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检索条件"主题词=string algorithms"

共 150 条记录，以下是121-130 订阅

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On Computing Average Common Substring Over Run Length Encoded Sequences

On Computing Average Common Substring Over Run Length Encode...

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2nd Student Conference on Mathematical Founcations in Bioinformatics

作者： Hooshmand, Sahar Tavakoli, Neda Abedin, Paniz Thankachan, Sharma V. Univ Cent Florida Dept Comp Sci 117 Harris Ctr Bldg 1164000 Cent Florida Blvd Orlando FL 32816 USA Georgia Inst Technol Sch Computat Sci & Engn Atlanta GA 30332 USA

The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS of a sequence X[1, x] w.r.t. another sequence Y[1, y] is ACS(X, Y) = 1/x Sigma(x)(i=1) max lcp(X[i, x], Y[j, y]) The lcp(., .) of two input sequences is the length of their longest common prefix. The ACS can be computed in O(n) space and time, where n = x + y is the input size. The compressed string matching is the study of string matching problems with the following twist: the input data is in a compressed format and the underling task must be performed with little or no decompression. In this paper, we revisit the ACS problem under this paradigm where the input sequences are given in their run-length encoded format. We present an algorithm to compute ACS(X, Y) in O(N logN) time using O(N) space, where N is the total length of sequences after run-length encoding.

关键词： string algorithms Suffix Trees RL Encoding Compression

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ACCELERATING THE UNDERSTANDING OF LIFE'S CODE THROUGH BETTER algorithms AND HARDWARE DESIGN

ACCELERATING THE UNDERSTANDING OF LIFE'S CODE THROUGH BETTER...

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作者： Mohammed H. K. Alser Bilkent University

学位级别：博士

Our understanding of human genomes today is affected by the ability of modern computing technology to quickly and accurately determine an individual's entire genome. Over the past decade, high throughput sequencing (HTS) technologies have opened the door to remarkable biomedical discoveries through its ability to generate hundreds of millions to billions of DNA segments per run along with a substantial reduction in time and cost. However, this flood of sequencing data continues to overwhelm the processing capacity of existing algorithms and hardware. To analyze a patient's genome, each of these segments - called reads - must be mapped to a reference genome based on the similarity between a read and "candidate" locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (1) it is implemented using quadratic-time dynamic programming algorithms, and (2) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. In this thesis, we introduce four new algorithms that function as a pre-alignment step and aim to filter out most incorrect candidate locations. We call our algorithms GateKeeper, Slider, MAGNET, and SneakySnake. The first key idea of our proposed pre-alignment filters is to provide high filtering accuracy by correctly detecting all similar segments shared between two sequences. The second key idea is to exploit the massively parallel architecture of modern FPGAs for accelerating our four proposed filtering algorithms. We also develop an efficient CPU implementation

关键词： Read Mapping Approximate string Matching Read Alignment Levenshtein Distance string algorithms Edit Distance fast pre-alignment filter field-programmable gate arrays (FPGA)

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On the Hardness and Inapproximability of Recognizing Wheeler Graphs 27

On the Hardness and Inapproximability of Recognizing Wheeler...

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27th Annual European Symposium on algorithms (ESA)

作者： Gibney, Daniel Thankachan, Sharma, V Univ Cent Florida Dept Comp Sci Orlando FL 32816 USA

ISBN: (纸本)9783959771245

In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these are used to index structures far more complex than a single string, as was originally done with the FM-index [Ferragina and Manzini, J. ACM 2005]. As such, there has been an increasing effort to better understand under which conditions such an indexing scheme is possible. This has led to the introduction of Wheeler graphs [Gagie et al., Theor. Comput. Sci., 2017]. Gagie et al. showed that de Bruijn graphs, generalized compressed suffix arrays, and several other BWT related structures can be represented as Wheeler graphs, and that Wheeler graphs can be indexed in a way which is space efficient. Hence, being able to recognize whether a given graph is a Wheeler graph, or being able to approximate a given graph by a Wheeler graph, could have numerous applications in indexing. Here we resolve the open question of whether there exists an efficient algorithm for recognizing if a given graph is a Wheeler graph. We present: - The problem of recognizing whether a given graph G = (V, E) is a Wheeler graph is NP-complete for any edge label alphabet of size sigma >= 2, even when G is a DAG. This holds even on a restricted, subset of graphs called d-NFA's for d >= 5. This is in contrast to recent results demonstrating the problem can be solved in polynomial time for d-NFA's where d <= 2. We also show the recognition problem can be solved in linear time for sigma = 1;- There exists an 2(e log sigma+O(n+e)) time exact algorithm where n = vertical bar V vertical bar and e = vertical bar E vertical bar. This algorithm relies on graph isomorphism being computable in strictly sub-exponential time;- We define an optimization variant of the problem called Wheeler Graph Violation, abbreviated WGV, where the aim is to remove the minimum number of edges in order to obtain a Wheeler graph. We show WGV is APX-hard, even when G is a DAG, implying there exists a

