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Efficiently Calculating Evolutionary Tree Measures Using SAT [chapter]

María Luisa Bonet, Katherine St. John
2009 Lecture Notes in Computer Science  
We develop techniques to calculate important measures in evolutionary biology by encoding to CNF formulas and using powerful SAT solvers.  ...  We use state-of-the-art SAT solvers to determine if the formula encoding the measure has a satisfying assignment.  ...  We use two different approaches to calculating these measures: exact calculation and an upper bound heuristic.  ... 
doi:10.1007/978-3-642-02777-2_3 fatcat:e7vxsy3yonhxrktnknjzrfi5fy

Comparison of Selection Strategies for Evolutionary Quantum Circuit Design [chapter]

André Leier, Wolfgang Banzhaf
2004 Lecture Notes in Computer Science  
In this paper we analyze different selection strategies, which are applied to the Deutsch-Jozsa problem and the 1-SAT problem using our GP system.  ...  Intermediate measurements providing a linear-tree structure [12] are disregarded. A detailed landscape analysis for landscapes regarding the 1-SAT problem has yet to be done.  ...  It was also found, that the mixing matrix can be implemented more efficiently by using simple Rx-Gates.  ... 
doi:10.1007/978-3-540-24855-2_65 fatcat:qacc6snvpzcinh37fugi3bgamy

Evolving Hogg's Quantum Algorithm Using Linear-Tree GP [chapter]

André Leier, Wolfgang Banzhaf
2003 Lecture Notes in Computer Science  
Intermediate measurements in quantum circuits compare to conditional branchings in programming languages. Due to this, quantum circuits have a natural linear-tree structure.  ...  It was applied to instances of the 1-SAT problem, resulting in evidently and "visibly" scalable quantum algorithms, which correspond to Hogg's quantum algorithm.  ...  In this way linear-tree GP naturally supports the use of measurements as an intermediate step in quantum circuits.  ... 
doi:10.1007/3-540-45105-6_48 fatcat:3ne3b32b3vdhjkvnnearxzduim

Phylogenetic Tree Reconstruction with Protein Linkage [chapter]

Junjie Yu, Henry Chi Ming Leung, Siu Ming Yiu, Yong Zhang, Francis Y. L. Chin, Nathan Hobbs, Amy Y. X. Wang
2012 Lecture Notes in Computer Science  
We also argue, by experiments, that trees with higher accuracy can be constructed by using linkage information than by using only hamming distance to measure the differences between the binary strings,  ...  We provide an efficient dynamic programming algorithm to solve the general problem in 4 and 4 time (compared to the straight-forward 4 and 4 time algorithm), depending on the versions of linkage distance  ...  Moreover, the effectiveness of these methods relies very much on the evolutionary distance measure being used.  ... 
doi:10.1007/978-3-642-30191-9_29 fatcat:gny4yhaytbabdppsenl7orsy5u

Responses of tree leaf gas exchange to elevated CO 2 combined with changes in temperature and water availability: A global synthesis

Zhaoguo Wang, Chuankuan Wang, Benjamin Poulter
2021 Global Ecology and Biogeography  
Aim: An elevated CO 2 concentration (eCO 2 ) can increase photosynthesis (A sat ) and reduce stomatal conductance (g s ); hence, it can benefit tree growth directly by increasing carbon availability and  ...  ACK N OWLED G M ENTS We thank all the researchers whose data were used in this metaanalysis. We also thank the editors, Dr Anthony P.  ...  (c) intrinsic water-use efficiency (iWUE) to eCO 2 grouped by phylogeny, leaf habit, tree age, canopy position and leaf age.  ... 
doi:10.1111/geb.13394 fatcat:o4gszrnrw5ep3dwmtboj56pjx4

Stomatal conductance and not stomatal density determines the long-term reduction in leaf transpiration of poplar in elevated CO2

Penny J. Tricker, Harriet Trewin, Olevi Kull, Graham J. J. Clarkson, Eve Eensalu, Matthew J. Tallis, Alessio Colella, C. Patrick Doncaster, Maurizio Sabatti, Gail Taylor
2005 Oecologia  
In year 5, measurements were also taken of leaf stomatal conductance (g s , lmol m À2 s À1 ), photosynthetic CO 2 fixation (A, mmol m À2 s À1 ), instantaneous water-use efficiency (A/E) and the ratio of  ...  Using a free-air CO 2 enrichment (FACE) experiment, poplar trees (Populus · euramericana clone I214) were exposed to either ambient or elevated [CO 2 ] from planting, for a 5-year period during canopy  ...  Pinel (University of Southampton) for allowing us access to unpublished results and anonymous reviewers for their helpful comments on a previous version of this manuscript.  ... 
doi:10.1007/s00442-005-0025-4 pmid:15909132 fatcat:kl2cnaglprfkbj4xh3rnkjp6oe

A Hybrid Quantum Genetic Algorithm and Local Search based DPLL for Max 3-SAT Problems

Abdesslem Layeb, Djamel-Eddine Saidouni
2014 Applied Mathematics & Information Sciences  
In this paper, we present a new framework for combining complete and incomplete methods in order to deal with the Max Sat problem.  ...  A new local search based on DPLL algorithm has been embodied in the quantum genetic algorithm leading to an efficient hybrid framework which achieves better balance between diversification and intensification  ...  Evolutionary algorithms have been applied to SAT problems. However, the use of a pure evolutionary algorithm has been unsuccessful in Max Sat problems.  ... 
doi:10.12785/amis/080109 fatcat:qmyh7erwejaovbuaxp4xe4gohi

Multi-objective Evolutionary Neural Network to Predict Graduation Success at the United States Military Academy

