Ensemble Clustering Classification Applied to Competing SVM and One-Class Classifiers Exemplified by Plant MicroRNAs Data

Malik Yousef 1 , Waleed Khalifa 2  and Loai AbdAllah 3 , 4
  • 1 Community Information Systems, Zefat Academic College, Zefat, Israel
  • 2 Computer Science, The College of Sakhnin, Sakhnin, Israel
  • 3 Computer Science, The College of Sakhnin, Sakhnin, Israel
  • 4 Management Information Systems, The Max Stern Yezreel Valley College, 19300, Afula, Israel


The performance of many learning and data mining algorithms depends critically on suitable metrics to assess efficiency over the input space. Learning a suitable metric from examples may, therefore, be the key to successful application of these algorithms. We have demonstrated that the k-nearest neighbor (kNN) classification can be significantly improved by learning a distance metric from labeled examples. The clustering ensemble is used to define the distance between points in respect to how they co-cluster. This distance is then used within the framework of the kNN algorithm to define a classifier named ensemble clustering kNN classifier (EC-kNN). In many instances in our experiments we achieved highest accuracy while SVM failed to perform as well. In this study, we compare the performance of a two-class classifier using EC-kNN with different one-class and two-class classifiers. The comparison was applied to seven different plant microRNA species considering eight feature selection methods. In this study, the averaged results show that EC-kNN outperforms all other methods employed here and previously published results for the same data. In conclusion, this study shows that the chosen classifier shows high performance when the distance metric is carefully chosen.

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Journal + Issues

The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.