Constructing the Maximum Consensus Tree from Rooted Triples

We investigated the problem of constructing the maximum consensus tree from rooted triples. We showed the NP-hardness of the problem and developed exact and heuristic algorithms. The exact algorithm is based on the dynamic programming strategy and runs in O((m + n ²)3 ⁿ ) time and O(2 ⁿ ) space. The heuristic algorithms run in polynomial time and their performances are tested and shown by comparing with the optimal solutions. In the tests, the worst and average relative error ratios are 1.200 and 1.072 respectively. We also implemented the two heuristic algorithms proposed by Gasieniec et al. The experimental result shows that our heuristic algorithm is better than theirs in most of the tests.     

Computational Comparison Studies of Quadratic Assignment Like Formulations for the In Silico Sequence Selection Problem in De Novo Protein Design

In this paper an O(n²) mathematical formulation for in silico sequence selection in de novo protein design proposed by Klepeis et al. (2003, 2004), in which the number of additional variables and linear constraints scales with the square of the number of binary variables, is compared to three O(n) formulations. It is found that the O(n²) formulation is superior to the O(n) formulations on most sequence search spaces. The superiority of the O(n²) formulation is due to the reformulation linearization techniques (RLTs), since the O(n²) formulation without RLTs is found to be computationally less efficient than the O(n) formulations. In addition, new algorithmic enhancing components of RLTs with inequality constraints, triangle inequalities, and Dead-End Elimination (DEE) type preprocessing are added to the O(n²) formulation. The current best O(n²) formulation, which is the original formulation from Klepeis et al. (2003, 2004) plus DEE type preprocessing, is proposed for in silico sequence search. For a test problem with a search space of 3.4×10⁴⁵ sequences, this new improved model is able to reduce the required CPU time by 67%.     

Parameterized lower bound and inapproximability of polylogarithmic string barcoding

String barcoding is a method that can identify microorganisms by analyzing their genome sequences. In this paper, we study the polylogarithmic string barcoding problem, where the lengths of the substrings in the testing set are polylogarithmically bounded. In particular, we show that the polylogarithmic string barcoding problem remains NP-hard and moreover, for a problem instance with n sequences, it is NP-hard to achieve an approximate ratio within dln n in polynomial time, where d is some constant. We then consider the parameterized polylogarithmic string barcoding problem, where the number of substrings in the test set is considered to be a fixed parameter k. We show that, unless W[2]=FPT, there does not exist a 2 ^O(k) n ^c algorithm that can decide whether a test set of size k exists or not, where c is a constant independent of n and k.     

A 2-approximation for the preceding-and-crossing structured 2-interval pattern problem

The 2-interval pattern problem over its various models and restrictions was proposed by Vialette (2004) for the application of RNA secondary structure prediction. We present an O(n ³logn)-time 2-approximation algorithm for the problem of finding a largest { < ,-structured subset of 2-intervals given an input 2-interval set of size n. This greatly improves the previous best approximation ratio of 6 by Crochemore et al. (2005).     

Min-energy broadcast in mobile ad hoc networks with restricted motion

This paper concerns about energy-efficient broadcasts in mobile ad hoc networks, yet in a model where each station moves on the plane with uniform rectilinear motion. Such restriction is imposed to discern which issues arise from the introduction of movement in the wireless ad hoc networks. Given a transmission range assignment for a set of n stations S, we provide an polynomial O(n ²)-time algorithm to decide whether a broadcast operation from a source station could be performed or not. Additionally, we study the problem of computing a transmission range assignment for S that minimizes the energy required in a broadcast operation. An O(n ³log?n)-time algorithm for this problem is presented, under the assumption that all stations have equally sized transmission ranges. However, we prove that the general version of such problem is NP-hard and not approximable within a (1?o(1))ln?n factor (unless NP?DTIME(n ^O(log?log?n))). We then propose a polynomial time approximation algorithm for a restricted version of that problem.     

