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Accurate prediction of drug-target interactions (DTIs) through biological data can reduce the time and economic cost of drug development. The prediction method of DTIs based on a similarity network is attracting increasing attention. Currently, many studies have focused on predicting DTIs. However, such approaches do not consider the features of drugs and targets in multiple networks or how to extract and merge them. In this study, we proposed a Network EmbeDding framework in mulTiPlex networks (NEDTP) to predict DTIs. NEDTP builds a similarity network of nodes based on 15 heterogeneous information networks. Next, we applied a random walk to extract the topology information of each node in the network and learn it as a low-dimensional vector. Finally, the Gradient Boosting Decision Tree model was constructed to complete the classification task. NEDTP achieved accurate results in DTI prediction, showing clear advantages over several state-of-the-art algorithms. The prediction of new DTIs was also verified from multiple perspectives. In addition, this study also proposes a reasonable model for the widespread negative sampling problem of DTI prediction, contributing new ideas to future research. Code and data are available at https://github.com/LiangYu-Xidian/NEDTP. [ABSTRACT FROM AUTHOR]

Modifications of protein, RNA and DNA play an important role in many biological processes and are related to some diseases. Therefore, accurate identification and comprehensive understanding of protein, RNA and DNA modification sites can promote research on disease treatment and prevention. With the development of sequencing technology, the number of known sequences has continued to increase. In the past decade, many computational tools that can be used to predict protein, RNA and DNA modification sites have been developed. In this review, we comprehensively summarized the modification site predictors for three different biological sequences and the association with diseases. The relevant web server is accessible at http://lab.malab.cn/∼acy/PTM%5fdata/ some sample data on protein, RNA and DNA modification can be downloaded from that website. [ABSTRACT FROM AUTHOR]

Accurate prediction of energy prices is crucial to the development of energy security and environmental policies in various countries. This paper proposes a novel multi-step prediction hybrid model with genetic algorithm for variational mode decomposition, improved complete ensemble empirical modal decomposition with adaptive noise, bidirectional gated recurrent unit, temporal convolutional network, and multi-layer perceptron (GVMD-ICEEMDAN-BIGRU-TCN-MLP) for predicting carbon and natural gas futures prices. First genetic algorithm (GA) is used to fix the parameters of VMD model, the carbon and natural gas prices are decomposed into subsequences. Then the difference between the original series and the VMD after decomposition is further decomposed into subseries using ICEEMDAN. Next, the highest frequency series is predicted using the MLP model, and other subsequences are predicted using the BIGRU-TCN model. Finally, each predicted value is added linearly to determine the final result of steps 1, 3, and 5 of the entire forecasting process. According to the experimental results, it is shown that the model has lower prediction errors than the comparison model under mean absolute error (MAE), root mean square error (RMSE), mean absolute percentage error (MAPE), coefficient of determination (R2), and modified Diebold-Mariano test (MDM). The good prediction results of the novel hybrid model are demonstrated in multi-step ahead integrated prediction experiments, especially in the experiments with 1-step ahead prediction, as well as in the experiments with varying training ratios. • GVMD-ICEEMDAN-BIGRU-TCN-MLP model is used to forecast energy prices. • ICEEMDAN is used to further decompose the residuals. • Hierarchical prediction based on subsequence features is better. • Multi-step forecasting integrated study of energy prices. [ABSTRACT FROM AUTHOR]