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Fuzzy Dominance Based Multi-objective GA-Simplex Hybrid Algorithms Applied to Gene Network Models [chapter]

Praveen Koduru, Sanjoy Das, Stephen Welch, Judith L. Roe
2004 Lecture Notes in Computer Science  
In this article, we apply a similar technique to estimate the parameters of a gene regulatory network for flowering time control in rice.  ...  The concept of fuzzy dominance is introduced, and a multi-objective simplex algorithm based on this concept is proposed as a part of the hybrid approach.  ...  Conclusions In this paper, we have proposed an effective approach to perform parameter estimation of gene regulatory network models.  ... 
doi:10.1007/978-3-540-24854-5_37 fatcat:4acdrerdyjfwvnjrjtioo6u7ou

A co-evolutionary hybrid algorithm for multi-objective optimization of gene regulatory network models

Praveen Koduru, Sanjoy Das, Stephen Welch, Judith L. Roe, Zenaida P. Lopez-Dee
2005 Proceedings of the 2005 conference on Genetic and evolutionary computation - GECCO '05  
We have modified the recently introduced concept of fuzzy dominance to hybridize the well-known Nelder Mead Simplex algorithm for better exploitation with a multi-objective genetic algorithm.  ...  In this paper, the parameters of a genetic network for rice flowering time control have been estimated using a multiobjective genetic algorithm approach.  ...  GENE REGULATORY NETWORK MODELS Molecular geneticists are rapidly deciphering the genomes of a great many organisms.  ... 
doi:10.1145/1068009.1068073 dblp:conf/gecco/KoduruDWRL05 fatcat:2bmpopex4bhapgwc2lbbs2ux4a

Stages of Gene Regulatory Network Inference: the Evolutionary Algorithm Role [chapter]

Alina Sirbu, Heather J., Martin Crane
2011 Evolutionary Algorithms  
Acknowledgements We wish to acknowledge the SFI/HEA Irish Centre for High-End Computing (ICHEC) for the provision of computational facilities and assistance.  ...  This work has been conducted with support from the Irish Research Council for Science Engineering and Technology EMBARK Initiative.  ...  Regulatory networks are intrinsically nonlinear systems and approaches that correctly model gene interactions are needed.  ... 
doi:10.5772/15182 fatcat:5kwdvbdzrnfythieaii3arhgxq

Evolutionary ComputationMethods for Fuzzy Decision Making on Load Dispatch Problems [chapter]

Guoli Zhang, Guangquan Zhang, Ya Gao, Jie Lu
2010 Computational Intelligence in Complex Decision Systems  
To solve load dispatch problems from day-ahead markets in power systems, a hybrid evolutionary computation method with a quasi-simplex technique, a weight point method for multi-objective programming,  ...  and a fuzzy-number-ranking-based optimization method for fuzzy multi-objective non-linear programming are developed.  ...  The reference point method is a relatively practical interactive approach to multi-objective optimization problems.  ... 
doi:10.2991/978-94-91216-29-9_11 fatcat:oy4awmn4srcktbjbhmxyezldzq

Hybridizing exact methods and metaheuristics: A taxonomy

L. Jourdan, M. Basseur, E.-G. Talbi
2009 European Journal of Operational Research  
First, we propose some natural approaches for the different schemes of cooperation encountered, and we analyse, for each model, some examples taken from the literature.  ...  In this paper, we propose to extend an existing taxonomy for hybrid methods involving heuristic approaches in order to consider cooperative schemes between exact methods and metaheuristics.  ...  [53] HRH(aB&B + CSA) (approximate, partial, specialist) parallel static Protein structure prediction [47] LTH (GA(Splx)) (approximate, partial, general) sequential Gene regulatory network models  ... 
doi:10.1016/j.ejor.2007.07.035 fatcat:uq3aphcfqbgujf5idpcdqxd66i

Computational optimization for S-type biological systems: Cockroach genetic algorithm

Shinq-Jen Wu, Cheng-Tao Wu
2013 Mathematical Biosciences  
A wide search space ([0, 100] for rate constants and [À100, 100] for kinetic orders) with random or bad initial starts are used to show the high exploration performance.  ...  Cockroaches live in nearly all habitats and survive for more than 300 million years.  ...  ] , the hybrid GA-FNN (fuzzy neural network) [45] , and the hybrid GA-PSO [46] [47] [48] .  ... 
doi:10.1016/j.mbs.2013.07.019 pmid:23927855 fatcat:puesyrd27fa43abtbobqp6gfg4

Evolutionary Dynamics in Gene Networks and Inference Algorithms

Daniel Aguilar-Hidalgo, María Lemos, Antonio Córdoba
2015 Computation  
Gene regulatory networks (GRNs) are directed networks that define interactions (links) among different genes/proteins involved in such processes.  ...  In recent years, this combination has become a powerful tool to fit models with the increasingly available experimental data.  ...  Other instances of hybrid methods are S-systems with SA [48] , GA with ANN [49] , GA with a Simplex method [43] , ANN with Fuzzy-logic [34] .  ... 
doi:10.3390/computation3010099 fatcat:f7el6e5wf5gdjdmn74buifmb7u

Evolutionary Algorithms [chapter]

