Related papers: Geometric-informed GFlowNets for Structure-Based D…

Deep generative models have shown significant promise in generating valid 3D molecular structures, with the GEOM-Drugs dataset serving as a key benchmark. However, current evaluation protocols suffer from critical flaws, including incorrect…

Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale…

Although Generative Flow Networks (GFlowNets) are designed to capture multiple modes of a reward function, they often suffer from mode collapse in practice, getting trapped in early-discovered modes and requiring prolonged training to find…

There are many frameworks for deep generative modeling, each often presented with their own specific training algorithms and inference methods. Here, we demonstrate the connections between existing deep generative models and the recently…

Recent remarkable advancements in geometric deep generative models, coupled with accumulated structural data, enable structure-based drug design (SBDD) using only target protein information. However, existing models often struggle to…

Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential…

Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…

Surgical phase recognition plays a critical role in developing intelligent assistance systems for minimally invasive procedures such as Endoscopic Submucosal Dissection (ESD). However, the high visual similarity across different phases and…

Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks…

While DeepMind has tentatively solved protein folding, its inverse problem -- protein design which predicts protein sequences from their 3D structures -- still faces significant challenges. Particularly, the lack of large-scale standardized…

Real-time immersive video communications, particularly high-fidelity 3D telepresence, necessitates a synergistic balance between instantaneous dynamic scene reconstruction and high-efficiency data transmission. While recent advancements in…

The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…

Protein-ligand binding prediction is central to virtual screening and affinity ranking, two fundamental tasks in drug discovery. While recent retrieval-based methods embed ligands and protein pockets into Euclidean space for…

Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural representations with molecular representations, and ensuring…

Molecular geometry prediction of flexible molecules, or conformer search, is a long-standing challenge in computational chemistry. This task is of great importance for predicting structure-activity relationships for a wide variety of…

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…

Computer-aided molecular design (CAMD) studies quantitative structure-property relationships and discovers desired molecules using optimization algorithms. With the emergence of machine learning models, CAMD score functions may be replaced…

Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, predictive modeling of such data remains…

Generative Flow Networks (GFlowNets) have emerged as an innovative learning paradigm designed to address the challenge of sampling from an unnormalized probability distribution, called the reward function. This framework learns a policy on…

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…