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Tighter Packed Bit-Parallel NFA for Approximate String Matching [chapter]

Heikki Hyyrö
<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 propose a new variant of the bit-parallel NFA of Baeza-Yates and Navarro (BPD) for approximate string matching [1] .  ...  We decrease this to (m − k)(k + 1), and also give a slightly more efficient simulation algorithm for the NFA.  ...  The methods used horizontal partitioning (see [1] ) when the NFA required more than one computer word.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11812128_32">doi:10.1007/11812128_32</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wqt65beckzfkhffymxt5i25x7i">fatcat:wqt65beckzfkhffymxt5i25x7i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304091427/http://pdfs.semanticscholar.org/bb30/f9bcdba06bba4c16a67ab9ed09d3754226b3.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/bb/30/bb30f9bcdba06bba4c16a67ab9ed09d3754226b3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11812128_32"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Fast Bit-Parallel Matching for Network and Regular Expressions [chapter]

Yusaku Kaneta, Shin-ichi Minato, Hiroki Arimura
<span title="">2010</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;
Following the study of Navarro (RECOMB, 2001) on the extended string matching, we introduce new operations called Scatter, Gather, and Propagate to efficiently compute ε-moves of the Thompson NFA using  ...  By using these operations and a property called the bi-monotonicity of the Thompson NFA, we present an efficient algorithm for the network expression matching that runs in O(ndm/w) time using O(dm) preprocessing  ...  To obtain above results, we devise the following techniques to achieve efficient bit-parallel simulation of Thompson NFA (TNFA, for short) for classes NET and EXNET.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-16321-0_39">doi:10.1007/978-3-642-16321-0_39</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fjdglam7ybdzjikh4m5kdi2q34">fatcat:fjdglam7ybdzjikh4m5kdi2q34</a> </span>
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Bit-parallel sequence-to-graph alignment [article]

Mikko Rautiainen, Veli Mäkinen, Tobias Marschall
<span title="2018-05-15">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The Shift-And algorithm works by simulating a nondeterministic finite automaton (NFA) that matches the pattern, and then feeding the text to it.  ...  Whenever a node's NFA state has changed, we add all outgoing edges to the list. A state change may set a bit but it cannot unset a bit.  ...  << chunkSize) + extra 7: x ← x * M lsb x now has the prefix sum of the set bits at each chunk boundary 8: return x 9: function AddC(x, y) Calculates the values x + y at each chunk in parallel 10:  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/323063">doi:10.1101/323063</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hetblw734recjjfaant4afidge">fatcat:hetblw734recjjfaant4afidge</a> </span>
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Bit-(Parallelism)2: Getting to the Next Level of Parallelism [chapter]

Domenico Cantone, Simone Faro, Emanuele Giaquinta
<span title="">2010</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;
These approaches are general enough to be applied to other bit-parallel algorithms.  ...  In particular, starting from an algorithm based on bit-parallelism, we propose two flexible approaches for boosting it with a higher level of parallelism.  ...  When the pattern size is small enough, in favorable situations it becomes possible to carry on in parallel the simulation of multiple copies of a same NFA or of multiple distinct NFAs, thus getting to  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-13122-6_18">doi:10.1007/978-3-642-13122-6_18</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sfkeerf5szefhekp46idh6d5ai">fatcat:sfkeerf5szefhekp46idh6d5ai</a> </span>
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Bit-Parallel Witnesses and Their Applications to Approximate String Matching

Heikki Hyyrö, Gonzalo Navarro
<span title="2004-09-08">2004</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qhi3z76be5c5xeihac5cyiid3m" style="color: black;">Algorithmica</a> </i> &nbsp;
The idea is to simulate another algorithm using bit-parallelism.  ...  The first bit-parallel algorithm for approximate searching [24] parallelized an automaton-based algorithm: a nondeterministic finite automaton (NFA) was simulated in O(k⌈m/w⌉n) time, where w is the number  ...  A Bit-Parallel Automaton Simulation (BPA) The idea of BPA [24] is to simulate the NFA of Figure 2 using bit-parallelism, so that each row i of the automaton fits in a computer word R i (each state  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00453-004-1108-z">doi:10.1007/s00453-004-1108-z</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rnpo3cqqnvbn3lnsz34wbqqmnm">fatcat:rnpo3cqqnvbn3lnsz34wbqqmnm</a> </span>
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Bit-parallel sequence-to-graph alignment