David Corne, Michael A. Lones
2018 Handbook of Heuristics  
However, this flexibility goes hand in hand with a cost: the tailoring of an EA's configuration and parameters, so as to provide robust performance for a given class of tasks, is often a complex and time-consuming  ...  Particularly well-known categories of EAs include genetic algorithms (GAs), Genetic Programming (GP), and Evolution Strategies (ES).  ...  This approach proved effective for reverse engineering the regulatory rules underlying differential gene expression within tissues.  ... 
doi:10.1007/978-3-319-07153-4_27-1 fatcat:fgaedapskbhkzh4h6riitzn3x4

Mathematical Modelling as a Tool for Optimized PHA Production

M. Novak
2015 Chemical and Biochemical Engineering Quarterly  
The modeling ability and the optimization power of hybrid ANN-GA model provided higher accuracy (considering optimal substrate concentrations) than hybrid RSM-GA model.  ...  An Eulerian approach was applied to model the gas-liquid interactions.  ...  Puchałka et al. 101 Pseudomonas putida KT2440 Genome-scale network reconstruction, FBA, FVA, C 13  ... 
doi:10.15255/cabeq.2014.2101 fatcat:sbnabwlayvh6ji4qfgy3t33adq

A Comprehensive Survey on Particle Swarm Optimization Algorithm and Its Applications

Yudong Zhang, Shuihua Wang, Genlin Ji
2015 Mathematical Problems in Engineering  
It is hoped that this survey would be beneficial for the researchers studying PSO algorithms.  ...  This survey presented a comprehensive investigation of PSO.  ...  [24] proposed a new approach, based on a hybrid algorithm combining of improved QPSO and simplex algorithms.  ... 
doi:10.1155/2015/931256 fatcat:ubc5eywnhzdjllxjaywe4czhnm

Advances in the Application of Machine Learning Techniques in Drug Discovery, Design and Development [chapter]

S. J. Barrett, W. B. Langdon
2006 Advances in Intelligent and Soft Computing  
They are inherently suitable for use with 'noisy', high dimensional (many variables) data, as is commonly used in cheminformatic (i.e.  ...  The authors wish to thank GSK colleagues, past and present, for their efforts in expressing the nature of their research.  ...  An ease of blending of these and other techniques incorporating multi-objective capabilities is awaited with anticipation for challenges in areas like gene regulatory mechanisms discovery [Burckin et  ... 
doi:10.1007/978-3-540-36266-1_10 fatcat:gdq5kxmbfjfbbaccdcjpsopg4e

Seeking Multiple Solutions: An Updated Survey on Niching Methods and Their Applications

Xiaodong Li, Michael G. Epitropakis, Kalyanmoy Deb, Andries Engelbrecht
2017 IEEE Transactions on Evolutionary Computation  
Epitropakis serves as a Reviewer for numerous high-impact journals and first tier conferences. He is a Founding Member and the Chair of the IEEE CIS Task Force on Multi-Modal Optimization. .  ...  Furthermore, the paper surveys previous attempts on leveraging the capabilities of niching to facilitate various optimization (e.g., multi-objective and dynamic optimization) and machine learning (e.g.  ...  ACKNOWLEDGMENT The authors would like to thank anonymous reviewers for their constructive comments which have greatly improved the quality of this paper.  ... 
doi:10.1109/tevc.2016.2638437 fatcat:7ol4ecd35bfjvkn6mujx37uocu

Inference and differential analysis of Extended Core Networks: A way to study anti-sense regulation

Marc Legeay, Beatrice Duval, Jean-Pierre Renou
2016 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
His laboratory has developed a number of algorithms for modeling and analyzing gene regulatory networks. He serves on the editorial board of PLos Computational Biology and BMC Genomics.  ...  Meanwhile, the analysis of dynamic networks has been a hot topic in data mining and social networks. Dynamic networks are structures with objects and links between the objects that vary in time.  ... 
doi:10.1109/bibm.2016.7822532 dblp:conf/bibm/LegeayDR16 fatcat:k33tacfd25flplfykeqfwkmzg4

Development of a Cournot-oligopoly model for competition of multi-product supply chains under government supervision

A. Hafezalkotob, S. Borhani, S. Zamani
2017 Scientia Iranica. International Journal of Science and Technology  
The paper proposes a Cournot-oligopoly model for green supply chain management.  ...  It provides a novel approach to construct a model that maximizes government tari and pro ts of the suppliers and manufacturers in all the GSCs.  ...  Their model was generated using Mixed Integer Linear Multi-Objective Programming, which was solved through a simulated annealing-based multi-objective meta-heuristics algorithm (MBSA).  ... 
doi:10.24200/sci.2017.4132 fatcat:nshdex32kvb5vgjxz5na2redqy

Integrated Omics: Tools, Advances, and Future Approaches

Biswapriya B Misra, Carl D Langefeld, Michael Olivier, Laura A Cox
2018 Journal of Molecular Endocrinology  
data files on a daily basis.  ...  We discuss recent approaches, existing tools, and potential caveats in the integration of omics datasets for development of standardized analytical pipelines that could be adopted by the global omics research  ...  Clearly, the authors concluded that network modeling from a large dataset and in vitro approaches helped predict key driver genes regulating non-alcoholic fatty liver disease.  ... 
doi:10.1530/jme-18-0055 pmid:30006342 fatcat:62c6xglxcbhhnkxgqo5gt7garq
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