Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization
Machine Learning - Special issue on applications in molecular biology
Computers and Operations Research
The Complexity of Some Problems on Subsequences and Supersequences
Journal of the ACM (JACM)
Journal of Global Optimization
FMGA: Finding Motifs by Genetic Algorithm
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
MDGA: motif discovery using a genetic algorithm
GECCO '05 Proceedings of the 7th annual conference on Genetic and evolutionary computation
Comparison of Multiobjective Evolutionary Algorithms: Empirical Results
Evolutionary Computation
Muiltiobjective optimization using nondominated sorting in genetic algorithms
Evolutionary Computation
Shuffling biological sequences with motif constraints
Journal of Discrete Algorithms
MOGAMOD: Multi-objective genetic algorithm for motif discovery
Expert Systems with Applications: An International Journal
Handbook of Parametric and Nonparametric Statistical Procedures
Handbook of Parametric and Nonparametric Statistical Procedures
GSA: A Gravitational Search Algorithm
Information Sciences: an International Journal
Bacterial Foraging Optimization Algorithm Integrating Tabu Search for Motif Discovery
BIBM '09 Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine
Motif Discovery Using Evolutionary Algorithms
SOCPAR '09 Proceedings of the 2009 International Conference of Soft Computing and Pattern Recognition
Finding motifs in DNA sequences applying a multiobjective artificial bee colony (MOABC) algorithm
EvoBIO'11 Proceedings of the 9th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Applying a multiobjective gravitational search algorithm (MO-GSA) to discover motifs
IWANN'11 Proceedings of the 11th international conference on Artificial neural networks conference on Advances in computational intelligence - Volume Part II
Multiobjective evolutionary algorithms: a comparative case studyand the strength Pareto approach
IEEE Transactions on Evolutionary Computation
A fast and elitist multiobjective genetic algorithm: NSGA-II
IEEE Transactions on Evolutionary Computation
A faster algorithm for calculating hypervolume
IEEE Transactions on Evolutionary Computation
Hybrid multiobjective artificial bee colony with differential evolution applied to motif finding
EvoBIO'13 Proceedings of the 11th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Designing a novel hybrid swarm based multiobjective evolutionary algorithm for finding DNA motifs
Proceedings of the 15th annual conference companion on Genetic and evolutionary computation
Journal of Global Optimization
A parallel cooperative team of multiobjective evolutionary algorithms for motif discovery
The Journal of Supercomputing
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In recent years, a huge number of biological problems have been successfully addressed through computational techniques, among all these computational techniques we highlight metaheuristics. Also, most of these biological problems are directly related to genomic, studying the microorganisms, plants, and animals genomes. In this work, we solve a DNA sequence analysis problem called Motif Discovery Problem (MDP) by using two novel algorithms based on swarm intelligence: Artificial Bee Colony (ABC) and Gravitational Search Algorithm (GSA). To guide the pattern search to solutions that have a better biological relevance, we have redefined the problem formulation and incorporated several biological constraints that should be satisfied by each solution. One of the most important characteristics of the problem definition is the application of multiobjective optimization (MOO), maximizing three conflicting objectives: motif length, support, and similarity. So, we have adapted our algorithms to the multiobjective context. This paper presents an exhaustive comparison of both multiobjective proposals on instances of different nature: real instances, generic instances, and instances generated according to a Markov chain. To analyze their operations we have used several indicators and statistics, comparing their results with those obtained by standard algorithms in multiobjective computation, and by 14 well-known biological methods.