Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework

Article


Ahmed, Fee Faysal, Khatun, Mst. Shamima, Mosharaf, Md. Parvez and Mollah, Md. Nurul Haque. 2021. "Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework." Current Bioinformatics. 16 (6), pp. 865-879. https://doi.org/10.2174/1574893616666210204145254
Article Title

Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework

ERA Journal ID36845
Article CategoryArticle
AuthorsAhmed, Fee Faysal, Khatun, Mst. Shamima, Mosharaf, Md. Parvez and Mollah, Md. Nurul Haque
Journal TitleCurrent Bioinformatics
Journal Citation16 (6), pp. 865-879
Number of Pages15
Year2021
Place of PublicationUnited Arab Emirates
ISSN1574-8936
Digital Object Identifier (DOI)https://doi.org/10.2174/1574893616666210204145254
Web Address (URL)https://www.eurekaselect.com/article/113978
Abstract

Background: Protein-protein interactions (PPI) play a vital role in a wide range of biological processes starting from cell-cell interactions to developmental control in all organisms. However, experimental identification of PPI is often laborious, time-consuming and costly compared to computational prediction. There are several computational prediction models in the literature based on complete training samples, but none of them dealt with the partial training samples.

Objective: The objective of this work was to develop an effective PPI prediction model for Arabidopsis Thaliana using partial training samples in a machine learning framework.

Methods: We proposed an effective computational PPI prediction model by combining random forest (RF) classifier and autocorrelation (AC) sequence encoding features with 1:2 ratio of positive-PPI and unknown-PPI samples.

Results: We observed that the proposed prediction model produces the highest average performance scores of sensitivity (94.62%), AUC (0.92) and pAUC (0.189) with the training datasets and sensitivity (88.14%), AUC (0.89) and pAUC (0.176) with the test datasets of 5-fold cross-validation compared to other candidate predictors based on LDA, LOGI, ADA, NB, KNN & SVM classifiers. It also computed the highest performance scores of TPR (91.82%) and pAUC (0.174) at FPR= 20% with AUC (0.948) compared to other candidate predictors.

Conclusion: Overall performance of the developed model revealed that our proposed predictor might be useful to elucidate the biological function of unseen PPIs from a large number of candidate proteins in Arabidopsis thaliana.

KeywordsArabidopsis thaliana; Interaction prediction; Machine learning ap-proach; Protein sequence; Protein-protein interaction; Random forest; Sequence encoding
Contains Sensitive ContentDoes not contain sensitive content
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Byline AffiliationsJashore University of Science and Technology, Bangladesh
University of Rajshahi, Bangladesh
Kyushu Institute of Technology, Japan
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