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Recent Advances in Text-to-Pattern Distance Algorithms [chapter]

Przemysław Uznański
2020 Lecture Notes in Computer Science  
Computing text-to-pattern distances is a fundamental problem in pattern matching.  ...  A huge efforts have been put into advancement of understanding of pattern matching by the community. One particular variant to consider is finding occurrences or almost-occurrences of P in T .  ...  If is a 2x-period of the pattern, then any two occurrences of the pattern in the text with at most x mismatches are at offset distance at least .  ... 
doi:10.1007/978-3-030-51466-2_32 fatcat:67g3nam6o5elfc6xeup7mqw7fi

Brain-Inspired Photonic Signal Processor for Generating Periodic Patterns and Emulating Chaotic Systems

Piotr Antonik, Marc Haelterman, Serge Massar
2017 Physical Review Applied  
Here we present a photonic reservoir computer with output feedback, and demonstrate its capacity to generate periodic time series and to emulate chaotic systems.  ...  In previous experiments the output was uncoupled from the system and in most cases simply computed offline on a post-processing computer.  ...  compressing it with an efficient compression algorithm (such as e.g.  ... 
doi:10.1103/physrevapplied.7.054014 fatcat:xqtszmdtxrcmvpdfxfbhtkwctu

Waves in active and passive periodic structures: A review

C. Elachi
1976 Proceedings of the IEEE  
This leads to a periodic change in the diameter of the channels with periodicities from a few angstroms to few tens of angstroms.  ...  The reader interested in that aspect of the field of waves in periodic structures is referred to that review paper or to a wide range of text books [ 246] .  ... 
doi:10.1109/proc.1976.10409 fatcat:7jipnulzdzgz7i7cl25s6rha5q

High Throughput Short Read Alignment via Bi-directional BWT

T. W. Lam, Ruiqiang Li, Alan Tam, Simon Wong, Edward Wu, S. M. Yiu
2009 2009 IEEE International Conference on Bioinformatics and Biomedicine  
When compared with existing software (Bowtie is the best), our software is at least 3 times faster for finding unique best alignments, and 25 times faster for finding all possible alignments.  ...  We believe that bi-directional BWT is an interesting data structure on its own and could be applied to other pattern matching problems.  ...  Matching a pattern of a few hundred characters with the human genome takes a few microseconds only. However, BWT is not designed for approximate pattern matching.  ... 
doi:10.1109/bibm.2009.42 dblp:conf/bibm/LamLTWWY09 fatcat:prausjgobffh5hv54o6ux5xgdu

Full-text and Keyword Indexes for String Searching [article]

Aleksander Cisłak
2015 arXiv   pre-print
Query times in the order of 1 microsecond were reported for one mismatch for a few-megabyte natural language dictionary on a medium-end PC.  ...  We compare our solution with other algorithms and we show that it is faster when the Hamming distance is used.  ...  The pattern size can vary from a few letters (NL words) to a few hundred (DNA reads), and the input text can be of almost arbitrary size.  ... 
arXiv:1508.06610v1 fatcat:5pmce2d72veuxpw3s5u6hbidim

Circular pattern matching with k mismatches

Panagiotis Charalampopoulos, Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, Wiktor Zuba
2020 Journal of computer and system sciences (Print)  
This is the circular pattern matching with k mismatches (k-CPM) problem.  ...  The k-mismatch problem has also been considered on compressed representations of the text [9] [10] [11] [12] [13] , in the parallel model [14] , in the streaming model [15, 6, 16] , and in the setting  ...  to influence the work reported in this paper.  ... 
doi:10.1016/j.jcss.2020.07.003 fatcat:jepd5jdl6jaghjib6jjy7pgx7q

General Pattern Matching [chapter]

Alberto Apostolico
2009 Algorithms and Theory of Computation Handbook, Second Edition, Volume 1  
Since then, the range of applications of the tools and methods developed in pattern matching has expanded to include text, image and signal processing, speech analysis and recognition, data compression  ...  Some initial pattern matching problems and techniques arose in the early Seventies in connection with emerging technologies and problems of the time, e.g., compiler design.  ...  Acknowledgements This work was supported in part by NSF Grants CCR-9201078 and CCR-9700276, by NATO  ... 
doi:10.1201/9781584888239-c15 fatcat:tma4hyzbabfifpwgzhokprih44

Towards Unified Approximate Pattern Matching for Hamming and L_1 Distance

Pawel Gawrychowski, Przemyslaw Uznanski, Michael Wagner
2018 International Colloquium on Automata, Languages and Programming  
We complement the trade-off with a matching conditional lower bound, showing that a significantly faster combinatorial algorithm is not possible, unless the combinatorial matrix multiplication conjecture  ...  Computing the distance between a given pattern of length n and a text of length m is defined as calculating, for every m-substring of the text, the distance between the pattern and the substring.  ...  Thus we see that k-mismatch pattern matching is reduced to a kernel where the -encoding of both the text and the pattern have few runs, that is, they both compress well with RLE.  ... 
doi:10.4230/lipics.icalp.2018.62 dblp:conf/icalp/GawrychowskiU18 fatcat:d2rerchbtjhqrl6kp52ypex44y

