A systematic assessment of machine learning for structural variant filtering

Background Accurate discrimination of true structural variants (SVs) from artifacts in long-read sequencing data remains a critical bottleneck. Numerous machine learning solutions have been proposed, ranging from classical models using engineered features to advanced deep learning and foundation model interpretability methods. However, a systematic comparison of their performance, efficiency, and practical utility is lacking. Results We conducted a comprehensive benchmark of five machine learning paradigms for SV filtering using standardized Genome in a Bottle (GIAB) data for samples HG002 and HG005. We evaluated classical Random Forest classifiers on 15 genomic features, computer vision models (ResNet/VICReg), diffusion-based anomaly detection, sparse autoencoders (SAEs) on the Evo2-7B foundation model, and multimodal ensembles. A simple Random Forest on interpretable features achieved a peak F1-score of 95.7%, effectively matching all more complex models (ResNet50: 95.9%, Diffusion: 95.8%). This study represents the first application of diffusion-based anomaly detection and sparse autoencoders to structural variant analysis; while diffusion models learned highly discriminative, disentangled representations and SAEs uncovered biologically interpretable features (including atoms that were specific for ALU deletions, chromosome X variants and insertion events), they did not significantly surpass this classification ceiling. Ensemble methods offered no performance benefit but may have future potential given the orthogonality of vision-based and linear features. Conclusions Our findings demonstrate that for the established task of germline SV filtering, simpler, interpretable models provide an optimal balance of accuracy, speed, and transparency. This benchmark establishes a pragmatic framework for method selection and argues that increased model complexity must be justified by clear, unmet biological needs rather than marginal predictive gains.