The results of the Co-DeepNet are compared with six other methods proposed in previous studies and a single CNN using four prediction accuracy measurements (R², MAD, MSE and RMSE). The effectiveness of the Co-DeepNet and superiority of its results is proved through the statistical analysis.