arXiv:2602.22551math.OCcs.LG2026-02

用高效算法快速找到癌症关键基因组合,无需超级计算机。

Identifying Multi-Hit Cancer Drivers Without Massive Parallelization: A CP, MIP, and Column Generation Framework

  • 提出约束规划与整数规划框架,优化基因组合选择。
  • 单核CPU下1分钟内完成计算,效果媲美超算。
  • 首次证明半数以上案例的解为最优,适合研究者探索新模型。

癌症常由2至9个基因突变组合驱动,识别这些多击组合对理解癌变机制和设计靶向治疗至关重要。本文将该问题形式化为多击癌症驱动集覆盖问题(MHCDSCP),目标是在最大化肿瘤覆盖的同时严格最小化正常样本误判。现有方法依赖穷举和大规模并行计算,而本文提出基于约束规划与混合整数规划的快速启发式算法。在真实癌症基因组数据上评估,该框架仅用单个通用CPU即可在1分钟内达到超算级性能。此外,提出的定价-分支启发式通过最优求解根节点,首次为超过一半基准实例提供可证明最优解,验证了快速启发式近似最优性。结果表明,实际问题实例的计算复杂度远低于以往认知,为探索此前不可行的多击建模假设提供了可及基线。

原文摘要 · Abstract (English)

Cancer is often driven by specific combinations of an estimated two to nine gene mutations, known as multi-hit combinations. Identifying these multi-hit combinations of gene mutations that drive cancer is critical for understanding carcinogenesis and designing targeted therapies. We formalize this challenge as the Multi-Hit Cancer Driver Set Cover Problem (MHCDSCP), optimizing the selection of gene combinations to maximize tumor coverage while strictly minimizing normal sample misclassification. While existing approaches rely on exhaustive enumeration and massive parallelization, we introduce fast heuristics based on constraint programming and mixed integer programming formulations. Evaluated on real-world cancer genomics data, our framework matches state-of-the-art supercomputing methods using a single commodity CPU in under a minute. We also propose a price-and-branch heuristic which, by solving the root node to optimality, provides the first provably optimal solutions for over half of the benchmark instances, thereby verifying the near-optimality of our fast heuristics. These findings demonstrate that on real-world problem instances, the MHCDSCP is far less computationally demanding than previously believed, providing an accessible baseline that enables the exploration of previously intractable multi-hit modeling assumptions.

癌症基因组合优化高效算法

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