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Network embedding has attracted an increasing attention over the past few years. As an effective approach to solve graph mining problems, network embedding aims to learn a low-dimensional feature vector representation for each node of a…

Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…

Molecular 3D conformations play a key role in determining how molecules interact with other molecules or protein surfaces. Recent deep learning advancements have improved conformation prediction, but slow training speeds and difficulties in…

Accurately predicting 3D structures and dynamics of physical systems is crucial in scientific applications. Existing approaches that rely on geometric Graph Neural Networks (GNNs) effectively enforce $\mathrm{E}(3)$-equivariance, but they…

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…

Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular…

The de novo design of drug molecules is recognized as a time-consuming and costly process, and computational approaches have been applied in each stage of the drug discovery pipeline. Variational autoencoder is one of the computer-aided…

Identifying molecules that exhibit some pre-specified properties is a difficult problem to solve. In the last few years, deep generative models have been used for molecule generation. Deep Graph Variational Autoencoders are among the most…

Currently, the field of structure-based drug design is dominated by three main types of algorithms: search-based algorithms, deep generative models, and reinforcement learning. While existing works have typically focused on comparing models…

Designing new molecules is essential for drug discovery and material science. Recently, deep generative models that aim to model molecule distribution have made promising progress in narrowing down the chemical research space and generating…

Pulmonary nodule detection plays an important role in lung cancer screening with low-dose computed tomography (CT) scans. It remains challenging to build nodule detection deep learning models with good generalization performance due to…

Anomaly detection is a challenging task for machine learning algorithms due to the inherent class imbalance. It is costly and time-demanding to manually analyse the observed data, thus usually only few known anomalies if any are available.…

Link prediction aims to infer missing links or predicting the future ones based on currently observed partial networks, it is a fundamental problem in network science with tremendous real-world applications. However, conventional link…

Structure-based drug design uses three-dimensional geometric information of macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric deep learning, an emerging concept of neural-network-based machine…

The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges but have not yet been experimentally validated. Here we apply…

In data-driven drug discovery, designing molecular descriptors is a very important task. Deep generative models such as variational autoencoders (VAEs) offer a potential solution by designing descriptors as probabilistic latent vectors…

Design of new drugs is a challenging process: a candidate molecule should satisfy multiple conditions to act properly and make the least side-effect -- perfect candidates selectively attach to and influence only targets, leaving off-targets…

Generative AI has the potential to revolutionize drug discovery. Yet, despite recent advances in deep learning, existing models cannot generate molecules that satisfy all desired physicochemical properties. Herein, we describe IDOLpro, a…

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…

Structure-Based Drug Design (SBDD) has revolutionized drug discovery by enabling the rational design of molecules for specific protein targets. Despite significant advancements in improving docking scores, advanced 3D-SBDD generative models…