An improved approximation lower bound for finding almost stable maximum matchings

In the stable marriage problem that allows incomplete preference lists, all stable matchings for a given instance have the same size. However, if we ignore the stability, there can be larger matchings. Biró et al. defined the problem of finding a maximum cardinality matching that contains minimum number of blocking pairs. They proved that this problem is not approximable within some constant δ>1 unless P=NP, even when all preference lists are of length at most 3. In this paper, we improve this constant δ to n1−ε for any ε>0, where n is the number of men in an input.     

An improved approximation ratio for the minimum linear arrangement problem

We observe that combining the techniques of Arora, Rao, and Vazirani, with the rounding algorithm of Rao and Richa yields an -approximation for the minimum-linear arrangement problem. This improves over the O(logn)-approximation of Rao and Richa.     

An improved lower bound on query complexity for quantum PAC learning

In this paper, we study the quantum PAC learning model, offering an improved lower bound on the query complexity. For a concept class with VC dimension d, the lower bound is for ? accuracy and 1−δ confidence, where e can be an arbitrarily small positive number. The lower bound is very close to the best lower bound known on query complexity for the classical PAC learning model, which is .     

On approximation algorithms for the terminal Steiner tree problem

The terminal Steiner tree problem is a special version of the Steiner tree problem, where a Steiner minimum tree has to be found in which all terminals are leaves. We prove that no polynomial time approximation algorithm for the terminal Steiner tree problem can achieve an approximation ratio less than (1−o(1))lnn unless NP has slightly superpolynomial time algorithms. Moreover, we present a polynomial time approximation algorithm for the metric version of this problem with a performance ratio of 2ρ, where ρ denotes the best known approximation ratio for the Steiner tree problem. This improves the previously best known approximation ratio for the metric terminal Steiner tree problem of ρ+2.     

A simple approximation algorithm for the weighted matching problem

We present a linear time approximation algorithm with a performance ratio of 1/2 for finding a maximum weight matching in an arbitrary graph. Such a result is already known and is due to Preis [STACS'99, Lecture Notes in Comput. Sci., Vol. 1563, 1999, pp. 259-269]. Our algorithm uses a new approach which is much simpler than the one given by Preis and needs no amortized analysis for its running time.     

An improved approximation algorithm for the metric maximum clustering problem with given cluster sizes

The input to the metric maximum clustering problem with given cluster sizes consists of a complete graph G=(V,E) with edge weights satisfying the triangle inequality, and integers c₁,…,cp. The goal is to find a partition of V into disjoint clusters of sizes c₁,…,cp, maximizing the sum of weights of edges whose two ends belong to the same cluster. We describe an approximation algorithms for this problem with performance guarantee that approaches 0.5 when the cluster sizes are large.     

Improved approximation algorithms for the Max Edge-Coloring problem

The Max Edge-Coloring problem asks for a proper edge-coloring of an edge-weighted graph minimizing the sum of the weights of the heaviest edges in the color classes. In this paper we present a PTAS for trees and a 1.74-approximation algorithm for bipartite graphs; we also adapt the last algorithm to one for general graphs of the same, asymptotically, approximation ratio.     

Approximation algorithms for the arc orienteering problem

In this article we present approximation algorithms for the Arc Orienteering Problem (AOP). We propose a polylogarithmic approximation algorithm in directed graphs, while in undirected graphs we give a (6+?+o(1))$(6+?+o(1))$ and a (4+?)$(4+?)$-approximation algorithm for arbitrary instances and instances of unit profit, respectively. Also, an inapproximability result for the AOP is obtained as well as approximation algorithms for the Mixed Orienteering Problem.     

On the approximation of protein threading

In this paper, we study the protein threading problem, which was proposed for predicting a folded 3D protein structure from an amino acid sequence. Since this problem was already proved to be NP-hard, we study polynomial time approximation algorithms. We show several hardness results for the approximation, which includes a MAX SNP-hardness result. We also show approximation algorithms for a special case and a general case, where a graph representing interactions between amino acid residues is restricted to be planar in a special case. For this special case, we obtain a constant approximation ratio.     

