Graph-based semi-supervised learning with genomic data integration using condition-responsive genes applied to phenotype classification

Journal of the American Medical Informatics Association : JAMIA
Abolfazl Doostparast Torshizi, Linda R Petzold

Abstract

Data integration methods that combine data from different molecular levels such as genome, epigenome, transcriptome, etc., have received a great deal of interest in the past few years. It has been demonstrated that the synergistic effects of different biological data types can boost learning capabilities and lead to a better understanding of the underlying interactions among molecular levels. In this paper we present a graph-based semi-supervised classification algorithm that incorporates latent biological knowledge in the form of biological pathways with gene expression and DNA methylation data. The process of graph construction from biological pathways is based on detecting condition-responsive genes, where 3 sets of genes are finally extracted: all condition responsive genes, high-frequency condition-responsive genes, and P-value-filtered genes. The proposed approach is applied to ovarian cancer data downloaded from the Human Genome Atlas. Extensive numerical experiments demonstrate superior performance of the proposed approach compared to other state-of-the-art algorithms, including the latest graph-based classification techniques. Simulation results demonstrate that integrating various data types enhances classification pe...Continue Reading

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Citations

Jul 11, 2020·Nature Reviews. Gastroenterology & Hepatology·Giovanni CammarotaGiampaolo Tortora
Jun 12, 2020·Journal of Biomedical Informatics·Zahra MomeniRiccardo Bellazzi
Jun 23, 2020·Reviews on Recent Clinical Trials·Payal BhardwajSojan Kurian

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