Filters








9,749 Hits in 3.2 sec

Optimal parallel suffix tree construction

Ramesh Hariharan
1994 Proceedings of the twenty-sixth annual ACM symposium on Theory of computing - STOC '94  
An O(m)-work, O(m)-space, O(log 4 m)-time CREW-PRAM algorithm for constructing the suffix tree of a string s of length m drawn from any fixed alphabet set is obtained.  ...  This is the first known work and space optimal parallel algorithm for this problem.  ...  We give the first work-optimal parallel algorithm to construct the suffix tree of a binary string s. The algorithm does O(m) work and takes O(log 4 m) time and O(m) space in the CREW-PRAM model.  ... 
doi:10.1145/195058.195162 dblp:conf/stoc/Hariharan94 fatcat:3pvihzwv6bgq5bgtvuytuxbhb4

Optimal Parallel Suffix Tree Construction

Ramesh Hariharan
1997 Journal of computer and system sciences (Print)  
An O(m)-work, O(m)-space, O(log 4 m)-time CREW-PRAM algorithm for constructing the suffix tree of a string s of length m drawn from any fixed alphabet set is obtained.  ...  This is the first known work and space optimal parallel algorithm for this problem.  ...  We give the first work-optimal parallel algorithm to construct the suffix tree of a binary string s. The algorithm does O(m) work and takes O(log 4 m) time and O(m) space in the CREW-PRAM model.  ... 
doi:10.1006/jcss.1997.1496 fatcat:qxlqdwooqbcsnnxwx774zhd6kq

Subject Index

2005 Journal of Discrete Algorithms  
total hop count on ATM tree networks, 101 Bioinformatics Distributed suffix trees, 176 Bit-parallelism Bit-parallel (δ, γ )-matching and suffix automata, 198; Bit-parallel approximate string matching  ...  Suffix sorting Space efficient linear time construction of suffix arrays, 143 Suffix trees Distributed suffix trees, 176 Tandemly repeated sequences An exact and polynomial distance-based algo-  ... 
doi:10.1016/s1570-8667(05)00042-0 fatcat:phytlwupp5hmtddg3ffue5546u

Efficient parallel construction of suffix trees for genomes larger than main memory

Matteo Comin, Montse Farreras
2013 Proceedings of the 20th European MPI Users' Group Meeting on - EuroMPI '13  
In this paper we presented Parallel Continuous Flow P CF , a parallel suffix tree construction method that is suitable for very long strings.  ...  The construction of suffix tree for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain.  ...  The optimal construction of suffix tree has been addressed by Ukkonen [27] and McCreight [22] .  ... 
doi:10.1145/2488551.2488579 dblp:conf/pvm/CominF13 fatcat:vmqlvbpairgbfoq7z2mnwydljq

Optimal logarithmic time randomized suffix tree construction [chapter]

Martin Farach, S. Muthukrishnan
1996 Lecture Notes in Computer Science  
We are also able to parallelize our algorithm so that we settle the main open problem in the construction of suffix trees: we give a Las Vegas CRCW PRAM algorithm that constructs the suffix tree of a binary  ...  As a result, we obtain the first work-optimal algorithm for suffix tree construction under the unbounded alphabet assumption.  ...  Efficient parallel construction of suffix trees has also proven to be a challenge.  ... 
doi:10.1007/3-540-61440-0_158 fatcat:6ba4benauba4fjl4m33jrpexn4

Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes

Matteo Comin, Montse Farreras
2014 Journal of Computational Biology  
In this article, we present parallel continuous flow (PCF), a parallel suffix tree construction method that is suitable for very long genomes.  ...  The construction of suffix trees for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain.  ...  PARALLEL CONTINUOUS FLOW: PARALLEL SUFFIX TREE CONSTRUCTION In this section we present our parallel suffix tree construction algorithm called parallel continuous flow (PCF).  ... 
doi:10.1089/cmb.2012.0256 pmid:24597675 pmcid:PMC3962650 fatcat:f4w5lxx4tra2fclghursejytxu

Optimal Parallel Construction of Minimal Suffix and Factor Automata

Dany Breslauer, Ramesh Hariharan
1995 BRICS Report Series  
The algorithms use recently discovered optimal parallel suffix tree construction algorithms together with data structures for the efficient manipulation of trees, exploiting the well known relation between  ...  This paper gives optimal parallel algorithms for the construction of the smallest deterministic finite automata recognizing all the suffixes and the factors of a string.  ...  benefit directly from using any of the recent optimal parallel suffix tree construction algorithms.  ... 
doi:10.7146/brics.v2i16.19884 fatcat:74l5vvy2anacxdfkfjcyc5pzoq

ERA Revisited: Theoretical and Experimental Evaluation [article]

