GPU-Powered Evolutionary Auxiliary Multitasking for Fast SNP Interaction Detection

Fangting Li, Ying Yin, Xin Wang, Changyong Yu, Yuhai Zhao, Ye Tian

Abstract: Identifying complex interactions among millions of single nucleotide polymorphisms (SNPs) is a key challenge in Genome-Wide Association Studies (GWAS), offering crucial insights into the genetic architecture of complex diseases. Evolutionary algorithm (EA)-based methods have gained significant attention for their global search capabilities, controllable runtime, and multi-objective optimization potential. However, when applied to high-dimensional GWAS datasets, many existing EA-based methods encounter challenges such as getting trapped in local optima and facing high computational demands. To address these issues, the evolutionary multitasking (EMT) paradigm presents a promising solution, enhancing population diversity and convergence speed through collaborative, cross-task knowledge sharing. Furthermore, the multi-tasking framework and EA can be seamlessly deployed across multiple Graphics Processing Units (GPUs), leveraging their high parallelism and aggregated memory bandwidth. Therefore, we introduce a GPU-powered evolutionary auxiliary multitasking algorithm (GEAMT) for fast SNP interaction detection. GEAMT first constructs a main task along with several low-dimensional auxiliary tasks to redefine the original task. The main task explores the entire search space, while the auxiliary tasks search distinct subspaces to enhance local optimization capabilities. In each iteration, the auxiliary tasks transfer high-quality information to the main task via an information transfer mechanism. Subsequently, an auxiliary task update strategy based on feature regrouping is employed to switch the search subspaces of the auxiliary tasks. The final results are derived from the Pareto-optimal solutions of the main task. Implemented across multiple GPUs, GEAMT achieves notable scalability and efficiency. Comprehensive experiments on both synthetic and real-world datasets demonstrate that GEAMT can significantly enhance search accuracy and speed up the search process.

External IDs:dblp:journals/tcbb/LiYWYZT25