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A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies.

ABSTRACT: Background:Biologists aim to understand the genetic background of diseases, metabolic disorders or any other genetic condition. Microarrays are one of the main high-throughput technologies for collecting information about the behaviour of genetic information on different conditions. In order to analyse this data, clustering arises as one of the main techniques used, and it aims at finding groups of genes that have some criterion in common, like similar expression profile. However, the problem of finding groups is normally multi dimensional, making necessary to approach the clustering as a multi-objective problem where various cluster validity indexes are simultaneously optimised. They are usually based on criteria like compactness and separation, which may not be sufficient since they can not guarantee the generation of clusters that have both similar expression patterns and biological coherence. Method:We propose a Multi-Objective Clustering algorithm Guided by a-Priori Biological Knowledge (MOC-GaPBK) to find clusters of genes with high levels of co-expression, biological coherence, and also good compactness and separation. Cluster quality indexes are used to optimise simultaneously gene relationships at expression level and biological functionality. Our proposal also includes intensification and diversification strategies to improve the search process. Results:The effectiveness of the proposed algorithm is demonstrated on four publicly available datasets. Comparative studies of the use of different objective functions and other widely used microarray clustering techniques are reported. Statistical, visual and biological significance tests are carried out to show the superiority of the proposed algorithm. Conclusions:Integrating a-priori biological knowledge into a multi-objective approach and using intensification and diversification strategies allow the proposed algorithm to find solutions with higher quality than other microarray clustering techniques available in the literature in terms of co-expression, biological coherence, compactness and separation.

SUBMITTER: Parraga-Alava J

PROVIDER: S-EPMC6081857 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies.

Parraga-Alava Jorge J Dorn Marcio M Inostroza-Ponta Mario M

BioData mining 20180807

<h4>Background</h4>Biologists aim to understand the genetic background of diseases, metabolic disorders or any other genetic condition. Microarrays are one of the main high-throughput technologies for collecting information about the behaviour of genetic information on different conditions. In order to analyse this data, clustering arises as one of the main techniques used, and it aims at finding groups of genes that have some criterion in common, like similar expression profile. However, the pr ...[more]

PMID: 30100924

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Project description:Since water supply association analysis plays an important role in attribution analysis of water supply fluctuation, how to carry out effective association analysis has become a critical problem. However, the current techniques and methods used for association analysis are not very effective because they are based on continuous data. In general, there is different degrees of monotone relationship between continuous data, which makes the analysis results easily affected by monotone relationship. The multicollinearity between continuous data distorts these analytical methods and may generate incorrect results. Meanwhile, we cannot know the association rules and value interval between features and water supply. Therefore, the lack of an effective analysis method hinders the water supply association analysis. Association rules and value interval of features obtained from association analysis are helpful to grasp cause of water supply fluctuation and know the fluctuation interval of water supply, so as to provide better support for water supply dispatching. But the association rules and value interval between features and water supply are not fully understood. In this study, a data mining method coupling kmeans clustering discretization and apriori algorithm was proposed. The kmeans was used for data discretization to obtain the one-hot encoding that can be recognized by apriori, and the discretization can also avoid the influence of monotone relationship and multicollinearity on analysis results. All the rules eventually need to be validated in order to filter out spurious rules. The results show that the method in this study is an effective association analysis method. The method can not only obtain the valid strong association rules between features and water supply, but also understand whether the association relationship between features and water supply is direct or indirect. Meanwhile, the method can also obtain value interval of features, the association degree between features and confidence probability of rules.

Dataset Information

A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies.

Publications

A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies.

Similar Datasets

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