GenEx: A Graph-Based Representational Paradigm for SARS-CoV-2 Variant Detection via Codon Co-occurrence Networks

arXiv cs.AIAugust 20, 2026en

arXiv:2608.18238v1 Announce Type: new Abstract: Genomic analysis on viruses such as SARS-CoV-2 variants: Beta, Gamma, Delta, and Omicron is heavily dominated by classical bioinformatics methods, including Sequence Alignment, Phylogenetic Analysis, and Mutation Frequency Statistics. These approaches use pairwise codon or nucleotide distance matrices to analyze gene sequences, treating them as linear strings rather than capturing their complex contextual interdependencies. We proposed GenEx, a pipeline that converts raw gene sequences into codon co-occurrence graphs and extracts more than 25 graph features. Our two most prominent techniques for graph generation and feature extraction are MSCG

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