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Quasi-Linear-Time Algorithm for Longest Common Circular Factor [article]

Mai Alzamel, Maxime Crochemore, Costas S. Iliopoulos, Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, Wiktor Zuba
2019 arXiv   pre-print
We introduce the Longest Common Circular Factor (LCCF) problem in which, given strings S and T of length n, we are to compute the longest factor of S whose cyclic shift occurs as a factor of T.  ...  It is a new similarity measure, an extension of the classic Longest Common Factor. We show how to solve the LCCF problem in O(n ^5 n) time.  ...  Conclusions We have presented an O(n log 5 n)-time algorithm for computing the Longest Common Circular Factor (LCCF) of two strings of length n.  ... 
arXiv:1901.11305v1 fatcat:wv63cl24p5a77n3ksyhve6dqwi

Quasi-Linear-Time Algorithm for Longest Common Circular Factor

Mai Alzamel, Maxime Crochemore, Costas S. Iliopoulos, Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Juliusz Straszynski, Tomasz Walen, Wiktor Zuba, Michael Wagner
2019 Annual Symposium on Combinatorial Pattern Matching  
We introduce the Longest Common Circular Factor (LCCF) problem in which, given strings S and T of length at most n, we are to compute the longest factor of S whose cyclic shift occurs as a factor of T  ...  It is a new similarity measure, an extension of the classic Longest Common Factor. We show how to solve the LCCF problem in O(n log 4 n) time using O(n log 2 n) space.  ...  Using Lemma 19 and a linear-time algorithm for constructing SA W and PA W (and SA Conclusions We have presented an O(n log 4 n)-time algorithm for computing the Longest Common Circular Factor (LCCF)  ... 
doi:10.4230/lipics.cpm.2019.25 dblp:conf/cpm/AlzamelCIKRRSWZ19 fatcat:wtvalihurvbchhbf7cnffw6fd4

Algorithms for determining transposons in gene sequences [article]

Yue Wang
2022 arXiv   pre-print
With the help of graph theory, we design fast algorithms for different scenarios. We also derive some results that might be of theoretical interests in combinatorics.  ...  copies, we classify the problem of determining transposons into four scenarios: (1) linear sequences without replicated genes; (2) circular sequences without replicated genes; (3) linear sequences with  ...  The author would like to thank Zhongkai Zhao for helping with designing Algorithm 1. The author would like to thank Lucas Böttcher for providing helpful comments.  ... 
arXiv:1506.02424v3 fatcat:w4njkzihwfetxgv3nuanbzrxlq

A Quasilinear-Time Algorithm for Tiling the Plane Isohedrally with a Polyomino [article]

Stefan Langerman, Andrew Winslow
2016 arXiv   pre-print
We give a O(n^2n)-time algorithm for deciding if a polyomino with n edges can tile the plane isohedrally.  ...  This improves on the O(n^18)-time algorithm of Keating and Vince and generalizes recent work by Brlek, Provençal, Fédou, and the second author.  ...  Acknowledgements The authors wish to thank anonymous reviewers for comments that improved the correctness of the paper.  ... 
arXiv:1507.02762v2 fatcat:nnkfqm63ajg53ia4v4nzsbf6da

Front Matter, Table of Contents, Preface, Conference Organization

Gonzalo Navarro, David Sankoff, Binhai Zhu, Marc Herbstritt
2018 Annual Symposium on Combinatorial Pattern Matching  
10:1-10:12 Locally Maximal Common Factors as a Tool for Efficient Dynamic String Algorithms Amihood Amir and Itai Boneh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  ...  Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications Tatsuya Akutsu, Colin de la Higuera, and Takeyuki Tamura . . . . . . . . . . . . . . . . . . . . . . .  ...  The goal is to design efficient algorithms based on the properties of these structures.  ... 
doi:10.4230/lipics.cpm.2018.0 dblp:conf/cpm/X18 fatcat:4t5f2esmfbg3xkfeyjpvxfgtk4

Motif trie: An efficient text index for pattern discovery with don't cares

Roberto Grossi, Giulia Menconi, Nadia Pisanti, Roberto Trani, Søren Vind
2018 Theoretical Computer Science  
Acknowledgement We are grateful to Giulia Punzi for having read a preliminary version of this paper.  ...  We show how to report only the maximal motifs in time linear in the size of the trie.  ...  The longest common prefix lcp(x, y) is the longest string such that x[1, | lcp(x, y)|] = y[1, | lcp(x, y)|] for any two strings x, y ∈ * .  ... 
doi:10.1016/j.tcs.2017.04.012 fatcat:piu4jjjgh5a6dnx3ioddwitesm

Two-stage reconstruction of a circular anomaly in electrical impedance tomography

Sampsa Pursiainen
2006 Inverse Problems  
This paper focuses on the development of effective reconstruction techniques for detection of a circular anomaly from an otherwise constant background.  ...  In the first stage, the ROI is determined using a quasi-Newton optimization algorithm and a smoothness prior, and in the second stage, the reconstruction is found using Markov chain Monte Carlo sampling  ...  Performing one step of the algorithm took about 15 s of CPU time.  ... 
doi:10.1088/0266-5611/22/5/010 fatcat:7gi52wkkajawjb4qnze2kske74

Topological Auto-Calibration of Central Imaging Sensors [chapter]

