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

Accurately predicting the binding conformation of small-molecule ligands to protein targets is a critical step in rational drug design. Although recent deep learning-based docking surpasses traditional methods in speed and accuracy, many…

Generative Flow Networks (GFlowNets, GFNs) are a generative framework for learning unnormalized probability mass functions over discrete spaces. Since their inception, GFlowNets have proven to be useful for learning generative models in…

Virtual screening plays a critical role in modern drug discovery by enabling the identification of promising candidate molecules for experimental validation. Traditional machine learning methods such, as Support Vector Machines (SVM) and…

We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the…

Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule…

Accurate modeling of fluid dynamics around complex geometries is critical for applications such as aerodynamic optimization and biomedical device design. While advancements in numerical methods and high-performance computing have improved…

Generative flow networks (GFlowNets) are a family of algorithms for training a sequential sampler of discrete objects under an unnormalized target density and have been successfully used for various probabilistic modeling tasks. Existing…

Navigating the vast chemical space of druggable compounds is a formidable challenge in drug discovery, where generative models are increasingly employed to identify viable candidates. Conditional 3D structure-based drug design (3D-SBDD)…

We present FlowNet3D++, a deep scene flow estimation network. Inspired by classical methods, FlowNet3D++ incorporates geometric constraints in the form of point-to-plane distance and angular alignment between individual vectors in the flow…

This paper is about the problem of learning a stochastic policy for generating an object (like a molecular graph) from a sequence of actions, such that the probability of generating an object is proportional to a given positive reward for…

While Markov chain Monte Carlo methods (MCMC) provide a general framework to sample from a probability distribution defined up to normalization, they often suffer from slow convergence to the target distribution when the latter is highly…

Generative Flow Networks (GFlowNets) enable structured generation with inherent diversity, but existing sampling strategies often rely on weak guided exploration, slowing early discovery of high-reward candidates. In tasks such as molecular…

Structure-based drug design (SBDD) focuses on designing small-molecule ligands that bind to specific protein pockets. Computational methods are integral in modern SBDD workflows and often make use of virtual screening methods via docking or…

Designing mRNA sequences is a major challenge in developing next-generation therapeutics, since it involves exploring a vast space of possible nucleotide combinations while optimizing sequence properties like stability, translation…

Generative flow networks (GFlowNets) are amortized variational inference algorithms that treat sampling from a distribution over compositional objects as a sequential decision-making problem with a learnable action policy. Unlike other…

Accurate prediction of protein-ligand binding affinity plays a pivotal role in accelerating the discovery of novel drugs and vaccines, particularly for gastrointestinal (GI) diseases such as gastric ulcers, Crohn's disease, and ulcerative…

Geometric graph neural networks (GNNs) that respect E(3) symmetries have achieved strong performance on small molecule modeling, but they face scalability and expressiveness challenges when applied to large biomolecules such as RNA and…

The field of geometric deep learning has had a profound impact on the development of innovative and powerful graph neural network architectures. Disciplines such as computer vision and computational biology have benefited significantly from…

Many generative applications, such as synthesis-based 3D molecular design, involve constructing compositional objects with continuous features. Here, we introduce Compositional Generative Flows (CGFlow), a novel framework that extends flow…

In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations:…