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Optimal parallel suffix tree construction

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

doi:10.1145/195058.195162
dblp:conf/stoc/Hariharan94
fatcat:3pvihzwv6bgq5bgtvuytuxbhb4
*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. ...##
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Optimal Parallel Suffix Tree Construction

1997
*
Journal of computer and system sciences (Print)
*

An O(m)-work, O(m)-space, O(log 4 m)-time CREW-PRAM algorithm for

doi:10.1006/jcss.1997.1496
fatcat:qxlqdwooqbcsnnxwx774zhd6kq
*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. ...##
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Subject Index

2005
*
Journal of Discrete Algorithms
*

total hop count on
ATM

doi:10.1016/s1570-8667(05)00042-0
fatcat:phytlwupp5hmtddg3ffue5546u
*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- ...##
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Efficient parallel construction of suffix trees for genomes larger than main memory

2013
*
Proceedings of the 20th European MPI Users' Group Meeting on - EuroMPI '13
*

In this paper we presented

doi:10.1145/2488551.2488579
dblp:conf/pvm/CominF13
fatcat:vmqlvbpairgbfoq7z2mnwydljq
*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] . ...##
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Optimal logarithmic time randomized suffix tree construction
[chapter]

1996
*
Lecture Notes in Computer Science
*

We are also able to

doi:10.1007/3-540-61440-0_158
fatcat:6ba4benauba4fjl4m33jrpexn4
*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. ...##
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Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes

2014
*
Journal of Computational Biology
*

In this article, we present

doi:10.1089/cmb.2012.0256
pmid:24597675
pmcid:PMC3962650
fatcat:f4w5lxx4tra2fclghursejytxu
*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). ...##
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Optimal Parallel Construction of Minimal Suffix and Factor Automata

1995
*
BRICS Report Series
*

The algorithms use recently discovered

doi:10.7146/brics.v2i16.19884
fatcat:74l5vvy2anacxdfkfjcyc5pzoq
*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. ...##
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ERA Revisited: Theoretical and Experimental Evaluation
[article]

2016
*
arXiv
*
pre-print

In this paper we focus on the fastest practical

arXiv:1609.09654v1
fatcat:on6g7keizbeapclcq6tbb656p4
*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. ...##
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Fast parallel construction of variable-length Markov chains

2021
*
BMC Bioinformatics
*

The scarcity of available fast, or even

doi:10.1186/s12859-021-04387-y
pmid:34627154
fatcat:j3cq7lokovhyhgcfnxnmk4qbsi
*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*. ...##
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ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings
[article]

2011
*
arXiv
*
pre-print

However, when the string and the resulting

arXiv:1109.6884v1
fatcat:sy74m75m6bb73dusd5nhz7bxje
*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. ...##
###
Suffix tree construction algorithms on modern hardware

2010
*
Proceedings of the 13th International Conference on Extending Database Technology - EDBT '10
*

In this paper, we propose cache-conscious

doi:10.1145/1739041.1739075
dblp:conf/edbt/TsirogiannisK10
fatcat:ij42ym6cabf7fng5usnmof5w2y
*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. ...##
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ERA

2011
*
Proceedings of the VLDB Endowment
*

However, when the string and the resulting

doi:10.14778/2047485.2047490
fatcat:nxquqdqdljholdfppfdmu6o5vi
*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. ...##
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Distributed suffix trees

2005
*
Journal of Discrete Algorithms
*

The method is based on a new linear time

doi:10.1016/j.jda.2004.08.004
fatcat:6mnw675kerdffejam6ykkqmwc4
*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] . ...##
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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. ...##
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Simple Linear Work Suffix Array Construction
[chapter]

2003
*
Lecture Notes in Computer Science
*

Since sorting is a well studied problem, we obtain

doi:10.1007/3-540-45061-0_73
fatcat:5l6a3kvv5fandemcha7yi4gj6e
*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. ...
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