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Although diffusion language models (DLMs) are evolving quickly, many recent models converge on a set of shared components. These components, however, are distributed across ad-hoc research codebases or lack transparent implementations,…

Automatically generating high-quality real world 3D scenes is of enormous interest for applications such as virtual reality and robotics simulation. Towards this goal, we introduce NeuralField-LDM, a generative model capable of synthesizing…

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…

Diffusion models have emerged as a leading framework in generative modeling, poised to transform the traditionally slow and costly process of drug discovery. This review provides a systematic comparison of their application in designing two…

Diffusion Language Models (DLMs) are rapidly emerging as a powerful and promising alternative to the dominant autoregressive (AR) paradigm. By generating tokens in parallel through an iterative denoising process, DLMs possess inherent…

In the past decade, Artificial Intelligence driven drug design and discovery has been a hot research topic, where an important branch is molecule generation by generative models, from GAN-based models and VAE-based models to the latest…

Diffusion Language Models (DLMs) offer a promising parallel generation paradigm but suffer from slow inference due to numerous refinement steps and the inability to use standard KV caching. We introduce CDLM (Consistency Diffusion Language…

Vision-language models (VLMs) have shown promise in 2D medical image analysis, but extending them to 3D remains challenging due to the high computational demands of volumetric data and the difficulty of aligning 3D spatial features with…

Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…

Diffusion Probabilistic Models (DPMs) have demonstrated significant potential in 3D medical image segmentation tasks. However, their high computational cost and inability to fully capture global 3D contextual information limit their…

Methods for jointly generating molecular graphs along with their 3D conformations have gained prominence recently due to their potential impact on structure-based drug design. Current approaches, however, often suffer from very slow…

Recent advances in 3D generation have improved the fidelity and geometric details of synthesized 3D assets. However, due to the inherent ambiguity of single-view observations and the lack of robust global structural priors caused by limited…

Bridging molecular structures and natural language is essential for controllable design. Autoregressive models struggle with long-range dependencies, while standard diffusion processes apply uniform corruption across positions, which can…

Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…

Molecular conformation generation plays key roles in computational drug design. Recently developed deep learning methods, particularly diffusion models have reached competitive performance over traditional cheminformatical approaches.…

Drug discovery is a complex process that involves multiple stages and tasks. However, existing molecular generative models can only tackle some of these tasks. We present Generalist Molecular generative model (GenMol), a versatile framework…

Recent advancements in large language models (LLMs) have demonstrated impressive performance in molecular generation, which offers potential to accelerate drug discovery. However, the current LLMs overlook a critical requirement for drug…

Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…

In the pursuit of efficient automated content creation, procedural generation, leveraging modifiable parameters and rule-based systems, emerges as a promising approach. Nonetheless, it could be a demanding endeavor, given its intricate…

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…