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Approximate pattern matching on elastic-degenerate text

Giulia Bernardini, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone
2019 Theoretical Computer Science  
The natural problem that arises is finding all matches of a deterministic pattern of length m in an elastic-degenerate text.  ...  In this paper, we study the same problem under the edit distance model and present an O(k 2 mG + kN)-time and O(m)-space algorithm, where G is the total number of strings in the elastic-degenerate text  ...  [k E -EDSM] Elastic-Degenerate String Matching under the edit distance model: Input: A deterministic pattern P of length m, an ED text T of length n and size N ≥ m, an integer 0 < k < m.  ... 
doi:10.1016/j.tcs.2019.08.012 fatcat:gkebn2b6znb53jhiyl5dtonzgq

SOPanG 2: online searching over a pan-genome without false positives [article]

Aleksander Cisłak, Szymon Grabowski
2020 arXiv   pre-print
Motivation: The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences.  ...  The additional stage for checking the matches yields a penalty of less than 3.5% relative speed in practice, which means that SOPanG 2 is able to report pattern matches in a pan-genome, mapping them onto  ...  While still using an elastic-degenerate text format, we eliminated its inherent limitation of false positive matches (i.e., matches not present in any individual genome) by augmenting it with the information  ... 
arXiv:2004.03033v2 fatcat:cvb567ziwvhjxoarobbxmalqvu

Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line

Solon P. Pissis, Ahmad Retha, Marc Herbstritt
2018 Symposium on Experimental and Efficient Algorithms  
For a standard pattern of length m, pattern matching in an elastic-degenerate text can be solved on-line in time O(nm 2 + N ) with pre-processing time and space O(m) (Grossi et al., CPM 2017).  ...  An elastic-degenerate string is a sequence of n sets of strings of total length N . It has been introduced to represent multiple sequence alignments of closely-related sequences in a compact form.  ...  solutions for exact pattern matching can be applied for fast average-case approximate pattern matching, similar to standard strings; (c) on-line solutions can be useful when one wants to search for a  ... 
doi:10.4230/lipics.sea.2018.16 dblp:conf/wea/PissisR18 fatcat:won7okgllredpgvtgmjj6b4t4e

Pattern Matching on Elastic-Degenerate Text with Errors [chapter]

Giulia Bernardini, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone
2017 Lecture Notes in Computer Science  
solutions for exact pattern matching can be applied for fast average-case approximate pattern matching similar to standard strings [2] ; (c) on-line solutions can be useful when one wants to search for  ...  [k E -EDSM] Elastic-Degenerate String Matching with Edit Distance: Input: A deterministic pattern P of length m, an elastic-degenerate textT of length n and size N ≥ m, and an integer 0 < k < m.  ... 
doi:10.1007/978-3-319-67428-5_7 fatcat:ylqke6jym5ds5oipgh44tencxu

On-Line Pattern Matching on Similar Texts

Roberto Grossi, Costas S. Iliopoulos, Chang Liu, Nadia Pisanti, Solon S. Pissis, Ahmad Retha, Giovanna Rosone, Fatima Vayani, Luca Versari, Marc Herbstritt
2017 Annual Symposium on Combinatorial Pattern Matching  
Our immediate target is to apply these on-line solutions for fast average-case approximate pattern matching or for multiple pattern matching on a set of similar texts.  ...  for a set of patterns in elastic-degenerate texts, similar to standard strings [1, 2] .  ... 
doi:10.4230/lipics.cpm.2017.9 dblp:conf/cpm/GrossiILPPRRVV17 fatcat:j5v4fj4o5zautf5medbysd4dpm

Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication

Giulia Bernardini, Pawel Gawrychowski, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone, Michael Wagner
2019 International Colloquium on Automata, Languages and Programming  
The ED string matching (EDSM) problem is to find all occurrences of a pattern of length m in an ED text.  ...  An elastic-degenerate (ED) string is a sequence of n sets of strings of total length N , which was recently proposed to model a set of similar sequences.  ...  This is the elastic-degenerate string matching (EDSM) problem.  ... 
doi:10.4230/lipics.icalp.2019.21 dblp:conf/icalp/0001GPPR19 fatcat:d7epfhuadraq5fjgd42hvi5yfe

Front Matter, Table of Contents, Preface, Conference Organization

Gonzalo Navarro, David Sankoff, Binhai Zhu, Marc Herbstritt
2018 Annual Symposium on Combinatorial Pattern Matching  
Thankachan 8:1-8:9 Faster Online Elastic Degenerate String Matching Kotaro Aoyama, Yuto Nakashima, Tomohiro I, Shunsuke Inenaga, . . 9:1-9:10 A Simple Linear- On Undetected Redundancy in the Burrows-Wheeler  ...  Matching Indeterminate Strings Susanne Albers (TU München) Rui Henriques, Alexandre P.  ...  pattern matching and discovery, string algorithms, string processing in databases, symbolic computation and text searching and indexing.  ... 
doi:10.4230/lipics.cpm.2018.0 dblp:conf/cpm/X18 fatcat:4t5f2esmfbg3xkfeyjpvxfgtk4

Topological Point Defects of Liquid Crystals in Quasi-Two-Dimensional Geometries

Kirsten Harth, Ralf Stannarius
2020 Frontiers in Physics  
Random defect patterns can be created by thermal quenching of the samples from lower ordered into higher ordered phases.  ...  From interactions and dynamic features observed in these LC systems, general conclusions on defect dynamics can be drawn.  ...  The defects repel each other, and the pattern rapidly expands, with eight defects moving radially outward and one remaining in the center. The defect cores are labeled by small circles (see text).  ... 
doi:10.3389/fphy.2020.00112 fatcat:ydbct7ufvzbvhhuworeoqw7kaq

