The longest common subsequence problem revisited

This paper re-examines, in a unified framework, two classic approaches to the problem of finding a longest common subsequence (LCS) of two strings, and proposes faster implementations for both. Letl be the length of an LCS between two strings of lengthm andn m, respectively, and let s be the alphabet size. The first revised strategy follows the paradigm of a previousO(ln) time algorithm by Hirschberg. The new version can be implemented in timeO(lm · min logs, logm, log(2n/m)), which is profitable when the input strings differ considerably in size (a looser bound for both versions isO(mn)). The second strategy improves on the Hunt-Szymanski algorithm. This latter takes timeO((r +n) logn), wherermn is the total number of matches between the two input strings. Such a performance is quite good (O(n logn)) whenrn, but it degrades to (mn logn) in the worst case. On the other hand the variation presented here is never worse than linear-time in the productmn. The exact time bound derived for this second algorithm isO(m logn +d log(2mn/d)), whered r is the number ofdominant matches (elsewhere referred to asminimal candidates) between the two strings. Both algorithms require anO(n logs) preprocessing that is nearly standard for the LCS problem, and they make use of simple and handy auxiliary data structures.     

A Technique to Speed Up Parallel Fully Dynamic Algorithms for MST

We provide a new EREW PRAM algorithm to maintain the minimum spanning tree (MST) of an undirected weighted graph. Our approach combines the sparsification data structure with a novel parallel technique which efficiently treats single edge deletions. The proposed parallel algorithm requires O(log n) time and O(n^2/3 log(m/n)) work, where n and m are respectively the number of nodes and edges of the given graph.     

Efficient Graph-Theoretic Algorithms on a Linear Array with a Reconfigurable Pipelined Bus System

We present efficient algorithms for solving several fundamental graph-theoretic problems on a Linear Array with a Reconfigurable Pipelined Bus System (LARPBS), one of the recently proposed models of computation based on optical buses. Our algorithms include finding connected components, minimum spanning forest, biconnected components, bridges and articulation points for an undirected graph. We compute the connected components and minimum spanning forest of a graph in O(log n) time using O(m+n) processors where m and n are the number of edges and vertices in the graph and m=O(n ²) for a dense graph. Both the processor and time complexities of these two algorithms match the complexities of algorithms on the Arbitrary and Priority CRCW PRAM models which are two of the strongest PRAM models. The algorithms for these two problems published by Li et al. [7] have been considered to be the most efficient on the LARPBS model till now. Their algorithm [7] for these two problems require O(log n) time and O(n ³/log n) processors. Hence, our algorithms have the same time complexity but require less processors. Our algorithms for computing biconnected components, bridges and articulation points of a graph run in O(log n) time on an LARPBS with O(n ²) processors. No previous algorithm was known for these latter problems on the LARPBS.     

The longest common subsequence problem revisited

This paper re-examines, in a unified framework, two classic approaches to the problem of finding a longest common subsequence (LCS) of two strings, and proposes faster implementations for both. Letl be the length of an LCS between two strings of lengthm andn ≥m, respectively, and let s be the alphabet size. The first revised strategy follows the paradigm of a previousO(ln) time algorithm by Hirschberg. The new version can be implemented in timeO(lm · min logs, logm, log(2n/m)), which is profitable when the input strings differ considerably in size (a looser bound for both versions isO(mn)). The second strategy improves on the Hunt-Szymanski algorithm. This latter takes timeO((r +n) logn), wherer≤mn is the total number of matches between the two input strings. Such a performance is quite good (O(n logn)) whenr～n, but it degrades to Θ(mn logn) in the worst case. On the other hand the variation presented here is never worse than linear-time in the productmn. The exact time bound derived for this second algorithm isO(m logn +d log(2mn/d)), whered ≤r is the number ofdominant matches (elsewhere referred to asminimal candidates) between the two strings. Both algorithms require anO(n logs) preprocessing that is nearly standard for the LCS problem, and they make use of simple and handy auxiliary data structures.     

An efficient distributed algorithm for finding all hinge vertices in networks

Let G=(V, E) be a graph with vertex set V of size n and edge set E of size m. A vertex v∈V is called a hinge vertex if there exist two vertices in V\{v} such that their distance becomes longer when v is removed. In this paper, we present a distributed algorithm that finds all hinge vertices on an arbitrary graph. The proposed algorithm works for named static asynchronous networks and achieves O(n ²) time complexity and O(m) message complexity. In particular, the total messages exchanged during the algorithm are at most 2m(log n+nlog n+1) bits.     

