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Mapper: an intelligent restriction mapping tool

J. A. Inglehart, P. C. Nelson, Y. Zou
1998 Bioinformatics  
Motivation: To determine the most powerful artificial intelligence techniques for automated restriction mapping, and use them to create a powerful multiple-enzyme restriction mapping tool.  ...  Additional experimentation led to the development of an input preprocessing module which significantly speeds up searches, and an output post-processing module which enables users to analyze large solution  ...  The authors are indebted to Steven Weaver and Donald Morrison of the University of Illinois at Chicago's Laboratory of Molecular Biology, who provided domain expertise in DNA restriction mapping, and to  ... 
doi:10.1093/bioinformatics/14.2.101 pmid:9545441 fatcat:lllpwl3fk5frzm7or63qny46yq

An EM-type Algorithm for Ordered Restriction Map Alignment

Hirotada Kobayashi, Hiroshi Imai
1999 Genome Informatics Series  
In this paper, we formulate the problem on the basis of the statistical maximum likelihood estimate, and propose a new efficient local search algorithm for this problem, by applying the Expectation-Maximization  ...  Our algorithm works well for a lot of sets of simulated data, some of which we believe more difficult than the actual cases.  ...  Acknowledgement This work was supported in part by the Grant-in-Aid for Scientific Research on Priority Areas , "Genome Science" from the Ministry of Ed ucation, Science, Sports and Culture of Japan.  ... 
doi:10.11234/gi1990.10.62 fatcat:vzeidp6yyfgerez3svxtnkrnzq

AGORA: Assembly Guided by Optical Restriction Alignment

Henry C Lin, Steve Goldstein, Lee Mendelowitz, Shiguo Zhou, Joshua Wetzel, David C Schwartz, Mihai Pop
2012 BMC Bioinformatics  
Prior work has used optical maps for validating assemblies and scaffolding contigs, after an initial assembly has been produced.  ...  Lastly, we show that a proper choice of restriction enzyme for the optical map may substantially improve the quality of the final assembly.  ...  Acknowledgements We would like to acknowledge Arthur Delcher for useful discussions.  ... 
doi:10.1186/1471-2105-13-189 pmid:22856673 pmcid:PMC3431216 fatcat:wzv42krzsvhgpm6pdk2ijtj7xy

Pattern-Guided Association Rule Mining for Complex Ontology Alignment

Beatriz Lima, Daniel Faria, Catia Pesquita
2021 International Semantic Web Conference  
This approach reduces the ARM search space, and enables the application of tailored semantic filtering algorithms for refining the mappings.  ...  Yet, most ontology alignment algorithms are restricted to finding simple equivalences between ontology entities.  ...  For each complex alignment pattern, an individual pattern matching algorithm iterates through the set of shared individuals, and, for each individual, it searches the hash-table data structures containing  ... 
dblp:conf/semweb/LimaFP21 fatcat:5gun73h4s5bb5bzrb35pvaxfvq

Dynamic Graph-Search Algorithm for Global Path Planning in Presence of Hazardous Weather

M. Garcia, A. Viguria, A. Ollero
2012 Journal of Intelligent and Robotic Systems  
It is also explained how to adapt graph search algorithms to be used for 3D trajectories with UAVs, and which design considerations should be taken into account (for example the discretization of the airspace  ...  Also, an extension of the Lazy Theta* algorithm is presented; a dynamic algorithm that calculates the trajectory while the weather hazards information is updated.  ...  Miguel Angel Trujillo for his unselfish help during the development of the experiments.  ... 
doi:10.1007/s10846-012-9704-7 fatcat:zva475hdsbbxnhhjcc54ib2d54

Solving string constraints lazily

Pieter Hooimeijer, Westley Weimer
2010 Proceedings of the IEEE/ACM international conference on Automated software engineering - ASE '10  
Our algorithm performs an explicit search for a satisfying assignment; the search space is constructed lazily based on an automata representation of the constraints.  ...  We present a constraint solving algorithm for equations over string variables. We focus on scalability with regard to the size of the input constraints.  ...  The search procedure performs an explicit search for satisfying assignments.  ... 
doi:10.1145/1858996.1859080 dblp:conf/kbse/HooimeijerW10 fatcat:3a53gpnl4bee5guzg46c63gsdi

Verifying Geostatistical Travel Time Properties on Routing Networks

Renaud De Landtsheer, Christophe Ponsard
2016 Proceedings of 5th the International Conference on Operations Research and Enterprise Systems  
It details our progress on developing efficient algorithmic modules to verifying such properties. We have applied our algorithms on the medical emergency infrastructures deployed in Belgium.  ...  We thanks Market-IP for sharing their fully featured maps and Raphael Michel for sharing his expertise on the Belgian emergency medical care.  ...  It can be used both for point to point search and for one-to-many exploration while other more efficient variants such as the A* (Hart, 1968) are focusing on directed search, and are restricted to point-to-point  ... 
doi:10.5220/0005794403960401 dblp:conf/icores/LandtsheerP16 fatcat:vqbfqrncize43nvc3j3xpyxnrm

