CAKR: commutative algebra k-mer representations for genomics

Abstract

Despite the availability of various sequence analysis models, comparative genomic analysis remains a challenge in genomics, genetics, and phylogenetics. Commutative algebra, a fundamental tool in algebraic geometry and number theory, has rarely been used in data and biological sciences. In this study, we introduce commutative algebra k-mer representations as a nonlinear algebraic framework for analyzing genomic sequences. This representation bridges commutative algebra, algebraic topology, combinatorics, and machine learning to establish a mathematical framework for comparative genomic analysis. We evaluate its effectiveness on three tasks including genetic variant classification, phylogenetic tree reconstruction, and viral classification, typically requiring alignment-based, alignment-free, and machine-learning approaches, respectively. In this work, we show that commutative algebra k-mer representations outperform five state-of-the-art sequence analysis methods across twelve primary datasets, with two additional supplementary fragment-placement benchmarks, especially in viral classification, and maintain relatively stable predictive accuracy as dataset size increases, underscoring scalability and robustness. Comparative genomic analysis remains a fundamental challenge in genomics, genetics and phylogenetics, motivating the development of new mathematical frameworks for sequence comparison. The authors introduce a commutative algebra k-mer representation that integrates concepts from algebra, topology, combinatorics and machine learning, and evaluate its application to genetic variant classification, phylogenetic tree reconstruction and viral classification.