Related papers: DiffDTM: A conditional structure-free framework fo…

Combining discrete and continuous data is an important capability for generative models. We present Discrete Flow Models (DFMs), a new flow-based model of discrete data that provides the missing link in enabling flow-based generative models…

Designing molecules that bind to specific target proteins is a fundamental task in drug discovery. Recent models leverage geometric constraints to generate ligand molecules that bind cohesively with specific protein pockets. However, these…

This work introduces the generative fractional diffusion model for protein generation (ProT-GFDM), a novel generative framework that employs fractional stochastic dynamics for protein backbone structure modeling. This approach builds on the…

Deep Neural Networks (DNNs) are increasingly deployed across applications. However, ensuring their reliability remains a challenge, and in many situations, alternative models with similar functionality and accuracy are available.…

Generative models, especially diffusion models (DMs), have achieved promising results for generating feature-rich geometries and advancing foundational science problems such as molecule design. Inspired by the recent huge success of Stable…

Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein sequence pretraining, pretraining for structural data which is…

Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…

Deep generative models are rapidly advancing structure-based drug design, offering substantial promise for generating small molecule ligands that bind to specific protein targets. However, most current approaches assume a rigid protein…

De novo design of molecules has recently enjoyed the power of generative deep neural networks. Current approaches aim to generate molecules either resembling the properties of the molecules of the training set or molecules that are…

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…

Denoising diffusion models have shown great potential in multiple research areas. Existing diffusion-based generative methods on de novo 3D molecule generation face two major challenges. Since majority heavy atoms in molecules allow…

The advent of deep learning has introduced efficient approaches for de novo protein sequence design, significantly improving success rates and reducing development costs compared to computational or experimental methods. However, existing…

Molecular generation with diffusion models has emerged as a promising direction for AI-driven drug discovery and materials science. While graph diffusion models have been widely adopted due to the discrete nature of 2D molecular graphs,…

Diffusion models (DMs) have demonstrated exceptional generative capabilities across various domains, including image, video, and so on. A key factor contributing to their effectiveness is the high quantity and quality of data used during…

A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D…

Recently Data-Free Knowledge Distillation (DFKD) has garnered attention and can transfer knowledge from a teacher neural network to a student neural network without requiring any access to training data. Although diffusion models are adept…

Solving medical imaging data scarcity through semantic image generation has attracted growing attention in recent years. However, existing generative models mainly focus on synthesizing whole-organ or large-tissue structures, showing…

Structure-based drug design has seen significant advancements with the integration of artificial intelligence (AI), particularly in the generation of hit and lead compounds. However, most AI-driven approaches neglect the importance of…

Much scientific enquiry across disciplines is founded upon a mechanistic treatment of dynamic systems that ties form to function. A highly visible instance of this is in molecular biology, where an important goal is to determine…

In medical imaging, the diffusion models have shown great potential for synthetic image generation tasks. However, these approaches often lack the interpretable connections between the generated and real images and can create anatomically…