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The Journal of Supercomputing

, Volume 72, Issue 10, pp 3708–3728 | Cite as

Improving the classification performance of biological imbalanced datasets by swarm optimization algorithms

  • Jinyan Li
  • Simon FongEmail author
  • Sabah Mohammed
  • Jinan Fiaidhi
Article

Abstract

Classification which is a popular supervised machine learning method has many applications in computational biology, where data samples are automatically categorized into predefined labels with the aid of data mining. Often the training samples contain very few instances of interest (e.g., medical anomalies, rare disease in a population, and unusual syndromes, etc.), but many normal instances. Such imbalanced ratio of data distributions among the target labels hampers the efficacy of classification algorithms, because the induced model has not been trained with sufficient amount of instances of the interesting label(s), but overwhelmed with ordinary training records. Traditional remedies attempt to rebalance the data distributions of the target classes, by inflating the interesting instances artificially, reducing the majority of the common instances or a combination of both. Though the fundamental concept is effective, there is no clear guideline on how to strike a balance between fabricating the rare samples and reducing the norms, with the purpose of maximizing the classification accuracy. In this paper, an optimization model using different swarm strategies (Bat-inspired algorithm and PSO) is proposed for adaptively balancing the increase/decrease of the class distribution, depending on the properties of the biological datasets. The optimization is extended for achieving the highest possible accuracy and Kappa statistics at the same time as well. The optimization model is tested on five imbalanced medical datasets, which are sourced from lung surgery logs and virtual screening of bioassay data. Computer simulation results show that the proposed optimization model outperforms other class balancing methods in medical data classification.

Keywords

Imbalanced biological data Medical classification  Swarm algorithm Parameter optimization 

Notes

Acknowledgments

The authors are thankful for the financial support from the research grant “Temporal Data Stream Mining by Using Incrementally Optimized Very Fast Decision Forest (iOVFDF)”, Grant No. MYRG2015-00128-FST, offered by the University of Macau, FST, and RDAO.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Jinyan Li
    • 1
  • Simon Fong
    • 1
    Email author
  • Sabah Mohammed
    • 2
  • Jinan Fiaidhi
    • 2
  1. 1.Department of Computer and Information ScienceUniversity of MacauTaipaMacau SAR
  2. 2.Department of Computer ScienceLakehead UniversityTaipaMacau SAR

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