GLAM: An adaptive graph learning method for automated molecular interactions and properties predictions

Improving drug discovery efficiency is a core and long-standing challenge in drug discovery. For this purpose, many graph learning methods have been developed to search potential drug candidates with fast speed and low cost. In fact, the pursuit of high prediction performance on a limited number of datasets has crystallized them, making them lose advantage in repurposing to new data generated in drug discovery. Here we propose a flexible method that can adapt to any dataset and make accurate predictions. The proposed method employs an adaptive pipeline to learn from a dataset and output a predictor. Without any manual intervention, the method achieves far better prediction performance on all tested datasets than traditional methods, which are based on hand-designed neural architectures and other fixed items. In addition, we found that the proposed method is more robust than traditional methods and can provide meaningful interpretability. Given the above, the proposed method can serve as a reliable method to predict molecular interactions and properties with high adaptability, performance, robustness and interpretability. This work would take a solid step forward to the purpose of aiding researchers to design better drugs with high efficiency.

Semisupervised Classification with High-Order Graph Learning Attention Neural Network

At present, the graph neural network has achieved good results in the semisupervised classification of graph structure data. However, the classification effect is greatly limited in those data without graph structure, incomplete graph structure, or noise. It has no high prediction accuracy and cannot solve the problem of the missing graph structure. Therefore, in this paper, we propose a high-order graph learning attention neural network (HGLAT) for semisupervised classification. First, a graph learning module based on the improved variational graph autoencoder is proposed, which can learn and optimize graph structures for data sets without topological graph structure and data sets with missing topological structure and perform regular constraints on the generated graph structure to make the optimized graph structure more reasonable. Then, in view of the shortcomings of graph attention neural network (GAT) that cannot make full use of the graph high-order topology structure for node classification and graph structure learning, we propose a graph classification module that extends the attention mechanism to high-order neighbors, in which attention decays according to the increase of neighbor order. HGLAT performs joint optimization on the two modules of graph learning and graph classification and performs semisupervised node classification while optimizing the graph structure, which improves the classification performance. On 5 real data sets, by comparing 8 classification methods, the experiment shows that HGLAT has achieved good classification results on both a data set with graph structure and a data set without graph structure.