Matevž Jekovec, Andrej Brodnik
2016 arXiv   pre-print
In this paper we focus on the fastest practical suffix tree construction algorithm to date, ERA.  ...  Efficient construction of the suffix tree given an input text is an active area of research from the time it was first introduced.  ...  Our long-pursuing goal is to design a theoretically optimal parallel suffix tree construction algorithm, which is also the fastest in practice.  ... 
arXiv:1609.09654v1 fatcat:on6g7keizbeapclcq6tbb656p4

Fast parallel construction of variable-length Markov chains

Joel Gustafsson, Peter Norberg, Jan R. Qvick-Wester, Alexander Schliep
2021 BMC Bioinformatics  
The scarcity of available fast, or even parallel software tools, prompted the development of a parallel implementation using lazy suffix trees and a hash-based alternative.  ...  Conclusions Our parallel implementation released as open-source under the GPLv3 license provides a practically useful alternative to the state-of-the-art which allows the construction of VLMCs even for  ...  Furthermore, since all children of the suffix tree and probabilistic suffix tree can be found by hash-lookup Pseudo-code for the parallel hash-map construction of the suffix tree.  ... 
doi:10.1186/s12859-021-04387-y pmid:34627154 fatcat:j3cq7lokovhyhgcfnxnmk4qbsi

ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings [article]

Essam Mansour, Amin Allam, Spiros Skiadopoulos, Panos Kalnis
2011 arXiv   pre-print
However, when the string and the resulting suffix tree are too large to fit into the main memory, most existing construction algorithms become very inefficient.  ...  This paper presents a disk-based suffix tree construction method, called Elastic Range (ERa), which works efficiently with very long strings that are much larger than the available memory.  ...  Then, it merges the suffix arrays of all partitions and generates suffix sub-trees. Note that the tree is constructed in batch at the final phase.  ... 
arXiv:1109.6884v1 fatcat:sy74m75m6bb73dusd5nhz7bxje

Suffix tree construction algorithms on modern hardware

Dimitris Tsirogiannis, Nick Koudas
2010 Proceedings of the 13th International Conference on Extending Database Technology - EDBT '10  
In this paper, we propose cache-conscious suffix tree construction algorithms that are tailored to CMP architectures.  ...  Suffix trees are indexing structures that enhance the performance of numerous string processing algorithms.  ...  The first work-optimal parallel suffix tree construction algorithm was presented in [15] . It does O(n) work and runs in O(log 4 n) time using n processors.  ... 
doi:10.1145/1739041.1739075 dblp:conf/edbt/TsirogiannisK10 fatcat:ij42ym6cabf7fng5usnmof5w2y

ERA

Essam Mansour, Amin Allam, Spiros Skiadopoulos, Panos Kalnis
2011 Proceedings of the VLDB Endowment  
However, when the string and the resulting suffix tree are too large to fit into the main memory, most existing construction algorithms become very inefficient.  ...  This paper presents a disk-based suffix tree construction method, called Elastic Range (ERa), which works efficiently with very long strings that are much larger than the available memory.  ...  Then, it merges the suffix arrays of all partitions and generates suffix sub-trees. Note that the tree is constructed in batch at the final phase.  ... 
doi:10.14778/2047485.2047490 fatcat:nxquqdqdljholdfppfdmu6o5vi

Distributed suffix trees

Raphaël Clifford
2005 Journal of Discrete Algorithms  
The method is based on a new linear time construction algorithm for subtrees of a suffix tree.  ...  While none of these operations on the DST require inter-process communication, many have optimal expected parallel running times.  ...  Suffix tree construction in parallel has also been studied, culminating in a linear work CREW PRAM algorithm presented in 1994 [15] .  ... 
doi:10.1016/j.jda.2004.08.004 fatcat:6mnw675kerdffejam6ykkqmwc4

Page 6361 of Mathematical Reviews Vol. , Issue 97J [page]

1997 Mathematical Reviews  
The algorithms use recently discovered optimal parallel suffix tree construction algorithms together with data structures for the efficient manipu- lation of trees, exploiting the well-known relation between  ...  suffix and factor automata and suffix trees.” 97j:68039 68Q22 68Q10 Farach, Martin (1-RTG-C; New Brunswick, NJ); Muthukrishnan, S. (4-WARW-C; Coventry) Optimal parallel randomized renaming.  ... 

Simple Linear Work Suffix Array Construction [chapter]

Juha Kärkkäinen, Peter Sanders
2003 Lecture Notes in Computer Science  
Since sorting is a well studied problem, we obtain optimal algorithms for several other models of computation, e.g. external memory with parallel disks, cache oblivious, and parallel.  ...  Being a simpler and more compact alternative to suffix trees, it is an important tool for full text indexing and other string processing tasks.  ...  Construct the suffix tree of the remaining suffixes using the result of the first step. 3. Merge the two suffix trees into one.  ... 
doi:10.1007/3-540-45061-0_73 fatcat:5l6a3kvv5fandemcha7yi4gj6e
« Previous Showing results 1 — 15 out of 9,749 results