Related papers: TD3B: Transition-Directed Discrete Diffusion for A…

Proteins in complex with small molecule ligands represent the core of structure-based drug discovery. However, three-dimensional representations are absent from most deep-learning-based generative models. We here present a graph-based…

Diffusion language models enable any-order generation and bidirectional conditioning, offering appealing flexibility for tasks such as infilling, rewriting, and self-correction. However, their formulation-predicting one part of a sequence…

In silico prediction of the ligand binding pose to a given protein target is a crucial but challenging task in drug discovery. This work focuses on blind flexible selfdocking, where we aim to predict the positions, orientations and…

Diffusion models offer a powerful means of capturing the manifold of realistic protein structures, enabling rapid design for protein engineering tasks. However, existing approaches observe critical failure modes when precise constraints are…

Proteins play a critical role in carrying out biological functions, and their 3D structures are essential in determining their functions. Accurately predicting the conformation of protein side-chains given their backbones is important for…

Reinforcement learning with stochastic optimal control offers a promising framework for diffusion fine-tuning, where a pre-trained diffusion model is optimized to generate paths that lead to a reward-tilted distribution. While these…

AlphaFold3 introduces a diffusion-based architecture that elevates protein structure prediction to all-atom resolution with improved accuracy. This state-of-the-art performance has established AlphaFold3 as a foundation model for diverse…

The exploration of transition state (TS) geometries is crucial for elucidating chemical reaction mechanisms and modeling their kinetics. Recently, machine learning (ML) models have shown remarkable performance for prediction of TS…

We present LTM3D, a Latent Token space Modeling framework for conditional 3D shape generation that integrates the strengths of diffusion and auto-regressive (AR) models. While diffusion-based methods effectively model continuous latent…

Diffusion Transformers (DiT)-based video generation models with 3D full attention exhibit strong generative capabilities. Trajectory control represents a user-friendly task in the field of controllable video generation. However, existing…

Recent advancements in Diffusion Transformer (DiT) models have significantly improved 3D point cloud generation. However, existing methods primarily focus on local feature extraction while overlooking global topological information, such as…

Proteins underpin most biological function, and the ability to design them with tailored structures and properties is central to advances in biotechnology. Diffusion-based generative models have emerged as powerful tools for protein design,…

Therapeutic antibody candidates often require extensive engineering to improve key functional and developability properties before clinical development. This can be achieved through iterative design, where starting molecules are optimized…

Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…

Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback-Leibler divergence (Dx) between…

The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein…

Structure-based drug design (SBDD) is a critical task in drug discovery, requiring the generation of molecular information across two distinct modalities: discrete molecular graphs and continuous 3D coordinates. However, existing SBDD…

Recent text-driven motion generation methods span both discrete token-based approaches and continuous-latent formulations. MotionGPT3 exemplifies the latter paradigm, combining a learned continuous motion latent space with a diffusion-based…

Orthodontic treatment hinges on tooth alignment, which significantly affects occlusal function, facial aesthetics, and patients' quality of life. Current deep learning approaches predominantly concentrate on predicting transformation…

Diffusion Transformers (DiT) have demonstrated remarkable generative capabilities but remain highly computationally expensive. Previous acceleration methods, such as pruning and distillation, typically rely on a fixed computational…