On the pathological behavior of adaptive differential evolution on hybrid objective functions

Most state-of-the-art Differential Evolution (DE) algorithms are adaptive DEs with online parameter adaptation. We investigate the behavior of adaptive DE on a class of hy-brid functions, where independent groups of variables are associated with different component objective functions. An experimental evaluation of 3 state-of-the-art adaptive DEs (JADE, SHADE, jDE) shows that hybrid functions are "ada-ptive-DE-hard". That is, adaptive DEs have signicant fail-ure rates on these new functions. In-depth analysis of the adaptive behavior of the DEs reveals that their parameter adaptation mechanisms behave in a pathological manner on this class of problems, resulting in over-adaptation for one of the components of the hybrids and poor overall performance. Thus, this class of deceptive benchmarks pose a signicant challenge for DE

A novel fuzzy and multi-objective evolutionary algorithm based gene assignment for clustering short time series expression data

Conventional clustering algorithms based on Euclidean distance or Pearson correlation coefficient are not able to include order information in the distance metric and also unable to distinguish between random and real biological patterns. We present template based clustering algorithm for time series gene expression data. Template profiles are defined based on up-down regulation of genes between consecutive time points. Assignment of genes to templates is based on fuzzy membership function. Multi-objective evolutionary algorithm is used to determine compact clusters with varying number of templates. Statistical significance of each template is determined using permutation based non-parametric test. Statistically significant profiles are further tested for their biological relevance using gene ontology analysis. The algorithm was able to distinguish between real and noisy pattern when tested on artificial and real biological data. The proposed algorithm has shown better or similar performance compared to STEM and better than k-means on a real biological data

Gene selection algorithms for microarray data based on least squares support vector machine

BACKGROUND: In discriminant analysis of microarray data, usually a small number of samples are expressed by a large number of genes. It is not only difficult but also unnecessary to conduct the discriminant analysis with all the genes. Hence, gene selection is usually performed to select important genes. RESULTS: A gene selection method searches for an optimal or near optimal subset of genes with respect to a given evaluation criterion. In this paper, we propose a new evaluation criterion, named the leave-one-out calculation (LOOC, A list of abbreviations appears just above the list of references) measure. A gene selection method, named leave-one-out calculation sequential forward selection (LOOCSFS) algorithm, is then presented by combining the LOOC measure with the sequential forward selection scheme. Further, a novel gene selection algorithm, the gradient-based leave-one-out gene selection (GLGS) algorithm, is also proposed. Both of the gene selection algorithms originate from an efficient and exact calculation of the leave-one-out cross-validation error of the least squares support vector machine (LS-SVM). The proposed approaches are applied to two microarray datasets and compared to other well-known gene selection methods using codes available from the second author. CONCLUSION: The proposed gene selection approaches can provide gene subsets leading to more accurate classification results, while their computational complexity is comparable to the existing methods. The GLGS algorithm can also better scale to datasets with a very large number of genes

Benchmark generator for CEC 2009 competition on dynamic optimization

Evolutionary algorithms(EAs) have been widely applied to solve stationary optimization problems. However, many real-world applications are actually dynamic. In order to study the performance of EAs in dynamic environments, one important task is to develop proper dynamic benchmark problems. Over the years, researchers have applied a number of dynamic test problems to compare the performance of EAs in dynamic environments, e.g., the “moving peaks ” benchmark (MPB) proposed by Branke [1], the DF1 generator introduced by Morrison and De Jong [6], the singleand multi-objective dynamic test problem generator by dynamically combining different objective functions of exiting stationary multi-objective benchmark problems suggested by Jin and Sendhoff [2], Yang and Yao’s exclusive-or (XOR) operator [10, 11, 12], Kang’s dynamic traveling salesman problem (DTSP) [3] and dynamic multi knapsack problem (DKP), etc. Though a number of DOP generators exist in the literature, there is no unified approach of constructing dynamic problems across the binary space, real space and combinatorial space so far. This report uses the generalized dynamic benchmark generator (GDBG) proposed in [4], which construct dynamic environments for all the three solution spaces. Especially, in the rea

Multi-class protein fold recognition using multi-objective evolutionary algorithms

Protein fold recognition (PFR) is an important approach to structure discovery without relying on sequence similarity. In pattern recognition terminology, PFR is a multiclass classification problem to be solved by employing feature analysis and pattern classification techniques. This work reformulates PFR into a multiobjective optimization problem and proposes a multiobjective feature analysis and selection algorithm (MOFASA). We use support vector machines as the classifier. Experimental results on the structural classification of protein (SCOP) data set indicate that MOFASA is capable of achieving comparable performances to the existing results. In addition, MOFASA identifies relevant features for further biological analysis

A machine learning approach for the identification of odorant binding proteins from sequence-derived properties

Background: Odorant binding proteins (OBPs) are believed to shuttle odorants from the environment to the underlying odorant receptors, for which they could potentially serve as odorant presenters. Although several sequence based search methods have been exploited for protein family prediction, less effort has been devoted to the prediction of OBPs from sequence data and this area is more challenging due to poor sequence identity between these proteins. Results: In this paper, we propose a new algorithm that uses Regularized Least Squares Classifier (RLSC) in conjunction with multiple physicochemical properties of amino acids to predict odorantbinding proteins. The algorithm was applied to the dataset derived from Pfam and GenDiS database and we obtained overall prediction accuracy of 97.7% (94.5% and 98.4% for positive and negative classes respectively). Conclusion: Our study suggests that RLSC is potentially useful for predicting the odorant binding proteins from sequence-derived properties irrespective of sequence similarity. Our method predicts 92.8% of 56 odorant binding proteins non-homologous to any protein in the swissprot database and 97.1% of the 414 independent dataset proteins, suggesting the usefulness of RLSC method for facilitating the prediction of odorant binding proteins from sequence information

A Comparative Analysis of Surface Characteristics of Enamel after Conventional Acid Etching and Er,Cr:YSSG Laser Irradiation

To evaluate the influence of Erbium, Chromium:Yttrium-Scandium-Gallium-Garnet (Er,Cr:YSGG) laser irradiation (2W 15Hz, 2W 25Hz) on Penetration Depth, Surface Roughness, Surface Morphology and Etching Pattern of enamel and to compare it with conventional