Fast algorithms for long transportation problems

The paper deals with large transportation problems in which the number of destinations (n) is much larger than the number of origins (m), and in which some or many of the paths from origins to destinations may be inadmissible. Using a new approach, with certain auxilary lists, it is proved that the ordinary simplex algorithm (“Most Negative Rule”) can be performed in O(m²+ m log n) computer operations per iteration, as against O(mn) in the usual approach. A search-in-a-row simplex algorithm (“Row Most Negative Rule”), for which the total number of iterations is probably only somewhat larger, is shown to require just O(m + σm log n) operations per iteration, where σ is the density of the cost matrix (i.e. the proportion of admissible paths). For these rigorous results one needs computer storage which is not considerably larger than that required for storing the cost matrix. For smaller memory an efficient algorithm is also proposed. A general tentative rule for die amount of scanning per iteration is introduced and applied. Computer experiments are reported, confirming theoretical estimates.     

Solving shortest paths efficiently on nearly acyclic directed graphs

Shortest path problems can be solved very efficiently when a directed graph is nearly acyclic. Earlier results defined a graph decomposition, now called the 1-dominator set, which consists of a unique collection of acyclic structures with each single acyclic structure dominated by a single associated trigger vertex. In this framework, a specialised shortest path algorithm only spends delete-min operations on trigger vertices, thereby making the computation of shortest paths through non-trigger vertices easier. A previously presented algorithm computed the 1-dominator set in O(mn) worst-case time, which allowed it to be integrated as part of an O(mn+nrlogr) time all-pairs algorithm. Here m and n respectively denote the number of edges and vertices in the graph, while r denotes the number of trigger vertices. A new algorithm presented in this paper computes the 1-dominator set in just O(m) time. This can be integrated as part of the O(m+rlogr) time spent solving single-source, improving on the value of r obtained by the earlier tree-decomposition single-source algorithm. In addition, a new bidirectional form of 1-dominator set is presented, which further improves the value of r by defining acyclic structures in both directions over edges in the graph. The bidirectional 1-dominator set can similarly be computed in O(m) time and included as part of the O(m+rlogr) time spent computing single-source. This paper also presents a new all-pairs algorithm under the more general framework where r is defined as the size of any predetermined feedback vertex set of the graph, improving the previous all-pairs time complexity from O(mn+nr²) to O(mn+r³).     

Listing all the minimum spanning trees in an undirected graph

Efficient polynomial time algorithms are well known for the minimum spanning tree problem. However, given an undirected graph with integer edge weights, minimum spanning trees may not be unique. In this article, we present an algorithm that lists all the minimum spanning trees included in the graph. The computational complexity of the algorithm is O(N(mn+n ² log n)) in time and O(m) in space, where n, m and N stand for the number of nodes, edges and minimum spanning trees, respectively. Next, we explore some properties of cut-sets, and based on these we construct an improved algorithm, which runs in O(N m log n) time and O(m) space. These algorithms are implemented in C language, and some numerical experiments are conducted for planar as well as complete graphs with random edge weights.     

An optimal parallel algorithm for computing cut vertices and blocks on interval graphs

In this paper, a parallel algorithm is presented to find all cut-vertices and blocks of an interval graph. If the list of sorted end points of the intervals of an interval graph is given then the proposed algorithm takes O(log n) time and O(n/log n) processors on an EREW PRAM, if the sorted list is not given then the time and processors complexities are respectively O(log n) and O(n).     

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.     

Parallel String Matching with Variable Length Don′t Cares

String matching is the problem of finding all the occurrences of a pattern P in a text T, where P and T are strings over a finite alphabet Σ. A variable length don′t care is a special character, not belonging to Σ, which can match any string in Σ*. The string-matching problem with variable length don′t cares is an extension of the classical string-matching problem in which the pattern P may contain an arbitrary number of don′t cares. An efficient parallel algorithm is given for solving the string-matching problem with variable length don′t cares. The EREW PRAM model of parallel computer with scan operations is used to obtain an O(log n) running time using O(mn/log n) processors, where m and n are, respectively, the lengths of P and T. The proposed parallel algorithm has an Ω(1/log n) processor utilization, since the fastest serial algorithm known so far has an O(mn/log n) running time.     

Faster Algorithms for Stable Allocation Problems

We consider a high-multiplicity generalization of the classical stable matching problem known as the stable allocation problem, introduced by Baïou and Balinski in 2002. By leveraging new structural properties and sophisticated data structures, we show how to solve this problem in O(mlog?n) time on a bipartite instance with n vertices and m edges, improving the best known running time of O(mn). Building on this algorithm, we provide an algorithm for the non-bipartite stable allocation problem running in O(mlog?n) time with high probability. Finally, we give a polynomial-time algorithm for solving the “optimal” variant of the bipartite stable allocation problem, as well as a 2-approximation algorithm for the NP-hard “optimal” variant of the non-bipartite stable allocation problem.     

