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Tighter Packed Bit-Parallel NFA for Approximate String Matching
[chapter]
<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>
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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. ...
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Fast Bit-Parallel Matching for Network and Regular Expressions
[chapter]
<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>
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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. ...
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Bit-parallel sequence-to-graph alignment
[article]
<span title="2018-05-15">2018</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
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<span class="release-stage" >pre-print</span>
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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: ...
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Bit-(Parallelism)2: Getting to the Next Level of Parallelism
[chapter]
<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>
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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 ...
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Bit-Parallel Witnesses and Their Applications to Approximate String Matching
<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>
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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 ...
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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>
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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. ...
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Trajectory Pattern Matching Based on Bit-Parallelism for Large GPS Data
<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>
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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. ...
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Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor
<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>
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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 ...
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Bit-Parallel Multiple Approximate String Matching based on GPU
<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>
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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. ...
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New Bit-Parallel Indel-Distance Algorithm
[chapter]
<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>
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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. ...
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On the bit-parallel simulation of the nondeterministic Aho–Corasick and suffix automata for a set of patterns
<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>
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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. ...
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A Bit-Parallel Tree Matching Algorithm for Patterns with Horizontal VLDC's
[chapter]
<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>
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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. ...
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Bit-parallel approximate string matching algorithms with transposition
<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>
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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 ...
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Bit-Parallel Approximate String Matching Algorithms with Transposition
[chapter]
<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>
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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 ...
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A SPACE EFFICIENT BIT-PARALLEL ALGORITHM FOR THE MULTIPLE STRING MATCHING PROBLEM
<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>
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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 [?] . ...
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