Dy-mer: An Explainable DNA Sequence Representation Scheme using Sparse Recovery

Abstract

DNA sequences encode vital genetic and biological information, yet these unfixed-length sequences cannot serve as the input of common data mining algorithms. Hence, various representation schemes have been developed to transform DNA sequences into fixed-length numerical representations. However, these schemes face difficulties in learning high-quality representations due to the complexity and sparsity of DNA data. Additionally, DNA sequences are inherently noisy because of mutations. While several schemes have been proposed for their effectiveness, they often lack semantic structure, making it difficult for biologists to validate and leverage the results. To address these challenges, we propose \textbf{Dy-mer}, an explainable and robust DNA representation scheme based on sparse recovery. Leveraging the underlying semantic structure of DNA, we modify the traditional sparse recovery to capture recurring patterns indicative of biological functions by representing frequent K-mers as basis vectors and reconstructing each DNA sequence through simple concatenation. Experimental results demonstrate that \textbf{Dy-mer} achieves state-of-the-art performance in DNA promoter classification, yielding a remarkable \textbf{13\%} increase in accuracy. Moreover, its inherent explainability facilitates DNA clustering and motif detection, enhancing its utility in biological research.