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String Matching with Variable Length Gaps [chapter]

Philip Bille, Inge Li Gørtz, Hjalte Wedel Vildhøj, David Kofoed Wind
2010 Lecture Notes in Computer Science  
We consider string matching with variable length gaps.  ...  Given a string T and a pattern P consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending positions of substrings in  ...  Hence, a variable length gap g{a, b}, represented by a constant length expression in P , is translated into a regular expression of length Ω(σb).  ... 
doi:10.1007/978-3-642-16321-0_40 fatcat:kdas2lruazgdzbru2cnlue7qoy

String matching with variable length gaps

Philip Bille, Inge Li Gørtz, Hjalte Wedel Vildhøj, David Kofoed Wind
2012 Theoretical Computer Science  
We consider string matching with variable length gaps.  ...  Given a string T and a pattern P consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending positions of substrings in  ...  Hence, a variable length gap g{a, b}, represented by a constant length expression in P, is translated into a regular expression of length Ω(σ b).  ... 
doi:10.1016/j.tcs.2012.03.029 fatcat:v77gdbj225ggfbiogabqlxvyma

String Matching with Variable Length Gaps [article]

Philip Bille, Inge Li Goertz, Hjalte Wedel Vildhøj, David Kofoed Wind
2011 arXiv   pre-print
We consider string matching with variable length gaps.  ...  Given a string T and a pattern P consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending positions of substrings in  ...  Hence, a variable length gap g{a, b}, represented by a constant length expression in P , is translated into a regular expression of length Ω(σb).  ... 
arXiv:1110.2893v1 fatcat:zofasbe2mjfunakohsyn3dr3va

On the limited role of target onset in the gap task: Support for the motor-preparation hypothesis

Martin Rolfs, Françoise Vitu
2007 Journal of Vision  
Analyses of anticipations and regular-latency errors corroborated this view.  ...  In Experiment 3, we manipulated target onset and target uncertainty (two, four, or eight potential target locations) in gap and overlap tasks.  ...  Fixation offset (gap vs. overlap) and target onset (yes vs. no) were orthogonally manipulated as independent variables within each block of trials, resulting in four conditions (gap target onset, gap no  ... 
doi:10.1167/7.10.7 pmid:17997676 fatcat:bexv6fyn7zhczlpfndaedmwdpa

The 3of5 web application for complex and comprehensive pattern matching in protein sequences

Markus Seiler, Alexander Mehrle, Annemarie Poustka, Stefan Wiemann
2006 BMC Bioinformatics  
The n-of-m pattern type offers an improved accuracy for pattern matching in combination with the ability to find all solutions, without compromising the user friendliness of regular expression terms.  ...  The n-of-m pattern type can be combined with common regular expression terms and thus also allows for a comprehensive description of complex patterns. 3of5 increases the fidelity of pattern matching and  ...  This work was supported by the German Federal Ministry of Education and Research (BMBF) as project within the National Genome Research Network (NGFN) with grant 01GR0420.  ... 
doi:10.1186/1471-2105-7-144 pmid:16542452 pmcid:PMC1523217 fatcat:kmteezpxqbg5tibehifuxzcslq

An Efficient Optimization Algorithm for Structured Sparse CCA, with Applications to eQTL Mapping

Xi Chen, Han Liu
2011 Statistics in Biosciences  
Our optimization algorithm is based on a general excessive gap optimization framework and can scale up to millions of variables.  ...  In this paper we develop an efficient optimization algorithm for solving canonical correlation analysis (CCA) with complex structured-sparsity-inducing penalties, including overlapping-group-lasso penalty  ...  Carbonell for the helpful discussion on the excessive gap methods and related first-order methods.  ... 
doi:10.1007/s12561-011-9048-z fatcat:sgqqjkdanbglbexchkpgnwwdne

Exploring medical expressions used by consumers and the media: an emerging view of consumer health vocabularies

Tony Tse, Dagobert Soergel
2003 AMIA Annual Symposium Proceedings  
Healthcare consumers often have difficulty expressing and understanding medical concepts.  ...  While 80% conceptual overlap was found between closely mapped lay (consumer and mediator) and technical (professional) medical terms, about half of these overlapping concepts contained lay forms different  ...  The frequency distribution of expressive variability within each vocabulary follows a Zipf-type curve, with the majority of concepts represented by a single form.  ... 
pmid:14728258 pmcid:PMC1479921 fatcat:oo3vrtkxefgp5hkgq5snjdkasy

Timing during transitions in Bengalese finch song: implications for motor sequencing

Todd W. Troyer, Michael S. Brainard, Kristofer E. Bouchard
2017 Journal of Neurophysiology  
In agreement with previous studies, we found that more probable transitions at divergence points occur with shorter intersyllable gaps.  ...  Together, our data suggest that syllable selection happens early during the gap, with gap timing determined chiefly by the latency to syllable initiation.  ...  This means that the gap length distributions for high-and low-probability transitions have very little overlap.  ... 
doi:10.1152/jn.00296.2017 pmid:28637816 fatcat:75t47bnfcncwha4ckwn32dwtmq

