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Weighted Ancestors in Suffix Trees Revisited [article]

Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, Rajeev Raman
<span title="2021-04-11">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Our solution is based on a novel approach using so-called irreducible LCP values.  ...  It is known to require Ω(loglog n) time for queries provided O(npolylog n) space is available and weights are from [0..n], where n is the number of tree nodes.  ...  C P M 2 0 2 1 35:14 Weighted Ancestors in Suffix Trees Revisited  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2103.00462v2">arXiv:2103.00462v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/45zcta5fszhpffbvmpn5bejpky">fatcat:45zcta5fszhpffbvmpn5bejpky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210414122001/https://arxiv.org/pdf/2103.00462v2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/43/8f/438fd8d570cdc5a7612a2e90441248942c8cd87e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2103.00462v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Range Shortest Unique Substring Queries [chapter]

Paniz Abedin, Arnab Ganguly, Solon P. Pissis, Sharma V. Thankachan
<span title="">2019</span> <i title="Springer International Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
In this paper, we introduce the range variant of this problem, which we call the Range Shortest Unique Substring problem.  ...  The task is to construct a data structure over T answering the following type of online queries efficiently.  ...  Range queries are a classic data structure topic [6, 7, 30] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-030-32686-9_18">doi:10.1007/978-3-030-32686-9_18</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4th7hkls2ngntj5z2podo4fvje">fatcat:4th7hkls2ngntj5z2podo4fvje</a> </span>
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Efficient Data Structures for Range Shortest Unique Substring Queries

Paniz Abedin, Arnab Ganguly, Solon P. Pissis, Sharma V. Thankachan
<span title="2020-10-30">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/63zsvf7vxzfznojpqgfvpyk2lu" style="color: black;">Algorithms</a> </i> &nbsp;
In this paper, we introduce the range variant of this problem, which we call the Range Shortest Unique Substring problem.  ...  Given a range [α,β], return a shortest substring T[i,j] of T with exactly one occurrence in [α,β].  ...  Range queries are a classic data structure topic [20] [21] [22] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/a13110276">doi:10.3390/a13110276</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jpcdb7tvdvhhnlckxgdo56rtqi">fatcat:jpcdb7tvdvhhnlckxgdo56rtqi</a> </span>
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Lempel-Ziv Factorization Revisited [chapter]

Enno Ohlebusch, Simon Gog
<span title="">2011</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
Solutions using S and suffix tree (ST) (Kolpakov and Kucherov) suffix array (SA) + longest common prefix array (LCP) (Crochemore et al.) ... SA + range minimum queries (RMQs) on SA (Chen et al.)  ...  31.30 26.30 26.30 19.10 chr22.dna4 8.90 24.60 14.80 14.60 12.30 12.20 10.00 2 Existing solutions 3 New fast algorithm 4 Experimental Results Experimental Results for Fast Algorithms test case LCP  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-21458-5_4">doi:10.1007/978-3-642-21458-5_4</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qb3oearydnca7dobd3c35xhfpe">fatcat:qb3oearydnca7dobd3c35xhfpe</a> </span>
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Cache-oblivious index for approximate string matching

Wing-Kai Hon, Tak-Wah Lam, Rahul Shah, Siu-Lung Tam, Jeffrey Scott Vitter
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/elaf5sq7lfdxfdejhkqbtz6qoq" style="color: black;">Theoretical Computer Science</a> </i> &nbsp;
This paper revisits the problem of indexing a text for approximate string matching.  ...  We define the LCP query of P with respect to T , denoted by LCP (P, T ), to be a query which reports (i) the SA range, [i, j], that corresponds to the SA region occupied by Q, and (ii) the LCP length,  ...  s data structure makes O(log k n) LCA, Pred, WLA and LCP queries, where LCP queries are in the form LCP (P i , T ) and LCP (P i , T ) where 1 ≤ i ≤ |P |.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tcs.2011.03.004">doi:10.1016/j.tcs.2011.03.004</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vvmascowjbg2jhbhbij2rw6oti">fatcat:vvmascowjbg2jhbhbij2rw6oti</a> </span>
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InstantDB: Enforcing Timely Degradation of Sensitive Data

Nicolas Anciaux, Luc Bouganim, Harold van Heerde, Philippe Pucheral, Peter M. G. Apers
<span title="">2008</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vuw5ktdyknehrehttg5qm4rfqm" style="color: black;">2008 IEEE 24th International Conference on Data Engineering</a> </i> &nbsp;
The storage of degradable attributes, indexes and logs have thus to be revisited in this light. How to speed up queries involving degradable attributes?  ...  LCPs express degradation triggered by time . LCPs are defined per degradable attribute .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/icde.2008.4497560">doi:10.1109/icde.2008.4497560</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/icde/AnciauxBHPA08.html">dblp:conf/icde/AnciauxBHPA08</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j3efvypaf5ad7ezbdiltng3g3i">fatcat:j3efvypaf5ad7ezbdiltng3g3i</a> </span>
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Improving suffix array locality for fast pattern matching on disk

