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Space-Efficient String Indexing for Wildcard Pattern Matching [article]

Moshe Lewenstein, Yakov Nekrich, Jeffrey Scott Vitter
2014 arXiv   pre-print
In this paper we describe compressed indexes that support pattern matching queries for strings with wildcards.  ...  These are the first non-trivial data structures for this problem that need o(n n) bits of space.  ...  Acknowledgement The second author wishes to thank Gonzalo Navarro for pointing him to [15] .  ... 
arXiv:1401.0625v1 fatcat:2d4s3h6rkfa7vmb2ryxv3bjp7a

Space-Efficient String Indexing for Wildcard Pattern Matching

Moshe Lewenstein, Yakov Nekrich, Jeffrey Scott Vitter, Marc Herbstritt
2014 Symposium on Theoretical Aspects of Computer Science  
In this paper we describe compressed indexes that support pattern matching queries for strings with wildcards.  ...  These are the first non-trivial data structures for this problem that need o(n log n) bits of space.  ...  Acknowledgement The second author wishes to thank Gonzalo Navarro for pointing him to [15] .  ... 
doi:10.4230/lipics.stacs.2014.506 dblp:conf/stacs/LewensteinNV14 fatcat:cln64vqf5fggtnwtzbd37psrru

String Indexing for Patterns with Wildcards [chapter]

Philip Bille, Inge Li Gørtz, Hjalte Wedel Vildhøj, Søren Vind
2012 Lecture Notes in Computer Science  
We introduce three new indexes and obtain several new bounds for string indexing with wildcards in the pattern.  ...  We consider the problem of indexing a string t of length n to report the occurrences of a query pattern p containing m characters and j wildcards.  ...  String indexing for patterns with variable length gaps is equivalent to string indexing for patterns with wildcards, with the addition of allowing optional wildcards in the pattern.  ... 
doi:10.1007/978-3-642-31155-0_25 fatcat:kw2lhwrhcbhlzpok77rwkws33y

String Indexing for Patterns with Wildcards [article]

Philip Bille, Inge Li Goertz, Hjalte Wedel Vildhøj, Søren Vind
2012 arXiv   pre-print
We consider the problem of indexing a string t of length n to report the occurrences of a query pattern p containing m characters and j wildcards.  ...  . - An index with query time O(m+j+occ) using space O(σ^k^2 n ^k n), where k is the maximum number of wildcards allowed in the pattern.  ...  String indexing for patterns with variable length gaps is equivalent to string indexing for patterns with wildcards, with the addition of allowing optional wildcards in the pattern.  ... 
arXiv:1110.5236v2 fatcat:afrg25lvifcabo5cqmdb2jenbq

Error Tree: A Tree Structure for Hamming & Edit Distances & Wildcards Matching [article]

Anas Al-Okaily
2015 arXiv   pre-print
Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, Hamming and edit distances, as well as the wildcards matching problem.  ...  The algorithm proposes for Hamming distance and wildcards matching a tree structure that needs O(nlog_Σ ^kn/k!) words and takes O(m^k/k! + occ)(O(m + log_Σ ^kn/k!  ...  The exact matching problem is the simplest form of the pattern matching problems, while the approximate and wildcards matching are more complicated.  ... 
arXiv:1506.04486v1 fatcat:atnw6j4q4bhvjacrmfg3oyct5a

Super-Linear Indices for Approximate Dictionary Searching [chapter]

Leonid Boytsov
2012 Lecture Notes in Computer Science  
A straightforward implementation that creates a hash index directly over residual strings (obtained by deletions from dictionary words) is not space efficient.  ...  These data are indexed using a perfect hash function computed for a set of residual dictionary strings [2].  ...  I am very grateful to my wife Anna for editorial assistance.  ... 
doi:10.1007/978-3-642-32153-5_12 fatcat:52enei4um5dp5hd55lstjviywu

Streaming Pattern Matching with d Wildcards

Shay Golan, Tsvi Kopelowitz, Ely Porat
2018 Algorithmica  
In this paper we introduce two new algorithms for the d wildcard pattern matching problem in the streaming model.  ...  A wildcard character matches any other character. The goal is to establish for each m-length substring of T whether it matches P .  ...  For any 0 ≤ δ ≤ 1 the online d wildcards pattern matching problem can be solved for patterns P with π P < d δ with a randomized Monte Carlo algorithm, inÕ(1) time per arriving text character and usingÕ  ... 
doi:10.1007/s00453-018-0521-7 fatcat:4o5dz44ja5gcdkci2kvbtlpwba

Dictionary matching and indexing with errors and don't cares

Richard Cole, Lee-Ad Gottlieb, Moshe Lewenstein
2004 Proceedings of the thirty-sixth annual ACM symposium on Theory of computing - STOC '04  
For example, for the indexing problem with n = |t| and m = |p|, the query time for k substitutions is O(m + (c 1 log n) k k! + # matches), with a data structure of size O(n (c 2 log n) k k!  ...  The specific problems we look at are: indexing, in which there is a single text t, and we seek locations where p matches a substring of t; dictionary queries, in which a collection of strings is given  ...  In each case, the data structure provides an efficient implementation of the following naive strategy for matching a query string q.  ... 
doi:10.1145/1007352.1007374 dblp:conf/stoc/ColeGL04 fatcat:pjs3bjdz4bhynfhc2ommprmaxu