Node-weighted Steiner tree approximation in unit disk graphs

Given a graph G=(V,E) with node weight w:V→R ⁺ and a subset S⊆V, find a minimum total weight tree interconnecting all nodes in S. This is the node-weighted Steiner tree problem which will be studied in this paper. In general, this problem is NP-hard and cannot be approximated by a polynomial time algorithm with performance ratio aln n for any 0<a<1 unless NP⊆DTIME(n ^O(log n)), where n is the number of nodes in s. In this paper, we are the first to show that even though for unit disk graphs, the problem is still NP-hard and it has a polynomial time constant approximation. We present a 2.5ρ-approximation where ρ is the best known performance ratio for polynomial time approximation of classical Steiner minimum tree problem in graphs. As a corollary, we obtain that there is a polynomial time (9.875+ε)-approximation algorithm for minimum weight connected dominating set in unit disk graphs, and also there is a polynomial time (4.875+ε)-approximation algorithm for minimum weight connected vertex cover in unit disk graphs.     

RNA multiple structural alignment with longest common subsequences

In this paper, we present a new model for RNA multiple sequence structural alignment based on the longest common subsequence. We consider both the off-line and on-line cases. For the off-line case, i.e., when the longest common subsequence is given as a linear graph with n vertices, we first present a polynomial O(n ²) time algorithm to compute its maximum nested loop. We then consider a slightly different problem—the Maximum Loop Chain problem and present an algorithm which runs in O(n ⁵) time. For the on-line case, i.e., given m RNA sequences of lengths n, compute the longest common subsequence of them such that this subsequence either induces a maximum nested loop or the maximum number of matches, we present efficient algorithms using dynamic programming when m is small. This research is partially supported by EPSCOR Visiting Scholar's Program and MSU Short-term Professional Development Program.     

Enumerating the edge-colourings and total colourings of a regular graph

In this paper, we are interested in computing the number of edge colourings and total colourings of a connected graph. We prove that the maximum number of k-edge-colourings of a connected k-regular graph on n vertices is k?((k?1)!) ^n/2. Our proof is constructive and leads to a branching algorithm enumerating all the k-edge-colourings of a connected k-regular graph in time O ^?(((k?1)!) ^n/2) and polynomial space. In particular, we obtain a algorithm to enumerate all the 3-edge-colourings of a connected cubic graph in time O ^?(2 ^n/2)=O ^?(1.4143 ⁿ ) and polynomial space. This improves the running time of O ^?(1.5423 ⁿ ) of the algorithm due to Golovach et al. (Proceedings of WG 2010, pp. 39–50, 2010). We also show that the number of 4-total-colourings of a connected cubic graph is at most 3?2^3n/2. Again, our proof yields a branching algorithm to enumerate all the 4-total-colourings of a connected cubic graph.     

Alignments with non-overlapping moves,inversions and tandem duplications in <Emphasis Type="Italic">O</Emphasis>(<Emphasis Type="Italic">n</Emphasis><Superscript>4</Superscript>) time

Sequence alignment is a central problem in bioinformatics. The classical dynamic programming algorithm aligns two sequences by optimizing over possible insertions, deletions and substitutions. However, other evolutionary events can be observed, such as inversions, tandem duplications or moves (transpositions). It has been established that the extension of the problem to move operations is NP-complete. Previous work has shown that an extension restricted to non-overlapping inversions can be solved in O(n ³) with a restricted scoring scheme. In this paper, we show that the alignment problem extended to non-overlapping moves can be solved in O(n ⁵) for general scoring schemes, O(n ⁴log n) for concave scoring schemes and O(n ⁴) for restricted scoring schemes. Furthermore, we show that the alignment problem extended to non-overlapping moves, inversions and tandem duplications can be solved with the same time complexities. Finally, an example of an alignment with non-overlapping moves is provided. A preliminary version of this paper appeared in the Proceedings of COCOON 2007, LNCS, vol. 4598, pp. 151–164.     

Polynomially solvable cases of the constant rank unconstrained quadratic 0-1 programming problem

In this paper we consider the constant rank unconstrained quadratic 0-1 optimization problem, CR-QP01 for short. This problem consists in minimizing the quadratic function 〈x, Ax〉 + 〈c, x〉 over the set {0,1} ⁿ where c is a vector in ℝ ⁿ and A is a symmetric real n × n matrix of constant rank r. We first present a pseudo-polynomial algorithm for solving the problem CR-QP01, which is known to be NP-hard already for r = 1. We then derive two new classes of special cases of the CR-QP01 which can be solved in polynomial time. These classes result from further restrictions on the matrix A. Finally we compare our algorithm with the algorithm of Allemand et al. (2001) for the CR-QP01 with negative semidefinite A and extend the range of applicability of the latter algorithm. It turns out that neither of the two algorithms dominates the other with respect to the class of instances which can be solved in polynomial time.     

