U-Net for genomic sequencing: A novel approach to DNA sequence classification

Abstract

The precise classification of DNA sequences is pivotal in genomics, holding significant implications for personalized medicine. The stakes are particularly high when classifying key genetic markers such as BRAC, related to breast cancer susceptibility; BRAF, associated with various malignancies; and KRAS, a recognized oncogene. Conventional machine learning techniques often necessitate intricate feature engineering and may not capture the full spectrum of sequence dependencies. To ameliorate these limitations, this study employs an adapted U-Net architecture, originally designed for biomedical image segmentation, to classify DNA sequences.The attention mechanism was also tested LONG WITH u-Net architecture to precisely classify DNA sequences into BRAC, BRAF, and KRAS categories. Our comprehensive methodology includes rigorous data preprocessing, model training, and a multi-faceted evaluation approach. The adapted U-Net model exhibited exceptional performance, achieving an overall accuracy of 0.96. The model also achieved high precision and recall rates across the classes, with precision ranging from 0.93 to 1.00 and recall between 0.95 and 0.97 for the key markers BRAC, BRAF, and KRAS. The F1-score for these critical markers ranged from 0.95 to 0.98. These empirical results substantiate the architecture's capability to capture local and global features in DNA sequences, affirming its applicability for critical, sequence-based bioinformatics challenges.

Keywords

• DNA sequence classification
• U-net architecture
• Deep learning
• Genomics
• Sequence data