The streaming k-mismatch problem [chapter]

Raphael Clifford, Tomasz Kociumaka, Ely Porat
2019 Proceedings of the Thirtieth Annual ACM-SIAM Symposium on Discrete Algorithms  
In our formulation, the pattern is also in the stream, arriving directly before the text.  ...  Full terms of use are available: Abstract We consider the streaming complexity of a fundamental task in approximate pattern matching: the k-mismatch problem.  ...  Let P be a pattern with a d-period p. Suppose that p is also an O(d + p)-period of the text T .  ... 
doi:10.1137/1.9781611975482.68 dblp:conf/soda/CliffordKP19 fatcat:fvx2bf6cfnep3jinkiyuc3r2jm

FPGA Acceleration of Sequence Alignment: A Survey [article]

Sahand Salamat, Tajana Rosing
2020 arXiv   pre-print
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few.  ...  Providing massive parallelism, FPGA-based accelerators have shown great performance in accelerating DNA alignment algorithms.  ...  reference Memory access pattern can be optimized Stores the reference sequence in the compressed format Exact matching or limited number of mismatches Exponential growth in computations w.r.t the #mismatches  ... 
arXiv:2002.02394v2 fatcat:xy4ryqloszfwrezo4kbuwmvgfi

Statistical properties of a sample of periodically variable B-type supergiants

K. Lefever, J. Puls, C. Aerts
2006 Astronomy and Astrophysics  
We applied the method to selected H, He and Si line profiles, measured with the high resolution CES spectrograph attached to the ESO CAT telescope in La Silla, Chile.  ...  Our goal is to test if their variability is compatible with opacity-driven non-radial oscillations.  ...  Crowther for providing us with the CTIO/JKT spectra for the stars we had in common, and A. A. Pamyatnykh for providing us with the theoretical instability domains B stars.  ... 
doi:10.1051/0004-6361:20066038 fatcat:ef7u76vjqfhx5fj74pwebcpzuy

Practical authenticated pattern matching with optimal proof size

Dimitrios Papadopoulos, Charalampos Papamanthou, Roberto Tamassia, Nikos Triandopoulos
2015 Proceedings of the VLDB Endowment  
(mis)match of 10 2 characters in a text of 10 6 characters, once the query has been evaluated.  ...  Answers to queries are verified by proofs of size at most 500 bytes for text pattern matching, and at most 243 bytes for exact path XML search, independently of the document or answer size.  ...  Research supported in part by the U.S. National Science Foundation under CNS grants 1012798, 1012910, and 1228485. REFERENCES  ... 
doi:10.14778/2752939.2752944 fatcat:ljy34xuibnckfhbhdelcvh6cba

Enhanced Hydrogen Storage Properties of Li-RHC System with In-House Synthesized AlTi3 Nanoparticles

Thi-Thu Le, Claudio Pistidda, Julián Puszkiel, María Victoria Castro Riglos, David Michael Dreistadt, Thomas Klassen, Martin Dornheim
2021 Energies  
In comparison with the pristine material, the Li-RHC doped with AlTi3 nanoparticles has about a nine times faster dehydrogenation rate.  ...  The effect of in-house-produced AlTi3 nanoparticles on the hydrogenation/dehydrogenation kinetics of the 2LiH + MgB2 (Li-RHC) system is explored in this work, with the aim of reaching high hydrogen storage  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/en14237853 fatcat:4ecsqhrmqbfshdsd5aeqdiwrx4

Inverted files versus signature files for text indexing

Justin Zobel, Alistair Moffat, Kotagiri Ramamohanarao
1998 ACM Transactions on Database Systems  
We have undertaken a detailed comparison of these two approaches in the context of text indexing, paying particular attention to query evaluation speed and space requirements.  ...  Our results also show that a synthetic text database can provide a realistic indication of the behavior of an actual text database.  ...  ACKNOWLEDGMENTS We are grateful to Alan Kent for help with the signature file system, Tim Shimmin for help with MG, and Despina Psaradellis for programming assistance.  ... 
doi:10.1145/296854.277632 fatcat:cqxnkypdurawdlbpp2eur6ktne

A multispectral view of the periodic events in η Carinae

A. Damineli, D. J. Hillier, M. F. Corcoran, O. Stahl, J. H. Groh, J. Arias, M. Teodoro, N. Morrell, R. Gamen, F. Gonzalez, N. V. Leister, H. Levato (+4 others)
2008 Monthly notices of the Royal Astronomical Society  
Simple eclipses and mechanisms effective only near periastron (e.g., shell ejection or accretion onto the secondary star) cannot account for the whole 5.5-yr cycle.  ...  The first, the 'slow variation' component, is revealed by slow changes in the ionization level of circumstellar matter across the whole cycle and is caused by gradual changes in the wind-wind collision  ...  Since the plots are compressed in the Y scale, the errors are of the order of the size of the symbols.  ... 
doi:10.1111/j.1365-2966.2008.13214.x fatcat:ms4w3ehk3veifat7k436k4gvp4
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