On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies

<p>Abstract</p> <p>Background</p> <p>The analysis of large-scale data sets via clustering techniques is utilized in a number of applications. Biclustering in particular has emerged as an important problem in the analysis of gene expression data since genes may only jointly respond over a subset of conditions. Biclustering algorithms also have important applications in sample classification where, for instance, tissue samples can be classified as cancerous or normal. Many of the methods for biclustering, and clustering algorithms in general, utilize simplified models or heuristic strategies for identifying the "best" grouping of elements according to some metric and cluster definition and thus result in suboptimal clusters.</p> <p>Results</p> <p>In this article, we present a rigorous approach to biclustering, OREO, which is based on the Optimal RE-Ordering of the rows and columns of a data matrix so as to globally minimize the dissimilarity metric. The physical permutations of the rows and columns of the data matrix can be modeled as either a network flow problem or a traveling salesman problem. Cluster boundaries in one dimension are used to partition and re-order the other dimensions of the corresponding submatrices to generate biclusters. The performance of OREO is tested on (a) metabolite concentration data, (b) an image reconstruction matrix, (c) synthetic data with implanted biclusters, and gene expression data for (d) colon cancer data, (e) breast cancer data, as well as (f) yeast segregant data to validate the ability of the proposed method and compare it to existing biclustering and clustering methods.</p> <p>Conclusion</p> <p>We demonstrate that this rigorous global optimization method for biclustering produces clusters with more insightful groupings of similar entities, such as genes or metabolites sharing common functions, than other clustering and biclustering algorithms and can reconstruct underlying fundamental patterns in the data for several distinct sets of data matrices arising in important biological applications.</p

Soft morphological filter optimization using a genetic algorithm for noise elimination

Digital image quality is of importance in almost all image processing applications. Many different approaches have been proposed for restoring the image quality depending on the nature of the degradation. One of the most common problems that cause such degradation is impulse noise. In general, well known median filters are preferred for eliminating different types of noise. Soft morphological filters are recently introduced and have been in use for many purposes. In this study, we present a Genetic Algorithm (GA) which combines different objectives as a weighted sum under a single evaluation function and generates a soft morphological filter to deal with impulse noise, after a training process with small images. The automatically generated filter performs better than the median filter and achieves comparable results to the best known filters from the literature over a set of benchmark instances that are larger than the training instances. Moreover, although the training process involves only impulse noise added images, the same evolved filter performs better than the median filter for eliminating Gaussian noise as well

Soft morphological filter optimization using a genetic algorithm for noise elimination

Digital image quality is of importance in almost all image processing applications. Many different approaches have been proposed for restoring the image quality depending on the nature of the degradation. One of the most common problems that cause such degradation is impulse noise. In general, well known median filters are preferred for eliminating different types of noise. Soft morphological filters are recently introduced and have been in use for many purposes. In this study, we present a Genetic Algorithm (GA) which combines different objectives as a weighted sum under a single evaluation function and generates a soft morphological filter to deal with impulse noise, after a training process with small images. The automatically generated filter performs better than the median filter and achieves comparable results to the best known filters from the literature over a set of benchmark instances that are larger than the training instances. Moreover, although the training process involves only impulse noise added images, the same evolved filter performs better than the median filter for eliminating Gaussian noise as well