Decreased IGF-1 level is associated with restrained amino acid metabolism in NSCLC with diabetes mellitus.

The discovery of a large number of small pulmonary nodules and early diagnosis of lung cancer in the diabetic patients prompt us to re-examine the relationship between diabetes and the occurrence and development of lung cancer. The aim of this study was to explore the underlying metabolites changes in diabetes with NSCLC or benign nodule patients, and further to investigate the association of serum IGF-1 level and differentially expressed metabolites (DEMs). An untargeted metabolomics method was used to detect the changes of metabolism in diabetic patients with NSCLC on the platform of HR-MS. Serum level of IGF-1 was measured by ELISA. The patients were divided to three groups, DM, DLB (nodule), and DLC (cancer). we have identified numerous DEMs, which include amino acid, choline, and fatty acid derivatives. Further analysis of the involved metabolic pathways suggested that linoleate metabolism, tryptophan metabolism, histidine metabolism, putative anti-Inflammatory metabolites formation from EPA, and arachidonic acid metabolism were considered to be the most significant metabolic pathways between groups. Networks analysis suggested that a series of metabolites were associated with serum IGF-1among the three groups, which can be divided into 6 categories. Nine metabolites have been identified as the main DEMs among the DLC, DLB, and DM groups. In conclusion, metabolomics is a powerful and promising tool for the cancer risk evaluation in diabetic patients. Our results suggest that decreased IGF-1 level is associated with restrained amino acid metabolism in NSCLC with diabetes mellitus.

Improving Network Representation Learning via Dynamic Random Walk, Self-Attention and Vertex Attributes-Driven Laplacian Space Optimization.

Network data analysis is a crucial method for mining complicated object interactions. In recent years, random walk and neural-language-model-based network representation learning (NRL) approaches have been widely used for network data analysis. However, these NRL approaches suffer from the following deficiencies: firstly, because the random walk procedure is based on symmetric node similarity and fixed probability distribution, the sampled vertices' sequences may lose local community structure information; secondly, because the feature extraction capacity of the shallow neural language model is limited, they can only extract the local structural features of networks; and thirdly, these approaches require specially designed mechanisms for different downstream tasks to integrate vertex attributes of various types. We conducted an in-depth investigation to address the aforementioned issues and propose a novel general NRL framework called dynamic structure and vertex attribute fusion network embedding, which firstly defines an asymmetric similarity and h-hop dynamic random walk strategy to guide the random walk process to preserve the network's local community structure in walked vertex sequences. Next, we train a self-attention-based sequence prediction model on the walked vertex sequences to simultaneously learn the vertices' local and global structural features. Finally, we introduce an attributes-driven Laplacian space optimization to converge the process of structural feature extraction and attribute feature extraction. The proposed approach is exhaustively evaluated by means of node visualization and classification on multiple benchmark datasets, and achieves superior results compared to baseline approaches.

CR-GCN: Channel-Relationships-Based Graph Convolutional Network for EEG Emotion Recognition.

Electroencephalography (EEG) is recorded by electrodes from different areas of the brain and is commonly used to measure neuronal activity. EEG-based methods have been widely used for emotion recognition recently. However, most current methods for EEG-based emotion recognition do not fully exploit the relationship of EEG channels, which affects the precision of emotion recognition. To address the issue, in this paper, we propose a novel method for EEG-based emotion recognition called CR-GCN: Channel-Relationships-based Graph Convolutional Network. Specifically, topological structure of EEG channels is distance-based and tends to capture local relationships, and brain functional connectivity tends to capture global relationships among EEG channels. Therefore, in this paper, we construct EEG channel relationships using an adjacency matrix in graph convolutional network where the adjacency matrix captures both local and global relationships among different EEG channels. Extensive experiments demonstrate that CR-GCN method significantly outperforms the state-of-the-art methods. In subject-dependent experiments, the average classification accuracies of 94.69% and 93.95% are achieved for valence and arousal. In subject-independent experiments, the average classification accuracies of 94.78% and 93.46% are obtained for valence and arousal.

Deep Link-Prediction Based on the Local Structure of Bipartite Networks.

Link prediction based on bipartite networks can not only mine hidden relationships between different types of nodes, but also reveal the inherent law of network evolution. Existing bipartite network link prediction is mainly based on the global structure that cannot analyze the role of the local structure in link prediction. To tackle this problem, this paper proposes a deep link-prediction (DLP) method by leveraging the local structure of bipartite networks. The method first extracts the local structure between target nodes and observes structural information between nodes from a local perspective. Then, representation learning of the local structure is performed on the basis of the graph neural network to extract latent features between target nodes. Lastly, a deep-link prediction model is trained on the basis of latent features between target nodes to achieve link prediction. Experimental results on five datasets showed that DLP achieved significant improvement over existing state-of-the-art link prediction methods. In addition, this paper analyzes the relationship between local structure and link prediction, confirming the effectiveness of a local structure in link prediction.