Gene Lesinski, Steven Corns
2018 Procedia Computer Science  
The inputs to the evolutionary neural network model are used to classify students as: graduates, late graduates, or non-graduates.  ...  The inputs to the evolutionary neural network model are used to classify students as: graduates, late graduates, or non-graduates.  ...  Evolutionary Algorithms and Multi-Objective Evolutionary Algorithms Evolutionary algorithms (EA) are a biologically inspired non-gradient optimization technique that allows the rapid and efficient exploration  ... 
doi:10.1016/j.procs.2018.10.329 fatcat:dqrfmh4eobehpfhhthhrx3la7a

Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA- Genome Oryza Species

Qun-Jie Zhang, Li-Zhi Gao
2017 G3: Genes, Genomes, Genetics  
Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes.  ...  Figure 5 5 Figure 5 Evolutionary dynamics of the OAL002 family across the eight AA-genome Oryza species. (A) Phylogenetic trees constructed using RT gene and 59-LTR sequences, respectively.  ...  A substitution rate of 1.3 • 10 28 per site per year was used to calculate insertion times (Baucom et al. 2009b; Vitte et al. 2007 ).  ... 
doi:10.1534/g3.116.037572 pmid:28413161 pmcid:PMC5473765 fatcat:lpl3vb76drbb5o72usfqpzgxpy

Automated generation of computationally hard feature models using evolutionary algorithms

Sergio Segura, José A. Parejo, Robert M. Hierons, David Benavides, Antonio Ruiz-Cortés
2014 Expert systems with applications  
In this article, we propose to model the problem of finding computationally hard feature models as an optimisation problem and we solve it using a novel evolutionary algorithm for optimised feature models  ...  Performance evaluation in this domain typically relies on the use of randomly generated feature models.  ...  This was not 1448 observed in our work in which the SAT solver was much 1449 more efficient than the CSP solver, i.e. random and 1450 evolutionary search were unable to find hard problems 1451 for SAT.  ... 
doi:10.1016/j.eswa.2013.12.028 fatcat:hcruibhleff3tdd44iphjussbi

Evolving Combinatorial Problem Instances That Are Difficult to Solve

Jano I. van Hemert
2006 Evolutionary Computation  
In this paper we demonstrate how evolutionary computation can be used to acquire difficult to solve combinatorial problem instances, thereby stress-testing the corresponding algorithms used to solve these  ...  This is the amount of nodes in the Davis-Putnum search tree, which both algorithms use.  ...  The two solvers used here, zChaff and Relsat, compete in this competition and score well. zChaff (Fu, 2004 ) is based on Chaff (Moskewicz et al., 2001) , a SAT solver that employs a particularly efficient  ... 
doi:10.1162/evco.2006.14.4.433 pmid:17109606 fatcat:togz2qqffrcptjkiwwbke42vl4

Rapid and recent evolution of LTR retrotransposons drives rice genome evolution during the speciation of AA- genome Oryza species [article]

Qun-Jie Zhang, Li-zhi Gao
2016 bioRxiv   pre-print
Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes.  ...  Sequence lengths were calculated for each retrotransposon lineage using Repeatmasker (Smit et al.)  ...  Figure 5 5 Evolutionary dynamics of the OAL002 family across the eight AAgenome Oryza species. (A) Phylogentic trees constructed using RT gene and 5' LTR sequences, respectively.  ... 
doi:10.1101/086041 fatcat:d3bfslfdlbcl3e4b4oisgeoe6y

Sussing merger trees: the impact of halo merger trees on galaxy properties in a semi-analytic model

Jaehyun Lee, Sukyoung K. Yi, Pascal J. Elahi, Peter A. Thomas, Frazer R. Pearce, Peter Behroozi, Jiaxin Han, John Helly, Intae Jung, Alexander Knebe, Yao-Yuan Mao, Julian Onions (+4 others)
2014 Monthly notices of the Royal Astronomical Society  
These differences should be carefully understood before merger trees are used as input for models of galaxy formation.  ...  We find that the z=0 galaxy properties in our model show differences between trees when using a common parameter set.  ...  PAT, CS, AK, FRP and AS organized the Sussing Merger Trees workshop at which this work was initiated.  ... 
doi:10.1093/mnras/stu2039 fatcat:oe7rjkxdabejdb4yualtg6ftlm

PhISCS-BnB: A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem [article]

Erfan Sadeqi Azer, Farid Rashidi Mehrabadi, Xuan Cindy Li, Salem Malikic, Alejandro A. Schaffer, E. Michael Gertz, Chi-Ping Day, Eva Perez-Guijarro, Kerrie Marie, Maxwell P. Lee, Glenn Merlino, Funda Ergun (+1 others)
2020 bioRxiv   pre-print
Hence, improving the efficiency of phylogenetic Comparison of PhISCS-BnB with SCITE with respect to the multi-labled tree similarity measure (MLTSM).  ...  Therefore efficient reduction of an NP-complete problem (such as PP) to max-SAT or TSP can 325 325 leverage existing software to solve the problem much more efficiently.  ... 
doi:10.1101/2020.02.06.938043 fatcat:mpacfaj7x5fhbhlyauj7c3cm6u

A Clonal Selection Algorithm Based Tabu Search for Satisfiability Problems

Abdesslem Layeb
2012 Journal of Advances in Information Technology  
In order to increase the performance of clonal selection to deal with Max Sat problem, an adaptive fitness function based on weighted clauses has been used.  ...  We present in this paper a new memetic algorithm to deal with the Max Sat problem.  ...  Evolutionary algorithms have been applied to SAT problems. However, the use of a pure evolutionary algorithm has been unsuccessful in Max Sat problems.  ... 
doi:10.4304/jait.3.2.138-146 fatcat:k7dk33lonnhkbptxsxynasvske
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