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Imbalanced multi-label data classification as a bi-level optimization problem: application to miRNA-related diseases diagnosis

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Abstract

In multi-label classification, each instance could be assigned multiple labels at the same time. In such a situation, the relationships between labels and the class imbalance are two serious issues that should be addressed. Despite the important number of existing multi-label classification methods, the widespread class imbalance among labels has not been adequately addressed. Two main issues should be solved to come up with an effective classifier for imbalanced multi-label data. On the one hand, the imbalance could occur between labels and/or within a label. The “Between-labels imbalance” occurs where the imbalance is between labels however the “Within-label imbalance” occurs where the imbalance is in the label itself and it could occur across multiple labels. On the other hand, the labels’ processing order heavily influences the quality of a multi-label classifier. To deal with these challenges, we propose in this paper a bi-level evolutionary approach for the optimized induction of multivariate decision trees, where the upper-level role is to design the classifiers while the lower-level approximates the optimal labels’ ordering for each classifier. Our proposed method, named BIMLC-GA (Bi-level Imbalanced Multi-Label Classification Genetic Algorithm), is compared to several state-of-the-art methods across a variety of imbalanced multi-label data sets from several application fields and then applied on the miRNA-related diseases case study. The statistical analysis of the obtained results shows the merits of our proposal.

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Data Availability

The data sets analysed during the current study are available in http://www.uco.es/kdis/mllresources/. The real human miRNA-disease associations were retrieved from HMDD v3.0 database [52].

Notes

  1. https://colab.research.google.com.

  2. https://pygad.readthedocs.io/en/latest/.

  3. https://pypi.org/project/scikit-obliquetree/.

  4. http://epistasislab.github.io/tpot/.

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No funding was received to assist with the preparation of this manuscript.

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Authors and Affiliations

  1. SMART Lab, ISG-Campus, University of Tunis, Liberty Street, 2000, Bardo, Tunis, Tunisia

    Marwa Chabbouh & Lamjed Ben Said

  2. IEEE SM, SMART Lab, ISG-Campus, University of Tunis, Liberty Street, 2000, Bardo, Tunis, Tunisia

    Slim Bechikh

  3. IEEE SM, Artificial Intelligence Research Institute, University of Veracruz, Calle Paseo 112, Col. Nueva Xalapa, 91097, Xalapa, Veracruz, México

    Efrén Mezura-Montes

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  1. Marwa Chabbouh
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Correspondence to Marwa Chabbouh.

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Chabbouh, M., Bechikh, S., Mezura-Montes, E. et al. Imbalanced multi-label data classification as a bi-level optimization problem: application to miRNA-related diseases diagnosis. Neural Comput & Applic 35, 16285–16303 (2023). https://doi.org/10.1007/s00521-023-08458-4

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