Related papers: Learning Joint 2D & 3D Diffusion Models for Comple…
Generative AI presents chemists with novel ideas for drug design and facilitates the exploration of vast chemical spaces. Diffusion models (DMs), an emerging tool, have recently attracted great attention in drug R\&D. This paper…
Generative models of graphs based on discrete Denoising Diffusion Probabilistic Models (DDPMs) offer a principled approach to molecular generation by systematically removing structural noise through iterative atom and bond adjustments.…
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…
3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language…
Diffusion-based image generators can now produce high-quality and diverse samples, but their success has yet to fully translate to 3D generation: existing diffusion methods can either generate low-resolution but 3D consistent outputs, or…
Graph generation is a critical yet challenging task, as empirical analyses require a deep understanding of complex, non-Euclidean structures. Diffusion models have recently made significant advances in graph generation, but these models are…
We introduce a new framework for molecular graph generation with 3D molecular generative models. Our Synthetic Coordinate Embedding (SyCo) framework maps molecular graphs to Euclidean point clouds via synthetic conformer coordinates and…
The paradigm shift toward structure-driven molecule generation has been propelled by advances in deep generative models, such as variational auto-encoders and diffusion models. However, these generative models for molecular design remain…
Generating molecular graphs is crucial in drug design and discovery but remains challenging due to the complex interdependencies between nodes and edges. While diffusion models have demonstrated their potentiality in molecular graph design,…
Learning the underlying distribution of molecular graphs and generating high-fidelity samples is a fundamental research problem in drug discovery and material science. However, accurately modeling distribution and rapidly generating novel…
Inspired by Geoffrey Hinton emphasis on generative modeling, To recognize shapes, first learn to generate them, we explore the use of 3D diffusion models for object classification. Leveraging the density estimates from these models, our…
Graph is a prevalent discrete data structure, whose generation has wide applications such as drug discovery and circuit design. Diffusion generative models, as an emerging research focus, have been applied to graph generation tasks.…
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,…
Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…
We introduce a framework for joint grounded scene graph - image generation, a challenging task involving high-dimensional, multi-modal structured data. To effectively model this complex joint distribution, we adopt a factorized approach:…
Diffusion models have emerged as the best approach for generative modeling of 2D images. Part of their success is due to the possibility of training them on millions if not billions of images with a stable learning objective. However,…
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…
Predictive machine learning models generally excel on in-distribution data, but their performance degrades on out-of-distribution (OOD) inputs. Reliable deployment therefore requires robust OOD detection, yet this is particularly…
This paper proposes a new 3D molecule generation framework, called GOAT, for fast and effective 3D molecule generation based on the flow-matching optimal transport objective. Specifically, we formulate a geometric transport formula for…
The de novo generation of molecules with targeted properties is crucial in biology, chemistry, and drug discovery. Current generative models are limited to using single property values as conditions, struggling with complex customizations…