String-matching with OBDDs

Ordered binary decision diagrams (OBDDs) are a very popular graph representation for Boolean functions. They can be viewed as finite automata recognizing sets of strings of a fixed length, where the letters of the input strings are read at most once in a predefined ordering. The string matching problem with string w as pattern, consists of determining, given an input string, whether or not it contains w as substring. We show that for a fraction of orderings tending to 1 when n increases arbitrarily, the minimal size of an OBDD solving the string matching problem for strings of length n has a growth which is an exponential in n.     

多序列的近似LCS改进算法

提出2种针对3条源序列的近似LCS算法,近似因子均为1/|?|。其中,线性近似LCS算法的时空复杂度均为 , 为最长源序列的长度,适于解决大规模问题。递归近似LCS算法时空复杂度均为O(nlogn),适于要求高精度问题。同时,这2种算法都能用于解决多序列的LCS和CLCS问题。实验验证了这2种算法的有效性。     

An Efficient Systolic Algorithm for the Longest Common Subsequence Problem

A longest common subsequence (LCS) of two strings is a common subsequence of the two strings of maximal length. The LCS problem is to find an LCS of two given strings and the length of the LCS (LLCS). In this paper, a fast linear systolic algorithm that improves on previous systolic algorithms for solving the LCS problem is presented. For two given strings of length m and n, where m n, the LLCS and an LCS can be found in m + 2n – 1 time steps. This algorithm achieves the tight lower bound of the time complexity under the situation where symbols are input sequentially to a linear array of n processors. The systolic algorithm can be modified to take only m + n steps on multicomputers by using the scatter operation.     

A design of time-optimum and register-number-minimum systolic convolvers

We present an optimum bit-parallel/word-sequential systolic convolver. Our design is the best one among the previous many convolvers in the sense that its optimality in time and space performances is simultaneously attained without augmenting any global control, broadcasting, initial-data-preloading, and/or multi-sequential or parallel I/O ports which were allowed in most of the previous designs. As an application of our convolver we give a systolic polynomial divider which can compute the polynomial division in exactly n + O(1) optimum steps on [min(n−m, m)/2]+O(1) systolic cells for the division of any degree n polynomial by any degree m polynomial (n m).     

Finding the minimum vertex distance between two disjoint convex polygons in linear time

Let V = v₁, v₂, …, v_m and W = w₁, w₂, …, w_n be two linearly separable convex polygons whose vertices are specified by their cartesian coordinates in order. An algorithm with O(m + n) worst-case time complexity is described for finding the minimum euclidean distance between a vertex v₁ in V and a vertex w_j in W. It is also shown that the algorithm is optimal.     

A parallel residue-to-binary conversion algorithm without trial division

In recent years, the conversion of residue numbers to a binary integer has been intensively studied. The Chinese Remainder Theorem (CRT) is a solution to this conversion problem of a number to the Residue Number System with a general moduli set. This paper presents a new division-free conversion approach for the conversion of residue numbers to a binary integer. The algorithm differs from others employing a great number of division instructions by using shift instructions instead. These simple instructions keep the power consumption lower. This algorithm can also be implemented with a lookup table or upon a vector machine. Both make the conversion process efficient. This division-free algorithm employs the concept of Montgomery multiplication algorithm. There are two variations of Montgomery algorithm proposed, which are algorithms MMA and IMA. The algorithm MMA is to transform the input number into the output presentation of Montgomery algorithm. Algorithm IMA is therefore inverse the computation of Montgomery algorithm to obtain the multiplicand. These two algorithms are in the complexity of O(n), where n is log₂ q_i. q_i is a modulus. The proposed algorithm for converting the residues to a binary integer therefore runs on O(n × log m) times on O(m) processors. There are O(log m) iterations of O(n) complexity. Compared with the traditional conversion algorithm, the advantages of this proposed algorithm are not only in employing simpler operations but also in performing fewer iterations.     

The unbounded single machine parallel batch scheduling problem with family jobs and release dates to minimize makespan

In this paper we consider the unbounded single machine parallel batch scheduling problem with family jobs and release dates to minimize makespan. We show that this problem is strongly NP-hard, and give an O(n(n/m+1)^m) time dynamic programming algorithm and an O(mk^k+1P^2k−1) time dynamic programming algorithm, where n is the number of jobs, m is the number of families, k is the number of distinct release dates and P is the sum of the processing times of all families. We further give a heuristic with a performance ratio 2. We also give a polynomial-time approximation scheme for the problem.     