Ricardo Galego, Ricardo Ferreira, Alexandre Bernardino, Etienne Grossmann, José Gaspar
2013 Lecture Notes in Computer Science  
Here we show that there is a quasi-linear relationship between time-correlation and angular inter-pixel distance, considering small angles and a simple scenario encompassing one bright light on a dark  ...  The topology reconstruction algorithm is therefore based on correlating time series (pixel streams) acquired by the pixels of the moving camera.  ...  We propose to further drop this requirement for small sensors by embedding the locations in a plane up to a scale factor.  ... 
doi:10.1007/978-3-642-38628-2_56 fatcat:bgascskhbnb63hhcbdkm4o2uhu

Stability constraints in modeling of multi-planet extrasolar systems [article]

K. Gozdziewski, C. Migaszewski, A. Musielinski
2008 arXiv   pre-print
We use dynamical stability constraints and quasi-global methods of optimization. As an illustration, we present new results derived for the RV data of the Sun-like dwarfs HD 155358 and τ^1 Gruis.  ...  G. thanks the organizers of the IAU 249 symposium for the invitation and great hospitality. We are grateful to the anonymous referee for comments that improved the manuscript.  ...  Many thanks to Boud Roukema for corrections of the text. This work is supported by the Polish Ministry of Science, Grant 1P03D 021 29.  ... 
arXiv:0802.0254v1 fatcat:rocwxz6xa5gjbefipvnrnqivuu

A Combinatorial Approach to Orthogonal Placement Problems [chapter]

Gunnar W. Klau
2003 Operations Research Proceedings 2002  
computation time.  ...  Often, our new algorithms are the first exact algorithms for the respective problem variant.  ...  A more detailed look at the running time behavior of the exact algorithm provides Figure  .. The longest running time needed for a real-world example is . seconds.  ... 
doi:10.1007/978-3-642-55537-4_4 dblp:conf/or/Klau02 fatcat:jgxvmhcijbdibafixism7iami4

Identification of aeroelastic forces and static drag coefficients of a twin cable bridge stay from full-scale ambient vibration measurements

A. Acampora, J.H.G. Macdonald, C.T. Georgakis, N. Nikitas
2014 Journal of Wind Engineering and Industrial Aerodynamics  
Finally, static drag coefficients are back-calculated from the full-scale vibration measurements, for first time, with reasonable agreement with direct wind tunnel measurements.  ...  Using the Eigenvalue Realization Algorithm (ERA), the damping and stiffness matrices are identified for different vibration modes of the cables, with sufficient accuracy to identify changes in the total  ...  Acknowledgments The authors would like to thank Femern A/S and Storebaelt A/S for their financial support, without which this work would not have been possible, and Øresundsbron for their help with installing  ... 
doi:10.1016/j.jweia.2013.10.009 fatcat:x7zs5t4s7rfupgegh7mt2ikt3m

A Literature Review on Circle and Sphere Packing Problems: Models and Methodologies

Mhand Hifi, Rym M'Hallah
2009 Advances in Operations Research  
This paper reviews the most relevant literature on efficient models and methods for packing circular objects/items into Euclidean plane regions where the objects/items and regions are either two- or three-dimensional  ...  They have been tackled using various approaches-based algorithms ranging from computer-aided optimality proofs, to branch-and-bound procedures, to constructive approaches, to multi-start nonconvex minimization  ...  The second author is grateful for their support.  ... 
doi:10.1155/2009/150624 fatcat:hqzj67rderbkrlo63pewqz7v5i

Non-uniform stochastic dynamics of nanoparticle clusters at a solid–liquid interface induced by laser trapping

Itsuo Hanasaki, Chie Hosokawa
2019 Japanese Journal of Applied Physics  
The nominal diffusion coefficient is larger than the bulk at sufficiently small time scale for sufficiently high laser powers, although it decreases as a function of time because of the confinement.  ...  Tatsunori Kishimoto for technical supports.  ...  However, the longer time span for our system of interest basically gives smaller value of β due to the confinement effect and we have a limited time span on the longest side.  ... 
doi:10.7567/1347-4065/ab0887 fatcat:wamify5otfdkblh76hytop5oyi

The accuracy of prostate volume measurement from ultrasound images: A quasi-Monte Carlo simulation study using magnetic resonance imaging

David-Olivier D. Azulay, Philip Murphy, Jim Graham
2013 Computerized Medical Imaging and Graphics  
A quasi-Monte Carlo (qMC) approach is used to simulate multiple probe positions and angles within prescribed limits resulting in a range of dimensions.  ...  However, using an appropriate linear regression model, accurate volume estimates can be made using prostate diameters calculated from a single scanning plane.  ...  We have demonstrated the use of a simulation study for interrogating sources of variability in estimating prostate volumes.  ... 
doi:10.1016/j.compmedimag.2013.09.001 pmid:24119334 fatcat:vs5u5yxtmrhyhlidbnqus7e5na

Coherent wave activity in Mercury's magnetosheath

Torbjörn Sundberg, Scott A. Boardsen, David Burgess, James A. Slavin
2015 Journal of Geophysical Research - Space Physics  
Their occurrence rates maximize at the near-parallel shock, where they are present approximately 10% of the time, and where they also show their largest wave powers.  ...  Lefthanded electromagnetic ion-cyclotron waves are commonly found behind the quasi-perpendicular section of the bow shock, where they are present in ~50% of the spacecraft crossings of the magnetosheath  ...  Acknowledgements We thank MESSENGER mission, the MESSENGER Magnetometer Instrument team, and the Planetary Data System (https://pds.nasa.gov) for providing the data used in this study.  ... 
doi:10.1002/2015ja021499 fatcat:nzfepgr54zbvrhe6wskg7xente
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