DNA binding proteins (DBPs) not only play an important role in all aspects of genetic activities such as DNA replication, recombination, repair, and modification but also are used as key components of antibiotics, steroids, and anticancer drugs in the field of drug discovery. Identifying DBPs becomes one of the most challenging problems in the domain of proteomics research.Considering the high-priced and inefficient of the experimental method, constructing a detailed DBPs prediction model becomes an urgent problem for researchers. In this paper, we propose a stacked ensemble classifier based method for predicting DBPs called StackPDB. Firstly, pseudo amino acid composition (PseAAC), pseudo position-specific scoring matrix (PsePSSM), position-specific scoring matrix-transition probability composition (PSSM-TPC), evolutionary distance transformation (EDT), and residue probing transformation (RPT) are applied to extract protein sequence features. Secondly, extreme gradient boosting-recursive feature elimination (XGB-RFE) is employed to gain an excellent feature subset. Finally, the best features are applied to the stacked ensemble classifier composed of XGBoost, LightGBM, and SVM to construct StackPDB. After applying leave-one-out cross-validation (LOOCV), StackPDB obtains high ACC and MCC on PDB1075,93.44% and 0.8687, respectively. Besides, the ACC of the independent test datasets PDB186 and PDB180 are 84.41% and 90.00%, respectively. The MCC of the independent test datasets PDB186 and PDB180 are 0.6882 and 0.7997, respectively. The results on the training dataset and the independent test dataset show that StackPDB has a great predictive Corresponding author.
Early risk prediction of diabetes could help doctors and patients to pay attention to the disease and intervene as soon as possible, which can effectively reduce the risk of complications. In this paper, a GA-stacking ensemble learning model is proposed to improve the accuracy of diabetes risk prediction. Firstly, genetic algorithms (GA) based on Decision Tree (DT) is used to select individuals with high adaptability, that is, a subset of attributes suitable for diabetes risk prediction. Secondly, the optimized convolutional neural network (CNN) and support vector machine (SVM) are used as the primary learners of stacking to learn attribute subsets, respectively. Then, the output of CNN and SVM is used as the input of the mate learner, the fully connected layer, for classification. Qingdao desensitization physical examination data from 1 January 2017 to 31 December 2019 is used, which includes body temperature, BMI, waist circumference, and other indicators that may be related to early diabetes. We compared the performance of GA-stacking with K-nearest neighbor (KNN), SVM, logistic regression (LR), Naive Bayes (NB), and CNN before and after adding GA through the average prediction time, accuracy, precision, sensitivity, specificity, and F1-score. Results show that prediction efficiency can be improved by adding GA. GA-stacking has higher prediction accuracy. Moreover, the strong generalization ability and high prediction efficiency of GA-stacking have also been verified on the early-stage diabetes risk prediction dataset published by UCI.
DNA binding proteins (DBPs) not only play an important role in all aspects of genetic activities such as DNA replication, recombination, repair, and modification but also are used as key components of antibiotics, steroids, and anticancer drugs in the field of drug discovery. Identifying DBPs becomes one of the most challenging problems in the domain of proteomics research. Considering the high-priced and inefficient of the experimental method, constructing a detailed DBPs prediction model becomes an urgent problem for researchers. In this paper, we propose a stacked ensemble classifier based method for predicting DBPs called StackPDB. Firstly, pseudo amino acid composition (PseAAC), pseudo position-specific scoring matrix (PsePSSM), position-specific scoring matrix-transition probability composition (PSSM-TPC), evolutionary distance transformation (EDT), and residue probing transformation (RPT) are applied to extract protein sequence features. Secondly, extreme gradient boosting-recursive feature elimination (XGB-RFE) is employed to gain an excellent feature subset. Finally, the best features are applied to the stacked ensemble classifier composed of XGBoost, LightGBM, and SVM to construct StackPDB. After applying leave-one-out cross-validation (LOOCV), StackPDB obtains high ACC and MCC on PDB1075, 93.44% and 0.8687, respectively. Besides, the ACC of the independent test datasets PDB186 and PDB180 are 84.41% and 90.00%, respectively. The MCC of the independent test datasets PDB186 and PDB180 are 0.6882 and 0.7997, respectively. The results on the training dataset and the independent test dataset show that StackPDB has a great predictive ability to predict DBPs.
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