Approximate Pattern Matching with the <Emphasis Type="Italic">L</Emphasis><Subscript>1</Subscript>, <Emphasis Type="Italic">L</Emphasis><Subscript>2</Subscript> and <Emphasis Type="Italic">L</Emphasis><Subscript>∞</Subscript> Metrics

Given an alphabet Σ={1,2,…,|Σ|} text string T∈Σ ⁿ and a pattern string P∈Σ ^m , for each i=1,2,…,n−m+1 define L _p (i) as the p-norm distance when the pattern is aligned below the text and starts at position i of the text. The problem of pattern matching with L _p distance is to compute L _p (i) for every i=1,2,…,n−m+1. We discuss the problem for d=1,2,∞. First, in the case of L ₁ matching (pattern matching with an L ₁ distance) we show a reduction of the string matching with mismatches problem to the L ₁ matching problem and we present an algorithm that approximates the L ₁ matching up to a factor of 1+ε, which has an O(\frac1e²nlogmlog|S|)O(\frac{1}{\varepsilon^{2}}n\log m\log|\Sigma|) run time. Then, the L ₂ matching problem (pattern matching with an L ₂ distance) is solved with a simple O(nlog m) time algorithm. Finally, we provide an algorithm that approximates the L _∞ matching up to a factor of 1+ε with a run time of O(\frac1enlogmlog|S|)O(\frac{1}{\varepsilon}n\log m\log|\Sigma|) . We also generalize the problem of String Matching with mismatches to have weighted mismatches and present an O(nlog ⁴ m) algorithm that approximates the results of this problem up to a factor of O(log m) in the case that the weight function is a metric.     

A parallel algorithm for preemptive scheduling of uniform machines

In this paper we describe a fast parallel algorithm for preemptive scheduling of n independent jobs on m uniform machines. Each job has a processing requirement, and each machine processes jobs at a different rate. The goal of the scheduling algorithm is to find a schedule which minimizes the time at which the last job is completed. T. Gonzalez and S. Sahni have developed a sequential algorithm which solves this problem in O(n + m log m) time. We develop a parallel version of this algorithm for a Concurrent Read Exclusive Write (CREW) shared memory computer. The algorithm runs in O(log n + log³m) time using n processors.     

An efficient top-down search algorithm for learning Boolean networks of gene expression

Boolean networks provide a simple and intuitive model for gene regulatory networks, but a critical defect is the time required to learn the networks. In recent years, efficient network search algorithms have been developed for a noise-free case and for a limited function class. In general, the conventional algorithm has the high time complexity of O(2^{2k mn k+1}) where m is the number of measurements, n is the number of nodes (genes), and k is the number of input parents. Here, we suggest a simple and new approach to Boolean networks, and provide a randomized network search algorithm with average time complexity O ^{(mn k+1}/ (log m)^(k−1)). We show the efficiency of our algorithm via computational experiments, and present optimal parameters. Additionally, we provide tests for yeast expression data. Editor: David Page     

3D object perception using gradient descent

A new algorithm is presented for interpreting two-dimensional (2D) line drawings as three-dimensional (3D) objects without models. Even though no explicit models or additional heuristics are included, the algorithm tends to reach the same 3D interpretations of 2D line drawings that humans do. The algorithm explicitly calculates the partial derivatives of Marill's Minimum Standard Deviation of Angles (MSDA) with respect to all adjustable parameters, and follows this gradient to minimize SDA. For an image with lines meeting atm points formingn angles, the gradient descent algorithm requiresO(n) time to adjust all the points, while Marill's method requiredO(mn) time to do so. Experimental results on various line drawing objects show that this gradient descent algorithm running on a Macintosh II is one to two orders of magnitude faster than the MSDA algorithm running on a Symbolics, while still giving comparable results.     