Two minimum spanning forest algorithms on fixed-size hypercube computers

Two parallel algorithms for finding minimum spanning forest (MSF) of a weighted undirected graph on hypercube computers, consisting of a fixed number of processors, are presented. One algorithm is suited for sparse graphs, the other for dense graphs. Our design strategy is based on successive elimination of non-MSF edges. The input graph is partitioned equally among different processors, which then repeatedly eliminate non-MSF edges and merge results to gradually construct the desired MSF of the entire graph. Low communication overhead is achieved by restricting the message-flow to between the neighboring processors in the hypercube topology. The correctness of our approach is due to a theorem which states that with total-ordered edges, if an edge of an arbitrary subgraph does not belong to its MSF, then it does not belong to the MSF of the entire graph. For a graph of n vertices and m edges, our first algorithm finds an MSF in O(m log m)/p) time using p processors for p ≤ (mlog m)/n(1+log(m/n)). The second algorithm, efficient for dense graphs, requires O(n²/p) time for p≤n/log n.     

Parallel clustering algorithms

Clustering techniques play an important role in exploratory pattern analysis, unsupervised learning and image segmentation applications. Many clustering algorithms, both partitional clustering and hierarchical clustering, require intensive computation, even for a modest number of patterns. This paper presents two parallel clustering algorithms. For a clustering problem with N = 2ⁿ patterns and M = 2^m features, the time complexity of the traditional partitional clustering algorithm on a single processor computer is O(MNK), where K is the number of clusters. The proposed algorithm on anSIMD computer with MN processors has a time complexity O(K(n + m)). The time complexity of the proposed single-link hierarchical clustering algorithm is reduced from O(MN²) of the uniprocessor algorithm to O(nN) with MN processors.     

Minimum cost source location problem with vertex-connectivity requirements in digraphs

Given a digraph (or an undirected graph) G=(V,E) with a set V of vertices v with nonnegative real costs w(v), and a set E of edges and a positive integer k, we deal with the problem of finding a minimum cost subset SV such that, for each vertex vV−S, there are k vertex-disjoint paths from S to v. In this paper, we show that the problem can be solved by a greedy algorithm in time in a digraph (or in time in an undirected graph), where n=|V| and m=|E|. Based on this, given a digraph and two integers k and ℓ, we also give a polynomial time algorithm for finding a minimum cost subset SV such that for each vertex vV−S, there are k vertex-disjoint paths from S to v as well as ℓ vertex-disjoint paths from v to S.     

Approximate Matching of Run-Length Compressed Strings

We focus on the problem of approximate matching of strings that have been compressed using run-length encoding. Previous studies have concentrated on the problem of computing the longest common subsequence (LCS) between two strings of length m and n , compressed to m' and n' runs. We extend an existing algorithm for the LCS to the Levenshtein distance achieving O(m'n+n'm) complexity. Furthermore, we extend this algorithm to a weighted edit distance model, where the weights of the three basic edit operations can be chosen arbitrarily. This approach also gives an algorithm for approximate searching of a pattern of m letters (m' runs) in a text of n letters (n' runs) in O(mm'n') time. Then we propose improvements for a greedy algorithm for the LCS, and conjecture that the improved algorithm has O(m'n') expected case complexity. Experimental results are provided to support the conjecture.     

A new routing algorithm for multirate rearrangeable Clos networks

In this paper, we study the problem of finding routing algorithms on the multirate rearrangeable Clos networks which use as few number of middle-stage switches as possible. We propose a new routing algorithm called the “grouping algorithm”. This is a simple algorithm which uses fewer middle-stage switches than all known strategies, given that the number of input-stage switches and output-stage switches are relatively small compared to the size of input and output switches. In particular, the grouping algorithm implies that m = 2n+(n−1)/2^k is a sufficient number of middle-stage switches for the symmetric three-stage Clos network C(n,m,r) to be multirate rearrangeable, where k is any positive integer and rn/(2^k−1).     

Constrained multibody system dynamics an automated approach

The governing equations for constrained multibody systems are formulated in a manner suitable for their automated, numerical development and solution. Specifically, the “closed loop” problem of multibody chain systems is addressed.

The governing equations are developed by modifying dynamical equations obtained from Lagrange's form of d'Alembert's principle. This modification, which is based upon a solution of the constraint equations obtained through a “zero eigenvalues theorem,” is, in effect, a contraction of the dynamical equations.

It is observed that, for a system with n generalized coordinates and m constraint equations, the coefficients in the constraint equations may be viewed as “constraint vectors” in n-dimensional space. Then, in this setting the system itself is free to move in the n−m directions which are “orthogonal” to the constraint vectors.     