Ranjan Sinha, Simon Puglisi, Alistair Moffat, Andrew Turpin
<span title="">2008</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vxrc3vebzzachiwy3nopwi3h5u" style="color: black;">Proceedings of the 2008 ACM SIGMOD international conference on Management of data - SIGMOD &#39;08</a> </i> &nbsp;
Here we address the problem of arranging a suffix array on disk so that querying is fast in practice.  ...  We show that the combination of a small trie and a suffix array-like blocked data structure allows queries to be answered as much as three times faster than the best alternative disk-based suffix array  ...  range.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1376616.1376683">doi:10.1145/1376616.1376683</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/sigmod/SinhaPMT08.html">dblp:conf/sigmod/SinhaPMT08</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ij5tit5dibdrpnmcsvamv62c3e">fatcat:ij5tit5dibdrpnmcsvamv62c3e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20090914005234/http://www.seg.rmit.edu.au/research/download.php?manuscript=247" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d0/f0/d0f072a6e61db8e6f8555ea7d380ef66a449ea4d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1376616.1376683"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Compressed Indexes for Approximate String Matching [chapter]

Ho-Leung Chan, Tak-Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Swee-Seong Wong
<span title="">2006</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
We revisit the problem of indexing a string S[1..n] to support searching all substrings in S that match a given pattern P [1..m] with at most k errors.  ...  [5] proposed an O( log 2 n)-bit LCP data structure to answer each subsequent LCP query in O(log log n) time.  ...  Given a pattern P , finding the 1-error matches can be reduced to a number of prefix matching queries on the insertion suffixes and LCP queries.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11841036_21">doi:10.1007/11841036_21</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pag7vro2oretbimngsdszaeiee">fatcat:pag7vro2oretbimngsdszaeiee</a> </span>
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Compressed Indexes for Approximate String Matching

Ho-Leung Chan, Tak-Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Swee-Seong Wong
<span title="2008-12-17">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qhi3z76be5c5xeihac5cyiid3m" style="color: black;">Algorithmica</a> </i> &nbsp;
We revisit the problem of indexing a string S[1..n] to support searching all substrings in S that match a given pattern P [1..m] with at most k errors.  ...  [5] proposed an O( log 2 n)-bit LCP data structure to answer each subsequent LCP query in O(log log n) time.  ...  Given a pattern P , finding the 1-error matches can be reduced to a number of prefix matching queries on the insertion suffixes and LCP queries.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00453-008-9263-2">doi:10.1007/s00453-008-9263-2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yhukilfdn5gshdu6rivuwec7ay">fatcat:yhukilfdn5gshdu6rivuwec7ay</a> </span>
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The longest common extension problem revisited and applications to approximate string searching

Lucian Ilie, Gonzalo Navarro, Liviu Tinta
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/usw2n4yaarcurchx7i4on2iqea" style="color: black;">Journal of Discrete Algorithms</a> </i> &nbsp;
The two known approaches use powerful algorithms: either constant-time computation of the Lowest Common Ancestor in trees or constant-time computation of Range Minimum Queries in arrays.  ...  We compare it with the more widely used Ukkonen's cutoff algorithm and show that it behaves better for a significant range of error thresholds.  ...  The second, more efficient, uses constant-time computation of Range Minimum Queries (RMQ) in arrays [2, 1, 4, 5] applied to the LCP array.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jda.2010.08.004">doi:10.1016/j.jda.2010.08.004</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dmqrg2nwmvdzrhjiidcg5ipl5u">fatcat:dmqrg2nwmvdzrhjiidcg5ipl5u</a> </span>
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ERA Revisited: Theoretical and Experimental Evaluation [article]

Matevž Jekovec, Andrej Brodnik
<span title="2016-09-30">2016</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
They allow answering three main queries: 1) is the given query string P present in the text, 2) where are all its' occurrences located in the text, and 3) finding the longest prefix of the given query  ...  is not defined, 1 ≤ i ≤ |SA| − 1 do 17 cp is the common prefix of Buf [i − 1] and Buf [i] 18 if |cp| < range then 19 LCP [i] ← (Buf [i − 1][|cp|], Buf [i][|cp|], start + |cp|) 20 if LCP [i − 1] is defined  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1609.09654v1">arXiv:1609.09654v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/on6g7keizbeapclcq6tbb656p4">fatcat:on6g7keizbeapclcq6tbb656p4</a> </span>
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Pattern Matching on Grammar-Compressed Strings in Linear Time [article]

