Classification of SARS-CoV-2 viral genome sequences using Neurochaos Learning

• Published in: Medical & biological engineering & computing Vol. 60; no. 8; pp. 2245 - 2255
• Main Authors: Harikrishnan, N. B., Pranay, S. Y., Nagaraj, Nithin
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.08.2022; Springer Nature B.V
• Subjects: Algorithms; Bayesian analysis; Biomedical and Life Sciences; Biomedical Engineering and Bioengineering; Biomedicine; Classification; Clinical trials; Computer Applications; Coronaviruses; Deep learning; Gene sequencing; Genomes; Human Physiology; Imaging; Influenza; Learning algorithms; Machine learning; Neural networks; Nucleotide sequence; Original; Original Article; Pest outbreaks; Public health; Radiology; Rhinovirus; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Training; Viral diseases; Viruses; Neurochaos; SARS-CoV-2; Genome classification; Machine learning; Universal approximation theorem
• ISSN: 0140-0118; 1741-0444
• DOI: 10.1007/s11517-022-02591-3

The high spread rate of SARS-CoV-2 virus has put the researchers all over the world in a demanding situation. The need of the hour is to develop novel learning algorithms that can effectively learn a general pattern by training with fewer genome sequences of coronavirus. Learning from very few training samples is necessary and important during the beginning of a disease outbreak when sequencing data is limited. This is because a successful detection and isolation of patients can curb the spread of the virus. However, this poses a huge challenge for machine learning and deep learning algorithms as they require huge amounts of training data to learn the pattern and distinguish from other closely related viruses. In this paper, we propose a new paradigm – Neurochaos Learning (NL) for classification of coronavirus genome sequence that addresses this specific problem. NL is inspired from the empirical evidence of chaos and non-linearity at the level of neurons in biological neural networks. The average sensitivity, specificity and accuracy for NL are 0.998, 0.999 and 0.998 respectively for the multiclass classification problem (SARS-CoV-2, Coronaviridae, Metapneumovirus, Rhinovirus and Influenza) using leave one out crossvalidation. With just one training sample per class for 1000 independent random trials of training, we report an average macro F1-score > 0.99 for the classification of SARS-CoV-2 from SARS-CoV-1 genome sequences. We compare the performance of NL with K-nearest neighbours (KNN), logistic regression, random forest, SVM, and naïve Bayes classifiers. We foresee promising future applications in genome classification using NL with novel combinations of chaotic feature engineering and other machine learning algorithms. Graphical abstract