Neural Computing and Applications

, Volume 31, Issue 7, pp 2311–2327 | Cite as

Neural networks ensemble for automatic DNA microarray spot classification

  • Juan Carlos Rojas-Thomas
  • Marco Mora
  • Matilde SantosEmail author
Original Article


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.


DNA microarray images Spot classification Neural networks ensemble Optimization Sequential forward selection Image processing 



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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


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Copyright information

© The Natural Computing Applications Forum 2017

Authors and Affiliations

  1. 1.Facultad de InformáticaUniversidad Complutense de MadridMadridSpain
  2. 2.Department of Computer ScienceUniversidad Católica del MauleTalcaChile

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