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首页> 外文期刊>Annals of Biomedical Engineering >An Optimal Cutting-Plane Algorithm for Solving the Non-Unique Probe Selection Problem
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An Optimal Cutting-Plane Algorithm for Solving the Non-Unique Probe Selection Problem

机译：解决非唯一探针选择问题的最优割平面算法

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The non-unique probe selection problem consists of selecting oligonucleotide probes for use in hybridization experiments in which target viruses or bacteria are to be identified in biological samples. The presence or absence of these targets is determined by observing whether selected probes bind to their corresponding sequences. The goal is to select a probe set that is able to uniquely identify targets while containing a minimal number of probes. This paper contributes the first exact method for finding optimal solutions to the non-unique probe selection problem within practical computational limits, without the a priori elimination of candidate probes. Previously published methods have employed heuristics to find approximate solutions that are not provably optimal, and as a result, no knowledge has been obtained regarding the quality of those solutions relative to optimality. We demonstrate that our approach consistently finds an optimal solution to the non-unique probe selection problem within 10 min, and is capable of reducing the number of probes required over state-of-the-art heuristic techniques by as much as 20%.
机译：非唯一探针选择问题包括选择用于杂交实验的寡核苷酸探针，其中要在生物样品中鉴定靶病毒或细菌。通过观察所选探针是否结合至其相应序列来确定这些靶标的存在与否。目的是选择一种探针集，该探针集能够在包含最少数量的探针的同时唯一地识别目标。本文为在不事先消除候选探针的情况下，在实际计算范围内找到非唯一探针选择问题的最佳解决方案提供了第一种精确方法。先前发布的方法已采用启发式方法来找到无法证明是最优的近似解，因此，尚未获得有关这些解相对于最优性的质量的知识。我们证明了我们的方法始终能够在10分钟内找到针对非唯一探针选择问题的最佳解决方案，并且能够将最先进的启发式技术所需的探针数量减少多达20％。

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