<span title="2019-10-01">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
The Shift-And algorithm works by simulating a nondeterministic finite automaton (NFA) that matches the pattern, and then feeding the text to it.  ...  We believe that this can also be applied to the bit-parallel version of graph alignment.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz162">doi:10.1093/bioinformatics/btz162</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30851095">pmid:30851095</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6761980/">pmcid:PMC6761980</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wvalpmnmirhfhlgctq2gume7la">fatcat:wvalpmnmirhfhlgctq2gume7la</a> </span>
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Trajectory Pattern Matching Based on Bit-Parallelism for Large GPS Data

Hirohito Sasakawa, Hiroki Arimura
<span title="">2012</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zbve6t6jwrdqlpyjrojwweoora" style="color: black;">2012 IIAI International Conference on Advanced Applied Informatics</a> </i> &nbsp;
Then, we present an efficient bit-parallel string matching algorithm on encoded texts for the classes of multi-resolution trajectory patterns.  ...  Fig. 2 , we present an algorithm RUNTIME that simulates the NFA N for a pattern using bit-parallelism on encoded texts in multi-resolution tagged coding.  ...  In runtime phase, we simulate the string matching of the NFA based on the given set of bit-masks by using bit-and arithmetic operations on registers.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/iiai-aai.2012.22">doi:10.1109/iiai-aai.2012.22</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/iiaiaai/SasakawaA12.html">dblp:conf/iiaiaai/SasakawaA12</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gu3ajpfzzvcuhgbgb6zqn5p4ii">fatcat:gu3ajpfzzvcuhgbgb6zqn5p4ii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810000810/http://www-ikn.ist.hokudai.ac.jp/~sasakawa/drafts/sasakawa_arim_eskm12cam.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/ef/a9/efa91d71c3cb98d356a0f6b6c3a32c9fb0f30cae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/iiai-aai.2012.22"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor

Tuan Tu Tran, Simon Schindel, Yongchao Liu, Bertil Schmidt
<span title="">2014</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fdx47zt2hbb7ph2yhsec3zdkme" style="color: black;">2014 IEEE 26th International Symposium on Computer Architecture and High Performance Computing</a> </i> &nbsp;
values by a single bit operation; • Directly simulates all states of the NFA (Wu-Manber algorithm [Wu and Manber, 1992] ); • Limited by the size of machine words.  ...  / 27 Bit-parallel Approximate Pattern Matching with the prefix automaton Bit-parallelism: • Encodes calculated values into a machine work, seen as a bit array; • Allows for simultaneous updates of multiple  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/sbac-pad.2014.37">doi:10.1109/sbac-pad.2014.37</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/sbac-pad/TranSLS14.html">dblp:conf/sbac-pad/TranSLS14</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cazay7utjffuhoq4vgl6nw4tmy">fatcat:cazay7utjffuhoq4vgl6nw4tmy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808051118/http://sbac.lip6.fr/2014/session%206/1-BitParallel.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/11/85/118563903efc3c325e0a288485074f1cb8951307.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/sbac-pad.2014.37"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Bit-Parallel Multiple Approximate String Matching based on GPU

Kefu Xu, Wenke Cui, Yue Hu, Li Guo
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cx3f4s3qmfe6bg4qvuy2cxezyu" style="color: black;">Procedia Computer Science</a> </i> &nbsp;
This paper proposed a bit-parallel multiple approximate string match algorithm, and developed a GPU implementation which achieved speedups about 28 relative to a single-thread CPU code.  ...  The third, one of the most successful approaches, is based on the bit-parallel simulation of other approaches.  ...  It packs each row i of the NFA in a different machine word R i , with each state represented by a bit.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.procs.2013.05.067">doi:10.1016/j.procs.2013.05.067</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mjongpxrafenrdgd2xaz4dbogu">fatcat:mjongpxrafenrdgd2xaz4dbogu</a> </span>
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New Bit-Parallel Indel-Distance Algorithm [chapter]

Heikki Hyyrö, Yoan Pinzon, Ayumi Shinohara
<span title="">2005</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;
Recently, in [3] , the IndelMYE, In-delWM and IndelBYN algorithms where introduced as modified version of the bit-parallel algorithms of Myers [6], Wu&Manber [10] and Baeza-Yates&Navarro [1], respectively  ...  In this paper we present an improved version of IndelMYE that makes a better use of the bit-operations and runs 24.5 percent faster in practice.  ...  The O(k m/w n) algorithm of Wu and Manber [10] and the O( (k + 2)(m − k)/w n) algorithm of Baeza-Yates and Navarro [1] simulate a non-deterministic finite automaton (NFA) by using bitvectors.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11427186_33">doi:10.1007/11427186_33</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q2puyzdrljg3bmztlhhbwdcvu4">fatcat:q2puyzdrljg3bmztlhhbwdcvu4</a> </span>
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On the bit-parallel simulation of the nondeterministic Aho–Corasick and suffix automata for a set of patterns

