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Prediction of Protein-protein Interactions in Arabidopsis Thaliana using Partial Training Samples in a Machine Learning Framework


Fee Faysal Ahmed, Mst Shamima Khatun, Md. Parvez Mosharaf and Md. Nurul Haque Mollah*   Pages 1 - 15 ( 15 )


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.


Protein-protein interaction, Interaction prediction, Protein sequence, Sequence encoding, Machine learning approach, Random forest, Arabidopsis thaliana.


Department of Mathematics, Jashore University of Science and Technology, Jashore-7408, Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi-6205, Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi-6205

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