Pairwise gene GO-based measures for biclustering of high-dimensional expression data

Background: Biclustering algorithms search for groups of genes that share the same behavior under a subset of samples in gene expression data. Nowadays, the biological knowledge available in public repositories can be used to drive these algorithms to find biclusters composed of groups of genes functionally coherent. On the other hand, a distance among genes can be defined according to their information stored in Gene Ontology (GO). Gene pairwise GO semantic similarity measures report a value for each pair of genes which establishes their functional similarity. A scatter search-based algorithm that optimizes a merit function that integrates GO information is studied in this paper. This merit function uses a term that addresses the information through a GO measure. Results: The effect of two possible different gene pairwise GO measures on the performance of the algorithm is analyzed. Firstly, three well known yeast datasets with approximately one thousand of genes are studied. Secondly, a group of human datasets related to clinical data of cancer is also explored by the algorithm. Most of these data are high-dimensional datasets composed of a huge number of genes. The resultant biclusters reveal groups of genes linked by a same functionality when the search procedure is driven by one of the proposed GO measures. Furthermore, a qualitative biological study of a group of biclusters show their relevance from a cancer disease perspective. Conclusions: It can be concluded that the integration of biological information improves the performance of the biclustering process. The two different GO measures studied show an improvement in the results obtained for the yeast dataset. However, if datasets are composed of a huge number of genes, only one of them really improves the algorithm performance. This second case constitutes a clear option to explore interesting datasets from a clinical point of view.Ministerio de Economía y Competitividad TIN2014-55894-C2-

A statistical learning based approach for parameter fine-tuning of metaheuristics

Metaheuristics are approximation methods used to solve combinatorial optimization problems. Their performance usually depends on a set of parameters that need to be adjusted. The selectionof appropriate parameter values causes a loss of efficiency, as it requires time, and advanced analytical and problem-specific skills. This paper provides an overview of the principal approaches to tackle the Parameter Setting Problem, focusing on the statistical procedures employed so far by the scientific community. In addition, a novel methodology is proposed, which is tested using an already existing algorithm for solving the Multi-Depot Vehicle Routing Problem.Peer Reviewe

Review, challenges, design, and development

Peres, F., & Castelli, M. (2021). Combinatorial optimization problems and metaheuristics: Review, challenges, design, and development. Applied Sciences (Switzerland), 11(14), 1-39. [6449]. https://doi.org/10.3390/app11146449In the past few decades, metaheuristics have demonstrated their suitability in addressing complex problems over different domains. This success drives the scientific community towards the definition of new and better-performing heuristics and results in an increased interest in this research field. Nevertheless, new studies have been focused on developing new algorithms without providing consolidation of the existing knowledge. Furthermore, the absence of rigor and formalism to classify, design, and develop combinatorial optimization problems and metaheuristics represents a challenge to the field’s progress. This study discusses the main concepts and challenges in this area and proposes a formalism to classify, design, and code combinatorial optimization problems and metaheuristics. We believe these contributions may support the progress of the field and increase the maturity of metaheuristics as problem solvers analogous to other machine learning algorithms.publishersversionpublishe

An Improved Excitation Matching Method based on an Ant Colony Optimization for Suboptimal-Free Clustering in Sum-Difference Compromise Synthesis

Dealing with an excitation matching method, this paper presents a global optimization strategy for the optimal clustering in sum-difference compromise linear arrays. Starting from a combinatorial formulation of the problem at hand, the proposed technique is aimed at determining the sub-array configuration expressed as the optimal path inside a directed acyclic graph structure modelling the solution space. Towards this end, an ant colony metaheuristic is used to benefit of its hill-climbing properties in dealing with the non-convexity of the sub-arraying as well as in managing graph searches. A selected set of numerical experiments are reported to assess the efficiency and current limitations of the ant-based strategy also in comparison with previous local combinatorial search methods. (c) 2009 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works