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Graph-structured data plays a vital role in numerous domains, such as social networks, citation networks, commonsense reasoning graphs and knowledge graphs. While graph neural networks have been employed for graph processing, recent…

Overcoming the challenge of limited data availability within materials science is crucial for the broad-based applicability of machine learning within materials science. One pathway to overcome this limited data availability is to use the…

Graph neural network (GNN) is a powerful learning approach for graph-based recommender systems. Recently, GNNs integrated with contrastive learning have shown superior performance in recommendation with their data augmentation schemes,…

Machine learning (ML) and deep learning (DL) techniques have gained significant attention as reduced order models (ROMs) to computationally expensive structural analysis methods, such as finite element analysis (FEA). Graph neural network…

Graph Neural Networks (GNNs) are popular for graph machine learning and have shown great results on wide node classification tasks. Yet, they are less popular for practical deployments in the industry owing to their scalability challenges…

Explainable artificial intelligence (XAI) approaches have been increasingly applied in drug discovery to learn molecular representations and identify substructures driving property predictions. However, building end-to-end explainable…

Accurate prediction of binding sites of a given protein, to which ligands can bind, is a critical step in structure-based computational drug discovery. Recently, Equivariant Graph Neural Networks (GNNs) have emerged as a powerful paradigm…

Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify…

To design a drug given a biological molecule by using deep learning methods, there are many successful models published recently. People commonly used generative models to design new molecules given certain protein. LiGAN was regarded as…

The graph neural network (GNN) has been a powerful deep-learning tool in chemistry domain, due to its close connection with molecular graphs. Most GNN models collect and update atom and molecule features from the fed atom (and, in some…

Text-rich graphs, which exhibit rich textual information on nodes and edges, are prevalent across a wide range of real-world business applications. Large Language Models (LLMs) have demonstrated remarkable abilities in understanding text,…

Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand…

Graph Convolutional Neural Networks (GCNNs) are generalizations of CNNs to graph-structured data, in which convolution is guided by the graph topology. In many cases where graphs are unavailable, existing methods manually construct graphs…

Link prediction in graph data uses various algorithms and Graph Nerual Network (GNN) models to predict potential relationships between graph nodes. These techniques have found widespread use in numerous real-world applications, including…

Link prediction is a classical problem in graph analysis with many practical applications. For directed graphs, recently developed deep learning approaches typically analyze node similarities through contrastive learning and aggregate…

Graph Machine Learning (GML) has numerous applications, such as node/graph classification and link prediction, in real-world domains. Providing human-understandable explanations for GML models is a challenging yet fundamental task to foster…

Is it feasible to create an analysis paradigm that can analyze and then accurately and quickly predict known drugs from experimental data? PharML.Bind is a machine learning toolkit which is able to accomplish this feat. Utilizing deep…

In this survey, we dive into Tabular Data Learning (TDL) using Graph Neural Networks (GNNs), a domain where deep learning-based approaches have increasingly shown superior performance in both classification and regression tasks compared to…

Graph neural networks (GNNs) have been widely applied in the recommendation tasks and have obtained very appealing performance. However, most GNN-based recommendation methods suffer from the problem of data sparsity in practice. Meanwhile,…

Gradient Boosting (GB) is a popular methodology used to solve prediction problems by minimizing a differentiable loss function, $L$. GB performs very well on tabular machine learning (ML) problems; however, as a pure ML solver it lacks the…