Prediction of antifreeze proteins using machine learning

Living organisms including fishes, microbes, and animals can live in extremely cold weather. To stay alive in cold environments, these species generate antifreeze proteins (AFPs), also referred to as ice-binding proteins. Moreover, AFPs are extensively utilized in many important fields including medical, agricultural, industrial, and biotechnological. Several predictors were constructed to identify AFPs. However, due to the sequence and structural heterogeneity of AFPs, correct identification is still a challenging task. It is highly desirable to develop a more promising predictor. In this research, a novel computational method, named AFP-LXGB has been proposed for prediction of AFPs more precisely. The information is explored by Dipeptide Composition (DPC), Grouped Amino Acid Composition (GAAC), Position Specific Scoring Matrix-Segmentation-Autocorrelation Transformation (Sg-PSSM-ACT), and Pseudo Position Specific Scoring Matrix Tri-Slicing (PseTS-PSSM). Keeping the benefits of ensemble learning, these feature sets are concatenated into different combinations. The best feature set is selected by Extremely Randomized Tree-Recursive Feature Elimination (ERT-RFE). The models are trained by Light eXtreme Gradient Boosting (LXGB), Random Forest (RF), and Extremely Randomized Tree (ERT). Among classifiers, LXGB has obtained the best prediction results. The novel method (AFP-LXGB) improved the accuracies by 3.70% and 4.09% than the best methods. These results verified that AFP-LXGB can predict AFPs more accurately and can participate in a significant role in medical, agricultural, industrial, and biotechnological fields.