RNA二级结构预测中动态规划的优化和有效并行

基于最小自由能模型的方法是计算生物学中RNA二级结构预测的主要方法,而计算最小自由能的动态规划算法需要O(n⁴)的时间,其中n是RNA序列的长度.目前有两种降低时间复杂度的策略:限制二级结构中内部环的大小不超过k,得到O(n²×k²)算法;Lyngso方法根据环的能量规则,不限制环的大小,在O(n3)的时间内获得近似最优解.通过使用额外的O(n)的空间,计算内部环中的冗余计算大为减少,从而在同样不限制环大小的情况下,在O(n³)的时间内能够获得最优解.然而,优化后的算法仍然非常耗时,通过有效的负载平衡方法,在机群系统上实现并行程序.实验结果表明,并行程序获得了很好的加速比.     

Exact Algorithms for Exact Satisfiability and Number of Perfect Matchings

We present exact algorithms with exponential running times for variants of n-element set cover problems, based on divide-and-conquer and on inclusion–exclusion characterizations. We show that the Exact Satisfiability problem of size l with m clauses can be solved in time 2 ^m l ^O(1) and polynomial space. The same bounds hold for counting the number of solutions. As a special case, we can count the number of perfect matchings in an n-vertex graph in time 2 ⁿ n ^O(1) and polynomial space. We also show how to count the number of perfect matchings in time O(1.732 ⁿ ) and exponential space. We give a number of examples where the running time can be further improved if the hypergraph corresponding to the set cover instance has low pathwidth. This yields exponential-time algorithms for counting k-dimensional matchings, Exact Uniform Set Cover, Clique Partition, and Minimum Dominating Set in graphs of degree at most three. We extend the analysis to a number of related problems such as TSP and Chromatic Number.     

Communication-Efficient Broadcasting in Complete Networks with Dynamic Faults

We consider the problem of message (and bit) efficient broadcasting in complete networks with dynamic faults. Despite the simplicity of the setting, the problem turned out to be surprisingly interesting from the algorithmic point of view. In this paper we show an Ω(n + t f ^{t/(t – 1)}) lower bound on the number of messages sent by any t-step broadcasting algorithm, where f is the number of faults per step. The core of the paper contains a constructive O(n + t f ^{(t + 1)/t} ) upper bound. The algorithms involved are of time complexity O(t), not strictly t. In addition, we present a bit-efficient algorithm of O(n log² n) bit and O(log n) time complexities. We also show that it is possible to achieve the same message complexity even if the nodes do not know the id’s of their neighbours, but instead have only a Weak Sense of Direction.     

An efficient algorithm for finding ideal schedules

We study the problem of scheduling unit execution time jobs with release dates and precedence constraints on two identical processors. We say that a schedule is ideal if it minimizes both maximum and total completion time simultaneously. We give an instance of the problem where the min-max completion time is exceeded in every preemptive schedule that minimizes total completion time for that instance, even if the precedence constraints form an intree. This proves that ideal schedules do not exist in general when preemptions are allowed. On the other hand, we prove that, when preemptions are not allowed, then ideal schedules do exist for general precedence constraints, and we provide an algorithm for finding ideal schedules in O(n ³) time, where n is the number of jobs. In finding such ideal schedules we resolve a conjecture of Baptiste and Timkovsky (Math. Methods Oper. Res. 60(1):145–153, 2004) Further, our algorithm for finding min-max completion-time schedules requires only O(n ³) time, while the most efficient solution to date has required O(n ⁹) time.     

Path-distance heuristics for the Steiner problem in undirected networks

An integrative overview of the algorithmic characteristics of three well-known polynomialtime heuristics for the undirected Steiner minimum tree problem:shortest path heuristic (SPH),distance network heuristic (DNH), andaverage distance heuristic (ADH) is given. The performance of thesesingle-pass heuristics (and some variants) is compared and contrasted with several heuristics based onrepetitive applications of the SPH. It is shown that two of these repetitive SPH variants generate solutions that in general are better than solutions obtained by any single-pass heuristic. The worst-case time complexity of the two new variants isO(pn ³) andO(p ³ n ²), while the worst-case time complexity of the SPH, DNH, and ADH is respectivelyO(pn ²),O(m + n logn), andO(n ³) wherep is the number of vertices to be spanned,n is the total number of vertices, andm is the total number of edges. However, use of few simple tests is shown to provide large reductions of problem instances (both in terms of vertices and in term of edges). As a consequence, a substantial speed-up is obtained so that the repetitive variants are also competitive with respect to running times.     

Order Statistics in the Farey Sequences in Sublinear Time and Counting Primitive Lattice Points in Polygons

We present the first sublinear-time algorithms for computing order statistics in the Farey sequence and for the related problem of ranking. Our algorithms achieve a running times of nearly O(n ^2/3), which is a significant improvement over the previous algorithms taking time O(n). We also initiate the study of a more general problem: counting primitive lattice points inside planar shapes. For rational polygons containing the origin, we obtain a running time proportional to D ^6/7, where D is the diameter of the polygon. This work represents a merging of 19 and 21, with additional extensions.     