A strong lower bound for approximate nearest neighbor searching

We prove a lower bound of d^1−o(1) on the query time for any deterministic algorithms that solve approximate nearest neighbor searching in Yao's cell probe model. Our result greatly improves the best previous lower bound for this problem, which is [A. Chakrabarti et al., in: Proc. 31st Ann. ACM Symp. Theory of Computing, 1999, pp. 305-311]. Our proof is also much simpler than the proof of A. Chakrabarti et al.     

Upper bound for the approximation ratio of a class of hypercube segmentation algorithms

The Hypercube Segmentation problem was recently introduced by Kleinberg et al. [J. ACM 51 (2004) 263-280], along with several algorithms that select each segment's prototype vector from the segment. The algorithms were shown to have an approximation ratio of at least . We show that a lemma used in this proof is tight, and that the asymptotic approximation ratio of no algorithm of this type can exceed 5/6≈0.833.     

Combinatorial algorithms for DNA sequence assembly

The trend toward very large DNA sequencing projects, such as those being undertaken as part of the Human Genome Program, necessitates the development of efficient and precise algorithms for assembling a long DNA sequence from the fragments obtained by shotgun sequencing or other methods. The sequence reconstruction problem that we take as our formulation of DNA sequence assembly is a variation of the shortest common superstring problem, complicated by the presence of sequencing errors and reverse complements of fragments. Since the simpler superstring problem is NP-hard, any efficient reconstruction procedure must resort to heuristics. In this paper, however, a four-phase approach based on rigorous design criteria is presented, and has been found to be very accurate in practice. Our method is robust in the sense that it can accommodate high sequencing error rates, and list a series of alternate solutions in the event that several appear equally good. Moreover, it uses a limited form of multiple sequence alignment to detect, and often correct, errors in the data. Our combined algorithm has successfully reconstructed nonrepetitive sequences of length 50,000 sampled at error rates of as high as 10%.This research was supported by the National Library of Medicine under Grant R01-LM4960, by a postdoctoral fellowship from the Program in Mathematics and Molecular Biology of the University of California at Berkeley under National Science Foundation Grant DMS-8720208, and by a fellowship from the Centre de recherches mathématiques of the Université de Montréal.     

An in-place algorithm for Klee's measure problem in two dimensions

We present the first in-place algorithm for solving Klee's measure problem for a set of n axis-parallel rectangles in the plane. Our algorithm runs in O(n3/2logn) time and uses O(1) extra words in addition to the space needed for representing the input. The algorithm is surprisingly simple and thus very likely to yield an implementation that could be of practical interest. As a byproduct, we develop an optimal algorithm for solving Klee's measure problem for a set of n intervals; this algorithm runs in optimal time O(nlogn) and uses O(1) extra space.     

Improved approximation algorithms for minimum AND-circuits problem via k-set cover

Arpe and Manthey [J. Arpe, B. Manthey, Approximability of minimum AND-circuits, Algorithmica 53 (3) (2009) 337-357] recently studied the minimum AND-circuit problem, which is a circuit minimization problem, and showed some results including approximation algorithms, APX-hardness and fixed parameter tractability of the problem. In this note, we show that algorithms via the k-set cover problem yield improved approximation ratios for the minimum AND-circuit problem with maximum degree three. In particular, we obtain an approximation ratio of 1.199 for the problem with maximum degree three and unbounded multiplicity.     

A 2-approximation algorithm for genome rearrangements by reversals and transpositions

Recently, a new approach to analyze genomes evolving which is based on comparision of gene orders versus traditional comparision of DNA sequences was proposed (Sankoff et al. 1992). The approach is based on the global rearrangements (e.g., inversions and transpositions of fragments). Analysis of genomes evolving by inversions and transpositions leads to a combinatorial problem of sorting by reversals and transpositions, i.e., sorting of a permutation using reversals and transpositions of arbitrary fragments. We study sorting of signed permutations by reversals and transpositions, a problem which adequately models genome rearrangements, as the genes in DNA are oriented. We establish a lower bound and give a 2-approximation algorithm for the problem.     

