Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.

Abstract

The DyGAF model, which stands for Dynamic Gene Attention Focus, is specifically designed and tailored to address the challenges in biomarker detection, progression reporting of pathogen infection, and disease diagnostics. The DyGAF model introduced a novel dual-model attention-based mechanism within neural networks, combined with machine learning algorithms to enhance the process of biomarker identification. The model transcended traditional diagnostic approaches by meticulously analyzing gene expression data. DyGAF not only identified but also ranked genes based on their significance, revealing a comprehensive list of the top genes essential for disease detection and prognosis. In addition, KEGG pathways, Wiki Pathways, and Gene Ontology-based analyses provided a multileveled evaluation of the genes' roles. In our analyses, we tailored COVID-19 gene expression profile from nasopharyngeal swabs that offer a more nuanced view of the intricate interplay between the host and the virus. The genes ranked by the DyGAF model were compared against those selected by differential expression analysis and random forest feature selection methods for further validation of our model. DyGAF demonstrated its prowess in identifying important biomarkers that could enrich gene ontologies and pathways crucial for elucidating the pathogenesis of COVID-19. Furthermore, DyGAF was also employed for diagnosing COVID-19 patients by classifying gene-expression profiles with an accuracy of 94.23%. Benchmarking against other conventional models revealed DyGAF's superior performance, highlighting its effectiveness in identifying and categorizing COVID-19 cases. In summary, DyGAF model represents a significant advancement in genomic research, providing a more comprehensive and precise tool for identifying key genetic markers and unraveling the complex biological insights of a disease. The DyGAF model is available as a software package at the following link: https://github.com/hiddenntreasure/DyGAF.