MMF-SV: A Multi-Modal Feature Fusion-Based Structural Variant Caller

摘要

Structural variant (SV) calling plays a critical role in understanding genome diversity and disease mechanisms. Although deep learning techniques have been increasingly applied to SV identification, existing general-purpose models still face significant challenges, including incomplete extraction of alignment signals, limited accuracy and efficiency, and poor performance in highly polymorphic or structurally complex genomic regions. These limitations lead to suboptimal detection accuracy in current SV callers. In this work, we present MMF-SV, a multi-modal feature fusion-based model (MMF) for SV calling. MMF-SV integrates matching patterns and statistical information from CIGAR signals with textual features extracted from alignment information, enabling comprehensive representation of diverse SV signals. We trained MMF-SV using CLIP, and the trained model achieved over 96% F1 score for classifying various types of variations. We validated the stability and robustness of the MMF-SV model through 5-fold cross-validation. Compared to existing long-read SV callers, MMF-SV achieves higher accuracy and can be effectively integrated with them to significantly reduce the number of false positives in the calling results.