Improved Dynamic Programming in Connection with an FPTAS for the Knapsack Problem

A vector merging problem is introduced where two vectors of length n are merged such that the k-th entry of the new vector is the minimum over of the -th entry of the first vector plus the sum of the first k – + 1 entries of the second vector. For this problem a new algorithm with O(n log n) running time is presented thus improving upon the straightforward O(n ²) time bound.The vector merging problem can appear in different settings of dynamic programming. In particular, it is applied for a recent fully polynomial time approximation scheme (FPTAS) for the classical 0–1 knapsack problem by the same authors.     

Polynomial time approximation schemes for minimum disk cover problems

The following planar minimum disk cover problem is considered in this paper: given a set D\mathcal{D} of n disks and a set ℘ of m points in the Euclidean plane, where each disk covers a subset of points in ℘, to compute a subset of disks with minimum cardinality covering ℘. This problem is known to be NP-hard and an algorithm which approximates the optimal disk cover within a factor of (1+ε) in O(mn^{O(\frac1e2log2\frac1e)})\mathcal{O}(mn^{\mathcal{O}(\frac{1}{\epsilon^{2}}\log^{2}\frac{1}{\epsilon})}) time is proposed in this paper. This work presents the first polynomial time approximation scheme for the minimum disk cover problem where the best known algorithm can approximate the optimal solution with a large constant factor. Further, several variants of the minimum disk cover problem such as the incongruent disk cover problem and the weighted disk cover problem are considered and approximation schemes are designed.     

Approximating multilinear monomial coefficients and maximum multilinear monomials in multivariate polynomials

This paper is our third step towards developing a theory of testing monomials in multivariate polynomials and concentrates on two problems: (1) How to compute the coefficients of multilinear monomials; and (2) how to find a maximum multilinear monomial when the input is a ΠΣΠ polynomial. We first prove that the first problem is #P-hard and then devise a O ^?(3 ⁿ s(n)) upper bound for this problem for any polynomial represented by an arithmetic circuit of size s(n). Later, this upper bound is improved to O ^?(2 ⁿ ) for ΠΣΠ polynomials. We then design fully polynomial-time randomized approximation schemes for this problem for ΠΣ polynomials. On the negative side, we prove that, even for ΠΣΠ polynomials with terms of degree ≤2, the first problem cannot be approximated at all for any approximation factor ≥1, nor “weakly approximated” in a much relaxed setting, unless P=NP. For the second problem, we first give a polynomial time λ-approximation algorithm for ΠΣΠ polynomials with terms of degrees no more a constant λ≥2. On the inapproximability side, we give a n ^(1??)/2 lower bound, for any ?>0, on the approximation factor for ΠΣΠ polynomials. When terms in these polynomials are constrained to degrees ≤2, we prove a 1.0476 lower bound, assuming P≠NP; and a higher 1.0604 lower bound, assuming the Unique Games Conjecture.     

Finding longest increasing and common subsequences in streaming data

We present algorithms and lower bounds for the Longest Increasing Subsequence (LIS) and Longest Common Subsequence (LCS) problems in the data-streaming model. To decide if the LIS of a given stream of elements drawn from an alphabet αbet has length at least k, we discuss a one-pass algorithm using O(k log αbetsize) space, with update time either O(log k) or O(log log αbetsize); for αbetsize = O(1), we can achieve O(log k) space and constant-time updates. We also prove a lower bound of Ω(k) on the space requirement for this problem for general alphabets αbet, even when the input stream is a permutation of αbet. For finding the actual LIS, we give a ⌈log (1 + 1/ɛ)-pass algorithm using O(k^1+ɛlog αbetsize) space, for any ɛ > 0. For LCS, there is a trivial Θ(1)-approximate O(log n)-space streaming algorithm when αbetsize = O(1). For general alphabets αbet, the problem is much harder. We prove several lower bounds on the LCS problem, of which the strongest is the following: it is necessary to use Ω(n/ρ²) space to approximate the LCS of two n-element streams to within a factor of ρ, even if the streams are permutations of each other. A preliminary version of this paper appears in the Proceedings of the 11th International Computing and Combinatorics Conference (COCOON'05), August 2005, pp. 263–272.     

