DNA methylation-based age prediction using cell separation algorithm

Abstract

The age of each individual can be predicted based on the alteration rule of DNA methylation with age. In this paper, an age prediction method is developed in order to solve multivariate regression problems from DNA methylation data, by optimizing the artificial neural network (ANN) model using a new proposed algorithm named the Cell Separation Algorithm (CSA). The CSA imitates cell separation action by using a differential centrifugation process involving multiple centrifugation steps and increasing the rotor speed in each step. The CSA performs similar to the centrifugal force in separating the solutions based on their objective function in different steps, with velocity increasing in each step. Firstly, 25 test functions are used to test the CSA. Secondly, the CSA is examined on three forms of age prediction problems from two body fluids (blood and saliva). The healthy blood samples, diseased blood samples and saliva samples are used to test the method's capability. The results of the CSA are compared not only with other methods proposed in previous studies, but also with the results from stochastic gradient descent (SGD), ADAM, and genetic algorithm (GA). The model results of CSA are extremely better than the four methods proposed in previous works that have not used ANN training process. The CSA also outperformed SGD, ADAM that employ the ANN model without ANN optimization by meta-heuristics. The CSA results are comparable (even superior) to the GA model which takes the advantages of both ANN and meta-heuristics.

Keywords: Age prediction; Cell separation algorithm; DNA methylation data; Regression.