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## Filters

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ERA Revisited: Theoretical and Experimental Evaluation
[article]

2016
*
arXiv
*
pre-print

Efficient

arXiv:1609.09654v1
fatcat:on6g7keizbeapclcq6tbb656p4
*construction**of**the**suffix**tree*given an input text is an active area*of*research from*the*time it was first introduced. ... Both theoretical computer scientists and engineers tackled*the*problem. In this paper we focus*on**the*fastest practical*suffix**tree**construction*algorithm to date, ERA. ... Therefore,*one*cannot expect to directly*construct**the**suffix**tree*using a*tree*traversal and a single scan*of**the*input string. ...##
###
Distributed Splay Suffix Arrays: A New Structure For Distributed String Search

2007
*
Zenodo
*

This data structure combines

doi:10.5281/zenodo.1071981
fatcat:aipel2ylvba2pngyzvhujlse2a
*the*features*of*splay*tree*and*suffix*arrays into a new approach which is suitable to implementation*on*both conventional and clustered computers. ... But if*the*string access pattern follows*the*"90/10" rule,*suffix*array can not take advantage*of**the*fact that we often find something that we have just found. ...*The**complexity*will be ( ) O R . c) Use Manber and Myer's string*sorting*method [7] to finish*the**construction**of**suffix*array in each node. ...##
###
Construction of Aho Corasick automaton in linear time for integer alphabets

2006
*
Information Processing Letters
*

A new, efficient implementation

doi:10.1016/j.ipl.2005.11.019
fatcat:vjfshafuqbdtvcjv3o7pkwznji
*of*nodes in*the*Aho Corasick automaton is introduced, which works for*suffix**trees*as well. ... We present a new simple algorithm that*constructs*an Aho Corasick automaton for a set*of*patterns, P ,*of*total length n, in O(n) time and space for integer alphabets. ...*The*patterns can be*sorted*using*suffix*arrays, by*constructing**the**suffix*array for S P , thus*sorting*all*suffixes**of*S P ; out*of*these, we can filter only*the*complete words and receive their*sorted*...##
###
Construction of Aho Corasick Automaton in Linear Time for Integer Alphabets
[chapter]

2005
*
Lecture Notes in Computer Science
*

A new, efficient implementation

doi:10.1007/11496656_15
fatcat:kyby4hj5iffnfbku6zyrzzovia
*of*nodes in*the*Aho Corasick automaton is introduced, which works for*suffix**trees*as well. ... We present a new simple algorithm that*constructs*an Aho Corasick automaton for a set*of*patterns, P ,*of*total length n, in O(n) time and space for integer alphabets. ...*The*patterns can be*sorted*using*suffix*arrays, by*constructing**the**suffix*array for S P , thus*sorting*all*suffixes**of*S P ; out*of*these, we can filter only*the*complete words and receive their*sorted*...##
###
Practical methods for constructing suffix trees

2005
*
The VLDB journal
*

Second, we present a new disk-based

doi:10.1007/s00778-005-0154-8
fatcat:bthtthcevrgqzag7huffc5ckci
*suffix**tree**construction*algorithm that is based*on*a*sort*-merge paradigm, and show that for*constructing*very large*suffix**trees*with very little resources, this algorithm ... Even when*the**suffix**tree*fits in memory, it turns out that*the*processor cache behavior*of*theoretically optimal*suffix**tree**construction*methods is poor, resulting in poor performance. ... We would like to thank*the*reviewers*of*this paper for their careful study*of*our previous manuscript, and their*constructive*suggestions. Their comments have helped strengthen this paper. ...##
###
Suffix-Sorting via Shannon-Fano-Elias Codes

2010
*
Algorithms
*

Given T ,

doi:10.3390/a3020145
fatcat:xvxmbjzzm5dbpgoufhqxwqfes4
*the**suffix**sorting*problem is to*construct*its*suffix*array.*The*direct*suffix**sorting*problem is to*construct**the**suffix*array*of*T directly without using*the**suffix**tree*data structure. ... Some methods for*constructing**suffix*arrays first build*the**suffix**tree*, and then*construct**the**suffix*array by performing an inorder traversal*of**the**suffix**tree*. ... A short version*of*this paper was presented at*the*2008 IEEE Data Compression Conference, Snowbird, Utah. ...##
###
Subject Index

2005
*
Journal of Discrete Algorithms
*

*construction*

*of*suf- fix arrays, 143

*Suffix*

*sorting*Space efficient linear time

*construction*

*of*

*suffix*arrays, 143

*Suffix*

*trees*Distributed

*suffix*

*trees*, 176 Tandemly repeated sequences An exact ...

*of*minisatellites, 375

*Complexity*analysis

*On*

*the*analysis

*of*a simple evolutionary algorithm

*on*quadratic pseudo-boolean functions, 61 Computational biology Space efficient linear time

*construction*...