Succincter Text Indexing with Wildcards [article]

Chris Thachuk
2011 arXiv   pre-print
The query algorithm for our wildcard index is faster than previous approaches using reasonable working space.  ...  matching queries.  ...  The author would like to thank Anne Condon for helpful discussions, detailed feedback and suggestions on this manuscript.  ... 
arXiv:1101.5376v1 fatcat:dabhlgpq6vdkbkf6xj4ymnqnv4

Space Lower Bounds for Online Pattern Matching [article]

Raphael Clifford, Markus Jalsenius, Ely Porat, Benjamin Sach
2011 arXiv   pre-print
We present space lower bounds for online pattern matching under a number of different distance measures.  ...  In the former case which includes, as an example, pattern matching with character classes, we give Omega(m) bit space lower bounds.  ...  We reduce from Indexing: Alice has a string T = {a, b} m and Bob has an index n. Alice initialises a pattern matching algorithm A on the pattern P = {x} m and feeds in her string T .  ... 
arXiv:1106.4412v1 fatcat:rfiitmtbfba2pccq53huc3md6y

Space Lower Bounds for Online Pattern Matching [chapter]

Raphaël Clifford, Markus Jalsenius, Ely Porat, Benjamin Sach
2011 Lecture Notes in Computer Science  
We present space lower bounds for online pattern matching under a number of different distance measures.  ...  In the former case which includes, as an example, pattern matching with character classes, we give Ω(m) bit space lower bounds.  ...  We reduce from Indexing: Alice has a string T = {a, b} m and Bob has an index n. Alice initialises a pattern matching algorithm A on the pattern P = {x} m and feeds in her string T .  ... 
doi:10.1007/978-3-642-21458-5_17 fatcat:obhotgwuandzzkywnsy7a4vtli

Space lower bounds for online pattern matching

Raphaël Clifford, Markus Jalsenius, Ely Porat, Benjamin Sach
2013 Theoretical Computer Science  
We present space lower bounds for online pattern matching under a number of different distance measures.  ...  In the former case which includes, as an example, pattern matching with character classes, we give Ω(m) bit space lower bounds.  ...  We reduce from Indexing: Alice has a string T = {a, b} m and Bob has an index n. Alice initialises a pattern matching algorithm A on the pattern P = {x} m and feeds in her string T .  ... 
doi:10.1016/j.tcs.2012.06.012 fatcat:vihdt22zwjfvfhr2ljhhuae2wa

Streaming Pattern Matching with d Wildcards [article]

Shay Golan, Tsvi Kopelowitz, Ely Porat
2017 arXiv   pre-print
In this paper we introduce two new algorithms for the d wildcard pattern matching problem in the streaming model.  ...  A wildcard character matches any other character. The goal is to establish for each m-length substring of T whether it matches P.  ...  Fingerprints with Wildcards Using fingerprints together with wildcards seems to be a difficult task, since for any string S with x wildcards there are |Σ| x different strings over Σ that match the string  ... 
arXiv:1704.01646v1 fatcat:uj56nfjx7zc4fbwyq43c5cdn6q

Compressed Text Indexing with Wildcards [chapter]

Wing-Kai Hon, Tsung-Han Ku, Rahul Shah, Sharma V. Thankachan, Jeffrey Scott Vitter
2011 Lecture Notes in Computer Science  
The text indexing with wildcards problem is to index T such that when we are given a query pattern P , we can locate the occurrences of P in T efficiently.  ...  In this paper, we present the first compressed index for this problem, which takes only nH h + o(n log σ) + O(d log n) bits space, where H h is the hth-order empirical entropy (h = o(log σ n)) of T .  ...  wildcards, our objective is to construct an index for T for locating all the occurrences of an online pattern P of length p efficiently.  ... 
doi:10.1007/978-3-642-24583-1_26 fatcat:xem3emzjhngntkereloc4qaena

Compressed text indexing with wildcards

Wing-Kai Hon, Tsung-Han Ku, Rahul Shah, Sharma V. Thankachan, Jeffrey Scott Vitter
2013 Journal of Discrete Algorithms  
The text indexing with wildcards problem is to index T such that when we are given a query pattern P , we can locate the occurrences of P in T efficiently.  ...  In this paper, we present the first compressed index for this problem, which takes only nH h + o(n log σ) + O(d log n) bits space, where H h is the hth-order empirical entropy (h = o(log σ n)) of T .  ...  wildcards, our objective is to construct an index for T for locating all the occurrences of an online pattern P of length p efficiently.  ... 
doi:10.1016/j.jda.2012.12.003 fatcat:snw2ro2ofzf2tdhgovwfmdac6y
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