A new approximation algorithm for sorting of signed permutations

Sequence comparison leads to a combinatorial optimization problem of sorting permutations by reversals and transpositions.Namely,given any two permutations,find the shortest distance between them.This problem is related with genome rearrangement,genes are oriented in DNA sequences.The transpositions which have been studied in the liteature can be viewed as operations working on two consecutive segments of the genome.In this paper,a new kind of transposition which can work on two arbitrary segments of the genome is proposed,and the sorting of signed permutations by reversals and this new kind of transpostitions are studied.After establishing a lower bound on the number of operations needed,a 2-approximation algorithm is presented for this problem and an example is given to show that the performance ratio of the algorithm cannot be improved.     

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).     

A new approximation algorithm for cut-and-paste sorting of unsigned circular permutations

A cut-and-paste operation can be a reversal, a transposition, or a transreversal on circular or linear permutations. There are several approximation algorithms for sorting signed permutations by combinations of these operations. For sorting unsigned permutations, we only know an algorithm with performance ratio 3 and its improved version with performance ratio $2.8386+\delta$ allowing reversals and transpositions. In this paper, we present a 2.25-approximation algorithm for sorting unsigned circular permutations by cut-and-paste operations. A structure called tie is proposed to represent the alternating path of length 5. We can classify the ties into 6 types and find ways to remove the breakpoints for each type of ties, so that every cut-and-paste operation can reduce at least $\frac{4}{3}$ breakpoints averagely. Our algorithm can be used to sort unsigned linear permutations and achieve the performance ratio 2.25 if another operation named revrev is allowed.     

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.     

Efficient Parallel Algorithms for Permutation Graphs

In this paper, we present optimal O(log n) time, O(n/log n) processor EREW PRAM parallel algorithms for finding the connected components, cut vertices, and bridges of a permutation graph. We also present an O(log n) time, O(n) processor, CREW PRAM model parallel algorithm for finding a Breadth First Search (BFS) spanning tree of a permutation graph rooted at vertex 1 and use the same to derive an efficient parallel algorithm for the All Pairs Shortest Path problem on permutation graphs.     

Fast Generation of Random Permutations Via Networks Simulation

We consider the problem of generating random permutations with uniform distribution. That is, we require that for an arbitrary permutation π of n elements, with probability 1/n! the machine halts with the i th output cell containing π(i) , for 1 ≤ i ≤ n . We study this problem on two models of parallel computations: the CREW PRAM and the EREW PRAM. The main result of the paper is an algorithm for generating random permutations that runs in O(log log n) time and uses O(n ^1+o(1) ) processors on the CREW PRAM. This is the first o(log n) -time CREW PRAM algorithm for this problem. On the EREW PRAM we present a simple algorithm that generates a random permutation in time O(log n) using n processors and O(n) space. This algorithm outperforms each of the previously known algorithms for the exclusive write PRAMs. The common and novel feature of both our algorithms is first to design a suitable random switching network generating a permutation and then to simulate this network on the PRAM model in a fast way. Received November 1996; revised March 1997.     

Minimizing total weighted flow time under uncertainty using dominance and a stability box

We consider an uncertain single-machine scheduling problem, in which the processing time of a job can take any real value on a given closed interval. The criterion is to minimize the total weighted flow time of the n jobs, where there is a weight associated with a job. We calculate a number of minimal dominant sets of the job permutations (a minimal dominant set contains at least one optimal permutation for each possible scenario). We introduce a new stability measure of a job permutation (a stability box) and derive an exact formula for the stability box, which runs in O(n log n) time. We investigate properties of a stability box. These properties allow us to develop an O(n²)-algorithm for constructing a permutation with the largest volume of a stability box. If several permutations have the largest volume of a stability box, the developed algorithm selects one of them due to a simple heuristic. The efficiency of the constructed permutation is demonstrated on a large set of randomly generated instances with 10≤n≤1000.     

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.     

<Emphasis Type="Italic">O</Emphasis>(log*<Emphasis Type="Italic">n</Emphasis>) algorithms on a Sum-CRCW PRAM

We present work- and cost-optimal O(log*n) algorithms for prefix sums and linear integer sorting on a Sum-CRCW PRAM.     

Virtual Shared Memory: Algorithms and Complexity

We consider the Block PRAM model of Aggarwal et al. (in "Proceedings, First Annual ACM Symposium on Parallel Algorithms and Architectures, 1989," pp. 11-21). For a Block PRAM model with n/log n processors and communication latency l = O(log n), we show that prefix sums can be performed in time O(l log n/log l), but list ranking requires time Ω(l log n); these bounds are tight. These results justify an intuitive observation of Gazit et al. (in "Proceedings, 1987 Princeton Workshop on Algorithm, Architecture and Technology Issues for Models of Concurrent Computation," pp. 139-156) that algorithm designers should, when possible, replace the list ranking procedure with the prefix sums procedure. We demonstrate the value of this technique in choosing between two optimal PRAM algorithms for finding the connected components of dense graphs. We also give theoretical improvements for integer sorting and many other algorithms based on prefix sums, and suggest a relationship between the issue of graph density for the connected components problem and alternative approaches to integer sorting.     

