Related papers: Towards Multiscale Graph-based Protein Learning wi…

Geometric Graph Neural Networks (GNNs) and Transformers have become state-of-the-art for learning from 3D protein structures. However, their reliance on message passing prevents them from capturing the hierarchical interactions that govern…

Graph Neural Networks (GNNs) have become powerful tools for learning from graph-structured data, finding applications across diverse domains. However, as graph sizes and connectivity increase, standard GNN training methods face significant…

Graph Neural Networks (GNNs) have been widely employed for feature representation learning in molecular graphs. Therefore, it is crucial to enhance the expressiveness of feature representation to ensure the effectiveness of GNNs. However, a…

The graph structure is a commonly used data storage mode, and it turns out that the low-dimensional embedded representation of nodes in the graph is extremely useful in various typical tasks, such as node classification, link prediction ,…

Graphs as a type of data structure have recently attracted significant attention. Representation learning of geometric graphs has achieved great success in many fields including molecular, social, and financial networks. It is natural to…

Graph neural networks (GNNs) are shown to be successful in modeling applications with graph structures. However, training an accurate GNN model requires a large collection of labeled data and expressive features, which might be inaccessible…

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…

Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which amino-acid residues are in close spatial proximity given the amino-acid sequence…

In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…

Graph neural networks (GNNs) are a class of deep models that operate on data with arbitrary topology represented as graphs. We introduce an efficient memory layer for GNNs that can jointly learn node representations and coarsen the graph.…

Graph Nerual Networks (GNNs) are effective models in graph embedding. It extracts shallow features and neighborhood information by aggregating neighbor information to learn the embedding representation of different nodes. However, the local…

Graph neural networks (GNNs) have been applied into a variety of graph tasks. Most existing work of GNNs is based on the assumption that the given graph data is optimal, while it is inevitable that there exists missing or incomplete edges…

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model…

Graph Neural Networks (GNNs) have attracted increasing attention in recent years and have achieved excellent performance in semi-supervised node classification tasks. The success of most GNNs relies on one fundamental assumption, i.e., the…

Graph neural network (GNN) is a popular tool to learn the lower-dimensional representation of a graph. It facilitates the applicability of machine learning tasks on graphs by incorporating domain-specific features. There are various options…

Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in…

Graphs can model complicated interactions between entities, which naturally emerge in many important applications. These applications can often be cast into standard graph learning tasks, in which a crucial step is to learn low-dimensional…

Graph neural networks (GNNs) are a powerful tool to learn representations on graphs by iteratively aggregating features from node neighbourhoods. Many variant models have been proposed, but there is limited understanding on both how to…

Recently, there have been some breakthroughs in graph analysis by applying the graph neural networks (GNNs) following a neighborhood aggregation scheme, which demonstrate outstanding performance in many tasks. However, we observe that the…

Graphs serve as fundamental descriptors for systems composed of interacting elements, capturing a wide array of data types, from molecular interactions to social networks and knowledge graphs. In this paper, we present an exhaustive review…