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iAFP-gap-SMOTE: An Efficient Feature Extraction Scheme Gapped Dipeptide Composition is Coupled with an Oversampling Technique for Identification of Antifreeze Proteins

[ Vol. 16 , Issue. 4 ]

Author(s):

Shahid Akbar, Maqsood Hayat*, Muhammad Kabir and Muhammad Iqbal   Pages 294 - 302 ( 9 )

Abstract:


Antifreeze proteins (AFPs) perform distinguishable roles in maintaining homeostatic conditions of living organisms and protect their cell and body from freezing in extremely cold conditions. Owing to high diversity in protein sequences and structures, the discrimination of AFPs from non- AFPs through experimental approaches is expensive and lengthy. It is, therefore, vastly desirable to propose a computational intelligent and high throughput model that truly reflects AFPs quickly and accurately. In a sequel, a new predictor called “iAFP-gap-SMOTE” is proposed for the identification of AFPs. Protein sequences are expressed by adopting three numerical feature extraction schemes namely; Split Amino Acid Composition, G-gap di-peptide Composition and Reduce Amino Acid alphabet composition. Usually, classification hypothesis biased towards majority class in case of the imbalanced dataset. Oversampling technique Synthetic Minority Over-sampling Technique is employed in order to increase the instances of the lower class and control the biasness. 10-fold cross-validation test is applied to appraise the success rates of “iAFP-gap-SMOTE” model. After the empirical investigation, “iAFP-gap-SMOTE” model obtained 95.02% accuracy. The comparison suggested that the accuracy of” iAFP-gap-SMOTE” model is higher than that of the present techniques in the literature so far. It is greatly recommended that our proposed model “iAFP-gap-SMOTE” might be helpful for the research community and academia.

Keywords:

Antifreeze proteins, Smote, KNN, PNN, SVM, AFPs.

Affiliation:

Department of Computer Science, Abdul Wali Khan University, Mardan, KP 23200, Department of Computer Science, Abdul Wali Khan University, Mardan, KP 23200, Department of Computer Science, Abdul Wali Khan University, Mardan, KP 23200, Department of Computer Science, Abdul Wali Khan University, Mardan, KP 23200

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