Finding a maximum matching in a permutation graph

We present anO(n log logn) time algorithm for finding a maximum matching in a permutation graph withn vertices, assuming that the input graph is represented by a permutation.     

Parallel permutation generation on linear array

Given n items, a parallel algorithm for generating all the n! permutations is presented. The computational model used is a linear array which consists of n identical processing elements with a simple structure. One permutation is produced at each other time step. The elapsed time to produce a permutation is independent of the integer n. The basic idea used is the iterative method and the exchange of two consecutive components in an existing permutation. The design procedures of this algorithm are considered in detail. The ranking and unranking functions of the required permutations are also discussed.     

An Optimal Shortest Path Parallel Algorithm for Permutation Graphs

We present an optimal parallel algorithm for the single-source shortest path problem for permutation graphs. The algorithm runs in O(log n) time using O(n/log n) processors on an EREW PRAM. As an application, we show that a minimum connected dominating set in a permutation graph can be found in O(log n) time using O(n/log n) processors.     

Fast algorithms for the dominating set problem on permutation graphs

AnO(n log logn) (resp.O(n² log² n)) algorithm is presented to solve the minimum cardinality (resp. weight) dominating set problem on permutation graphs, assuming the input is a permutation. The best-known previous algorithm was given by FÄrber and Keil, where they use dynamic programming to get anO(n² (resp.O(n³)) algorithm. Our improvement is based on the following three factors: (1) an observation on the order among the intermediate terms in the dynamic programming, (2) a new construction formula for the intermediate terms, and (3) efficient data structures for manipulating these terms.This research was supported in part by the National Science Foundation under Grant CCR-8905415 to Northwestern University.     

Fully Dynamic Algorithm for Recognition and Modular Decomposition of Permutation Graphs

This paper considers the problem of maintaining a compact representation (O(n) space) of permutation graphs under vertex and edge modifications (insertion or deletion). That representation allows us to answer adjacency queries in O(1) time. The approach is based on a fully dynamic modular decomposition algorithm for permutation graphs that works in O(n) time per edge and vertex modification. We thereby obtain a fully dynamic algorithm for the recognition of permutation graphs.     

The Minimum Weight Dominating Set Problem for Permutation Graphs Is in NC

In this paper, we show that the problem of finding a minimum weight dominating set in a permutation graph, where a positive weight is assigned to each vertex, is in NC by presenting an O(log n) parallel algorithm with polynomially many processors on the CRCW model.     

On Parallel Selection and Searching in Partial Orders: Sorted Matrices

Parallel algorithms for the problems of selection and searching on sorted matrices are formulated. The selection algorithm takesO(lognlog lognlog*n) time withO(n/lognlog*n) processors on an EREW PRAM. This algorithm can be generalized to solve the selection problem on a set of sorted matrices. The searching algorithm takesO(log logn) time withO(n/log logn) processors on a Common CRCW PRAM, which is optimal. We show that no algorithm using at mostnlog^cnprocessors,c≥ 1, can solve the matrix search problem in time faster than Ω(log logn) and that Ω(logn) steps are needed to solve this problem on any model that does not allow concurrent writes.     

Optimal routing algorithms for mesh-connected processor arrays

We show that there is a randomizedoblivious algorithm for routing any (partial) permutation on ann ×n grid in 2n +O(logn) parallel communication steps. The queues will not grow larger than Θ(logn/log logn) with high probability. We then modify this to obtain a (nonoblivious) algorithm with the same running time such that the size of the queues is bounded by a constant with high probability. For permutations withlocality, where each packet has to travel a distance at mostL, a generalization of the algorithm routes in time proportional toL with high probability. Finally, we identify a class of meshlike networks that have optimal or near-optimal diameter. These meshes have the potential of being adapted to run existing sorting and routing algorithms with corresponding reduction in their running times.     

Efficient parallel solutions to some geometric problems

This paper presents new algorithms for solving some geometric problems on a shared memory parallel computer, where concurrent reads are allowed but no two processors can simultaneously attempt to write in the same memory location. The algorithms are quite different from known sequential algorithms, and are based on the use of a new parallel divide-and-conquer technique. One of our results is an O(log n) time, O(n) processor algorithm for the convex hull problem. Another result is an O(log n log log n) time, O(n) processor algorithm for the problem of selecting a closest pair of points among n input points.