On the bottleneck tree alignment problems

Given a set W of k sequences (strings) and a tree structure T with k leaves, each of which is labeled with a unique sequence in W, a tree alignment is to label a sequence to each internal node of T. The weight of an edge of the tree alignment is the distance, such as Hamming distance, Levenshtein (edit) distance or reversal distance, between the two sequences labeled to the two ends of the edge. The bottleneck tree alignment problem is to find a tree alignment such that the weight of the largest edge is minimized. A lifted tree alignment is a tree alignment, where each internal node v is labeled one of the sequences that was labeled to the children of v. The bottleneck lifted tree alignment problem is to find a lifted tree alignment such that the weight of the largest edge is minimized. In this paper, we show that the bottleneck tree alignment problem is NP-complete even when the tree structure is the binary tree and the weight function is metric. For special cases, we present an exact algorithm to solve the bottleneck lifted tree alignment problem in polynomial time. If the weight function is ultrametric, we show that any lifted tree alignment is an optimal bottleneck tree alignment.KeywordsEdit distancebottleneck tree alignmentmetricultrametricNP-complete

Community search on attributed networks has recently attracted great deal of research interest. However, most of existing works require query users to specify some community structure parameters. This may not be always practical as sometimes a user does not have the knowledge and experience to decide the suitable parameters. In this paper, we propose a novel parameter-free contextual community model for attributed community search. The proposed model only requires a query context, i.e., a set of keywords describing the desired matching community context, while the community returned is both structure and attribute cohesive w.r.t. the provided query context. We theoretically show that both our exact and approximate contextual community search algorithms can be executed in worst case polynomial time. The exact algorithm is based on an elegant parametric maximum flow technique and the approximation algorithm that significantly improves the search efficiency is analyzed to have an approximation factor of 1/3. In the experiment, we use six real networks with ground-truth communities to evaluate the effectiveness of our contextual community model. Experimental results demonstrate that the proposed model can find near ground-truth communities. We also test both our exact and approximate algorithms using eight large real networks to demonstrate the high efficiency of the proposed algorithms.

This paper describes a dynamic programming algorithm to solve a family of problems in the reconstruction of evolutionary trees from protein sequence data, that of constructing "minimal" colorings. This dynamic programming formulation can be modified to efficiently enumerate the number of minimal colorings and thereby be used to calculate the average cost of any given edge, where the average is taken over the entire set of minimal colorings. An extension of our dynamic programming formulation allows for the calculation of average path costs amongst all minimal colorings. our results resolve questions raised in (Hendy and penny, 1987); in particular, we develop polynomial time procedures to find the minimum, maximum, and average (expected) cost of an edge, and more generally of a path, for a minimal coloring. Our algorithm is distinguished in its flexibility to address further distribution and statistical questions relating to the minimal colorings. Furthermore, the more general concept of calculating statistics describing the set of optimal solutions may be of interest in other combinatorial problems.

On the optimality of exact and approximation algorithms for scheduling problems

Implementing approximate regularities

Planar multifacility location problems with tree structure and finite dominating sets

The Random Shortest Path Problem with the second moment criterion is discussed in this paper. After the formulation of the problem, exact algorithms, based on general concepts for solving the Multi-objective Shortest Path Problem, are described. Next, several approximate algorithms are proposed. It is shown that the complexity of the exact algorithms is exponential, while the complexity of the approximate algorithms is only polynomial. Computational results for the exact and approximate algorithms, which were performed on large graphs, are shown.

In this paper we gather several improvements in the field of exact and approximate exponential-time algorithms for the Bandwidth problem. For graphs with treewidth t we present a O(n O(t) 2n) exact algorithm. Moreover for the same class of graphs we introduce a subexponential constant-approximation scheme – for any α> 0 there exists a (1 + α)-approximation algorithm running in \(O(\exp(c(t + \sqrt{n/\alpha})\log n))\) time where c is a universal constant. These results seem interesting since Unger has proved that Bandwidth does not belong to APX even when the input graph is a tree (assuming P ≠ NP). So somewhat surprisingly, despite Unger’s result it turns out that not only a subexponential constant approximation is possible but also a subexponential approximation scheme exists. Furthermore, for any positive integer r, we present a (4r − 1)-approximation algorithm that solves Bandwidth for an arbitrary input graph in \(O^*(2^{n\over r})\) time and polynomial space. Finally we improve the currently best known exact algorithm for arbitrary graphs with a O(4.473n) time and space algorithm.In the algorithms for the small treewidth we develop a technique based on the Fast Fourier Transform, parallel to the Fast Subset Convolution techniques introduced by Björklund et al. This technique can be also used as a simple method of finding a chromatic number of all subgraphs of a given graph in O *(2n) time and space, what matches the best known results.KeywordsFast Fourier TransformApproximation AlgorithmChromatic NumberExact AlgorithmInput GraphThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Article Free Access Share on Exact sampling and approximate counting techniques Author: Mark Huber School of Operations Research and Industrial Engineering, Cornell University, Ithaca, NY School of Operations Research and Industrial Engineering, Cornell University, Ithaca, NYView Profile Authors Info & Claims STOC '98: Proceedings of the thirtieth annual ACM symposium on Theory of computingMay 1998 Pages 31–40https://doi.org/10.1145/276698.276709Published:23 May 1998Publication History 25citation666DownloadsMetricsTotal Citations25Total Downloads666Last 12 Months66Last 6 weeks15 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF

• NP-Completeness and APX-Hardness • We prove that the problems MinFixMask OPT and MinFixMask BOUND are NP-complete. • We establish that FixMasks + is NP-complete and APX-hard. • We show NP-completeness of DFixMasks + . • Exact, FPT, and Approximation Algorithms for DFixMasks + • We design a fixed-parameter tractable (FPT) algorithm running in O *(2 M ) time, parameterized by the number of shield configurations M . • We present a polynomial-time 1 M -approximation algorithm. • We propose an exponential k M -approximation method (for a treatment plan length k ). • We provide a tight ( 1 − 1 e ) -approximation algorithm by exploiting monotonicity and submodularity of the objective function. • Quasi-Polynomial Algorithms and Logarithmic Approximations • We develop quasi-polynomial-time algorithms for MinFixMask OPT , MinFixMask OPT + , MinFixMask BOUND , and MinFixMask BOUND + , assuming that the maximum prescribed dose d ^ max is polynomially bounded. • Under the same assumption, we achieve polynomial-time approximation algorithms with a logarithmic factor log ( d ^ max ) for MinFixMask OPT and MinFixMask OPT + . • Polynomial-Time Solvable Special Cases • We identify polynomial-time solvable cases: FixMask and FixMasks + when M = 1 . • We show that the problems MinFixMask BOUND and MinFixMask BOUND + can be solved in polynomial time when T max 1, N ;. In this paper, we study a combinatorial problem which arises in the development of innovative treatment strategies and equipment using tunable shields in internal radiotherapy. From an algorithmic point of view, the problem is related to circular integer word decomposition into circular binary words under constraints. We consider several variants of the problem, depending on constraints and parameters and present exact, approximation, fixed parameter tractable algorithms and NP-hardness and APX-hardness results.

The area of parameterized approximation seeks to combine approximation and parameterized algorithms to obtain, e.g., (1+epsilon)-approximations in f(k,epsilon)n^O(1) time where k is some parameter of the input. The goal is to overcome lower bounds from either of the areas. We obtain the following results on parameterized approximability: - In the maximum independent set of rectangles problem (MISR) we are given a collection of n axis parallel rectangles in the plane. Our goal is to select a maximum-cardinality subset of pairwise non-overlapping rectangles. This problem is NP-hard and also W[1]-hard [Marx, ESA'05]. The best-known polynomial-time approximation factor is O(log log n) [Chalermsook and Chuzhoy, SODA'09] and it admits a QPTAS [Adamaszek and Wiese, FOCS'13; Chuzhoy and Ene, FOCS'16]. Here we present a parameterized approximation scheme (PAS) for MISR, i.e. an algorithm that, for any given constant epsilon>0 and integer k>0, in time f(k,epsilon)n^g(epsilon), either outputs a solution of size at least k/(1+epsilon), or declares that the optimum solution has size less than k. - In the (2-dimensional) geometric knapsack problem (2DK) we are given an axis-aligned square knapsack and a collection of axis-aligned rectangles in the plane (items). Our goal is to translate a maximum cardinality subset of items into the knapsack so that the selected items do not overlap. In the version of 2DK with rotations (2DKR), we are allowed to rotate items by 90 degrees. Both variants are NP-hard, and the best-known polynomial-time approximation factor is 2+epsilon [Jansen and Zhang, SODA'04]. These problems admit a QPTAS for polynomially bounded item sizes [Adamaszek and Wiese, SODA'15]. We show that both variants are W[1]-hard. Furthermore, we present a PAS for 2DKR. For all considered problems, getting time f(k,epsilon)n^O(1), rather than f(k,epsilon)n^g(epsilon), would give FPT time f'(k)n^O(1) exact algorithms by setting epsilon=1/(k+1), contradicting W[1]-hardness. Instead, for each fixed epsilon>0, our PASs give (1+epsilon)-approximate solutions in FPT time. For both MISR and 2DKR our techniques also give rise to preprocessing algorithms that take n^g(epsilon) time and return a subset of at most k^g(epsilon) rectangles/items that contains a solution of size at least k/(1+epsilon) if a solution of size k exists. This is a special case of the recently introduced notion of a polynomial-size approximate kernelization scheme [Lokshtanov et al., STOC'17].