Domenico Cantone, Simone Faro, Emanuele Giaquinta
<span title="">2012</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;
In this paper we present a method to simulate, using the bit-parallelism technique, the nondeterministic Aho-Corasick automaton and the nondeterministic suffix automaton induced by the trie and by the  ...  When the prefix redundancy is nonnegligible, this method yields-if compared to the original bit-parallel encoding with no prefix factorization-a representation that requires smaller bit-vectors and, correspondingly  ...  In this paper we present a new more general approach to the efficient bit-parallel simulation of the Aho-Corasick NFAs and suffix NFAs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jda.2011.02.001">doi:10.1016/j.jda.2011.02.001</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3fhi6yss7nautiylu34twvmbjy">fatcat:3fhi6yss7nautiylu34twvmbjy</a> </span>
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A Bit-Parallel Tree Matching Algorithm for Patterns with Horizontal VLDC's [chapter]

Hisashi Tsuji, Akira Ishino, Masayuki Takeda
<span title="">2005</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 adopt the bit-parallel technique to obtain a practically fast algorithm.  ...  Conclusion We addressed the problem of finding a regular hedge P within a ground hedge T , and presented an efficient algorithm basing on the bit-parallelism.  ...  We then adopt the bit-parallel technique to obtain a practically fast algorithm.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11575832_43">doi:10.1007/11575832_43</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lpp2t3jtxbhofclkqcz6cxdczu">fatcat:lpp2t3jtxbhofclkqcz6cxdczu</a> </span>
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Bit-parallel approximate string matching algorithms with transposition

Heikki Hyyrö
<span title="">2005</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;
Using bit-parallelism has resulted in fast and practical algorithms for approximate string matching under Levenshtein edit distance, which permits a single edit operation to insert, delete or substitute  ...  NFA of Baeza-Yates and Navarro The bit-parallel algorithm of Baeza-Yates and Navarro [2] is based on simulating the same NFA R as in the previous section.  ...  The bit-parallel NFA of Wu and Manber The bit-parallel approximate string matching algorithm of Wu and Manber [22] is based on representing a non-deterministic finite automaton (NFA) by using bit-vectors  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jda.2004.08.006">doi:10.1016/j.jda.2004.08.006</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/irjbfaokmnh5hgvttflek7v3ey">fatcat:irjbfaokmnh5hgvttflek7v3ey</a> </span>
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Bit-Parallel Approximate String Matching Algorithms with Transposition [chapter]

Heikki Hyyrö
<span title="">2003</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;
Using bit-parallelism has resulted in fast and practical algorithms for approximate string matching under Levenshtein edit distance, which permits a single edit operation to insert, delete or substitute  ...  NFA of Baeza-Yates and Navarro The bit-parallel algorithm of Baeza-Yates and Navarro [2] is based on simulating the same NFA R as in the previous section.  ...  The bit-parallel NFA of Wu and Manber The bit-parallel approximate string matching algorithm of Wu and Manber [22] is based on representing a non-deterministic finite automaton (NFA) by using bit-vectors  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-39984-1_8">doi:10.1007/978-3-540-39984-1_8</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/46irefwqkzgkfo466k4mxyya7a">fatcat:46irefwqkzgkfo466k4mxyya7a</a> </span>
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A SPACE EFFICIENT BIT-PARALLEL ALGORITHM FOR THE MULTIPLE STRING MATCHING PROBLEM

DOMENICO CANTONE, SIMONE FARO
<span title="">2006</span> <i title="World Scientific Pub Co Pte Lt"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yhcgkcmjlvfovferf3in5mkmpq" style="color: black;">International Journal of Foundations of Computer Science</a> </i> &nbsp;
Direct simulation of nondeterministic automata can be performed very efficiently using the bit-parallelism technique, though this is not necessarily true for factor-based automata.  ...  In this paper we present an algorithm for the multiple string matching problem, based on the bit-parallel simulation of nondeterministic factor-based automata which satisfy a particular ordering condition  ...  Thus, it would be desirable to be able to simulate efficiently the parallel computation of an NFA. This can be done using the bit-parallelism technique [?] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/s0129054106004388">doi:10.1142/s0129054106004388</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/buvts2fdhjfbtnl5alnjlplkna">fatcat:buvts2fdhjfbtnl5alnjlplkna</a> </span>
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