Improved LP-based algorithms for the closest string problem

In a recent paper by Liu et al. [Exact algorithm and heuristic for the closest string problem, Computers & Operations Research 2011;38:1513-20], a polynomial time heuristic procedure is proposed for the closest string problem (CSP). Such heuristic called LDDA_LSS is a combination of a previously published approximation algorithm and local search strategies. This paper points out that an instant algorithm deriving a feasible solution directly from the continuous relaxation solution of a standard ILP formulation of CSP already strongly outperforms LDDA_LSS both in terms of solution quality and computing time. Two core based procedures are then proposed that further improve the results of the instant algorithm. Based on these results, we conclude that such LP-based approaches for their efficiency and simplicity should be used as a benchmark for future heuristics on CSP.     

Exact and approximation algorithms for sorting by reversals,with application to genome rearrangement

Motivated by the problem in computational biology of reconstructing the series of chromosome inversions by which one organism evolved from another, we consider the problem of computing the shortest series of reversals that transform one permutation to another. The permutations describe the order of genes on corresponding chromosomes, and areversal takes an arbitrary substring of elements, and reverses their order.For this problem, we develop two algorithms: a greedy approximation algorithm, that finds a solution provably close to optimal inO(n ²) time and0(n) space forn-element permutations, and a branch- and-bound exact algorithm, that finds an optimal solution in0(mL(n, n)) time and0(n ²) space, wherem is the size of the branch- and-bound search tree, andL(n, n) is the time to solve a linear program ofn variables andn constraints. The greedy algorithm is the first to come within a constant factor of the optimum; it guarantees a solution that uses no more than twice the minimum number of reversals. The lower and upper bounds of the branch- and-bound algorithm are a novel application of maximum-weight matchings, shortest paths, and linear programming.In a series of experiments, we study the performance of an implementation on random permutations, and permutations generated by random reversals. For permutations differing byk random reversals, we find that the average upper bound on reversal distance estimatesk to within one reversal fork<1/2n andn<100. For the difficult case of random permutations, we find that the average difference between the upper and lower bounds is less than three reversals forn<50. Due to the tightness of these bounds, we can solve, to optimality, problems on 30 elements in a few minutes of computer time. This approaches the scale of mitochondrial genomes.This research was supported by a postdoctoral fellowship from the Program in Mathematics and Molecular Biology of the University of California at Berkeley under National Science Foundation Grant DMS-8720208, and by a fellowship from the Centre de recherches mathématiques of the Université de Montréal.This research was supported by grants from the Natural Sciences and Engineering Research Council of Canada, and the Fonds pour la formation de chercheurs et l'aide à la recherche (Québec). The author is a fellow of the Canadian Institute for Advanced Research.     

An approximation algorithm dependent on edge-coloring number for minimum maximal matching problem

We consider the minimum maximal matching problem, which is NP-hard (Yannakakis and Gavril (1980) [18]). Given an unweighted simple graph G=(V,E), the problem seeks to find a maximal matching of minimum cardinality. It was unknown whether there exists a non-trivial approximation algorithm whose approximation ratio is less than 2 for any simple graph. Recently, Z. Gotthilf et al. (2008) [5] presented a -approximation algorithm, where c is an arbitrary constant.In this paper, we present a -approximation algorithm based on an LP relaxation, where χ^′(G) is the edge-coloring number of G. Our algorithm is the first non-trivial approximation algorithm whose approximation ratio is independent of |V|. Moreover, it is known that the minimum maximal matching problem is equivalent to the edge dominating set problem. Therefore, the edge dominating set problem is also -approximable. From edge-coloring theory, the approximation ratio of our algorithm is , where Δ(G) represents the maximum degree of G. In our algorithm, an LP formulation for the edge dominating set problem is used. Fujito and Nagamochi (2002) [4] showed the integrality gap of the LP formulation for bipartite graphs is at least . Moreover, χ^′(G) is Δ(G) for bipartite graphs. Thus, as far as an approximation algorithm for the minimum maximal matching problem uses the LP formulation, we believe our result is the best possible.     

A lower bound method for quantum circuits

Quantum circuits, which are shallow, limited in the number of gates and additional workspace qubits, are popular for quantum computation because they form the simplest possible model similar to the classical model of a network of Boolean gates and capable of performing non-trivial computation. We give a new lower bound technique for such circuits and use it to give another proof that deterministic computation of the parity function cannot be performed by such circuits.