An algorithmic view of gene teams

Comparative genomics is a growing field in computational biology, and one of its typical problem is the identification of sets of orthologous genes that have virtually the same function in several genomes. Many different bioinformatics approaches have been proposed to define these groups, often based on the detection of sets of genes that are “not too far” in all genomes. In this paper, we propose a unifying concept, called gene teams, which can be adapted to various notions of distance. We present two algorithms for identifying gene teams formed by n genes placed on m linear chromosomes. The first one runs in O(mn log² n) and uses a divide and conquer approach based on the formal properties of gene teams. We next propose an optimization of the original algorithm, and, in order to better understand the complexity bound of the algorithms, we recast the problem in the Hopcroft's partition refinement framework. This allows us to analyze the complexity of the algorithms with elegant amortized techniques. Both algorithms require linear space. We also discuss extensions to circular chromosomes that achieve the same complexity.     

On the number of occurrences of all short factors in almost all words

We previously proved that almost all words of length n over a finite alphabet A with m letters contain as factors all words of length k(n) over A as n→∞, provided limsup_n→∞ k(n)/log n<1/log m.

In this note it is shown that if this condition holds, then the number of occurrences of any word of length k(n) as a factor into almost all words of length n is at least s(n), where lim_n→∞ log s(n)/log n=0. In particular, this number of occurrences is bounded below by C log n as n→∞, for any absolute constant C>0.     

A linear space algorithm for the LCS problem

Summary The LCS problem is to determine the longest common subsequence (LCS) of two strings. A new linear-space algorithm to solve the LCS problem is presented. The only other algorithm with linear-space complexity is by Hirschberg and has runtime complexity O(mn). Our algorithm, based on the divide and conquer technique, has runtime complexity O(n(m-p)), where p is the length of the LCS.     

Approximate Matching of Run-Length Compressed Strings

Abstract. We focus on the problem of approximate matching of strings that have been compressed using run-length encoding. Previous studies have concentrated on the problem of computing the longest common subsequence (LCS) between two strings of length m and n , compressed to m' and n' runs. We extend an existing algorithm for the LCS to the Levenshtein distance achieving O(m'n+n'm) complexity. Furthermore, we extend this algorithm to a weighted edit distance model, where the weights of the three basic edit operations can be chosen arbitrarily. This approach also gives an algorithm for approximate searching of a pattern of m letters (m' runs) in a text of n letters (n' runs) in O(mm'n') time. Then we propose improvements for a greedy algorithm for the LCS, and conjecture that the improved algorithm has O(m'n') expected case complexity. Experimental results are provided to support the conjecture.     

Efficient algorithms for single- and two-layer linear placement of parallel graphs

This paper outlines an algorithm for optimum linear ordering (OLO) of a weighted parallel graph with O(n log k) worst-case time complexity, and O(n + k log(n/k) log k) expected-case time complexity, where n is the total number of nodes and k is the number of chains in the parallel graph. Next, the two-layer OLO problem is considered, where the goal is to place the nodes linearly in two routing layers minimizing the total wire length. The two-layer problem is shown to subsume the maxcut problem and a befitting heuristic algorithm is proposed. Experimental results on randomly generated samples show that the heuristic algorithm runs very fast and outputs optimum solutions in more than 90% instances.     

A parallel algorithm solving a tridiagonal Toeplitz linear system

A new tridiagonal Toeplitz linear system (TTLS) solver is proposed. The solver first decomposes an n-dimensional strictly diagonally dominant TTLS equation into a number of m-dimensional subsystems employing a modified Gaussian elimination method. An analytic solution of a continued fraction is obtained to derive the solver. The solver based on the modified Gaussian elimination method fully exploits parallelism. Computation and communication complexities of the proposed algorithm are all shown to be O(n/m).     

Reaching a goal with directional uncertainty

We study two problems related to planar motion planning for robots with imperfect control, where, if the robot starts a linear movement in a certain commanded direction, we only know that its actual movement will be confined in a cone of angle centered around the specified direction.

First, we consider a single goal region, namely the “region at infinity”, and a set of polygonal obstacles, modeled as a set S of n line segments. We are interested in the region from where we can reach infinity with a directional uncertainty of . We prove that the maximum complexity of is O(n/⁵). Second, we consider a collection of k polygonal goal regions of total complexity m, but without any obstacles. Here we prove an O(k³m) bound on the complexity of the region from where we can reach a goal region with a directional uncertainty of . For both situations we also prove lower bounds on the maximum complexity, and we give efficient algorithms for computing the regions.