Protein Classification Using Machine Learning and Statistical Techniques

Abstract

Background: In recent era prediction of enzyme class from an unknown protein is one of the challenging tasks in bioinformatics. Day to day the number of proteins increases that causes difficulties in clinical verification and classification; as a result, the prediction of enzyme class gives a new opportunity to bioinformatics scholars. The machine learning classification technique helps in protein classification and predictions. But it is imperative to know which classification technique is more suited for protein classification. This study used human proteins data that is extracted from UniProtKB databank. Total 4368 protein data with 45 identified features has been used for experimental analysis. Objective: The prime objective of this article is to find an appropriate classification technique to classify the reviewed as well as un-reviewed human enzyme class of protein data. Also find the significance of different features in protein classification and prediction. Method: In this article, the ten most significant classification techniques such as CRT, QUEST, CHAID, C5.0, ANN, SVM, Bayesian, Random Forest, XgBoost and CatBoost has been used to classify the data and know the importance of features. To validate the result of different classification technique, the accuracy, precision, recall, F-measures, sensitivity, specificity, MCC, ROC and AUROC has been used. All experiment has been done with the help of SPSS Clementine and Python. Result: Above discussed classification techniques give different results and found that the data are imbalanced for class C4, C5, and C6. As a result, all of the classification technique gives acceptable accuracy above of 60% for these classes of data, but their precision value is very less or negligible. The experimental results highlight that the Random forest gives highest accuracy as well as AUROC among all, i.e., 96.84% and 0.945 respectively. And also have high precision and recall value. Conclusion: The experiment conducted and analyzed in this article highlight that the Random Forest classification technique can be used for protein of human enzyme classification and predictions.

Human Protein Sequence Classification using Machine Learning and Statistical Classification Techniques

“…The uniport databank contains two types of features (i) Profile Feature and (ii) Sequence Feature. Our previous study is based on the profile feature [40]. In this research we have consider the sequence-based features that are present in all seven class of protein data.…”