Hehe Lv

The cell cycle and biological processes rely on RNA and RNA-binding protein (RBP) interactions. It is crucial to identify the binding sites on RNA. Various deep-learning methods have been used for RNA-binding site prediction. However, they cannot extract the hierarchical features of the RNA secondary structure. Therefore, this paper proposes HPNet, which can automatically identify RNA-binding sites and -binding preferences. HPNet performs feature learning from the two perspectives of the RNA sequence and the RNA secondary structure. A convolutional neural network (CNN), a deep-learning method, is used to learn RNA sequence features in HPNet. To capture the hierarchical information for RNA, we introduced DiffPool into HPNet, a differentiable pooling graph neural network (GNN). A CNN and DiffPool were combined to improve the binding site prediction accuracy by leveraging both RNA sequence features and hierarchical features of the RNA secondary structure. Binding preferences can be extracted based on model outputs and parameters. Overall, the experimental results showed that HPNet achieved a mean area under the curve (AUC) of 94.5% for the benchmark dataset, which was more accurate than the state-of-the-art methods. Moreover, these results demonstrate that the hierarchical features of RNA secondary structure play an essential role in selecting RNA-binding sites.

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.

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.

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.

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.