Related papers: Deep Surrogate Docking: Accelerating Automated Dru…

Properties of molecules are indicative of their functions and thus are useful in many applications. With the advances of deep learning methods, computational approaches for predicting molecular properties are gaining increasing momentum.…

Stochastic gradient descent (SGD) is a standard optimization method to minimize a training error with respect to network parameters in modern neural network learning. However, it typically suffers from proliferation of saddle points in the…

Accurate prediction of molecular properties is essential in drug discovery and related fields. However, existing graph neural networks (GNNs) often struggle to simultaneously capture both local and global molecular structures. In this work,…

Code retrieval is to find the code snippet from a large corpus of source code repositories that highly matches the query of natural language description. Recent work mainly uses natural language processing techniques to process both query…

Deep generative models for graphs have exhibited promising performance in ever-increasing domains such as design of molecules (i.e, graph of atoms) and structure prediction of proteins (i.e., graph of amino acids). Existing work typically…

Deep Neural Networks (DNNs) have the potential for making various clinical procedures more time-efficient by automating medical image segmentation. Due to their strong, in some cases human-level, performance, they have become the standard…

Molecular docking aims to predict the 3D pose of a small molecule in a protein binding site. Traditional docking methods predict ligand poses by minimizing a physics-inspired scoring function. Recently, a diffusion model has been proposed…

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…

Resource is an important constraint when deploying Deep Neural Networks (DNNs) on mobile and edge devices. Existing works commonly adopt the cell-based search approach, which limits the flexibility of network patterns in learned cell…

This work presents a novel graph neural network (GNN) architecture, the Feature-specific Interpretable Graph Neural Network (FIGNN), designed to enhance the interpretability of deep learning surrogate models defined on unstructured grids in…

Dose-Volume Histogram (DVH) prediction is fundamental in radiation therapy that facilitate treatment planning, dose evaluation, plan comparison and etc. It helps to increase the ability to deliver precise and effective radiation treatments…

The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it…

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…

Graph Neural Networks (GNNs) have emerged as fundamental tools for a wide range of prediction tasks on graph-structured data. Recent studies have drawn analogies between GNN feature propagation and diffusion processes, which can be…

Accurate prediction of binding sites of a given protein, to which ligands can bind, is a critical step in structure-based computational drug discovery. Recently, Equivariant Graph Neural Networks (GNNs) have emerged as a powerful paradigm…

Continuous-time dynamic graphs (CTDGs) are essential for modeling interconnected, evolving systems. Traditional methods for extracting knowledge from these graphs often depend on feature engineering or deep learning. Feature engineering is…

Invasive ductal carcinoma is a prevalent, potentially deadly disease associated with a high rate of morbidity and mortality. Its malignancy is the second leading cause of death from cancer in women. The mammogram is an extremely useful…

The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…

This work introduces GeoDirDock (GDD), a novel approach to molecular docking that enhances the accuracy and physical plausibility of ligand docking predictions. GDD guides the denoising process of a diffusion model along geodesic paths…

Graph Neural Networks (GNNs) have recently been explored as surrogate models for numerical simulations. While their applications in computational fluid dynamics have been investigated, little attention has been given to structural problems,…