Related papers: Heterogeneous Molecular Graph Neural Networks for …

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…

Accurate short-term state forecasting is essential for efficient and stable operation of modern power systems, especially in the context of increasing variability introduced by renewable and distributed energy resources. As these systems…

Heterogeneous graph neural networks (HGNNs) excel at capturing structural and semantic information in heterogeneous graphs (HGs), while struggling to generalize across domains and tasks. With the rapid advancement of large language models…

Graph similarity learning (GSL), also referred to as graph matching in many scenarios, is a fundamental problem in computer vision, pattern recognition, and graph learning. However, previous GSL methods assume that graphs are homogeneous…

The high energy physics (HEP) community has a long history of dealing with large-scale datasets. To manage such voluminous data, classical machine learning and deep learning techniques have been employed to accelerate physics discovery.…

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect…

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…

Although substantial efforts have been made using graph neural networks (GNNs) for AI-driven drug discovery (AIDD), effective molecular representation learning remains an open challenge, especially in the case of insufficient labeled…

Molecule generation is a very important practical problem, with uses in drug discovery and material design, and AI methods promise to provide useful solutions. However, existing methods for molecule generation focus either on 2D graph…

Heterogeneous Graph Neural Networks (HGNNs) are powerful tools for deep learning on heterogeneous graphs. Typical HGNNs require repetitive message passing during training, limiting efficiency for large-scale real-world graphs. Recent…

Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…

Molecular representation learning (MRL) has long been crucial in the fields of drug discovery and materials science, and it has made significant progress due to the development of natural language processing (NLP) and graph neural networks…

By conceiving physical systems as 3D many-body point clouds, geometric graph neural networks (GNNs), such as SE(3)/E(3) equivalent GNNs, have showcased promising performance. In particular, their effective message-passing mechanics make…

Machine learning (ML) methods have gained increasing popularity in exploring and developing new materials. More specifically, graph neural network (GNN) has been applied in predicting material properties. In this work, we develop a novel…

Graph neural networks (GNNs) have achieved remarkable success in node classification. Building on this progress, heterogeneous graph neural networks (HGNNs) integrate relation types and node and edge semantics to leverage heterogeneous…

Graph neural networks (GNNs) have achieved great success in various graph problems. However, most GNNs are Message Passing Neural Networks (MPNNs) based on the homophily assumption, where nodes with the same label are connected in graphs.…

Background: Virtual Screening (VS) has become an essential tool in drug discovery, enabling the rapid and cost-effective identification of potential bioactive molecules. Among recent advancements, Graph Neural Networks (GNNs) have gained…

Leveraging domain knowledge including fingerprints and functional groups in molecular representation learning is crucial for chemical property prediction and drug discovery. When modeling the relation between graph structure and molecular…

Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of…

Learning from graph-structured data is an important task in machine learning and artificial intelligence, for which Graph Neural Networks (GNNs) have shown great promise. Motivated by recent advances in geometric representation learning, we…