##
###
Suffix Sorting via Shannon-Fano-Elias Codes

2008
*
Data Compression Conference (DCC), Proceedings
*

Given T ,

doi:10.1109/dcc.2008.99
dblp:conf/dcc/AdjerohN08
fatcat:qz2fzhsagfdg3hnpcrba57foqe
*the**suffix**sorting*problem is to*construct*its*suffix*array.*The*direct*suffix**sorting*problem is to*construct**the**suffix*array*of*T directly without using*the**suffix**tree*data structure. ... Some methods for*constructing**suffix*arrays first build*the**suffix**tree*, and then*construct**the**suffix*array by performing an inorder traversal*of**the**suffix**tree*. ... A short version*of*this paper was presented at*the*2008 IEEE Data Compression Conference, Snowbird, Utah. ...##
###
Space efficient linear time construction of suffix arrays

2005
*
Journal of Discrete Algorithms
*

Though

doi:10.1016/j.jda.2004.08.002
fatcat:y7s2hul265berbtc6spjsfy5z4
*the**suffix**tree**of*a string can be*constructed*in linear time and*the**sorted*order*of**suffixes*derived from it, a direct algorithm for*suffix**sorting*is*of*great interest due to*the*space requirements ... Our result improves upon*the*best known direct algorithm for*suffix**sorting*, which takes O(n log n) time. We also show how to*construct**suffix**trees*in linear time from our*suffix**sorting*result. ... It is well known that*the**suffix**tree**of*a string can be*constructed*from*the**sorted*order*of*its*suffixes*and*the*lcp array [FM96] . ...##
###
Simple Linear Work Suffix Array Construction
[chapter]

2003
*
Lecture Notes in Computer Science
*

A

doi:10.1007/3-540-45061-0_73
fatcat:5l6a3kvv5fandemcha7yi4gj6e
*suffix*array represents*the**suffixes**of*a string in*sorted*order. ...*sort**suffixes*beginning at positions i mod 3 = 0. 2.*sort**the*remaining*suffixes*using*the*information obtained in step*one*. 3. merge*the*two*sorted*sequences obtained in steps*one*and two. ...*Construct**the**suffix**tree**of**the*remaining*suffixes*using*the*result*of**the*first step. 3. Merge*the*two*suffix**trees*into*one*. ...##
###
Space Efficient Linear Time Construction of Suffix Arrays
[chapter]

2003
*
Lecture Notes in Computer Science
*

Though

doi:10.1007/3-540-44888-8_15
fatcat:3ij7vh5nsjfbtawz46w5ghgccu
*the**suffix**tree**of*a string can be*constructed*in linear time and*the**sorted*order*of**suffixes*derived from it, a direct algorithm for*suffix**sorting*is*of*great interest due to*the*space requirements ... Our result improves upon*the*best known direct algorithm for*suffix**sorting*, which takes O(n log n) time. We also show how to*construct**suffix**trees*in linear time from our*suffix**sorting*result. ... It is well known that*the**suffix**tree**of*a string can be*constructed*from*the**sorted*order*of*its*suffixes*and*the*lcp array [FM96] . ...##
###
RECONSTRUCTING A SUFFIX ARRAY

2006
*
International Journal of Foundations of Computer Science
*

In this paper we consider

doi:10.1142/s0129054106004418
fatcat:ojmxouxb4zdq3nexwbl6dgprka
*the*"reconstruction"*of*a*suffix*array based*on*a given reordering*of**the*alphabet, and we describe simple timeand space-efficient algorithms that accomplish it. ... It thus becomes*of*interest to study possible alternate orderings*of**the**suffixes*in these data structures, that may be easier to*construct*or more efficient to use. ... Acknowledgements*The*research was supported in part by*the*authors' research grants from*the*Natural Sciences and Engineering Research Council*of*Canada. ...##
###
Suffix Trees on Words

1999
*
Algorithmica
*

Since traditional

doi:10.1007/pl00009260
fatcat:gdguoegwyvdehotg3rn65xveie
*suffix**tree**construction*algorithms rely heavily*on**the*fact that all*suffixes*are inserted,*construction**of*a word*suffix**tree*is nontrivial, in particular when only O(m)*construction*... This word*suffix**tree*represents only*the*m*suffixes*that start at word boundaries. These boundaries are determined by delimiters, whose definition depends*on**the*application. ... Most*of**the*work done*on**suffix**tree**construction*seems to assume that a*suffix**tree*is implemented as a lexicographic trie. ...##
###
Suffix trees on words
[chapter]

1996
*
Lecture Notes in Computer Science
*

Since traditional

doi:10.1007/3-540-61258-0_9
fatcat:zkqalp6p4rbgjfmbn4hop75u3e
*suffix**tree**construction*algorithms rely heavily*on**the*fact that all*suffixes*are inserted,*construction**of*a word*suffix**tree*is nontrivial, in particular when only O(m)*construction*... This word*suffix**tree*represents only*the*m*suffixes*that start at word boundaries. These boundaries are determined by delimiters, whose definition depends*on**the*application. ... Most*of**the*work done*on**suffix**tree**construction*seems to assume that a*suffix**tree*is implemented as a lexicographic trie. ...##
###
Linear work suffix array construction

2006
*
Journal of the ACM
*

*Suffix*

*trees*and

*suffix*arrays are widely used and largely interchangeable index structures

*on*strings and sequences. ...

*The*algorithms for BSP and EREW-PRAM models are asymptotically faster than all previous

*suffix*

*tree*or array

*construction*algorithms. ... Consequently,

*the*

*complexity*

*of*

*constructing*

*the*

*suffix*

*tree*

*of*a string is

*the*same as

*the*

*complexity*

*of*

*sorting*

*the*characters

*of*

*the*string [19] . ...

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