A review of methods for predicting DNA N6-methyladenine sites.

Deoxyribonucleic acid(DNA) N6-methyladenine plays a vital role in various biological processes, and the accurate identification of its site can provide a more comprehensive understanding of its biological effects. There are several methods for 6mA site prediction. With the continuous development of technology, traditional techniques with the high costs and low efficiencies are gradually being replaced by computer methods. Computer methods that are widely used can be divided into two categories: traditional machine learning and deep learning methods. We first list some existing experimental methods for predicting the 6mA site, then analyze the general process from sequence input to results in computer methods and review existing model architectures. Finally, the results were summarized and compared to facilitate subsequent researchers in choosing the most suitable method for their work.

Mul-SNO: A Novel Prediction Tool for S-Nitrosylation Sites Based on Deep Learning Methods.

Protein s-nitrosylation (SNO) is one of the most important post-translational modifications and is formed by the covalent modification of nitric oxide and cysteine residues. Extensive studies have shown that SNO plays a pivotal role in the plant immune response and treating various major human diseases. In recent years, SNO sites have become a hot research topic. Traditional biochemical methods for SNO site identification are time-consuming and costly. In this study, we developed an economical and efficient SNO site prediction tool named Mul-SNO. Mul-SNO ensembled current popular and powerful deep learning model bidirectional long short-term memory (BiLSTM) and bidirectional encoder representations from Transformers (BERT). Compared with existing state-of-the-art methods, Mul-SNO obtained better ACC of 0.911 and 0.796 based on 10-fold cross-validation and independent data sets, respectively.

A Review of Approaches for Predicting Drug-Drug Interactions Based on Machine Learning.

Drug-drug interactions play a vital role in drug research. However, they may also cause adverse reactions in patients, with serious consequences. Manual detection of drug-drug interactions is time-consuming and expensive, so it is urgent to use computer methods to solve the problem. There are two ways for computers to identify drug interactions: one is to identify known drug interactions, and the other is to predict unknown drug interactions. In this paper, we review the research progress of machine learning in predicting unknown drug interactions. Among these methods, the literature-based method is special because it combines the extraction method of DDI and the prediction method of DDI. We first introduce the common databases, then briefly describe each method, and summarize the advantages and disadvantages of some prediction models. Finally, we discuss the challenges and prospects of machine learning methods in predicting drug interactions. This review aims to provide useful guidance for interested researchers to further promote bioinformatics algorithms to predict DDI.

Modification Effects of Carbon Nanotube Dispersion on the Mechanical Properties, Pore Structure, and Microstructure of Cement Mortar.

Carbon nanotubes (CNTs) are very effective in improving the performance of cement-based materials. Mechanical properties and pore structure were investigated for cement mortar with CNTs. Meanwhile, the composite morphology of CNT-cement material and the evolution of hydration products were observed by scanning electron microscope (SEM), and the quantitative relationship between mechanical properties and pore structure was analyzed. The results indicated that the strength of mortar increased with the addition of 0.05% CNTs and decreased when the fraction of CNTs increased to 0.5%. The porosity of mortar with dispersed CNTs increased significantly, as these pores may be introduced by the dispersant. The quantitative relationship between porosity and strength proved that the increased porosity is the reason for the decreased strength of mortar with 0.5% CNT content, while mortar matrix strength with 0.05% and 0.5% CNTs increased by 44.03% and 71.18%, respectively. SEM images show that CNTs are dispersed uniformly in the mortar without obvious agglomeration and that the CNTs and hydration products form a meshwork structure, which is the mechanism by which CNTs can enhance the strength of the cement matrix.

Hysteretic Noisy Chaotic Neural Networks for Resource Allocation in OFDMA System.

This paper addresses two-stage resource allocation in the orthogonal frequency division multiplexing access system. In the subcarrier allocation stage, hysteretic noisy chaotic neural network (HNCNN) with a newly established energy function is proposed for subcarrier allocation to improve the optimization performance and reduce the computational complexity. Activation functions with both anticlockwise and clockwise hysteretic loops are applied to the HNCNN. A new energy function is established for an objective function, which can be calculated offline, resulting in a lower computational complexity in solving subcarrier allocation than the previous energy function. In the power allocation stage, the water-filling algorithm is employed to attain optimal power allocation. Simulation results show that the energy function established in this paper can decrease the runtimes of the neural networks, and that the HNCNN with both anticlockwise and clockwise hysteretic-loop activation functions can improve probabilities of feasible and optimal solutions at higher noises. The two-stage algorithm in this paper outperforms the previous algorithms in fairness, system throughput, and resource utilization.

Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer.