CAttSleepNet: Automatic End-to-End Sleep Staging Using Attention-Based Deep Neural Networks on Single-Channel EEG.

Accurate sleep staging results can be used to measure sleep quality, providing a reliable basis for the prevention and diagnosis of sleep-related diseases. The key to sleep staging is the feature representation of EEG signals. Existing approaches rarely consider local features in feature extraction, and fail to distinguish the importance of critical and non-critical local features. We propose an innovative model for automatic sleep staging with single-channel EEG, named CAttSleepNet. We add an attention module to the convolutional neural network (CNN) that can learn the weights of local sequences of EEG signals by exploiting intra-epoch contextual information. Then, a two-layer bidirectional-Long Short-Term Memory (Bi-LSTM) is used to encode the global correlations of successive epochs. Therefore, the feature representations of EEG signals are enhanced by both local and global context correlation. Experimental results achieved on two real-world sleep datasets indicate that the CAttSleepNet model outperforms existing models. Moreover, ablation experiments demonstrate the validity of our proposed attention module.

Predicting DNA binding protein-drug interactions based on network similarity.

BACKGROUND: The study of DNA binding protein (DBP)-drug interactions can open a breakthrough for the treatment of genetic diseases and cancers. Currently, network-based methods are widely used for protein-drug interaction prediction, and many hidden relationships can be found through network analysis. We proposed a DCA (drug-cluster association) model for predicting DBP-drug interactions. The clusters are some similarities in the drug-binding site trimmers with their physicochemical properties. First, DBPs-drug binding sites are extracted from scPDB database. Second, each binding site is represented as a trimer which is obtained by sliding the window in the binding sites. Third, the trimers are clustered based on the physicochemical properties. Fourth, we build the network by generating the interaction matrix for representing the DCA network. Fifth, three link prediction methods are detected in the network. Finally, the common neighbor (CN) method is selected to predict drug-cluster associations in the DBP-drug network model. RESULT: This network shows that drugs tend to bind to positively charged sites and the binding process is more likely to occur inside the DBPs. The results of the link prediction indicate that the CN method has better prediction performance than the PA and JA methods. The DBP-drug network prediction model is generated by using the CN method which predicted more accurately drug-trimer interactions and DBP-drug interactions. Such as, we found that Erythromycin (ERY) can establish an interaction relationship with HTH-type transcriptional repressor, which is fitted well with silico DBP-drug prediction. CONCLUSION: The drug and protein bindings are local events. The binding of the drug-DBPs binding site represents this local binding event, which helps to understand the mechanism of DBP-drug interactions.

DLS: A Link Prediction Method Based on Network Local Structure for Predicting Drug-Protein Interactions.

The studies on drug-protein interactions (DPIs) had significant for drug repositioning, drug discovery, and clinical medicine. The biochemical experimentation (in vitro) requires a long time and high cost to be confirmed because it is difficult to estimate. Therefore, a feasible solution is to predict DPIs efficiently with computers. We propose a link prediction method based on drug-protein interaction (DPI) local structural similarity (DLS) for predicting the DPIs. The DLS method combines link prediction and binary network structure to predict DPIs. The ten-fold cross-validation method was applied in the experiment. After comparing the predictive capability of DLS with the improved similarity-based network prediction method, the results of DLS on the test set are significantly better. Moreover, several candidate proteins were predicted for three approved drugs, namely captopril, desferrioxamine and losartan, and these predictions are further validated by the literature. In addition, the combination of the Common Neighborhood (CN) method and the DLS method provides a new idea for the integrated application of the link prediction method.

SmoPSI: Analysis and Prediction of Small Molecule Binding Sites Based on Protein Sequence Information.

The analysis and prediction of small molecule binding sites is very important for drug discovery and drug design. The traditional experimental methods for detecting small molecule binding sites are usually expensive and time consuming, and the tools for single species small molecule research are equally inefficient. In recent years, some algorithms for predicting binding sites of protein-small molecules have been developed based on the geometric and sequence characteristics of proteins. In this paper, we have proposed SmoPSI, a classification model based on the XGBoost algorithm for predicting the binding sites of small molecules, using protein sequence information. The model achieved better results with an AUC of 0.918 and an ACC of 0.913. The experimental results demonstrate that our method achieves high performances and outperforms many existing predictors. In addition, we also analyzed the binding residues and nonbinding residues and finally found the PSSM; hydrophilicity, hydrophobicity, charge, and hydrogen bonding have obviously different effects on the binding-site predictions.