EVOLUTIONARY OPTIMIZATION OF SEQUENCE KERNELS FOR DETECTION OF BACTERIAL GENE STARTS

2007 ◽  
Vol 17 (05) ◽  
pp. 369-381 ◽  
Author(s):  
BRITTA MERSCH ◽  
TOBIAS GLASMACHERS ◽  
PETER MEINICKE ◽  
CHRISTIAN IGEL
Keyword(s):  
Cross Validation ◽  
Classification Performance ◽  
Sequence Classification ◽  
Biological Sequence ◽  
Bacterial Gene ◽  
Covariance Matrix Adaptation ◽  
Multiple Kernel ◽  
Specific Choice ◽  
Shine Dalgarno Sequence ◽  
Adaptation Evolution

Oligo kernels for biological sequence classification have a high discriminative power. A new parameterization for the K-mer oligo kernel is presented, where all oligomers of length K are weighted individually. The task specific choice of these parameters increases the classification performance and reveals information about discriminative features. For adapting the multiple kernel parameters based on cross-validation the covariance matrix adaptation evolution strategy is proposed. It is applied to optimize the trimer oligo kernels for the detection of bacterial gene starts. The resulting kernels lead to higher classification rates, and the adapted parameters reveal the importance of particular triplets for classification, for example of those occurring in the Shine-Dalgarno Sequence.

scholarly journals A comparison of optimisation algorithms for high-dimensional particle and astrophysics applications

2021 ◽  
Vol 2021 (5) ◽  
Author(s):  
Csaba Balázs ◽  
◽  
Melissa van Beekveld ◽  
Sascha Caron ◽  
Barry M. Dillon ◽  
...  
Keyword(s):  
Random Sampling ◽  
Detailed Comparison ◽  
Global Optimisation ◽  
Adaptive Memory ◽  
Test Functions ◽  
Bee Colony ◽  
Covariance Matrix Adaptation ◽  
Global Fit ◽  
Adaptation Evolution ◽  
Optimisation Algorithms

Abstract Optimisation problems are ubiquitous in particle and astrophysics, and involve locating the optimum of a complicated function of many parameters that may be computationally expensive to evaluate. We describe a number of global optimisation algorithms that are not yet widely used in particle astrophysics, benchmark them against random sampling and existing techniques, and perform a detailed comparison of their performance on a range of test functions. These include four analytic test functions of varying dimensionality, and a realistic example derived from a recent global fit of weak-scale supersymmetry. Although the best algorithm to use depends on the function being investigated, we are able to present general conclusions about the relative merits of random sampling, Differential Evolution, Particle Swarm Optimisation, the Covariance Matrix Adaptation Evolution Strategy, Bayesian Optimisation, Grey Wolf Optimisation, and the PyGMO Artificial Bee Colony, Gaussian Particle Filter and Adaptive Memory Programming for Global Optimisation algorithms.

Optimization Design of Trusses Based on Covariance Matrix Adaptation Evolution Strategy Algorithm

2012 ◽  
Vol 215-216 ◽  
pp. 133-137
Author(s):  
Guo Shao Su ◽  
Yan Zhang ◽  
Zhen Xing Wu ◽  
Liu Bin Yan
Keyword(s):  
Stochastic Optimization ◽  
Covariance Matrix ◽  
Optimization Problems ◽  
Fitness Function ◽  
Optimization Methods ◽  
Evolution Strategy ◽  
Covariance Matrix Adaptation ◽  
Study Results ◽  
Highly Nonlinear ◽  
Adaptation Evolution

Covariance matrix adaptation evolution strategy algorithm (CMA-ES) is a newly evolution algorithm. It has become a powerful tool for solving highly nonlinear multi-peak optimization problems. In many real-world optimization problems, the location of multiple optima is often required in a search space. In order to evaluate the solution, thousands of fitness function evaluations are involved that is a time consuming or expensive processes. Therefore, conventional stochastic optimization methods meet a special challenge for a very large number of problem function evaluations. Aiming to overcome the shortcoming of stochastic optimization methods in the high calculation cost, a truss optimal method based on CMA-ES algorithm is proposed and applied to solve the section and shape optimization problems of trusses. The study results show that the method is feasible and has the advantages of high accuracy, high efficiency and easy implementation.

scholarly journals Mirrored Orthogonal Sampling for Covariance Matrix Adaptation Evolution Strategies

2019 ◽  
Vol 27 (4) ◽  
pp. 699-725 ◽  
Author(s):  
Hao Wang ◽  
Michael Emmerich ◽  
Thomas Bäck
Keyword(s):  
Convergence Rate ◽  
Covariance Matrix ◽  
Sampling Technique ◽  
Black Box ◽  
Evolution Strategies ◽  
High Dimensional ◽  
Major Purpose ◽  
Search Spaces ◽  
Covariance Matrix Adaptation ◽  
Adaptation Evolution

Generating more evenly distributed samples in high dimensional search spaces is the major purpose of the recently proposed mirrored sampling technique for evolution strategies. The diversity of the mutation samples is enlarged and the convergence rate is therefore improved by the mirrored sampling. Motivated by the mirrored sampling technique, this article introduces a new derandomized sampling technique called mirrored orthogonal sampling. The performance of this new technique is both theoretically analyzed and empirically studied on the sphere function. In particular, the mirrored orthogonal sampling technique is applied to the well-known Covariance Matrix Adaptation Evolution Strategy (CMA-ES). The resulting algorithm is experimentally tested on the well-known Black-Box Optimization Benchmark (BBOB). By comparing the results from the benchmark, mirrored orthogonal sampling is found to outperform both the standard CMA-ES and its variant using mirrored sampling.

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