Shrinking of a condensed fermionic cloud in a trap approaching the Bose-Einstein condensation limit

A. Perali, P. Pieri, G. C. Strinati
2003 Physical Review A. Atomic, Molecular, and Optical Physics  
We find a significant decrease of the size of the atomic cloud as it evolves from the weak-coupling (BCS) regime of overlapping Cooper pairs to the strong-coupling (Bose-Einstein) regime of non-overlapping  ...  Most significantly, we find a pronounced increase of the value of the density at the center of the trap (even by an order of magnitude) when evolving between the two regimes.  ...  states, and then regularizing the ensuing ultraviolet divergence of the gap equation in terms of the scattering length a F of the associated fermionic twobody problem ͓10,11͔.  ... 
doi:10.1103/physreva.68.031601 fatcat:jlfcyi5p3bfehphaf4xsklcbl4

Bayesian Classifier for Anchored Protein Sorting Discovery

Fan Zhang, Jianjun Hu
2009 2009 IEEE International Conference on Bioinformatics and Biomedicine  
in which a highly conserved anchor is present along with a less conserved motif regions.  ...  Transportation of these proteins from their synthesis sites to their target locations within or outside of the cell is precisely controlled by protein sorting signals.  ...  We appreciate the discussion with other members of the Machine Learning and Evolutionary Laboratory at USC. The web server for this program will be made available at http://mleg.cse.sc.edu/sortmotif.  ... 
doi:10.1109/bibm.2009.43 dblp:conf/bibm/ZhangH09 fatcat:ebijbygsybfchmt2ywnmrdq37a

Defect layer method to capture effect of gaps and overlaps in variable stiffness laminates made by Automated Fiber Placement

Kazem Fayazbakhsh, Mahdi Arian Nik, Damiano Pasini, Larry Lessard
2013 Composite structures  
Laminates with variable stiffness design can be manufactured with Automated Fiber Placement (AFP) technology.  ...  Then, a methodology is developed to locate gaps and overlaps and calculate their area percentages.  ...  We introduce here a defect layer, which can be a regular composite material with an embedded defect (gap or overlap).  ... 
doi:10.1016/j.compstruct.2012.10.031 fatcat:6zsthldz7zfbrgf2u4hkypyisy

SMOTIF: efficient structured pattern and profile motif search

Yongqiang Zhang, Mohammed J Zaki
2006 Algorithms for Molecular Biology  
A structured motif allows variable length gaps between several components, where each component is a simple motif, which allows either no gaps or only fixed length gaps.  ...  It can effectively search for LTR retrotransposons and is well suited to searching for motifs with long range gaps.  ...  Anrep [3, 4] provides a unified biosequence pattern representation by using network expressions with spacers, where a network expression is a regular expression without Kleene closure.  ... 
doi:10.1186/1748-7188-1-22 pmid:17118189 pmcid:PMC1679804 fatcat:npasf5kn55el7fnjoniuxlbuda

What neural pathways mediate express saccades?

Marc A. Sommer, Peter H. Schiller, Robert M. McPeek
1993 Behavioral and Brain Sciences  
This target article puts together pieces of experimental evidence in oculomotor and related research -with special emphasis on the express saccade -to enhance our present understanding of the coordination  ...  interactive "skywriting" discussion with the world psychological community.  ...  The proposed distribution of saccade latencies into regular (R), fast regular (FR), and express (E) populations, depending on overlap or gap length. Figure 2 ( 2 Wenban-Smith).  ... 
doi:10.1017/s0140525x00031824 fatcat:kjfqazq4zjhqrk7krgxb4xyl7i

Express saccades and visual attention

B. Fischer, H. Weber
1993 Behavioral and Brain Sciences  
This target article puts together pieces of experimental evidence in oculomotor and related research -with special emphasis on the express saccade -to enhance our present understanding of the coordination  ...  interactive "skywriting" discussion with the world psychological community.  ...  The proposed distribution of saccade latencies into regular (R), fast regular (FR), and express (E) populations, depending on overlap or gap length. Figure 2 ( 2 Wenban-Smith).  ... 
doi:10.1017/s0140525x00031575 fatcat:z6co6bds6fgvppgxpk7jz2vbku

Partial Enumeration and Curvature Regularization

Carl Olsson, Johannes Ulen, Yuri Boykov, Vladimir Kolmogorov
2013 2013 IEEE International Conference on Computer Vision  
Our main application of interest is curvature regularization.  ...  Energies with high-order non-submodular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard.  ...  Unlike length or squared curvature regularization, this term does not add shrinking or ballooning bias.  ... 
doi:10.1109/iccv.2013.365 dblp:conf/iccv/OlssonUBK13 fatcat:iyrvh6cecfg7fdv5tnu6vnck2u
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