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arXiv 2004.14351math.COcs.DS
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链圈图最短变换的几乎精确线性复杂度算法

An Almost Exact Linear Complexity Algorithm of the Shortest Transformation of Chain-Cycle Graphs

K. Yu. Gorbunov, V. A. Lyubetsky

摘要:

“基因组结构”是具有度为1或2的顶点的标记的有向图。在这样的图上的一组操作是固定的,并且每个操作都有一定的成本,严格为正数。转换问题包括以下内容:对于给定的结构a和b以及给定的成本,找到将a转换为b的操作的最小总成本序列(“a到b的最短转换”)。每个操作对应于一个“事件”,后者是由执行一个操作引起的图中的变化。分配不同成本的可能性在应用程序中很重要,因为它允许区分频繁和罕见的事件。显然,任意的成本使得问题成为NP难问题,这导致了从一个成本限制到另一个成本限制的非平凡性,如果问题是通过线性或至少多项式算法解决的(假设P不等于NP)。我们提出了一种新的线性时间和空间算法,该算法构造了一个操作序列,将a转换为b,总成本接近或等于绝对极小值。也就是说,如果所有所谓的DCJ操作具有相同的成本w,并且如果删除和插入的成本都大于或小于w,则算法输出a到b的变换,其中总成本与绝对极小值相差至多2w(在前一种情况下)或等于2w(在后一种情况下)。在某些情况下,算法输出精确解,例如,在圆形基因组结构的情况下。关于删除和插入的代价的条件可以省略(尽管下面描述的证明不包括这种一般情况)。

英文摘要:

A "genome structure" is a labeled directed graph with vertices of degree 1 or 2. A set of operations over such graphs is fixed, and each of the operations has a certain cost, a strictly positive number. The transformation problem consists in the following: for given structures a and b and given costs, find a minimum total cost sequence of operations transforming a into b ("the shortest transformation of a into b"). Each operation corresponds to an "event", the latter being a change in the graph caused by executing one of the operations over it. The possibility of assigning different costs is important in applications, since it allows to distinguish between frequent and rare events. Apparently, arbitrary costs make the problem NP-hard, which results in nontriviality of passing from one restriction on costs to another, if the problem is solved by a linear or at least polynomial algorithm (assuming that P is not equal NP). We propose a novel linear time and space algorithm which constructs a sequence of operations transforming a to b with total cost close or equal to the absolute minimum. Namely, if all the so-called DCJ operations have the same cost w and if deletions and insertions have costs either both larger or both less than w, then the algorithm outputs a transformation of a into b with the total cost differing from the absolute minimum by at most 2w (in the former case) or equal to it (in the latter case). In some cases, the algorithm outputs an exact solution, e.g., in the case of circular genome structures. The condition on the costs of deletions and insertions can be omitted (although the proof described below does not include this general case).

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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