Based on the operation data from a certain wastewater treatment plant(WWTP) in northeast China, the models of back propagation neural network(BP NN) and radial basis function neural network(RBF NN) have been designed ...Based on the operation data from a certain wastewater treatment plant(WWTP) in northeast China, the models of back propagation neural network(BP NN) and radial basis function neural network(RBF NN) have been designed respectively and the ability of convergence and generalization has been analyzed separately. As for BP NN, the effects of numbers of layers and nodes have been studied; as for RBF NN, the influences of the number of nodes and the RBF′s width have been studied. It is concluded that BP NN has converged much slowly in comparison with RBF NN. The conclusion that the RBF NN is suitable for modeling activated sludge system has been drawn. An automatically optimum design program for RBF NN has been developed, through which the RBF NN model of traditional activated sludge system has been established.展开更多
Subcellular location is one of the key biological characteristics of proteins. Position-specific profiles （PSP） have been introduced as important characteristics of proteins in this article. In this study, to obtain...Subcellular location is one of the key biological characteristics of proteins. Position-specific profiles （PSP） have been introduced as important characteristics of proteins in this article. In this study, to obtain position-specific profiles, the Position Specific lterative-Basic Local Alignment Search Tool （PSI-BLAST） has been used to search for protein sequences in a database. Position-specific scoring matrices are extracted from the profiles as one class of characteristics. Four-part amino acid compositions and lst-7th order dipeptide compositions have also been calculated as the other two classes of characteristics. Therefore, twelve characteristic vectors are extracted from each of the protein sequences. Next, the characteristic vectors are weighed by a simple weighing function and inputted into a BP neural network predictor named PSP-Weighted Neural Network （PSP-WNN）. The Levenberg-Marquardt algorithm is employed to adjust the weight matrices and thresholds during the network training instead of the error back propagation algorithm. With a jackknife test on the RH2427 dataset, PSP-WNN has achieved a higher overall prediction accuracy of 88.4% rather than the prediction results by the general BP neural network, Markov model, and fuzzy k-nearest neighbors algorithm on this dataset. In addition, the prediction performance of PSP-WNN has been evaluated with a five-fold cross validation test on the PK7579 dataset and the prediction results have been consistently better than those of the previous method on the basis of several support vector machines, using compositions of both amino acids and amino acid pairs. These results indicate that PSP-WNN is a powerful tool for subcellular localization prediction. At the end of the article, influences on prediction accuracy using different weighting proportions among three characteristic vector categories have been discussed. An appropriate proportion is considered by increasing the prediction accuracy.展开更多
文摘Based on the operation data from a certain wastewater treatment plant(WWTP) in northeast China, the models of back propagation neural network(BP NN) and radial basis function neural network(RBF NN) have been designed respectively and the ability of convergence and generalization has been analyzed separately. As for BP NN, the effects of numbers of layers and nodes have been studied; as for RBF NN, the influences of the number of nodes and the RBF′s width have been studied. It is concluded that BP NN has converged much slowly in comparison with RBF NN. The conclusion that the RBF NN is suitable for modeling activated sludge system has been drawn. An automatically optimum design program for RBF NN has been developed, through which the RBF NN model of traditional activated sludge system has been established.
基金the National Natural Science Foundation of China (No. 60471003).
文摘Subcellular location is one of the key biological characteristics of proteins. Position-specific profiles （PSP） have been introduced as important characteristics of proteins in this article. In this study, to obtain position-specific profiles, the Position Specific lterative-Basic Local Alignment Search Tool （PSI-BLAST） has been used to search for protein sequences in a database. Position-specific scoring matrices are extracted from the profiles as one class of characteristics. Four-part amino acid compositions and lst-7th order dipeptide compositions have also been calculated as the other two classes of characteristics. Therefore, twelve characteristic vectors are extracted from each of the protein sequences. Next, the characteristic vectors are weighed by a simple weighing function and inputted into a BP neural network predictor named PSP-Weighted Neural Network （PSP-WNN）. The Levenberg-Marquardt algorithm is employed to adjust the weight matrices and thresholds during the network training instead of the error back propagation algorithm. With a jackknife test on the RH2427 dataset, PSP-WNN has achieved a higher overall prediction accuracy of 88.4% rather than the prediction results by the general BP neural network, Markov model, and fuzzy k-nearest neighbors algorithm on this dataset. In addition, the prediction performance of PSP-WNN has been evaluated with a five-fold cross validation test on the PK7579 dataset and the prediction results have been consistently better than those of the previous method on the basis of several support vector machines, using compositions of both amino acids and amino acid pairs. These results indicate that PSP-WNN is a powerful tool for subcellular localization prediction. At the end of the article, influences on prediction accuracy using different weighting proportions among three characteristic vector categories have been discussed. An appropriate proportion is considered by increasing the prediction accuracy.
