Overlapping Clusters and Support Vector Machines Based Interval Type-2 Fuzzy System for the Prediction of Peptide Binding Affinity

Uslan, Volkan; Seker, Huseyin; John, Robert

Abstract

In the post-genome era, it is becoming more complex to process high dimensional, low-instance available, and nonlinear biological datasets. This paper aims to address these characteristics as they have adverse effects on the performance of predictive models in bioinformatics. In this paper, an interval type-2 Takagi Sugeno fuzzy predictive model is proposed in order to manage high-dimensionality and nonlinearity of such datasets which is the common feature in bioinformatics. A new clustering framework is proposed for this purpose to simplify antecedent operations for an interval type-2 fuzzy system. This new clustering framework is based on overlapping regions between the clusters. The cluster analysis of partitions and statistical information derived from them has identified the upper and lower membership functions forming the premise part. This is further enhanced by adapting the regression version of support vector machines in the consequent part. The proposed method is used in experiments to quantitatively predict affinities of peptide bindings to biomolecules. This case study imposes a challenge in post-genome studies and remains an open problem due to the complexity of the biological system, diversity of peptides, and curse of dimensionality of amino acid index representation characterizing the peptides. Utilizing four different peptide binding affinity datasets, the proposed method resulted in better generalization ability for all of them yielding an improved prediction accuracy of up to 58.2% on unseen peptides in comparison with the predictive methods presented in the literature. Source code of the algorithm is available at https://github.com/sekerbigdatalab.

Citation

Uslan, V., Seker, H., & John, R. (2019). Overlapping Clusters and Support Vector Machines Based Interval Type-2 Fuzzy System for the Prediction of Peptide Binding Affinity. IEEE Access, 7, 49756-49764. https://doi.org/10.1109/access.2019.2910078

• Journal Article Type: Article
• Acceptance Date: Mar 25, 2019
• Publication Date: Apr 11, 2019
• Deposit Date: May 14, 2019
• Publicly Available Date: May 14, 2019
• Journal: IEEE Access
• Electronic ISSN: 2169-3536
• Publisher: Institute of Electrical and Electronics Engineers
• Peer Reviewed: Peer Reviewed
• Volume: 7
• Pages: 49756-49764
• DOI: https://doi.org/10.1109/access.2019.2910078
• Keywords: Interval Type-2 Fuzzy Systems, Support Vector, Regression, Overlapping Clusters, Peptide Binding Affinity,
• Public URL: https://nottingham-repository.worktribe.com/output/2050020
• Publisher URL: https://ieeexplore.ieee.org/document/8685099
• Additional Information: © 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
• Contract Date: May 14, 2019