Complexity and algorithms for Swap median and relation to other consensus problems

Abstract

Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to transform one genome into another. In a general scenario, more than two genomes are considered and we have new challenges. The {\sc Median} problem consists in finding, given three permutations and a distance metric, a permutation $s$ that minimizes the sum of the distances between $s$ and each input. We study the {\sc median} problem over \emph{swap} distances in permutations, for which the computational complexity has been open for almost 20 years (Eriksen, \emph{Theor. Compt. Sci.}, 2007). We consider this problem through some branches. We associate median solutions and interval convex sets, where the concept of graph convexity inspires the following investigation: Does a median permutation belong to every shortest path between one of the pairs of input permutations? We are able to partially answer this question, and as a by-product we solve a long open problem by proving that the {\sc Swap Median} problem is NP-hard. Furthermore, using a similar approach, we show that the {\sc Closest} problem, which seeks to minimize the maximum distance between the solution and the input permutations, is NP-hard even considering three input permutations. This gives a sharp dichotomy into the P vs. NP-hard approaches, since considering two input permutations the problem is easily solvable and considering any number of input permutations it is known to be NP-hard since 2007 (Popov, \emph{Theor. Compt. Sci.}, 2007). In addition, we show that {\sc Swap Median} and {\sc Swap Closest} are APX-hard problems.