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A versatile divide and conquer technique for optimal string alignment

David R. Powell, Lloyd Allison, Trevor I. Dix
1999 Information Processing Letters  
Common string alignment algorithms such as the basic dynamic programming algorithm (DPA) and the time efficient Ukkonen algorithm use quadratic space to determine an alignment between two strings.  ...  In this paper we present a technique that can be applied to these algorithms to obtain an alignment using only linear space, while having little or no effect on the time complexity.  ...  In this paper we briefly discuss the basic DPA and Hirschberg's [8] divide and conquer algorithm that allows the DPA to compute an alignment in O(n) space.  ... 
doi:10.1016/s0020-0190(99)00053-8 fatcat:cz3plijqzvhj7fyhmk34pbfjue

Large multiple sequence alignments with a root-to-leaf regressive method

Edgar Garriga, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, Cedric Notredame
2019 Nature Biotechnology  
It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity.  ...  Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive  ...  Riddihough for revisions and comments on the manuscript and O. Gascuel for suggestions. Europe PMC Funders Author Manuscripts Europe PMC Funders Author Manuscripts  ... 
doi:10.1038/s41587-019-0333-6 pmid:31792410 pmcid:PMC6894943 fatcat:h3pgl3fwqnbszfvud6sfsl4pzq

EasyFJP: Providing hybrid parallelism as a concern for divide and conquer java applications

Cristian Mateos, Alejandro Zunino, Mat´ıas Hirsch
2013 Computer Science and Information Systems  
Finally, EasyFJP relies on PaaC by means of source code generation techniques to wire applications and parallel-specific code together.  ...  In this paper, we present EasyFJP, an approach that implicitly exploits parallelism in Java applications based on the concept of fork-join synchronization pattern, a simple but effective abstraction for  ...  , but by proposing a simpler approach to PaaC for a family of applications, i.e., divide and conquer codes.  ... 
doi:10.2298/csis120712021m fatcat:opgqu3ty75etxjjnls72hl6w6y

Nomadic genetic algorithm for multiple sequence alignment (MSANGA)

S. Siva Sathya, S. Kuppuswami, K. Syam Babu
2009 International Journal of Adaptive and Innovative Systems  
of NGA over SGA and all other tools to produce quality alignment at a faster rate.  ...  Genetic algorithms (GA) are adaptive search procedures that try to produce a globally optimum solution for problems of huge search space.  ...  Divide and conquer multiple sequence alignment (DCA) is a program for producing fast, high quality simultaneous MSAs of amino acid, RNA, or DNA sequences.  ... 
doi:10.1504/ijais.2009.022002 fatcat:k3edjd4qkvexvnz4hthusz3jsa

Parallel sequence alignment in limited space

J A Grice, R Hughey, D Speck
1995 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
While the innovative O(n2)-time and O(n)-space serial algorithm has been parallelized for multiple-instruction, multiple-data stream (MIMD) computers with only a communication-time slowdown, typically  ...  Unfortunately, the twin problem of sequence alignment, finding the optimal character-by-character correspondence between two sequences, is more complicated.  ...  Acknowledgments We especially thank Kevin Karplus for his many useful discussions and the anonymous reviewers for their helpful comments.  ... 
pmid:7584431 fatcat:vv6yu3eh55fvzij6e2sg2sqxcq

An approach for non-intrusively adding malleable fork/join parallelism into ordinary JavaBean compliant applications

Cristian Mateos, Alejandro Zunino, Marcelo Campo
2010 Computer languages, systems & structures  
In this paper, we present EasyFJP, a new approach for semi-automatically injecting parallelism into sequential Java applications that offers a convenient balance to these four aspects.  ...  There is a substantial body of efforts in the form of parallel libraries and frameworks that supply developers with programming tools to exploit parallelism in their applications.  ...  Acknowledgments We thank Cristian Clasadonte for his good predisposition and valuable help managing the computing infrastructure used for conducting the experiments described in this paper.  ... 
doi:10.1016/j.cl.2009.12.003 fatcat:235q7ihgpnbdph7ggx4gihgray

Aggregating Heterogeneous Sensor Ontologies with Fuzzy Debate Mechanism

Xingsi Xue, Xiaojing Wu, Jie Zhang, Lingyu Zhang, Hai Zhu, Guojun Mao, James Ying
2021 Security and Communication Networks  
The robustness and effectiveness of the proposed method are proved by comparing it with the advanced ontology matching techniques.  ...  The testing cases from Bibliographic data which is furnished by the Ontology Alignment Evaluation Initiative (OAEI) and six sensor ontology matching tasks are used to evaluate the performance of our scheme  ...  Acknowledgments is work was supported by the Natural Science Foundation of Fujian Province (No. 2020J01875) and the National Natural Science Foundation of China (Nos. 61773415, 61801527, and 61103143).  ... 
doi:10.1155/2021/2878684 fatcat:lqrm6keknfhkbff6d2mx3yv7p4

Ontology Matching: State of the Art and Future Challenges

P. Shvaiko, J. Euzenat
2013 IEEE Transactions on Knowledge and Data Engineering  
These results show a measurable improvement in the field, the speed of which is albeit slowing down.  ...  We conjecture that significant improvements can be obtained only by addressing important challenges for ontology matching.  ...  Falcon is an automatic divide-and-conquer approach to ontology matching [40] . It handles ontologies in RDFS and OWL.  ... 
doi:10.1109/tkde.2011.253 fatcat:kswkwny4vreyjlpf2ybpgxpmam

