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Entity interaction prediction is essential in many important applications such as chemistry, biology, material science, and medical science. The problem becomes quite challenging when each entity is represented by a complex structure,…

Recent works have shown that exploiting multi-scale representations deeply learned via convolutional neural networks (CNN) is of tremendous importance for accurate contour detection. This paper presents a novel approach for predicting…

In the wake of the growing popularity of machine learning in particle physics, this work finds a new application of geometric deep learning on Feynman diagrams to make accurate and fast matrix element predictions with the potential to be…

Graph neural networks (GNNs) have been successfully applied in many structured data domains, with applications ranging from molecular property prediction to the analysis of social networks. Motivated by the broad applicability of GNNs, we…

Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…

The distance-geometric graph representation adopts a unified scheme (distance) for representing the geometry of three-dimensional(3D) graphs. It is invariant to rotation and translation of the graph and it reflects pair-wise node…

The combination of deep learning algorithm and materials science has made significant progress in predicting novel materials and understanding various behaviours of materials. Here, we introduced a new model called as the Crystal…

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…

Graphs serve as fundamental descriptors for systems composed of interacting elements, capturing a wide array of data types, from molecular interactions to social networks and knowledge graphs. In this paper, we present an exhaustive review…

The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are…

This paper presents new designs of graph convolutional neural networks (GCNs) on 3D meshes for 3D object segmentation and classification. We use the faces of the mesh as basic processing units and represent a 3D mesh as a graph where each…

Generating novel graph structures that optimize given objectives while obeying some given underlying rules is fundamental for chemistry, biology and social science research. This is especially important in the task of molecular graph…

The ability to design complex neural network architectures which enable effective training by stochastic gradient descent has been the key for many achievements in the field of deep learning. However, developing such architectures remains a…

While deep neural networks (DNN) have become an effective computational tool, the prediction results are often criticized by the lack of interpretability, which is essential in many real-world applications such as health informatics.…

Nowadays, the coupling of electronic structure and machine learning techniques serves as a powerful tool to predict chemical and physical properties of a broad range of systems. With the aim of improving the accuracy of predictions, a large…

Designing accurate deep learning models for molecular property prediction plays an increasingly essential role in drug and material discovery. Recently, due to the scarcity of labeled molecules, self-supervised learning methods for learning…

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats…

Molecular graph neural networks (GNNs) often focus exclusively on XYZ-based geometric representations and thus overlook valuable chemical context available in public databases like PubChem. This work introduces a multimodal framework that…

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,…

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…