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DrML: Probabilistic Modeling of Gene Duplications

Paweł Górecki, Oliver Eulenstein
2014 Journal of Computational Biology  
The program implements novel algorithms that efficiently infer most likely scenarios of gene duplication and loss events.  ...  DrML is a software program for inferring evolutionary scenarios from a gene tree and a species tree with speciation time estimates that is based on a general maximum likelihood model.  ...  Pawe1 Górecki and Oliver Eulenstein were supported by a grant from NCN (2011/01/B/ST6/02777). Oliver Eulenstein was supported in part by NSF awards 0830012 and 10117189.  ... 
doi:10.1089/cmb.2013.0078 pmid:24073895 pmcid:PMC3880059 fatcat:lm3fixxtqba4vhsggfyfmetr2m

WCET-driven branch prediction aware code positioning

Sascha Plazar, Jan Kleinsorge, Heiko Falk, Peter Marwedel
2011 Proceedings of the 14th international conference on Compilers, architectures and synthesis for embedded systems - CASES '11  
In the past decades, embedded system designers moved from simple, predictable system designs towards complex systems equipped with caches, branch prediction units and speculative execution.  ...  The ILP models the worst-case execution path (WCEP) of a program and takes branch prediction effects into account.  ...  A special thank also goes to the Computer Engineering and Networks Laboratory (TIK) of the Swiss Federal Institute of Technology Zurich (ETHZ) for supplying the PISA framework.  ... 
doi:10.1145/2038698.2038724 dblp:conf/cases/PlazarKFM11 fatcat:vqtpwx53kra5jkmldihe2i62eu

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses

Pawel Górecki, Gordon J Burleigh, Oliver Eulenstein
2011 BMC Bioinformatics  
Results: We introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths.  ...  We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model.  ...  Acknowledgements Financial support was partially provided by MNiSW grant N301 065236 and by NSF awards #0830012 and #1017189.  ... 
doi:10.1186/1471-2105-12-s1-s15 pmid:21342544 pmcid:PMC3044269 fatcat:q7sxcsqdpvdwdbp2vosqgx7jri

Combining Metaheuristics and Exact Algorithms in Combinatorial Optimization: A Survey and Classification [chapter]

Jakob Puchinger, Günther R. Raidl
2005 Lecture Notes in Computer Science  
Among the exact methods are branch-and-bound (B&B), dynamic programming, Lagrangian relaxation based methods, and linear and integer programming  ...  Altogether, the surveyed work on combinations of exact algorithms and metaheuristics documents the usefulness and strong potential of this research direction.  ...  B&B is used as an operator embedded in the evolutionary algorithm.  ... 
doi:10.1007/11499305_5 fatcat:z4rpx5szfjayhe7sningqweymm

Page 4360 of Mathematical Reviews Vol. , Issue 99f [page]

1999 Mathematical Reviews  
These relaxations are embedded within a globally convergent branch-and-bound algorithm that additionally incorporates certain range-reduction strategies and a new branching variable selection procedure  ...  Our approach combines a semidefin- ite relaxation with a cutting plane technique, and is applied in a branch and bound setting.  ... 

Finding consensus trees by evolutionary, variable neighborhood search, and hybrid algorithms

Sandro Pirkwieser, Günther R. Raidl
2008 Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08  
To find fully resolved (binary) consensus trees of high quality, we consider the fine-grained TreeRank similarity measure and extend a previously presented evolutionary algorithm (EA) to a memetic algorithm  ...  Furthermore, we propose a variable neighborhood search (VNS) with an embedded variable neighborhood descent (VND) based on the same neighborhood structures.  ...  A previously presented evolutionary algorithm using the fine-grained TreeRank similarity measure has been extended to several memetic algorithm variants by embedding a randomized local search utilizing  ... 
doi:10.1145/1389095.1389152 dblp:conf/gecco/PirkwieserR08 fatcat:lp2mgqrimzeebgelyzrp5dgqlu

Certified Global Minima for a Benchmark of Difficult Optimization Problems [article]

Charlie Vanaret, Jean-Baptiste Gotteland, Nicolas Durand, Jean-Marc Alliot
2020 arXiv   pre-print
The global optima that we report have been numerically certified using Charibde (Vanaret et al., 2013), a hybrid algorithm that combines an evolutionary algorithm and interval-based methods.  ...  We provide the global optimization community with new optimality proofs for six deceptive benchmark functions (five bound-constrained functions and one nonlinearly constrained problem).  ...  Charibde combines an Interval Branch and Contract algorithm and a Differential Evolution algorithm in a cooperative way: neither of the algorithms is embedded within the other, but they run in parallel  ... 
arXiv:2003.09867v1 fatcat:jpjx5dagpveataqbz66bht5nh4

Evolutionary White-Box Software Test with the EvoTest Framework: A Progress Report