The Hamming center problem for a set S of k binary strings, each of length n, is to find a binary string fl of length n that minimizes the maximum Hamming distance between p and any string in S. Its decision version is known to be NP-complete [2]. We provide several approximation algorithms for the Hamming center problem. Our main result is a randomized ($ + E)approximation algorithm running in polynomial time if the Hamming radius of S is at least superlogarithmic in k. Furthermore, we show how to find in polynomial time a set B of O(log k) strings of length n such that for each string in S there is at least one string in B within Hamming distance not exceeding the radius of S.

The Group Steiner Tree (GST) problem is a classical problem in combinatorial optimization and theoretical computer science. In the Edge-Weighted Group Steiner Tree (EW-GST) problem, we are given an undirected graph G = (V, E) on n vertices with edge costs c : E → ℝ≥ 0, a source vertex s and a collection of subsets of vertices, called groups, S1, . . . , Sk ⊆ V. The goal is to find a minimum-cost tree H ⊆ G that connects s to some vertex from each group Si, for all i = 1, 2, . . . , k. The Node-Weighted Group Steiner Tree (NW-GST) problem has the same setting, but the costs are associated with nodes. The goal is to find a minimum-cost node set X ⊆ V such that G[X] connects every group to the source.When G is a tree, both EW-GST and NW-GST admit a polynomial-time O(log n log k) approximation algorithm due to the seminal result of [Garg et al., SODA'98 and J. Algorithm]. The matching hardness of log2−ϵn is known even for tree instances of EW-GST and NW-GST [Halperin and Krauthgamer STOC'03]. In general graphs, most of polynomial-time approximation algorithms for EW-GST reduce the problem to a tree instance using the metric-tree embedding, incurring a loss of O(log n) on the approximation factor [Bartal, FOCS'96; Fakcharoenphol et al., FOCS'03 and JCSS]. This yields an approximation ratio of O(log2n log k) for EW-GST. Using metric-tree embedding, this factor cannot be improved: The loss of Ω(log n) is necessary on some input graphs (e.g., grids and expanders). There are alternative approaches that avoid metric-tree embedding, e.g., the algorithm of [Chekuri and Pal, FOCS'05], which gives a tight approximation ratio, but none of which achieves polylogarithmic approximation in polynomial-time. This state of the art shows a clear lack of understanding of GST in general graphs beyond the metric-tree embedding technique. For NW-GST (for which the metric-tree embedding does not apply), not even a polynomial-time polylogarithmic approximation algorithm is known.In this paper, we present O(log n log k) approximation algorithms that run in time nO(tw(G)2) for both NW-GST and EW-GST1, where tw(G) denotes the treewidth of graph G. The key to both results is a different type of "tree-embedding" that produces a tree of much bigger size, but does not cause any loss on the approximation factor. Our embedding is inspired by dynamic programming, a technique which is typically not applicable to Group Steiner problems.

An improved approximation algorithm for the partial-terminal Steiner tree problem with edge cost 1 or 2

We consider the bin packing problem with d different item sizes s i and item multiplicities a i , where all numbers are given in binary encoding. This problem formulation is also known as the one-dimensional cutting stock problem . In this work, we provide an algorithm that, for constant d , solves bin packing in polynomial time. This was an open problem for all d\ge 3 . In fact, for constant d our algorithm solves the following problem in polynomial time: Given two d -dimensional polytopes P and Q , find the smallest number of integer points in P whose sum lies in Q . Our approach also applies to high multiplicity scheduling problems in which the number of copies of each job type is given in binary encoding and each type comes with certain parameters such as release dates, processing times, and deadlines. We show that a variety of high multiplicity scheduling problems can be solved in polynomial time if the number of job types is constant.