Longest common subsequence between run-length-encoded strings: a new algorithm with improved parallelism

Data compression can be used to simultaneously reduce memory, communication and computation requirements of string comparison. In this paper we address the problem of computing the length of the longest common subsequence (LCS) between run-length-encoded (RLE) strings. We exploit RLE both to reduce the complexity of LCS computation from O(M×N) to O(mN+Mn−mn), where M and N are the lengths of the original strings and m and n the number of runs in their RLE representation, and to improve the inherent parallelism of the proposed algorithm, so that it may execute in O(m+n) steps on a systolic array of M+N units.We also discuss the application of the proposed algorithm to the related problem of edit distance (ED) computation.     

A fast and simple algorithm for computing the longest common subsequence of run-length encoded strings

Let X and Y be two strings of lengths n and m, respectively, and k and l, respectively, be the numbers of runs in their corresponding run-length encoded forms. We propose a simple algorithm for computing the longest common subsequence of two given strings X and Y in O(kl+min{p₁,p₂}) time, where p₁ and p₂ denote the numbers of elements in the bottom and right boundaries of the matched blocks, respectively. It improves the previously known time bound O(min{nl,km}) and outperforms the time bounds O(kllogkl) or O((k+l+q)log(k+l+q)) for some cases, where q denotes the number of matched blocks.     

An almost-linear time and linear space algorithm for the longest common subsequence problem

There are two general approaches to the longest common subsequence problem. The dynamic programming approach takes quadratic time but linear space, while the nondynamic-programming approach takes less time but more space. We propose a new implementation of the latter approach which seems to get the best for both time and space for the DNA application.     

A fast algorithm for computing a longest common increasing subsequence

Let A=〈a₁,a₂,…,am〉 and B=〈b₁,b₂,…,bn〉 be two sequences, where each pair of elements in the sequences is comparable. A common increasing subsequence of A and B is a subsequence 〈ai₁=bj₁,ai₂=bj₂,…,ail=bjl〉, where i₁<i₂<?<il and j₁<j₂<?<jl, such that for all 1?k<l, we have aik<aik+1. A longest common increasing subsequence of A and B is a common increasing subsequence of the maximum length. This paper presents an algorithm for delivering a longest common increasing subsequence in O(mn) time and O(mn) space.     

Variants of constrained longest common subsequence

We consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s₁ and s₂ over an alphabet Σ, a set Cs of strings, and a function Co:Σ→N, the DC-LCS problem consists of finding the longest subsequence s of s₁ and s₂ such that s is a supersequence of all the strings in Cs and such that the number of occurrences in s of each symbol σ∈Σ is upper bounded by Co(σ). The DC-LCS problem provides a clear mathematical formulation of a sequence comparison problem in Computational Biology and generalizes two other constrained variants of the LCS problem that have been introduced previously in the literature: the Constrained LCS and the Repetition-Free LCS. We present two results for the DC-LCS problem. First, we illustrate a fixed-parameter algorithm where the parameter is the length of the solution which is also applicable to the more specialized problems. Second, we prove a parameterized hardness result for the Constrained LCS problem when the parameter is the number of the constraint strings (|Cs|) and the size of the alphabet Σ. This hardness result also implies the parameterized hardness of the DC-LCS problem (with the same parameters) and its NP-hardness when the size of the alphabet is constant.     

Edit distance of run-length encoded strings

Let X and Y be two run-length encoded strings, of encoded lengths k and l, respectively. We present a simple O(|X|l+|Y|k) time algorithm that computes their edit distance.     

Classes of cost functions for string edit distance

Finding a sequence of edit operations that transforms one string of symbols into another with the minimum cost is a well-known problem. The minimum cost, or edit distance, is a widely used measure of the similarity of two strings. An important parameter of this problem is the cost function, which specifies the cost of each insertion, deletion, and substitution. We show that cost functions having the same ratio of the sum of the insertion and deletion costs divided by the substitution cost yield the same minimum cost sequences of edit operations. This leads to a partitioning of the universe of cost functions into equivalence classes. Also, we show the relationship between a particular set of cost functions and the longest common subsequence of the input strings. This work was supported in part by the U.S. Department of Defense and the U.S. Department of Energy.     