Moses Ganardi, Paweł Gawrychowski
<span title="2021-11-09">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Instead of answering a rooted LCP query for u t , we answer a rooted LCP query for p[i t ..m].  ...  Now the reduction from unrooted LCP queries to rooted LCP queries proceeds as follows. We retrieve the heavy path h containing v.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2111.05016v1">arXiv:2111.05016v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/etruqpzm3jf3zmv5uex555w5wu">fatcat:etruqpzm3jf3zmv5uex555w5wu</a> </span>
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Fast circular dictionary-matching algorithm

TANVER ATHAR, CARL BARTON, WIDMER BLAND, JIA GAO, COSTAS S. ILIOPOULOS, CHANG LIU, SOLON P. PISSIS
<span title="2015-05-11">2015</span> <i title="Cambridge University Press (CUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jdpukxfslnfmradqb65llq43na" style="color: black;">Mathematical Structures in Computer Science</a> </i> &nbsp;
Let SA denote the array of positions of the sorted suffixes of string x of length n, i.e. for all 1 6 r < n, -Preprocess array LCP for range minimum queries, we denote this by RMQ LCP (Fischer and Heun  ...  In this article, we revisit the following two problems in the average-case setting.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s0960129515000134">doi:10.1017/s0960129515000134</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x67nwwgzzrcd3owmmxsou7ou44">fatcat:x67nwwgzzrcd3owmmxsou7ou44</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724122943/https://www.cambridge.org/core/services/aop-cambridge-core/content/view/267FE13D0A1E3948C2C0C8966979D3FB/S0960129515000134a.pdf/div-class-title-fast-circular-dictionary-matching-algorithm-div.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ba/1c/ba1c03abd43495d9154dfaa3c1338ccea19cb3d4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s0960129515000134"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> cambridge.org </button> </a>

On searching compressed string collections cache-obliviously

Paolo Ferragina, Roberto Grossi, Ankur Gupta, Rahul Shah, Jeffrey Scott Vitter
<span title="">2008</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xtq6wnwaszaebg4qf7aw6mllwi" style="color: black;">Proceedings of the twenty-seventh ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems - PODS &#39;08</a> </i> &nbsp;
Our second contribution is a novel dictionary encoding scheme that builds upon such linearizations and achieves nearly optimal space, offers competitive I/O-search time, and is also conscious of the query  ...  It goes without saying that hashing is not suitable for the string dictionary problem, because it cannot support the Prefix Range(P ) query.  ...  P [lcp + 1].  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1376916.1376943">doi:10.1145/1376916.1376943</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/pods/FerraginaGGSV08.html">dblp:conf/pods/FerraginaGGSV08</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5n2owp2vbbc5ho3mowrmdblm7q">fatcat:5n2owp2vbbc5ho3mowrmdblm7q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809102139/http://www.ittc.ku.edu/~jsv/Papers/FGG08.SearchingCompressed.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/c3/f0c385d37b3587823d0eb56012379c464bbd956c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1376916.1376943"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

A Lagrangian approach for storage of spatio-temporal network datasets

Michael R. Evans, KwangSoo Yang, James M. Kang, Shashi Shekhar
<span title="">2010</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q6tw7qmnszfgbikw4mpyjrokkm" style="color: black;">Proceedings of the 18th SIGSPATIAL International Conference on Advances in Geographic Information Systems - GIS &#39;10</a> </i> &nbsp;
Experimental evaluation using the Minneapolis, MN road network showed that LCP outperforms traditional orthogonal approaches.  ...  .), which may produce excessive I/O costs when performing traversal-based spatio-temporal network queries (e.g., route evaluation, arrival time prediction, etc) due to the desired nodes not being allocated  ...  Figure 16(a) shows the ATSS method compared to the LCP method. ATSS was run with six different time interval parameter values, which range from a interval length of 2 time steps to 20.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1869790.1869822">doi:10.1145/1869790.1869822</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/gis/EvansYKS10.html">dblp:conf/gis/EvansYKS10</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ukavefy745ezplfehmirqjygju">fatcat:ukavefy745ezplfehmirqjygju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110913140726/http://www-users.cs.umn.edu/~mevans/p212-evans.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/65/a1/65a145606b097f8d0bdba490ad52a2729d1720af.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1869790.1869822"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>
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