Related papers: Reliable Graph Neural Networks for Drug Discovery …

Predicting drug-gene associations is crucial for drug development and disease treatment. While graph neural networks (GNN) have shown effectiveness in this task, they face challenges with data sparsity and efficient contrastive learning…

Graph-based Neural Networks (GNNs) are recent models created for learning representations of nodes (and graphs), which have achieved promising results when detecting patterns that occur in large-scale data relating different entities. Among…

Graph neural networks (GNNs) have emerged as one of the most effective ML techniques for drug effect prediction from drug molecular graphs. Despite having immense potential, GNN models lack performance when using datasets that contain…

Despite Graph Neural Networks (GNNs) have achieved remarkable accuracy, whether the results are trustworthy is still unexplored. Previous studies suggest that many modern neural networks are over-confident on the predictions, however,…

Graph Neural Networks (GNNs) have gained traction in the complex domain of drug discovery because of their ability to process graph-structured data such as drug molecule models. This approach has resulted in a myriad of methods and models…

Graph Neural Networks (GNNs) are proficient in graph representation learning and achieve promising performance on versatile tasks such as node classification and link prediction. Usually, a comprehensive hyperparameter tuning is essential…

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their…

Since multidrug combination is widely applied, the accurate prediction of drug-drug interaction (DDI) is becoming more and more critical. In our method, we use graph to represent drug-drug interaction: nodes represent drug; edges represent…

Graph Neural Networks (GNNs) have emerged as powerful tools for predicting outcomes in graph-structured data. However, a notable limitation of GNNs is their inability to provide robust uncertainty estimates, which undermines their…

Probabilistic graphical models provide a powerful tool to describe complex statistical structure, with many real-world applications in science and engineering from controlling robotic arms to understanding neuronal computations. A major…

Graph Neural Networks (GNNs) has been widely used in a variety of fields because of their great potential in representing graph-structured data. However, lacking of rigorous uncertainty estimations limits their application in high-stakes.…

With the capacity to capture high-order collaborative signals, Graph Neural Networks (GNNs) have emerged as powerful methods in Recommender Systems (RS). However, their efficacy often hinges on the assumption that training and testing data…

Graph Convolutional Networks (GCNs) have recently attracted vast interest and achieved state-of-the-art performance on graphs, but its success could typically hinge on careful training with amounts of expensive and time-consuming labeled…

Graph Neural Networks (GNNs) have emerged as potent tools for predicting outcomes in graph-structured data. Despite their efficacy, a significant drawback of GNNs lies in their limited ability to provide robust uncertainty estimates, posing…

Fast screening of drug molecules based on the ligand binding affinity is an important step in the drug discovery pipeline. Graph neural fingerprint is a promising method for developing molecular docking surrogates with high throughput and…

Graph transformation that predicts graph transition from one mode to another is an important and common problem. Despite much progress in developing advanced graph transformation techniques in recent years, the fundamental assumption…

Graph neural networks (GNN) have recently emerged as a vehicle for applying deep network architectures to graph and relational data. However, given the increasing size of industrial datasets, in many practical situations the message passing…

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the…

Predicting the supply and demand of transport systems is vital for efficient traffic management, control, optimization, and planning. For example, predicting where from/to and when people intend to travel by taxi can support fleet managers…

In this paper, we review recent developments and the role of Graph Neural Networks (GNNs) in computational drug discovery, including molecule generation, molecular property prediction, and drug-drug interaction prediction. By summarizing…