Related papers: ProT-GFDM: A Generative Fractional Diffusion Model…

Score-based stochastic denoising models have recently been demonstrated as powerful machine learning tools for conditional and unconditional image generation. The existing methods are based on a forward stochastic process wherein the…

Diffusion models (DMs) are a class of generative machine learning methods that sample a target distribution by transforming samples of a trivial (often Gaussian) distribution using a learned stochastic differential equation. In standard…

Diffusion models generate data by learning to reverse a forward process, where samples are progressively perturbed with Gaussian noise according to a predefined noise schedule. From a geometric perspective, each noise schedule corresponds…

Diffusion models are state-of-the-art generative models on data modalities such as images, audio, proteins and materials. These modalities share the property of exponentially decaying variance and magnitude in the Fourier domain. Under the…

Coarse-grained (CG) models play a crucial role in the study of protein structures, protein thermodynamic properties, and protein conformation dynamics. Due to the information loss in the coarse-graining process, backmapping from CG to…

The dynamics of short-lived mRNA results in bursts of protein production in gene regulatory networks. We investigate the propagation of bursting noise between different levels of mathematical modelling, and demonstrate that conventional…

Generative models have the potential to accelerate key steps in the discovery of novel molecular therapeutics and materials. Diffusion models have recently emerged as a powerful approach, excelling at unconditional sample generation and,…

We present an investigation into diffusion models for molecular generation, with the aim of better understanding how their predictions compare to the results of physics-based calculations. The investigation into these models is driven by…

We propose in this paper an analytically new construct of a diffusion model whose drift and diffusion parameters yield an exponentially time-decaying Signal to Noise Ratio in the forward process. In reverse, the construct cleverly carries…

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates…

Diffusion models have demonstrated significant potential in producing high-quality images in medical image translation to aid disease diagnosis, localization, and treatment. Nevertheless, current diffusion models have limited success in…

Accurate forecasting of spatiotemporal data remains challenging due to complex spatial dependencies and temporal dynamics. The inherent uncertainty and variability in such data often render deterministic models insufficient, prompting a…

We propose a new class of generative models that naturally handle data of varying dimensionality by jointly modeling the state and dimension of each datapoint. The generative process is formulated as a jump diffusion process that makes…

Protein design with desirable properties has been a significant challenge for many decades. Generative artificial intelligence is a promising approach and has achieved great success in various protein generation tasks. Notably, diffusion…

Diffusion models have emerged as powerful generative frameworks by progressively adding noise to data through a forward process and then reversing this process to generate realistic samples. While these models have achieved strong…

Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function.…

Recent advances in generative modeling with diffusion processes (DPs) enabled breakthroughs in image synthesis. Despite impressive image quality, these models have various prompt compliance problems, including low recall in generating…

This paper introduces a discrete diffusion model (DDM) framework for text-aligned speech tokenization and reconstruction. By replacing the auto-regressive speech decoder with a discrete diffusion counterpart, our model achieves…

Recent advances in generative modeling -- particularly diffusion models and flow matching -- have achieved remarkable success in synthesizing discrete data such as images and videos. However, adapting these models to physical applications…

This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from…