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.     

A new relevance feedback technique for iconic image retrieval based on spatial relationships

Due to the popularity of Internet and the growing demand of image access, the volume of image databases is exploding. Hence, we need a more efficient and effective image searching technology. Relevance feedback technique has been popularly used with content-based image retrieval (CBIR) to improve the precision performance, however, it has never been used with the retrieval systems based on spatial relationships. Hence, we propose a new relevance feedback framework to deal with spatial relationships represented by a specific data structure, called the 2D B_e-string. The notions of relevance estimation and query reformulation are embodied in our method to exploit the relevance knowledge. The irrelevance information is collected in an irrelevant set to rule out undesired pictures and to expedite the convergence speed of relevance feedback. Our system not only handles picture-based relevance feedback, but also deals with region-based feedback mechanism, such that the efficacy and effectiveness of our retrieval system are both satisfactory.     

Implementing Gaussian elimination on a matrix-matrix multiplication systolic array

We show that any systolic array dedicated to matrix-matrix multiplication can also execute Gaussian elimination.     

Parallel generation of permutations on systolic arrays

We present a systolic algorithm to generate all the n! permutations of n given items. The computational model used is a linear systolic array consisting of n identical PEs. This algorithm requires n! time steps to solve this problem. Since any PE is identical and executes the same program, it is suitable for VLSI implementation. The correctness of the algorithm is proved. We also consider the ranking and unranking functions of permutations in this parallel algorithm     

Parallel distance transforms on a linear array architecture

Distance transformation (DT) has been widely used for image matching and shape analysis. In this paper, a parallel algorithm for computing distance transformation is presented. First, it is shown that the algorithm has an execution time of 6N−4 cycles, for an N×N image using a parallel architecture that requires ⌈N/2⌉ parallel processors. By doing so, the real time requirement is fulfilled and its execution time is independent of the image contents. In addition, a partition method is developed to process an image when the parallel architecture has a fixed number of processing elements (PEs); say two or more. The total execution time for an N×N image by employing a fixed number of PEs is 2[N²/M+2(M−1)], when M is the fixed number of PEs.     

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.     

Computing all-pairs shortest paths on a linear systolic array and hardware realization on a reprogrammable FPGA platform

In this paper a regular bidirectional linear systolic array (RBLSA) for computing all-pairs shortest paths of a given directed graph is designed. The obtained array is optimal with respect to a number of processing elements (PE) for a given problem size. The execution time of the array has been minimized. To obtain RBLSA with optimal number of PEs, the accommodation of the inner computation space of the systolic algorithm to the projection direction vector is performed. Finally, FPGA-based reprogrammable systems are revolutionizing certain types of computation and digital logic, since as logic emulation systems they offer some orders of magnitude speedup over software simulation; herein, a FPGA realization of the RBLSA is investigated and the performance evaluation results are discussed.     

Longest common subsequence problem for unoriented and cyclic strings

Given a finite set of strings X, the Longest Common Subsequence problem (LCS) consists in finding a subsequence common to all strings in X that is of maximal length. LCS is a central problem in stringology and finds broad applications in text compression, conception of error-detecting codes, or biological sequence comparison. However, in numerous contexts, words represent cyclic or unoriented sequences of symbols and LCS must be generalized to consider both orientations and/or all cyclic shifts of the strings involved. This occurs especially in computational biology when genetic material is sequenced from circular DNA or RNA molecules.In this work, we define three variants of LCS when the input words are unoriented and/or cyclic. We show that these problems are -hard, and -hard if parameterized in the number of input strings. These results still hold even if the three LCS variants are restricted to input languages over a binary alphabet. We also settle the parameterized complexity of our problems for most relevant parameters. Moreover, we study the approximability of these problems: we discuss the existence of approximation bounds depending on the cardinality of the alphabet, on the length of the shortest sequence, and on the number of input sequences. For this we prove that Maximum Independent Set in r-uniform hypergraphs is -hard if parameterized in the cardinality of the sought independent set and at least as hard to approximate as Maximum Independent Set in graphs.     