BACKGROUND: Lung cancer, especially non-small cell lung cancer, is a leading cause of malignant tumor death worldwide. Understanding the mechanisms employed by the main regulators, such as microRNAs (miRNAs) and transcription factors (TFs), still remains elusive. The patterns of their cooperation and biological functions in the synergistic regulatory network have rarely been studied. RESULTS: Here, we describe the first miRNA-TF synergistic regulation network in human lung cancer. We identified important regulators (MYC, NFKB1, miR-590, and miR-570) and significant miRNA-TF synergistic regulatory motifs by random simulations. The two most significant motifs were the co-regulation of miRNAs and TFs, and TF-mediated cascade regulation. We also developed an algorithm to uncover the biological functions of the human lung cancer miRNA-TF synergistic regulatory network (regulation of apoptosis, cellular protein metabolic process, and cell cycle), and the specific functions of each miRNA-TF synergistic subnetwork. We found that the miR-17 family exerted important effects in the regulation of non-small cell lung cancer, such as in proliferation and cell cycle regulation by targeting the retinoblastoma protein (RB1) and forming a feed forward loop with the E2F1 TF. We proposed a model for the miR-17 family, E2F1, and RB1 to demonstrate their potential roles in the occurrence and development of non-small cell lung cancer. CONCLUSIONS: This work will provide a framework for constructing miRNA-TF synergistic regulatory networks, function analysis in diseases, and identification of the main regulators and regulatory motifs, which will be useful for understanding the putative regulatory motifs involving miRNAs and TFs, and for predicting new targets for cancer studies.

Noise-tuning-based hysteretic noisy chaotic neural network for broadcast scheduling problem in wireless multihop networks.

Compared with noisy chaotic neural networks (NCNNs), hysteretic noisy chaotic neural networks (HNCNNs) are more likely to exhibit better optimization performance at higher noise levels, but behave worse at lower noise levels. In order to improve the optimization performance of HNCNNs, this paper presents a novel noise-tuning-based hysteretic noisy chaotic neural network (NHNCNN). Using a noise tuning factor to modulate the level of stochastic noises, the proposed NHNCNN not only balances stochastic wandering and chaotic searching, but also exhibits stronger hysteretic dynamics, thereby improving the optimization performance at both lower and higher noise levels. The aim of the broadcast scheduling problem (BSP) in wireless multihop networks (WMNs) is to design an optimal time-division multiple-access frame structure with minimal frame length and maximal channel utilization. A gradual NHNCNN (G-NHNCNN), which combines the NHNCNN with the gradual expansion scheme, is applied to solve BSP in WMNs to demonstrate the performance of the NHNCNN. Simulation results show that the proposed NHNCNN has a larger probability of finding better solutions compared to both the NCNN and the HNCNN regardless of whether noise amplitudes are lower or higher.

Novel hysteretic noisy chaotic neural network for broadcast scheduling problems in packet radio networks.

Noisy chaotic neural network (NCNN), which can exhibit stochastic chaotic simulated annealing (SCSA), has been proven to be a powerful tool in solving combinatorial optimization problems. In order to retain the excellent optimization property of SCSA and improve the optimization performance of the NCNN using hysteretic dynamics without increasing network parameters, we first construct an equivalent model of the NCNN and then control noises in the equivalent model to propose a novel hysteretic noisy chaotic neural network (HNCNN). Compared with the NCNN, the proposed HNCNN can exhibit both SCSA and hysteretic dynamics without introducing extra system parameters, and can increase the effective convergence toward optimal or near-optimal solutions at higher noise levels. Broadcast scheduling problem (BSP) in packet radio networks (PRNs) is to design an optimal time-division multiple-access (TDMA) frame structure with minimal frame length, maximal channel utilization, and minimal average time delay. In this paper, the proposed HNCNN is applied to solve BSP in PRNs to demonstrate its performance. Simulation results show that the proposed HNCNN with higher noise amplitudes is more likely to find an optimal or near-optimal TDMA frame structure with a minimal average time delay than previous algorithms.

A novel chaotic neural network with the ability to characterize local features and its application.

To provide an ability to characterize local features for the chaotic neural network (CNN), Gauss wavelet is used for the self-feedback of the CNN with the dilation parameter acting as the bifurcation parameter. The exponentially decaying dilation parameter and the chaotically varying translation parameter not only govern the wavelet self-feedback transform but also enable the CNN to generate complex dynamics behavior preventing the network from being trapped in the local minima. Analysis of the energy function of the CNN indicates that the local characterization ability of the proposed CNN is effectively provided by the wavelet self-feedback in the manner of inverse wavelet transform and that the proposed CNN can achieve asymptotical stability. The experimental results on traveling salesman problem (TSP) suggest that the proposed CNN has a higher average success rate for obtaining globally optimal or near-optimal solutions.