A machine learning-based treatment prediction model using whole genome variants of hepatitis C virus

Hiroaki Haga, Hidenori Sato, Ayumi Koseki, Takafumi Saito, Kazuo Okumoto, Kyoko Hoshikawa, Tomohiro Katsumi, Kei Mizuno, Taketo Nishina and Yoshiyuki Ueno

PLOS ONE, 2020, vol. 15, issue 11, 1-12

Abstract: In recent years, the development of diagnostics using artificial intelligence (AI) has been remarkable. AI algorithms can go beyond human reasoning and build diagnostic models from a number of complex combinations. Using next-generation sequencing technology, we identified hepatitis C virus (HCV) variants resistant to directing-acting antivirals (DAA) by whole genome sequencing of full-length HCV genomes, and applied these variants to various machine-learning algorithms to evaluate a preliminary predictive model. HCV genomic RNA was extracted from serum from 173 patients (109 with subsequent sustained virological response [SVR] and 64 without) before DAA treatment. HCV genomes from the 109 SVR and 64 non-SVR patients were randomly divided into a training data set (57 SVR and 29 non-SVR) and a validation-data set (52 SVR and 35 non-SVR). The training data set was subject to nine machine-learning algorithms selected to identify the optimized combination of functional variants in relation to SVR status following DAA therapy. Subsequently, the prediction model was tested by the validation-data set. The most accurate learning method was the support vector machine (SVM) algorithm (validation accuracy, 0.95; kappa statistic, 0.90; F-value, 0.94). The second-most accurate learning algorithm was Multi-layer perceptron. Unfortunately, Decision Tree, and Naive Bayes algorithms could not be fitted with our data set due to low accuracy (

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0242028

DOI: 10.1371/journal.pone.0242028

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