关键词： Burrows-Wheeler transform string algorithms suffix trees NP-completeness

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6th Annual Symposium on Combinatorial Pattern Matching (CPM 95)

作者： Bafna, V Muthukrishnan, S Ravi, R PRINCETON UNIV DEPT COMP SCIDIMACSPRINCETONNJ 08544

ISBN: (纸本)3540600442

Ribonucleic acid (RNA) strings are strings over the four-letter alphabet (A,C,G,U) with a secondary structure of base-pairing between A-U and C - G pairs in the string(1). Edges are drawn between two bases that are paired in the secondary structure and these edges have traditionally been assumed to be noncrossing. The noncrossing base-pairing naturally leads to a tree-like representation of the secondary structure of RNA strings. In this paper, we address several notions of similarity between two RNA strings that take into account both the primary sequence and secondary base-pairing structure of the strings. We present efficient algorithms for exact matching and approximate matching between two RNA strings. We define a notion of alignment between two RNA strings and devise algorithms based on dynamic programming. We then present a method for optimally aligning a given RNA string with unknown secondary structure to one with known sequence and structure, thus attacking the structure prediction problem in the case when the structure of a closely related sequence is known. The techniques employed to prove our results include reductions to well-known string matching problems allowing wild cards and ranges, and speeding up dynamic programming by using the tree structures implicit in the secondary structure of RNA strings.

关键词： Approximate matching Edit distances RNA structure string algorithms Trees

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Methods for Reducing Unnecessary Computation on False Mappings in Read Mapping

Methods for Reducing Unnecessary Computation on False Mappin...

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作者： Hongyi Xin Carnegie Mellon University

学位级别：博士

Advancements in sequencing technology have brought a large increase in the quantity of raw sequencing data. To cope with the ever growing sequence data sets, efficient read mappers are developed to accurately reconstruct entire genomes from fragments, by mapping fragments of the genome of an organism to a high quality reference genome. For each fragment, a mapper tries to find a distinct correspond- ing highly similar sequence in the reference, or multiple highly similar sequences if applicable. Despite improvements of the mapping software, modern state-of-the-art mappers struggle between speed and sensitivity: as a mapper increases sensitiv- ity to tolerate more sequencer errors and genetic variations, it inevitably enlarges the search space and spend more time comparing fragments against increasingly dissimilar reference sequences. Comparisons over such false mappings are often unnecessary and wasteful, as dissimilar reference sequences are not considered as meaningful mappings. Furthermore, although only a small fraction of all DNA frag- ments require high mapping sensitivity due to large number of embedded errors, mappers have to raise sensitivity against all fragments, as the error profile of each fragment is unknown to the mapper. In this dissertation, we provide multiple algorithms and implementations that aim to reduce the amount of unnecessary computation spent on false mappings while achieving high sensitivity by 1) quickly and accurately filtering out false mappings and 2) reducing the total number of false mappings without sacrificing sensitivity through improved seeding mechanisms. Specifically, we designed SIMD-friendly algorithms that quickly identify false mappings with high accuracy. We also ex- tended a previously proposed approximate string matching algorithm to better suit biological applications. Finally, we developed multiple methods that enhance the popular seed-and-extend mapping strategy by increasing seed selectivity without re- ducing mapp

关键词： Read Mapping Approximate string Matching Seed-and-Extend Landau-Vishkin Error Tolerance string algorithms Suffix Trie Edit Distance Affine Gap

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Multiple pattern matching revisited 18

Multiple pattern matching revisited

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18th Prague stringology Conference, PSC 2014

作者： Susik, Robert Grabowski, Szymon Fredriksson, Kimmo Lodz University of Technology Institute of Applied Computer Science Al. Politechniki 11 Lódź90-924 Poland School of Computing University of Eastern Finland P.O.B. 1627 KuopioFI-70211 Finland

ISBN: (纸本)9788001055472

We consider the classical exact multiple string matching problem. Our solution is based on q-grams combined with pattern superimposition, bit-parallelism and alphabet size reduction. We discuss the pros and cons of the various alternatives of how to achieve best combination. Our method is closely related to previous work by (Salmela et al., 2006). The experimental results show that our method performs well on different alphabet sizes and that they scale to large pattern sets. © Czech Technical University in Prague, Czech Republic.

关键词： Combinatorial problems Q-grams string algorithms Word-level parallelism

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Space efficient construction of Lyndon arrays in linear time 47

Space efficient construction of Lyndon arrays in linear time

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47th International Colloquium on Automata, Languages, and Programming, ICALP 2020

作者： Bille, Philip Ellert, Jonas Fischer, Johannes Gørtz, Inge Li Kurpicz, Florian Ian Munro, J. Rotenberg, Eva DTU Compute Technical University of Denmark Lyngby Denmark Department of Computer Science Technical University of Dortmund Germany Cheriton School of Computer Science University of Waterloo Canada