Double pipelines and fast systolic designs on linear arrays

The fast systolic computation and double pipelines were designed to achieve implementations that use less processors to execute the algorithm in less time then the conventional systolic algorithms. H. T. Kung and C. S. Leiserson in [1-3] proposed systolic algorithms realized on a bidirectional linear array where two data streams flow in opposite directions. The data flow introduced for this solution requires data elements to appear in the data stream at each second time step, which is the only way to meet all the elements from the other data stream.

In [4, 5] the authors proposed a linear array where one data stream is double mapped while the elements from the other data stream flow in consecutive time moments. The procedure to obtain such a solution is called a fast systolic design. It was shown in [5] that double pipeline solutions are obtained by separating and grouping techniques in addition to this design.

Several more efficient systolic designs have been proposed for the matrix vector multiplication algorithm in [4, 5]. Here we implement these techniques on other linear array algorithms such as triangular linear system solver, string comparison, convolution, correlation, MA and AR filter.     

Parallel sorting with cooperating heaps in a linear array of processors

A parallel sorting algorithm using cooperating heaps in a linear array of processors is presented. It can sort a sequence whose length is much larger than the number of processors. Because the output begins one step after all the items have been input, sorting n items requires 2n + 1 steps. Two independent modifications of the algorithm are possible; one tries to reduce the number of processors used, and the other can sort more items on the same array.     

Using static suffix array in dynamic application: Case of text compression by longest first substitution

Over the last decade, enhanced suffix arrays (ESA) have replaced suffix trees in many applications. Algorithms based on ESAs require less space, while allowing the same time efficiency as those based on suffix trees. However, this is only true when a suffix structure is used as a static index. Suffix trees can be updated faster than suffix arrays, which is a clear advantage in applications that require dynamic indexing. We show that for some dynamic applications a suffix array and the derived LCP-interval tree can be used in such a way that the actual index updates are not necessary. We demonstrate this in the case of grammar text compression with longest first substitution and provide the source code. The proposed algorithm has O(N²)$O(N^2)$ worst case time complexity but runs in O(N)$O(N)$ time in practice.     

Intermediate-level vision tasks on a memory array architecture

With the fast advances in the area of computer vision and robotics there is a growing need for machines that can understand images at very high speed. A conventional von Neumann computer is not suitable for this purpose, because it takes a tremendous amount of time to solve most typical image analysis problems. Thus, it is now imperative to study computer vision in a parallel processing framework in order to reduce the processing time. In this paper we demonstrate the applicability of a simple memory array architecture to some intermediate-level computer vision tasks. This architecture, called theAccess Constrained Memory Array Architecture (ACMAA) has a linear array of processors which concurrently access distinct rows or columns of an array of memory modules. Because of its efficient local and global communication capabilities ACMAA is well suited for low-level as well as intermediate-level vision tasks. This paper presents algorithms for connected component labeling, determination of area, perimeter and moments of a labeled region, convex hull of a region, and Hough transform of an image. ACMAA is well suited to an efficient hardware implementation because it has a modular structure, simple interconnect and limited global control.     

A sum-over-paths extension of edit distances accounting for all sequence alignments

This paper introduces a simple Sum-over-Paths (SoP) formulation of string edit distances accounting for all possible alignments between two sequences, and extends related previous work from bioinformatics to the case of graphs with cycles. Each alignment ℘, with a total cost C(℘), is assigned a probability of occurrence P(℘)=exp[−θC(℘)]/Z where Z is a normalization factor. Therefore, good alignments (having a low cost) are favored over bad alignments (having a high cost). The expected cost ∑_℘∈PC(℘)exp[−θC(℘)]/Z computed over all possible alignments ℘∈P defines the SoP edit distance. When θ→∞, only the best alignments matter and the measure reduces to the standard edit distance. The rationale behind this definition is the following: for some applications, two sequences sharing many good alignments should be considered as more similar than two sequences having only one single good, optimal, alignment in common. In other words, sub-optimal alignments could also be taken into account. Forward/backward recurrences allowing to efficiently compute the expected cost are developed. Virtually any Viterbi-like sequence comparison algorithm computed on a lattice can be generalized in the same way; for instance, a SoP longest common subsequence is also developed. Pattern classification tasks performed on five data sets show that the new measures usually outperform the standard ones and, in any case, never perform significantly worse, at the expense of tuning the parameter θ.