Efficient Conformance Checking using Approximate Alignment Computation with Tandem Repeats [article]

Daniel Reißner, Abel Armas-Cervantes, Marcello La Rosa
2022 arXiv   pre-print
Given a cost function, an alignment is optimal when it contains the least number of mismatches between a log trace and a model trace.  ...  Alignments are an established technique to compute the distance between a trace in the event log and the closest execution trace of a corresponding process model.  ...  Divide-and-conquer approaches. In divide-and-conquer approaches, the process model is split into smaller parts to speed up the computation of alignments by reducing the size of the search space.  ... 
arXiv:2004.01781v2 fatcat:rdxjmb3oxvdltnx3zc76c4hdcu

Shear-solvo defect annihilation of diblock copolymer thin films over a large area

Ye Chan Kim, Tae Joo Shin, Su-Mi Hur, Seok Joon Kwon, So Youn Kim
2019 Science Advances  
Sequential shear alignment and solvent vapor annealing generate perfectly aligned nanopatterns with a low defect density over centimeter-scale areas, outperforming previous single or sequential combinations  ...  Here, we demonstrate a new experimental strategy for defect annihilation while conserving structural order and enhancing uniformity of nanopatterns.  ...  Son at KIST for helpful communications.  ... 
doi:10.1126/sciadv.aaw3974 fatcat:46oggqtjivc3zfpvdqbnombuuq

A Spline-based Volumetric Data Modeling Framework and Its Applications [article]

Bo Li
2013 arXiv   pre-print
This methodology can represent both boundary/volumetric geometry and real volumetric physical attributes in a compact and continuous fashion.  ...  These properties make our techniques highly preferable in many physically-based applications including mechanical analysis, shape deformation and editing, virtual surgery training, etc.  ...  Combining volumetric decomposition, parameterization with trivariate splines, we successfully and effectively solve a variety of problems in the areas of geometric shape design and modeling.  ... 
arXiv:1308.0869v1 fatcat:hiscx3juzzgivfzjdjcahp7une

Aligned Cluster Analysis for temporal segmentation of human motion

Feng Zhou, Fernando De la Torre, Jessica K. Hodgins
2008 2008 8th IEEE International Conference on Automatic Face & Gesture Recognition  
Temporal segmentation of human motion into actions is a crucial step for understanding and building computational models of human motion. Several issues contribute to the challenge of this task.  ...  In particular, this paper proposes Aligned Cluster Analysis (ACA), a robust method to temporally segment streams of motion capture data into actions.  ...  [3] developed a string-based motif-finding algorithm which allows for a user-controlled compromise between motif length and the number of motions in a motif.  ... 
doi:10.1109/afgr.2008.4813468 dblp:conf/fgr/ZhouTH08 fatcat:fhodsqak7bewnkwatvpsw3xlpi

Recent Advances in Solving the Protein Threading Problem [article]

Rumen Andonov, Jean-François Gibrat, Nikola Yanev
2007 arXiv   pre-print
In this paper, we present the diverse components of FROST, emphasizing on the recent advances in formulating and solving new versions of the PTP and on the way of solving on a computer cluster a million  ...  The fold recognition methods are promissing tools for capturing the structure of a protein by its amino acid residues sequence but their use is still restricted by the needs of huge computational resources  ...  Uberbacher and colleagues [17] , a couple of years later, described another algorithm based on a divide & conquer approach.  ... 
arXiv:0707.3750v2 fatcat:hh3s2ztm2jg5zezxarwulzjr3m

Matching large XML schemas

Erhard Rahm, Hong-Hai Do, Sabine Maßmann
2004 SIGMOD record  
The high expressive power and versatility of this schema language, in particular its type system and support for distributed schemas and namespaces, introduce new issues.  ...  Current schema matching approaches still have to improve for very large and complex schemas.  ...  We thank Phil Bernstein and Sergey Melnik for helpful comments. The second author is supported by DFG grant BIZ 6/1-1. References  ... 
doi:10.1145/1041410.1041415 fatcat:gj63vtt57vd2nmclyhh7wwaola

Interactive Reconstruction of Archaeological Fragments in a Collaborative Environment

Yifan Lu, Henry Gardner, Huidong Jin, Nianjun Liu, Rhys Hawkins, Ian Farrington
2007 9th Biennial Conference of the Australian Pattern Recognition Society on Digital Image Computing Techniques and Applications (DICTA 2007)  
A computer-aided and collaborative approach is proposed for the reconstruction of archaeological artefacts based on the boundary-matching estimation by string registration.  ...  iii Abstract The problem of reassembling archaeological artefacts from a collection of fragments that may include other fragments from several artefact has been addressed and widely studied.  ...  Acknowledgements Thanks to Supervisors Rhys Hawkins and Dr. Henry Gadner for guidance of the project.  ... 
doi:10.1109/dicta.2007.4426771 dblp:conf/dicta/LuGJLHF07 fatcat:ptf33dnwwjgixn3i7zgos3c5vy
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