ISBN: (纸本)9783959771382

Given a string S of length n, its Lyndon array identifies for each suffix S[i..n] the next lexicographically smaller suffix S[j..n], i.e. the minimal index j > i with S[i..n] S[j..n]. Apart from its plain (n log2 n)-bit array representation, the Lyndon array can also be encoded as a succinct parentheses sequence that requires only 2n bits of space. While linear time construction algorithms for both representations exist, it has previously been unknown if the same time bound can be achieved with less than Ω(n lg n) bits of additional working space. We show that, in fact, o(n) additional bits are sufficient to compute the succinct 2n-bit version of the Lyndon array in linear time. For the plain (n log2 n)-bit version, we only need O(1) additional words to achieve linear time. Our space efficient construction algorithm makes the Lyndon array more accessible as a fundamental data structure in applications like full-text indexing. © Philip Bille, Jonas Ellert, Johannes Fischer, Inge Li Gørtz, Florian Kurpicz, J. Ian Munro, and Eva Rotenberg;licensed under Creative Commons License CC-BY 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020).

关键词： Lyndon array Lyndon word Nearest smaller suffixes Nearest smaller values string algorithms string suffixes Succinct data structures

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Computing Abelian covers and Abelian runs 18

Computing Abelian covers and Abelian runs

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18th Prague stringology Conference, PSC 2014

作者： Matsuda, Shohei Inenaga, Shunsuke Bannai, Hideo Takeda, Masayuki Department of Informatics Kyushu University Japan

ISBN: (纸本)9788001055472

Two strings u and v are said to be Abelian equivalent if u is a permutation of the characters of v. We introduce two new regularities on strings w.r.t. Abelian equivalence, called Abelian covers and Abelian runs, which are generalizations of covers and runs of strings, respectively. We show how to determine in O(n) time whether or not a given string w of length n has an Abelian cover. Also, we show how to compute an O(n2)-size representation of (possibly exponentially many) Abelian covers of w in O(n2) time. Moreover, we present how to compute all Abelian runs in w in O(n2) time, and state that the maximum number of all Abelian runs in a string of length n is Ω(n2). © Czech Technical University in Prague, Czech Republic.

关键词： Abelian equivalence on strings Abelian repetitions Covers of strings Parikh vectors string algorithms

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New refinement techniques for longest common subsequence algorithms

New refinement techniques for longest common subsequence alg...

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10th International Symposium on string Processing and Information Retrieval

作者： Bergroth, L Hakonen, H Väisänen, J Turku Univ Dept Informat Technol Programming Tech Salo 24280 Finland Turku Univ Dept Informat Technol Turku 20520 Finland

ISBN: (纸本)3540201777

Certain properties of the input strings have dominating influence on the running time of an algorithm selected to solve the longest common subsequence (lcs) problem of two input strings. It has turned out to be difficult - as well theoretically as practically - to develop an lcs algorithm which would be superior for all problem instances. Furthermore, implementing the most evolved lcs algorithms presented recently is laborious. This paper shows that it is still beneficial to refine the traditional lcs algorithms to get new algorithm variants that are in practice competitive to the modern lcs methods in certain problem instances. We present and analyse a general-purpose algorithm NKY-MODIF, which has a moderate time and space efficiency and can easily be implemented correctly. The algorithm bases on the so-called diagonal-wise method of Nakatsu, Kambayashi and Yajima (NKY). The NKY algorithm was selected for our further consideration due to its algorithmic independence of the size of the input alphabet and its light preprocessing phase. The NKY-MODIF algorithm refines the NKY method essentially in three ways: by reducing unnecessary scanning over the input sequences, storing the intermediate results more locally, and utilizing lower and upper bound knowledge about the lcs. In order to demonstrate that the some of the presented ideas are not specific for the NKY only, we apply lower bound information on two lcs algorithms having a different processing approach than the NKY has. This introduces a new way to solve the lcs problem. The lcs problem has two variants: calculating only the length of the lcs, and determining also the symbols belonging to one instance of the lcs. We verify the presented ideas for both of these problem types by extensive test runs.

关键词： longest common subsequence string algorithms heuristic algorithms

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Methodology for Detecting Similarity of Program Code Based on Combining algorithms

Methodology for Detecting Similarity of Program Code Based o...

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2024 Conference of Young Researchers in Electrical and Electronic Engineering, ElCon 2024

作者： Novotochinov, Maksim E. Solomatin, Dmitry I. Chernenkii, Andrei V. Voronezh State University Voronezh Russia Polytechnic University Peter the Great St. Petersburg St. Petersburg Russia

ISBN: (纸本)9798350360646

In this paper, the main existing strategies used in plagiarism of program code were investigated, as well as the most popular approaches used to identify copied texts were analyzed. Based on the results of the analysis of various approaches, as well as the analysis of the subject area itself, the requirements for the new system were formulated. Further, this system was successfully designed, implemented and tested. The most suitable areas for the application of the developed system are education (universities, colleges and other educational institutions can use the system to check the code written by students in order to detect plagiarism) and programming competitions. © 2024 IEEE.

关键词： C++ code parsing dynamic programming expression parsing hashes plagiarism programming languages Python string algorithms system development tokenization

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