Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners

Abstract

This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a non-gradient neural network. Biological sequences can be viewed as data components with higher non-fixed dimensions, which correspond to the length of the sequences. Through computational procedures such as one-hot encoding, numerical encoding plays an important role in DNA sequence evaluation (OHE). However, the OHE method has some disadvantages: (1) It does not add any details that could result in an additional predictive variable, and (2) if the variable has many classes, OHE significantly expands the feature space. To address these shortcomings, this chapter proposes a computationally efficient framework for classifying DNA sequences of living organisms in the image domain. A multilayer perceptron trained by a pseudoinverse learning autoencoder (PILAE) algorithm is used in the proposed strategy. The learning control parameters and the number of hidden layers do not have to be specified during the PILAE training process. As a result, the PILAE classifier outperforms other deep neural network (DNN) strategies such as the VGG-16 and Xception models.