Hamilton Gross, Peter M. Kruse, Joachim Wegener, Tanja Vos
2009 2009 International Conference on Software Testing, Verification, and Validation Workshops  
Four case studies, each consisting of an embedded software module from the automotive industry implemented in the C language, were evaluated with the tool.  ...  Evolutionary white-box software testing has been extensively researched but is not yet applied in industry.  ...  ACKNOWLEDGMENT Many thanks go to Arthur Baars, Department of Information Systems and Computation, Technical University of Valencia, Spain, for assistance in the preparation of this paper and for support  ... 
doi:10.1109/icstw.2009.38 dblp:conf/icst/GrossKWV09 fatcat:odcogmng6felvjei4ij33xosqq

Hybridizing exact methods and metaheuristics: A taxonomy

L. Jourdan, M. Basseur, E.-G. Talbi
2009 European Journal of Operational Research  
Then we recall and complement the proposed grammar and provide an annotated bibliography.  ...  Indeed, more and more papers about cooperation between heuristics and exact techniques are published.  ...  The alpha branch and bound algorithm is a global optimization algorithm based on a branch and bound algorithm.  ... 
doi:10.1016/j.ejor.2007.07.035 fatcat:uq3aphcfqbgujf5idpcdqxd66i

Globally Convergent Particle Swarm Optimization via Branch-and-Bound

Zaiyong Tang, Kallol Kumar Bagchi
2010 Computer and Information Science  
We propose to combine the branch-and-bound framework with the particle swarm optimization algorithm.  ...  We have developed and implemented the BB-PSO algorithm that combines the efficiency of PSO and effectiveness of the branch-and-bound method.  ...  achieved through the branch and bound framework within which PSO operates.  ... 
doi:10.5539/cis.v3n4p60 fatcat:l65zqarn6vhnfdu3fg6gp3qnv4

A Survey Of Discrete Facility Location Problems

Z. Ulukan, E. Demircioğlu
2015 Zenodo  
as transportation, distribution, production, supply chain decisions and telecommunication.  ...  problems that have been studied, indicating how they are formulated and what are proposed by researchers to tackle the problem.  ...  Ulukan, Z. and Demircioğlu, E. are with Industrial Engineering Department, Galatasaray University, Istanbul (e-mail:,  ... 
doi:10.5281/zenodo.1108651 fatcat:svz4w677anchhewav4pf6qxwjq

Addition of Darwin's Third Dimension to Phyletic Trees

Theodora Pinou, Tamar Schlick, Bin Li, H.G. Dowling
1996 Journal of Theoretical Biology  
Second, linear connections are added to suggest a visual representation of the differing evolutionary trajectories of the organisms involved on the basis of a 2D tree algorithm.  ...  A three-dimensional (3D) approach for visualizing the phyletic relationship of living animals is proposed and developed as an alternative to current two-dimensional (2D) evolutionary trees.  ...  Suse Broyde for introducing the group of authors to one another and inspiring this collaboration, and Mr.  ... 
doi:10.1006/jtbi.1996.0191 pmid:8944896 fatcat:f3jyy5maoja2fbtrjhxgarrq54

A Unified View on Hybrid Metaheuristics [chapter]

Günther R. Raidl
2006 Lecture Notes in Computer Science  
Manifold possibilities of hybridizing individual metaheuristics with each other and/or with algorithms from other fields exist.  ...  A large number of publications documents the benefits and great success of such hybrids.  ...  Denzinger and Offermann [27] presented a similar multi-agent based approach for achieving cooperation between search-systems with different search paradigms, such as evolutionary algorithms and branch-and-bound  ... 
doi:10.1007/11890584_1 fatcat:opiskaru25gqpajnmmdua7b6uu

Parallel and Distributed Optimization of Dynamic Data Structures for Multimedia Embedded Systems [chapter]

José L. Risco-Martín, David Atienza, J. Ignacio Hidalgo, Juan Lanchares
2010 Studies in Computational Intelligence  
We propose a parallel Multi-Objective Evolutionary Algorithm (MOEA) which combines NSGA-II and SPEA2.  ...  In this work, we propose a method that uses parallel processing and evolutionary computation to explore DDTs in the design of embedded applications.  ...  We explore several classical Multi-Objective Evolutionary Algorithms (MOEA) [11] and propose an algorithm which combines NSGA-II and SPEA2 within a DEVS/SOA framework.  ... 
doi:10.1007/978-3-642-10675-0_12 fatcat:drjtcctg3jc3rnftrpgujw4fjq

Preventing Premature Convergence and Proving the Optimality in Evolutionary Algorithms [chapter]

Charlie Vanaret, Jean-Baptiste Gotteland, Nicolas Durand, Jean-Marc Alliot
2014 Lecture Notes in Computer Science  
The contribution of this paper is a hybrid algorithm called Charibde in which a particular EA, Differential Evolution, cooperates with a Branch and Bound algorithm endowed with interval propagation techniques  ...  Evolutionary Algorithms (EA) usually carry out an efficient exploration of the search-space, but get often trapped in local minima and do not prove the optimality of the solution.  ...  Few approaches attempted to hybridize EA and Branch and Bound algorithms in which lower bounds are computed using Interval Analysis. Integrative methods embed one algorithm within the other.  ... 
doi:10.1007/978-3-319-11683-9_3 fatcat:o2ardasw5vd5zlrrotyamcvubu
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