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Graphs representation learning has been a very active research area in recent years. The goal of graph representation learning is to generate graph representation vectors that capture the structure and features of large graphs accurately.…

Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…

Although artificial intelligence (AI) has made significant progress in understanding molecules in a wide range of fields, existing models generally acquire the single cognitive ability from the single molecular modality. Since the hierarchy…

Graph Neural Networks (GNNs) are powerful techniques in representation learning for graphs and have been increasingly deployed in a multitude of different applications that involve node- and graph-wise tasks. Most existing studies solve…

Graph Neural Networks (GNNs) are gaining increasing attention on graph data learning tasks in recent years. However, in many applications, graph may be coming in an incomplete form where attributes of graph nodes are partially…

Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making…

The use of machine learning is becoming increasingly common in computational materials science. To build effective models of the chemistry of materials, useful machine-based representations of atoms and their compounds are required. We…

The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Based on the postulates of quantum mechanics, we introduce a hierarchy of representations which meet…

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab-initio calculations) and at speeds suitable for molecular dynam- ics simulation. Best…

Machine-learning models in chemistry - when based on descriptors of atoms embedded within molecules - face essential challenges in transferring the quality of predictions of local electronic structures and their associated properties across…

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…

Although hypergraph neural networks (HGNNs) have emerged as a powerful framework for analyzing complex datasets, their practical performance often remains limited. On one hand, existing networks typically employ a single type of attention…

Graph classification has gained significant attention due to its applications in chemistry, social networks, and bioinformatics. While Graph Neural Networks (GNNs) effectively capture local structural patterns, they often overlook global…

Brain graph representation learning serves as the fundamental technique for brain diseases diagnosis. Great efforts from both the academic and industrial communities have been devoted to brain graph representation learning in recent years.…

In this paper, we introduce a self-supervised learning method to enhance the graph-level representations with the help of a set of subgraphs. For this purpose, we propose a universal framework to generate subgraphs in an auto-regressive way…

For several decades, chemical knowledge has been published in written text, and there have been many attempts to make it accessible, for example, by transforming such natural language text to a structured format. Although the discovered…

Deep Learning has been shown to learn efficient representations for structured data such as image, text or audio. In this chapter, we present neural network architectures that are able to learn efficient representations of molecules and…

Quantum Graph Neural Networks (QGNNs) offer a promising approach to combining quantum computing with graph-structured data processing. While classical Graph Neural Networks (GNNs) are scalable and robust, existing QGNNs often lack…

Applying machine learning to molecules is challenging because of their natural representation as graphs rather than vectors.Several architectures have been recently proposed for deep learning from molecular graphs, but they suffer from…

Graph Neural Networks(GNNs) are a family of neural models tailored for graph-structure data and have shown superior performance in learning representations for graph-structured data. However, training GNNs on large graphs remains…