Related papers: Co-Evolution-Based Metal-Binding Residue Predictio…

Graph neural networks (GNNs) demonstrate a robust capability for representation learning on graphs with complex structures, showcasing superior performance in various applications. The majority of existing GNNs employ a graph convolution…

Multi-view data containing complementary and consensus information can facilitate representation learning by exploiting the intact integration of multi-view features. Because most objects in real world often have underlying connections,…

Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…

As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally…

We present a simple, modular graph-based convolutional neural network that takes structural information from protein-ligand complexes as input to generate models for activity and binding mode prediction. Complex structures are generated by…

Predicting protein properties is paramount for biological and medical advancements. Current protein engineering mutates on a typical protein, called the wild-type, to construct a family of homologous proteins and study their properties.…

By folding into particular 3D structures, proteins play a key role in living beings. To learn meaningful representation from a protein structure for downstream tasks, not only the global backbone topology but the local fine-grained…

The recent success of graph neural networks has significantly boosted molecular property prediction, advancing activities such as drug discovery. The existing deep neural network methods usually require large training dataset for each…

Human motion prediction is a challenging task due to the stochasticity and aperiodicity of future poses. Recently, graph convolutional network has been proven to be very effective to learn dynamic relations among pose joints, which is…

Graph neural networks (GNNs) can learn effective node representations that significantly improve link prediction accuracy. However, most GNN-based link prediction algorithms are incompetent to predict weak ties connecting different…

Graph Neural Networks (GNNs) have been widely used for the representation learning of various structured graph data. While promising, most existing GNNs oversimplified the complexity and diversity of the edges in the graph, and thus…

Modeling the effects of mutations on the binding affinity plays a crucial role in protein engineering and drug design. In this study, we develop a novel deep learning based framework, named GraphPPI, to predict the binding affinity changes…

Materials informatics (MI), emerging from the integration of materials science and data science, is expected to significantly accelerate material development and discovery. The data used in MI are derived from both computational and…

Predicting interactions between structured entities lies at the core of numerous tasks such as drug regimen and new material design. In recent years, graph neural networks have become attractive. They represent structured entities as graphs…

While Graph Neural Network (GNN) has shown superiority in learning node representations of homogeneous graphs, leveraging GNN on heterogeneous graphs remains a challenging problem. The dominating reason is that GNN learns node…

Graph convolutional learning has led to many exciting discoveries in diverse areas. However, in some applications, traditional graphs are insufficient to capture the structure and intricacies of the data. In such scenarios, multigraphs…

The accurate prediction of changes in protein stability under multiple amino acid substitutions is essential for realising true in-silico protein re-design. To this purpose, we propose improvements to state-of-the-art Deep learning (DL)…

Due to the lack of a method to efficiently represent the multimodal information of a protein, including its structure and sequence information, predicting compound-protein binding affinity (CPA) still suffers from low accuracy when applying…

Graph Convolutional Networks (GCNs) have recently been shown to be quite successful in modeling graph-structured data. However, the primary focus has been on handling simple undirected graphs. Multi-relational graphs are a more general and…

Graph networks are a new machine learning (ML) paradigm that supports both relational reasoning and combinatorial generalization. Here, we develop universal MatErials Graph Network (MEGNet) models for accurate property prediction in both…