Related papers: Geometric Deep Learning on Molecular Representatio…

Geometric deep learning (GDL) has demonstrated huge power and enormous potential in molecular data analysis. However, a great challenge still remains for highly efficient molecular representations. Currently, covalent-bond-based molecular…

Protein engineering is experiencing a paradigmatic shift through the integration of geometric deep learning into computational design workflows. While traditional strategies, such as rational design and directed evolution, have enabled…

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…

Geometric Deep Learning (GDL) unifies a broad class of machine learning techniques from the perspectives of symmetries, offering a framework for introducing problem-specific inductive biases like Graph Neural Networks (GNNs). However, the…

Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…

Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…

Accurate and efficient prediction of polymer properties is of key importance for polymer design. Traditional experimental tools and density function theory (DFT)-based simulations for polymer property evaluation, are both expensive and…

Motivation: Despite its great success in various physical modeling, differential geometry (DG) has rarely been devised as a versatile tool for analyzing large, diverse and complex molecular and biomolecular datasets due to the limited…

Deep learning (DL) is one of the fastest growing topics in materials data science, with rapidly emerging applications spanning atomistic, image-based, spectral, and textual data modalities. DL allows analysis of unstructured data and…

Probabilistic generative deep learning for molecular design involves the discovery and design of new molecules and analysis of their structure, properties and activities by probabilistic generative models using the deep learning approach.…

Geometric deep learning (GDL) deals with supervised learning on data domains that go beyond Euclidean structure, such as data with graph or manifold structure. Due to the demand that arises from application-related data, there is a need to…

Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top…

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…

Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in…

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…

Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful…

Molecular property prediction refers to the task of labeling molecules with some biochemical properties, playing a pivotal role in the drug discovery and design process. Recently, with the advancement of machine learning, deep…

Effective molecular representation learning is of great importance to facilitate molecular property prediction, which is a fundamental task for the drug and material industry. Recent advances in graph neural networks (GNNs) have shown great…

In structure-based drug design, accurately estimating the binding affinity between a candidate ligand and its protein receptor is a central challenge. Recent advances in artificial intelligence, particularly deep learning, have demonstrated…

Recently, Geometric Deep Learning (GDL) has been introduced as a novel and versatile framework for computer-aided disease classification. GDL uses patient meta-information such as age and gender to model patient cohort relations in a graph…