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Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular behavior and development of protein-based…

Denoising diffusion probabilistic models (DDPMs) have emerged as competitive generative models yet brought challenges to efficient sampling. In this paper, we propose novel bilateral denoising diffusion models (BDDMs), which take…

Despite the proliferation of generative models, achieving fast sampling during inference without compromising sample diversity and quality remains challenging. Existing models such as Denoising Diffusion Probabilistic Models (DDPM) deliver…

The widespread application of Artificial Intelligence (AI) techniques has significantly influenced the development of new therapeutic agents. These computational methods can be used to design and predict the properties of generated…

Creating large-scale datasets for training high-performance generative models is often prohibitively expensive, especially when associated attributes or annotations must be provided. As a result, merging existing datasets has become a…

AI-assisted protein design has emerged as a critical tool for advancing biotechnology, as deep generative models have demonstrated their reliability in this domain. However, most existing models primarily utilize protein sequence or…

This paper proposes DiffPF, a differentiable particle filter that leverages diffusion models for state estimation in dynamic systems. Unlike conventional differentiable particle filters, which require importance weighting and typically rely…

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…

Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery.…

Generative AIBIM, a successful structural design pipeline, has proven its ability to intelligently generate high-quality, diverse, and creative shear wall designs that are tailored to specific physical conditions. However, the current…

Motivation: Despite its great success in various physical modeling, differential geometry (DG) has rarely been devised as a versatile tool for analyzing large, diverse and complex molecular and biomolecular datasets due to the limited…

Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes…

Structure-based drug design (SBDD) leverages the 3D structure of biomolecular targets to guide the creation of new therapeutic agents. Recent advances in generative models, including diffusion models and geometric deep learning, have…

Discrete diffusion models generate sequences by iteratively denoising samples corrupted by categorical noise, offering an appealing alternative to autoregressive decoding for structured and symbolic generation. However, standard training…

In this paper, we consider the conditional generation problem by guiding off-the-shelf unconditional diffusion models with differentiable loss functions in a plug-and-play fashion. While previous research has primarily focused on balancing…

Reparameterized diffusion models (RDMs) have recently matched autoregressive methods in protein generation, motivating their use for challenging tasks such as designing membrane proteins, which possess interleaved soluble and transmembrane…

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as…

We introduce the Multi-Motion Discrete Diffusion Models (M2D2M), a novel approach for human motion generation from textual descriptions of multiple actions, utilizing the strengths of discrete diffusion models. This approach adeptly…

Current SMILES-based diffusion models for molecule generation typically support only unimodal constraint. They inject conditioning signals at the start of the training process and require retraining a new model from scratch whenever the…

Structure-based drug design is drawing growing attentions in computer-aided drug discovery. Compared with the virtual screening approach where a pre-defined library of compounds are computationally screened, de novo drug design based on the…