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Neural networks ensemble for automatic DNA microarray spot classification

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Abstract

In this work, a new step for the DNA microarray image analysis pipeline is proposed using neural computing techniques. We perform the classification of the spots into morphology-derived classes in order to assist the segmentation procedure that is traditionally performed after the gridding process. Our method consists of extracting multiple features from each individual spot area (or cell—derived from the gridding process) that are then reduced to a presumably optimal subset using a feature selection process, the sequential forward selection algorithm. Classification is then realized by means of a neural network ensemble with a tree-like structure, made up of seven multi-layer perceptron networks. The architecture of each neural network has been obtained through an exhaustive automatic searching process that optimizes the size of the network as a function of the classification error rate. The neural ensemble classifier is tested on two sub-grids extracted from real microarray DNA images and is shown to achieve high accuracy rates over the seven different classes of spot. In addition, a dataset with more than 1000 samples of classes of spot has been generated and made freely available.

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Notes

  1. Available at https://puma.princeton.edu/.

  2. Available at http://smd.princeton.edu/.

  3. Available at http://new.litrp.cl/index.php/data-repository.

  4. Available at http://dmery.ing.puc.cl/index.php/balu.

  5. Available at http://www.litrp.cl.

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Acknowledgements

The authors are grateful for the resources made available by the “Laboratorio de Investigaciones Tecnológicas en Reconocimiento de Patrones”, Universidad Católica del Maule, Talca, Chile.

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Authors and Affiliations

  1. Facultad de Informática, Universidad Complutense de Madrid, C/Profesor García Santesmases 9, 28040, Madrid, Spain

    Juan Carlos Rojas-Thomas & Matilde Santos

  2. Department of Computer Science, Universidad Católica del Maule, Avenida San Miguel 3605, Talca, Chile

    Marco Mora

Authors
  1. Juan Carlos Rojas-Thomas
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  2. Marco Mora
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  3. Matilde Santos
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Correspondence to Matilde Santos.

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Rojas-Thomas, J.C., Mora, M. & Santos, M. Neural networks ensemble for automatic DNA microarray spot classification. Neural Comput & Applic 31, 2311–2327 (2019). https://doi.org/10.1007/s00521-017-3190-6

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  • DOI: https://doi.org/10.1007/s00521-017-3190-6

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