Testing the Quality of Manufactured Disks and Balls

We consider the problem of testing the roundness of manufactured disks and balls using the finger probing model of Cole and Yap. The running time of our procedures depends on the quality of the object being considered. Quality is a parameter that is negative when the object is not sufficiently round and positive when it is. Quality values close to zero represent objects that are close to the boundary between sufficiently round and insufficiently round. When the object being tested is a disk and its center is known, we describe a procedure that uses O(n) probes and O(n) computation time. (Here n =| 1/q|, where q is the quality of the object.) When the center of the object is not known, a procedure using O(n) probes and O(n log n) computation time is described. When the object is a ball, we describe a procedure that requires O(n²) probes and O(n⁴) computation time. Lower bounds are also given that show that these procedures are optimal in terms of the number of probes used. These results extend previous results in two directions by relaxing some of the assumptions required by previous results and by extending these results for three-dimensional objects.     

Approximating Tree Edit Distance through String Edit Distance

We present an algorithm to approximate edit distance between two ordered and rooted trees of bounded degree. In this algorithm, each input tree is transformed into a string by computing the Euler string, where labels of some edges in the input trees are modified so that structures of small subtrees are reflected to the labels. We show that the edit distance between trees is at least 1/6 and at most O(n ^3/4) of the edit distance between the transformed strings, where n is the maximum size of two input trees and we assume unit cost edit operations for both trees and strings. The algorithm works in O(n ²) time since computation of edit distance and reconstruction of tree mapping from string alignment takes O(n ²) time though transformation itself can be done in O(n) time.     

Fast Dynamic Transitive Closure with Lookahead

In this paper we consider the problem of dynamic transitive closure with lookahead. We present a randomized one-sided error algorithm with updates and queries in O(n ^{ω(1,1,ε)−ε} ) time given a lookahead of n ^ε operations, where ω(1,1,ε) is the exponent of multiplication of n×n matrix by n×n ^ε matrix. For ε≤0.294 we obtain an algorithm with queries and updates in O(n ^2−ε ) time, whereas for ε=1 the time is O(n ^ω−1). This is essentially optimal as it implies an O(n ^ω ) algorithm for boolean matrix multiplication. We also consider the offline transitive closure in planar graphs. For this problem, we show an algorithm that requires O(n^\fracw2)O(n^{\frac{\omega}{2}}) time to process n^\frac12n^{\frac{1}{2}} operations. We also show a modification of these algorithms that gives faster amortized queries. Finally, we give faster algorithms for restricted type of updates, so called element updates. All of the presented algorithms are randomized with one-sided error. All our algorithms are based on dynamic algorithms with lookahead for matrix inverse, which are of independent interest.     

An Approximation Algorithm for the Minimum Co-Path Set Problem

We present an approximation algorithm for the problem of finding a minimum set of edges in a given graph G whose removal from G leaves a graph in which each connected component is a path. It achieves a ratio of \frac 107\frac {10}{7} and runs in O(n ^1.5) time, where n is the number of vertices in the input graph. The previously best approximation algorithm for this problem achieves a ratio of 2 and runs in O(n ²) time.     

Efficient parallel and sequential algorithms for 4-coloring perfect planar graphs

We present an efficient algorithm for 4-coloring perfect planar graphs. The best previously known algorithm for this problem takesO(n ^3/2) sequential time, orO(log⁴ n) parallel time withO(n³) processors. The sequential implementation of our algorithm takesO(n logn) time. The parallel implementation of our algorithm takesO(log³ n) time withO(n) processors on a PRAM.     

Computing the Quartet Distance between Evolutionary Trees in Time O( n log n)

Evolutionary trees describing the relationship for a set of species are central in evolutionary biology, and quantifying differences between evolutionary trees is therefore an important task. The quartet distance is a distance measure between trees previously proposed by Estabrook, McMorris, and Meacham. The quartet distance between two unrooted evolutionary trees is the number of quartet topology differences between the two trees, where a quartet topology is the topological subtree induced by four species. In this paper we present an algorithm for computing the quartet distance between two unrooted evolutionary trees of n species, where all internal nodes have degree three, in time O(n log n. The previous best algorithm for the problem uses time O(n ²).     

Visibility of disjoint polygons

Consider a collection of disjoint polygons in the plane containing a total ofn edges. We show how to build, inO(n ²) time and space, a data structure from which inO(n) time we can compute the visibility polygon of a given point with respect to the polygon collection. As an application of this structure, the visibility graph of the given polygons can be constructed inO(n ²) time and space. This implies that the shortest path that connects two points in the plane and avoids the polygons in our collection can be computed inO(n ²) time, improving earlierO(n ² logn) results.     

