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Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…

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…

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…

Molecular property prediction is of crucial importance in many disciplines such as drug discovery, molecular biology, or material and process design. The frequently employed quantitative structure-property/activity relationships…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Predicting the properties of a molecule from its structure is a challenging task. Recently, deep learning methods have improved the state of the art for this task because of their ability to learn useful features from the given data. By…

Graph neural networks (GNNs) are increasingly used to model biological systems, yet the reliability of post-hoc explanation methods for recovering meaningful molecular mechanisms remains unclear. Here, we systematically evaluate four widely…

Predicting the solubility of given molecules remains crucial in the pharmaceutical industry. In this study, we revisited this extensively studied topic, leveraging the capabilities of contemporary computing resources. We employed two…

Advances in machine learning have led to graph neural network-based methods for drug discovery, yielding promising results in molecular design, chemical synthesis planning, and molecular property prediction. However, current graph neural…

Graph neural networks (GNNs) are powerful graph-based deep-learning models that have gained significant attention and demonstrated remarkable performance in various domains, including natural language processing, drug discovery, and…

Accurate prediction of blood-brain barrier permeability (BBBP) is essential for central nervous system (CNS) drug development. While graph neural networks (GNNs) have advanced molecular property prediction, they often rely on molecular…

Molecular property prediction (MPP) is a fundamental but challenging task in the computer-aided drug discovery process. More and more recent works employ different graph-based models for MPP, which have made considerable progress in…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNN) have made remarkable advancements…

Drug synergy arises when the combined impact of two drugs exceeds the sum of their individual effects. While single-drug effects on cell lines are well-documented, the scarcity of data on drug synergy, considering the vast array of…

Synergistic drug combinations provide huge potentials to enhance therapeutic efficacy and to reduce adverse reactions. However, effective and synergistic drug combination prediction remains an open question because of the unknown causal…

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive…

Recent studies on Graph Neural Networks(GNNs) provide both empirical and theoretical evidence supporting their effectiveness in capturing structural patterns on both homophilic and certain heterophilic graphs. Notably, most real-world…

Scaling deep learning models has been at the heart of recent revolutions in language modelling and image generation. Practitioners have observed a strong relationship between model size, dataset size, and performance. However,…

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…