Incrementing Bipartite Digraph Edge-Connectivity

This paper solves the problem of increasing the edge-connectivity of a bipartite digraph by adding the smallest number of new edges that preserve bipartiteness. A natural application arises when we wish to reinforce a 2-dimensional square grid framework with cables. We actually solve the more general problem of covering a crossing family of sets with the smallest number of directed edges, where each new edge must join the blocks of a given bipartition of the elements. The smallest number of new edges is given by a min-max formula that has six infinite families of exceptional cases. We discuss a problem on network flows whose solution has a similar formula with three infinite families of exceptional cases. We also discuss a problem on arborescences whose solution has five infinite families of exceptions. We give an algorithm that increases the edge-connectivity of a bipartite digraph in the same time as the best-known algorithm for the problem without the bipartite constraint: O(km log n) for unweighted digraphs and O(nm log (n ²/m)) for weighted digraphs, where n, m and k are the number of vertices and edges of the given graph and the target connectivity, respectively.     

Improved algorithms for largest cardinality 2-interval pattern problem

The 2-INTERVAL PATTERN problem is to find the largest constrained pattern in a set of 2-intervals. The constrained pattern is a subset of the given 2-intervals such that any pair of them are R-comparable, where model . The problem stems from the study of general representation of RNA secondary structures. In this paper, we give three improved algorithms for different models. Firstly, an O(n{log} n +L) algorithm is proposed for the case , where is the total length of all 2-intervals (density d is the maximum number of 2-intervals over any point). This improves previous O(n ²log n) algorithm. Secondly, we use dynamic programming techniques to obtain an O(nlog n + dn) algorithm for the case R = { <, ⊏ }, which improves previous O(n ²) result. Finally, we present another algorithm for the case with disjoint support(interval ground set), which improves previous O(n ²□n) upper bound. A preliminary version of this article appears in Proceedings of the 16th Annual International Symposium on Algorithms and Computation, Springer LNCS, Vol. 3827, pp. 412–421, Hainan, China, December 19–21, 2005.     

Approximating the Independence Number and the Chromatic Number in Expected Polynomial Time

The independence number of a graph and its chromatic number are known to be hard to approximate. Due to recent complexity results, unless coRP = NP, there is no polynomial time algorithm which approximates any of these quantities within a factor of n ^1– for graphs on n vertices.We show that the situation is significantly better for the average case. For every edge probability p = p(n) in the range n ^–1/2+ p 3/4, we present an approximation algorithm for the independence number of graphs on n vertices, whose approximation ratio is O((np)^1/2/log n) and whose expected running time over the probability space G(n, p) is polynomial. An algorithm with similar features is described also for the chromatic number.A key ingredient in the analysis of both algorithms is a new large deviation inequality for eigenvalues of random matrices, obtained through an application of Talagrand's inequality.     

COMMON DUE-WINDOW SCHEDULING

In this paper, we solve common due-window scheduling problems within the just-in-time window concept, i.e., scheduling problems including both earliness and tardiness penalties. We assume that jobs share the same due window and incur no penalty as long as they are completed within the due window. We further assume that the earliness and tardiness penalty factors are constant and that the size of the window is a given parameter. For cases where the location of the due window is a decision variable, we provide a polynomial algorithm with complexity O(n * log (n)) to solve the problem. For cases where the location of the due window is a given parameter, we use dynamic programming with pseudopolynomial complexity to solve the problem.     

The web proxy location problem in general tree of rings networks

The Web proxy location problem in general networks is an NP-hard problem. In this paper, we study the problem in networks showing a general tree of rings topology. We improve the results of the tree case in literature and get an exact algorithm with time complexity O(nhk), where n is the number of nodes in the tree, h is the height of the tree (the server is in the root of the tree), and k is the number of web proxies to be placed in the net. For the case of networks with a general tree of rings topology we present an exact algorithm with O(kn ²) time complexity.This research has been supported by NSF of China (No. 10371028) and the Educational Department grant of Zhejiang Province (No. 20030622).