Background <p>Structural variations (SVs) are a pervasive and impactful class of genetic variation within the genome, significantly influencing gene function, impacting human health, and contributing to disease. Recent advances in deep learning have shown promise for SV detection; however, current methods still encounter key challenges in effective feature extraction and accurately predicting complex variations.</p> Methods <p>We introduce SVEA, an advanced deep learning model designed to address these challenges. SVEA employs a novel multi-channel image encoding approach that transforms SVs into multi-dimensional image formats, improving the model’s ability to capture subtle genomic variations. Additionally, SVEA integrates multi-head self-attention mechanisms and multi-scale convolution modules, enhancing its ability to capture global context and multi-scale features. The model was trained and tested on a diverse range of genomic datasets to evaluate its accuracy and generalizability.</p> Results <p>SVEA demonstrated superior performance in detecting complex SVs compared to existing methods, with improved accuracy across various genomic regions. The multi-channel encoding and advanced feature extraction techniques contributed to the model’s enhanced ability to predict subtle and complex variations.</p> Conclusions <p>This study presents SVEA, a deep learning model incorporating advanced encoding and feature extraction techniques to enhance structural variation prediction. The model demonstrates high accuracy, outperforming existing methods by approximately 4%, while also identifying areas for further optimization.</p>