A model for predicting ncRNA-protein interactions based on graph neural networks and community detection

Motion states identification of underwater glider based on complex networks and graph convolutional networks

Underwater glider (UG) plays an important role in ocean observation and exploration for a more efficient and deeper understanding of complex ocean environment. Timely identifying the motion states of UG is conducive for timely attitude adjustment and detection of potential anomalies, thereby improving the working reliability of UG. Combining limited penetrable visibility graph (LPVG) and graph convolutional networks (GCN) with self-attention mechanisms, we propose a novel method for motion states identification of UG, which is called as visibility graph and self-attention mechanism-based graph convolutional network (VGSA-GCN). Based on the actual sea trial data of UG, we chose the attitude angle signals of motion states related sensors collected by the control system of UG as the research object and constructed complex networks based on the LPVG method from pitch angle, roll angle, and heading angle data in diving and climbing states. Then, we build a self-attention mechanism-based GCN framework and classify the graphs under different motion states constructed by a complex network. Compared with support vector machines, convolutional neural network, and GCN without self-attention pooling layer, the proposed VGSA-GCN method can more accurately distinguish the diving and climbing states of UG. Subsequently, we analyze the variation of the transitivity coefficient corresponding to these two motion states. The results suggest that the coordination of the various sensors in the attitude adjustment unit during diving becomes closer and more efficient, which corresponds to the higher network measure of the diving state compared to the climbing state.

GATLGEMF: A graph attention model with line graph embedding multi-complex features for ncRNA-protein interactions prediction

Non-coding RNA (ncRNA) plays an important role in many fundamental biological processes, and it may be closely associated with many complex human diseases. NcRNAs exert their functions by interacting with proteins. Therefore, identifying novel ncRNA-protein interactions (NPIs) is important for understanding the mechanism of ncRNAs role. The computational approach has the advantage of low cost and high efficiency. Machine learning and deep learning have achieved great success by making full use of sequence information and structure information. Graph neural network (GNN) is a deep learning algorithm for complex network link prediction, which can extract and discover features in graph topology data. In this study, we propose a new computational model called GATLGEMF. We used a line graph transformation strategy to obtain the most valuable feature information and input this feature information into the attention network to predict NPIs. The results on four benchmark datasets show that our method achieves superior performance. We further compare GATLGEMF with the state-of-the-art existing methods to evaluate the model performance. GATLGEMF shows the best performance with the area under curve (AUC) of 92.41% and 98.93% on RPI2241 and NPInter v2.0 datasets, respectively. In addition, a case study shows that GATLGEMF has the ability to predict new interactions based on known interactions. The source code is available at https://github.com/JianjunTan-Beijing/GATLGEMF.