An algorithm for merging meaps

Summary We present an algorithm to merge priority queues organized as heaps. The worst case number of comparisons required to merge two heaps of sizes k and n is O(log(n)*log(k)). The algorithm requires O(k) +log(n)*log (k)) data movements if heaps are implemented using arrays and O(log(n)*log(k)) for a pointer-based implementation. Previous algorithms require either O(n+k) data movements and comparisons, or O(k*log(log(n+k))) comparisons and O(k*log(n+k)) data movements. The algorithm presented in this paper improves on the previous algorithms for the case when k>log(n).This work was done while the authors were at McGill University, Montréal, Canada     

Traversal of an Unknown Directed Graph by a Finite Robot

A covering path in a directed graph is a path passing through all vertices and arcs of the graph, with each arc being traversed only in the direction of its orientation. A covering path exists for any initial vertex only if the graph is strongly connected, i.e., any of its vertices can be reached from any other vertex by some path. The strong connectivity is the only restriction on the considered class of graphs. As is known, on the class of such graphs, the covering path length is (nm), where n is the number of vertices and m is the number of arcs. For any graph, there exists a covering path of length O(nm), and there exist graphs with covering paths of the minimum length (nm). The traversal of an unknown graph implies that the topology of the graph is not a priori known, and we learn it only in the course of traversing the graph. At each vertex, one can see which arcs originate from the vertex, but one can learn to which vertex a given arc leads only after traversing this arc. This is similar to the problem of traversing a maze by a robot in the case where the plan of the maze is not available. If the robot is a general-purpose computer without any limitations on the number of its states, then traversal algorithms with the same estimate O(nm) are known. If the number of states is bounded, then this robot is a finite automaton. Such a robot is an analogue of the Turing machine, where the tape is replaced by a graph and the cells are assigned to the graph vertices and arcs. Currently, the lower estimate of the length of the traversal by a finite robot is not known. In 1971, the author of this paper suggested a robot with the traversal length O(nm + n ²logn). The algorithm of the robot is based on the construction of the output directed spanning tree of the graph and on the breadth-first search (BFS) on this tree. In 1993, Afek and Gafni [1] suggested an algorithm with the same estimate of the covering path length, which was also based on constructing a spanning tree but used the depth-first search (DFS) method. In this paper, an algorithm is suggested that combines the breadth-first search with the backtracking (suggested by Afek and Gafni), which made it possible to reach the estimate O(nm + n ²loglogn). The robot uses a constant number of memory bits for each vertex and arc of the graph.     

Efficient Algorithms for k-Terminal Cuts on Planar Graphs

The minimum k-terminal cut problem is of considerable theoretical interest and arises in several applied areas such as parallel and distributed computing, VLSI circuit design, and networking. In this paper we present two new approximation and exact algorithms for this problem on an n-vertex undirected weighted planar graph G. For the case when the k terminals are covered by the boundaries of m > 1 faces of G, we give a min{O(n ² log n logm), O(m ² n ^1.5 log² n + k n)} time algorithm with a (2–2/k)-approximation ratio (clearly, m \le k). For the case when all k terminals are covered by the boundary of one face of G, we give an O(n k3 + (n log n)k ²) time exact algorithm, or a linear time exact algorithm if k = 3, for computing an optimal k-terminal cut. Our algorithms are based on interesting observations and improve the previous algorithms when they are applied to planar graphs. To our best knowledge, no previous approximation algorithms specifically for solving the k-terminal cut problem on planar graphs were known before. The (2–2/k)-approximation algorithm of Dahlhaus et al. (for general graphs) takes O(k n ² log n) time when applied to planar graphs. Our approximation algorithm for planar graphs runs faster than that of Dahlhaus et al. by at least an O(k/logm) factor (m \le k).     

Efficient Algorithms for <Emphasis Type="Italic">k</Emphasis>-Terminal Cuts on Planar Graphs

The minimum k-terminal cut problem is of considerable theoretical interest and arises in several applied areas such as parallel and distributed computing, VLSI circuit design, and networking. In this paper we present two new approximation and exact algorithms for this problem on an n-vertex undirected weighted planar graph G. For the case when the k terminals are covered by the boundaries of m > 1 faces of G, we give a min{O(n ² log n logm), O(m ² n ^1.5 log² n + k n)} time algorithm with a (2–2/k)-approximation ratio (clearly, m \le k). For the case when all k terminals are covered by the boundary of one face of G, we give an O(n k3 + (n log n)k ²) time exact algorithm, or a linear time exact algorithm if k = 3, for computing an optimal k-terminal cut. Our algorithms are based on interesting observations and improve the previous algorithms when they are applied to planar graphs. To our best knowledge, no previous approximation algorithms specifically for solving the k-terminal cut problem on planar graphs were known before. The (2–2/k)-approximation algorithm of Dahlhaus et al. (for general graphs) takes O(k n ² log n) time when applied to planar graphs. Our approximation algorithm for planar graphs runs faster than that of Dahlhaus et al. by at least an O(k/logm) factor (m \le k).