Computing the Quartet Distance between Evolutionary Trees in Time O ( n log n )

Evolutionary trees describing the relationship for a set of species are central in evolutionary biology, and quantifying differences between evolutionary trees is therefore an important task. The quartet distance is a distance measure between trees previously proposed by Estabrook, McMorris, and Meacham. The quartet distance between two unrooted evolutionary trees is the number of quartet topology differences between the two trees, where a quartet topology is the topological subtree induced by four species. In this paper we present an algorithm for computing the quartet distance between two unrooted evolutionary trees of n species, where all internal nodes have degree three, in time O(n log n. The previous best algorithm for the problem uses time O(n ²).     

Fitting a Step Function to a Point Set

We consider the problem of fitting a step function to a set of points. More precisely, given an integer k and a set P of n points in the plane, our goal is to find a step function f with k steps that minimizes the maximum vertical distance between f and all the points in P. We first give an optimal Θ(nlog n) algorithm for the general case. In the special case where the points in P are given in sorted order according to their x-coordinates, we give an optimal Θ(n) time algorithm. Then, we show how to solve the weighted version of this problem in time O(nlog ⁴ n). Finally, we give an O(nh ²log n) algorithm for the case where h outliers are allowed. The running time of all our algorithms is independent of k.     

A linear-time algorithm to construct a rectilinear Steiner minimal tree fork-extremal point sets

Ak-extremal point set is a point set on the boundary of ak-sided rectilinear convex hull. Given ak-extremal point set of sizen, we present an algorithm that computes a rectilinear Steiner minimal tree in timeO(k ⁴ n). For constantk, this algorithm runs inO(n) time and is asymptotically optimal and, for arbitraryk, the algorithm is the fastest known for this problem.     

Efficient parallel and sequential algorithms for 4-coloring perfect planar graphs

We present an efficient algorithm for 4-coloring perfect planar graphs. The best previously known algorithm for this problem takesO(n ^3/2) sequential time, orO(log⁴ n) parallel time withO(n³) processors. The sequential implementation of our algorithm takesO(n logn) time. The parallel implementation of our algorithm takesO(log³ n) time withO(n) processors on a PRAM.

     

PRAM和LARPBS模型上有向序列翻转距离并行算法

分别在两种重要并行计算模型中给出计算有向基因组排列的反转距离新的并行算法.基于Hannenhalli和Pevzner理论,分3个主要部分设计并行算法:构建断点图、计算断点图中圈数、计算断点图中障碍的数目.在CREW-PRAM模型上,算法使用O(n²)处理器,时间复杂度为O(log²n);在基于流水光总线的可重构线性阵列系统(linear array with a reconfigurable pipelined bus system, LARPBS)模型上,算法使用O(n³)处理器,计算时间复杂度为O(logn).     

Selection, Routing, and Sorting on the Star Graph

We consider the problems of selection, routing, and sorting on ann-star graph (withn! nodes), an interconnection network which has been proven to possess many special properties. We identify a tree like subgraph (which we call a “(k, 1,k) chain network”) of the star graph which enables us to design efficient algorithms for the above mentioned problems. We present an algorithm that performs a sequence ofnprefix computations inO(n²) time. This algorithm is used as a subroutine in our other algorithms. We also show that sorting can be performed on then-star graph in timeO(n³) and that selection of a set of uniformly distributednkeys can be performed inO(n²) time with high probability. Finally, we also present a deterministic (nonoblivious) routing algorithm that realizes any permutation inO(n³) steps on then-star graph. There exists an algorithm in the literature that can perform a single prefix computation inO(nlgn) time. The best-known previous algorithm for sorting has a run time ofO(n³lgn) and is deterministic. To our knowledge, the problem of selection has not been considered before on the star graph.     

Applying Modular Decomposition to Parameterized Cluster Editing Problems

A graph G is said to be a bicluster graph if G is a disjoint union of bicliques (complete bipartite subgraphs), and a cluster graph if G is a disjoint union of cliques (complete subgraphs). In this work, we study the parameterized versions of the NP-hard Bicluster Graph Editing and Cluster Graph Editing problems. The former consists of obtaining a bicluster graph by making the minimum number of modifications in the edge set of an input bipartite graph. When at most k modifications are allowed (Bicluster(k) Graph Editing problem), this problem is FPT, and can be solved in O(4 ^k nm) time by a standard search tree algorithm. We develop an algorithm of time complexity O(4 ^k +n+m), which uses a strategy based on modular decomposition techniques; we slightly generalize the original problem as the input graph is not necessarily bipartite. The algorithm first builds a problem kernel with O(k ²) vertices in O(n+m) time, and then applies a bounded search tree. We also show how this strategy based on modular decomposition leads to a new way of obtaining a problem kernel with O(k ²) vertices for the Cluster(k) Graph Editing problem, in O(n+m) time. This problem consists of obtaining a cluster graph by modifying at most k edges in an input graph. A previous FPT algorithm of time O(1.92 ^k +n ³) for this problem was presented by Gramm et al. (Theory Comput. Syst. 38(4), 373–392, 2005, Algorithmica 39(4), 321–347, 2004). In their solution, a problem kernel with O(k ²) vertices is built in O(n ³) time.