A new 1.375-approximation algorithm for sorting by transpositions

Background sorting by transpositions (SBT) is a classical problem in genome rearrangements. In 2012, SBT was proven to be $$\mathcal {NP}$$ NP -hard and the best approximation algorithm with a 1.375 ratio was proposed in 2006 by Elias and Hartman (EH algorithm). Their algorithm employs simplification, a technique used to transform an input permutation $$\pi$$ π into a simple permutation$${\hat{\pi }}$$ π ^ , presumably easier to handle with. The permutation $${\hat{\pi }}$$ π ^ is obtained by inserting new symbols into $$\pi$$ π in a way that the lower bound of the transposition distance of $$\pi$$ π is kept on $${\hat{\pi }}$$ π ^ . The simplification is guaranteed to keep the lower bound, not the transposition distance. A sequence of operations sorting $${\hat{\pi }}$$ π ^ can be mimicked to sort $$\pi$$ π . Results and conclusions First, using an algebraic approach, we propose a new upper bound for the transposition distance, which holds for all $$S_n$$ S n . Next, motivated by a problem identified in the EH algorithm, which causes it, in scenarios involving how the input permutation is simplified, to require one extra transposition above the 1.375-approximation ratio, we propose a new approximation algorithm to solve SBT ensuring the 1.375-approximation ratio for all $$S_n$$ S n . We implemented our algorithm and EH’s. Regarding the implementation of the EH algorithm, two other issues were identified and needed to be fixed. We tested both algorithms against all permutations of size n, $$2\le n \le 12$$ 2 ≤ n ≤ 12 . The results show that the EH algorithm exceeds the approximation ratio of 1.375 for permutations with a size greater than 7. The percentage of computed distances that are equal to transposition distance, computed by the implemented algorithms are also compared with others available in the literature. Finally, we investigate the performance of both implementations on longer permutations of maximum length 500. From the experiments, we conclude that maximum and the average distances computed by our algorithm are a little better than the ones computed by the EH algorithm and the running times of both algorithms are similar, despite the time complexity of our algorithm being higher.

Approximation Algorithms for the Capacitated Min–Max Correlation Clustering Problem

In this paper, we propose a so-called capacitated min–max correlation clustering model, a natural variant of the min–max correlation clustering problem. As our main contribution, we present an integer programming and its integrality gap analysis for the proposed model. Furthermore, we provide two approximation algorithms for the model, one of which is a bi-criteria approximation algorithm and the other is based on LP-rounding technique.

On the Parameterized Approximability of Contraction to Classes of Chordal Graphs

A graph operation that contracts edges is one of the fundamental operations in the theory of graph minors. Parameterized Complexity of editing to a family of graphs by contracting k edges has recently gained substantial scientific attention, and several new results have been obtained. Some important families of graphs, namely, the subfamilies of chordal graphs, in the context of edge contractions, have proven to be significantly difficult than one might expect. In this article, we study the F -Contraction problem, where F is a subfamily of chordal graphs, in the realm of parameterized approximation. Formally, given a graph G and an integer k , F -Contraction asks whether there exists X ⊆ E(G) such that G/X ∈ F and | X | ≤ k . Here, G/X is the graph obtained from G by contracting edges in X . We obtain the following results for the F - Contraction problem: • Clique Contraction is known to be FPT . However, unless NP⊆ coNP/ poly , it does not admit a polynomial kernel. We show that it admits a polynomial-size approximate kernelization scheme ( PSAKS ). That is, it admits a (1 + ε)-approximate kernel with O ( k f(ε)) vertices for every ε > 0. • Split Contraction is known to be W[1]-Hard . We deconstruct this intractability result in two ways. First, we give a (2+ε)-approximate polynomial kernel for Split Contraction (which also implies a factor (2+ε)- FPT -approximation algorithm for Split Contraction ). Furthermore, we show that, assuming Gap-ETH , there is no (5/4-δ)- FPT -approximation algorithm for Split Contraction . Here, ε, δ > 0 are fixed constants. • Chordal Contraction is known to be W[2]-Hard . We complement this result by observing that the existing W[2]-hardness reduction can be adapted to show that, assuming FPT ≠ W[1] , there is no F(k) - FPT -approximation algorithm for Chordal Contraction . Here, F(k) is an arbitrary function depending on k alone. We say that an algorithm is an h(k) - FPT -approximation algorithm for the F -Contraction problem, if it runs in FPT time, and on any input (G, k) such that there exists X ⊆ E(G) satisfying G/X ∈ F and | X | ≤ k , it outputs an edge set Y of size at most h(k) ċ k for which G/Y is in F .

A General Framework for Approximating Min Sum Ordering Problems

We consider a large family of problems in which an ordering (or, more precisely, a chain of subsets) of a finite set must be chosen to minimize some weighted sum of costs. This family includes variations of min sum set cover, several scheduling and search problems, and problems in Boolean function evaluation. We define a new problem, called the min sum ordering problem (MSOP), which generalizes all these problems using a cost and a weight function defined on subsets of a finite set. Assuming a polynomial time α-approximation algorithm for the problem of finding a subset whose ratio of weight to cost is maximal, we show that under very minimal assumptions, there is a polynomial time [Formula: see text]-approximation algorithm for MSOP. This approximation result generalizes a proof technique used for several distinct problems in the literature. We apply this to obtain a number of new approximation results. Summary of Contribution: This paper provides a general framework for min sum ordering problems. Within the realm of theoretical computer science, these problems include min sum set cover and its generalizations, as well as problems in Boolean function evaluation. On the operations research side, they include problems in search theory and scheduling. We present and analyze a very general algorithm for these problems, unifying several previous results on various min sum ordering problems and resulting in new constant factor guarantees for others.