FAST AND CHEAP GENOME WIDE HAPLOTYPE CONSTRUCTION VIA OPTICAL MAPPING

T.S. ANANTHARAMAN, V. MYSORE, B. MISHRA
2004 Biocomputing 2005  
We describe an efficient algorithm to construct genome wide haplotype restriction maps of an individual by aligning single molecule DNA fragments collected with Optical Mapping technology.  ...  The algorithms were tested by constructing the first genome wide haplotype restriction map of the microbe T. pseudoana, as well as constructing a haplotype restriction map of a 120 Mb region of Human chromosome  ...  Each DNA fragment is further mapped by cleavage with a restriction enzyme of choice and imaged by an imaging algorithm to produce an ordered sequence of "restriction fragment lengths" or equivalently,  ... 
doi:10.1142/9789812702456_0037 fatcat:zq2ihgkrmbdqti2rs5eqwbanpu

Improving computational efficiency for RNA secondary structure prediction via data-adaptive alignment constraints

Angela D'Orazio, Gaurav Sharma
2008 2008 IEEE International Workshop on Genomic Signal Processing and Statistics  
In this paper, a new, principled method for restricting the alignment search space in Dynalign [1] is introduced.  ...  In addition to dynamic programming, practical algorithms utilize heuristics to restrict the search space and further reduce time and memory requirements.  ...  The speed of this algorithm is still problematic, however, especially considering the time to search an entire genome for novel ncRNA.  ... 
doi:10.1109/gensips.2008.4555679 fatcat:3rkonut7enchvpwgxpqhtri4py

Learning semantically-annotated routes for context-aware recommendations on map navigation systems

Jose A. Mocholi, Javier Jaen, Kamil Krynicki, Alejandro Catala, Artzai Picón, Alejandro Cadenas
2012 Applied Soft Computing  
Besides, this section also presents the results of an empirical comparison between two well known search algorithms that have been widely used in the literature and the one proposed in this paper.  ...  Learning semantically-annotated routes for context-aware recommendations on map navigation systems. Applied Soft Computing. 12(9):3088-3098.  ...  In Figure 5 it can be seen how the routes obtained from the algorithm for a given restriction set are displayed on the map.  ... 
doi:10.1016/j.asoc.2012.05.010 fatcat:mccsfnqdcjbixhxipyf5w7b63q

ScienScan – An Efficient Visualization and Browsing Tool for Academic Search [chapter]

Daniil Mirylenka, Andrea Passerini
2013 Lecture Notes in Computer Science  
In this paper we present ScienScan 1 -a browsing and visualization tool for academic search. The tool operates in real time by post-processing the query results returned by an academic search engine.  ...  ScienScan discovers topics in the search results and summarizes them in the form of a concise hierarchical topic map.  ...  This research was partially supported by grant PRIN 2009LNP494 (Statistical Relational Learning: Algorithms and Applications) from Italian Ministry of University and Research.  ... 
doi:10.1007/978-3-642-40994-3_51 fatcat:bnfbmk3w75am7anlopsokr7wxy

StrSolve: solving string constraints lazily

Pieter Hooimeijer, Westley Weimer
2012 Automated Software Engineering : An International Journal  
Our approach performs an explicit search for a satisfying assignment, but constructs the search space lazily based on an automata representation.  ...  We find that our prototype is, on average, several orders of magnitude faster than the fastest existing approaches, and present evidence that our lazy search space enumeration accounts for most of that  ...  We achieve this by treating the constraint solving problem as an explicit search problem. A key feature of our algorithm is that we instantiate the search space in an on-demand fashion.  ... 
doi:10.1007/s10515-012-0111-x fatcat:s7qpi5zzv5fotbs4xntvksyhpa

Local Stereo Matching Using Combined Matching Cost and Adaptive Cost Aggregation

2015 KSII Transactions on Internet and Information Systems  
In this paper, a novel fractal coding algorithm with motion-vector-field-based motion estimation for depth map sequence is proposed.  ...  We firstly add pre-search restriction to rule the improper domain blocks out of the matching search process so that the number of blocks involved in the search process can be restricted to a smaller size  ...  The pre-search restriction algorithm is outlined in the pseudo-code as follows.  ... 
doi:10.3837/tiis.2015.01.013 fatcat:i6mxkea6szc4rmlbre2rnnur2a

Data association in stochastic mapping using the joint compatibility test

J. Neira, J.D. Tardos
2001 IEEE Transactions on Robotics and Automation  
We show experimentally that this restrictive criterion can be used to efficiently search for the best solution to data association.  ...  In this paper, we address the problem of robust data association for simultaneous vehicle localization and map building.  ...  We show experimentally that this restrictive criterion can be used to efficiently search for the best solution to data association.  ... 
doi:10.1109/70.976019 fatcat:mzgh6zoh6rcvtmie476hzkx4vy

Shortest path and vehicle trajectory aided map-matching for low frequency GPS data

Mohammed Quddus, Simon Washington
2015 Transportation Research Part C: Emerging Technologies  
The well-known A ⁄ search algorithm is employed to derive the shortest path between two points while taking into account both link connectivity and turn restrictions at junctions.  ...  Map-matching algorithms that utilise road segment connectivity along with other data (i.e. position, speed and heading) in the process of map-matching are normally suitable for high frequency (1 Hz or  ...  The author takes full responsibility for the content of the paper and any errors or omissions. Research data for this paper are available on request from Mohammed Quddus (m.a.quddus@lboro.ac.uk).  ... 
doi:10.1016/j.trc.2015.02.017 fatcat:zmpxg3yz3fhl7g4jtho4h27ztu
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