Controlling placement of nonspherical (boomerang) colloids in nematic cells with photopatterned director

Chenhui Peng, Taras Turiv, Rui Zhang, Yubing Guo, Sergij V Shiyanovskii, Qi-Huo Wei, Juan de Pablo, Oleg D Lavrentovich
2016 Journal of Physics: Condensed Matter  
Control of colloidal locations through patterned molecular orientation can be explored for future applications in microfluidic, lab on a chip, sensing and sorting devices.  ...  Nematic liquid crystals with spatially varying director patterns represent a promising approach to achieve a well-controlled placement of colloidal particles thanks to the elastic forces between the particles  ...  the shape of the boomerang (in particular, its opening angle) as well as on the anchoring strength of its surface, K is the elastic constant in the so-called one-constant approximation.  ... 
doi:10.1088/0953-8984/29/1/014005 pmid:27830662 fatcat:45fsditnfnffbfrfuxzko7xuwe

Topographically induced hierarchical assembly and geometrical transformation of focal conic domain arrays in smectic liquid crystals

A. Honglawan, D. A. Beller, M. Cavallaro, R. D. Kamien, K. J. Stebe, S. Yang
2012 Proceedings of the National Academy of Sciences of the United States of America  
inside of the pillar, removing a significant fraction of the elastic energy (SI Text).  ...  FCDs on the patterned substrate.  ...  FCDs on the patterned substrate.  ... 
doi:10.1073/pnas.1214708109 pmid:23213240 pmcid:PMC3538202 fatcat:di5hq32swjgsfglia3gpad4vry

Strain-induced bound states in transition-metal dichalcogenide bubbles

L Chirolli, E Prada, F Guinea, R Roldán, P San-Jose
2019 2D Materials  
Our results show that elastic bubbles in these materials are remarkably efficient at confining photocarriers.  ...  Bubbles ubiquitously form in two-dimensional crystals on top of a substrate by the competition between van der Waals forces and the hydrostatic pressure exerted by trapped fluid.  ...  A similar straininduced confinement effect has been recently explored in which the strain is extrinsic, produced in the TMDC by indentation with nanopillars patterned on the substrate [17] [18] [19] 22  ... 
doi:10.1088/2053-1583/ab0113 fatcat:ci7tpbnafjbihayn3mzztro3jq

Cymatics for the cloaking of flexural vibrations in a structured plate

D. Misseroni, D. J. Colquitt, A. B. Movchan, N. V. Movchan, I. S. Jones
2016 Scientific Reports  
The elastic lattice cloak shows an impressive efficiency within the predicted frequency range of 100-250Hz.  ...  We present a proof of concept design for a structured square cloak enclosing a void in an elastic lattice, subjected to flexural vibrations.  ...  Acknowledgements The authors would like to thank Prof Davide Bigoni for stimulating discussions and valuable suggestions on the text of the paper, and for his strong support.  ... 
doi:10.1038/srep23929 pmid:27068339 pmcid:PMC4828639 fatcat:qmwmeep52bclzicnfodhy4yuye

Elastic-Degenerate String Matching via Fast Matrix Multiplication [article]

Giulia Bernardini, Paweł Gawrychowski, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone
2021 arXiv   pre-print
The ED string matching (EDSM) problem is to find all occurrences of a pattern of length m in an ED text. An O(nm^1.5√(log m)+N)-time algorithm for EDSM is known [Aoyama et al., CPM 2018].  ...  An elastic-degenerate (ED) string is a sequence of n sets of strings of total length N, which was recently proposed to model a set of similar sequences.  ...  This is the elastic-degenerate string matching (EDSM) problem.  ... 
arXiv:1905.02298v3 fatcat:owglwrnjf5axbmwzqzomekd3ry

Emergent Structure of Multidislocation Ground States in Curved Crystals

Amir Azadi, Gregory M. Grason
2014 Physical Review Letters  
Employing a combination of numerical simulations and asymptotic analysis of continuum elasticity theory, we prove that an energetic hierarchy gives rise to a structural hierarchy, whereby dislocation number  ...  In the main text a scaling prediction for the n s dependence was made based on the distinct energetics associated with scar lengths and scar ends.  ...  In [16] , it was shown in the limit of narrow scars ( s /W 1) that the n s -degenerate energetics encoded in the elastic energy of asymptotic stress σ d ij correspond directly to the combination of relaxation  ... 
doi:10.1103/physrevlett.112.225502 pmid:24949777 fatcat:554wjqizcrdlfhhb2vlt4udz6i

Neutron occupancies and single-particle energies across the stable tin isotopes [article]

S. V. Szwec, D. K. Sharp, B. P. Kay, S. J. Freeman, J. P. Schiffer, P. Adsley, C. Binnersley, N. de Séréville, T. Faestermann, R. F. Garcia Ruiz, F. Hammache, R. Hertenberger (+5 others)
2021 arXiv   pre-print
Two of the five orbitals are nearly degenerate, below N=64, and approximately two MeV more bound than the other three, which are also degenerate.  ...  In each case, the reactions were chosen to have good angular-momentum matching for transfer to the low- and high-ℓ orbitals present in this valence space.  ...  The dashed lines are to guide the eye and the 0g 7/2 data with open symbols have been adjusted using an approximation discussed in the text.  ... 
arXiv:2106.01848v1 fatcat:lkiyie2vwvfnnifzsm2cur2mhi
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