Journal
COMPUTERS IN BIOLOGY AND MEDICINE
Volume 160, Issue -, Pages -Publisher
PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.compbiomed.2023.106935
Keywords
SARS-CoV-2 phosphorylation sites; Multi -view feature fusion; Differential evolution algorithm; Group LASSO; Multi -head attention mechanism
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In this paper, a new prediction model called DE-MHAIPs is proposed to accurately identify phosphorylation sites of SARS-CoV-2. The model combines six feature extraction methods, utilizes differential evolution algorithm to learn feature weights, and employs Group LASSO for feature selection. The experimental results demonstrate that DE-MHAIPs method shows excellent predictive ability compared with other methods.
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) around the world affects the normal lives of people all over the world. The computational methods can be used to accurately identify SARS-CoV-2 phosphorylation sites. In this paper, a new prediction model of SARS-CoV-2 phosphorylation sites, called DE-MHAIPs, is proposed. First, we use six feature extraction methods to extract protein sequence information from different perspectives. For the first time, we use a differential evolution (DE) algorithm to learn individual feature weights and fuse multi-information in a weighted combination. Next, Group LASSO is used to select a subset of good features. Then, the important protein information is given higher weight through multi-head attention. After that, the processed data is fed into long short-term memory network (LSTM) to further enhance model's ability to learn features. Finally, the data from LSTM are input into fully connected neural network (FCN) to predict SARS-CoV-2 phosphorylation sites. The AUC values of the S/T and Y datasets under 5 -fold cross-validation reach 91.98% and 98.32%, respectively. The AUC values of the two datasets on the inde-pendent test set reach 91.72% and 97.78%, respectively. The experimental results show that the DE-MHAIPs method exhibits excellent predictive ability compared with other methods.
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