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We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of…

Far from equilibrium, neural systems self-organize across multiple scales. Exploiting multiscale self-organization in neuroscience and artificial intelligence requires a computational framework for modeling the effective non-equilibrium…

Accelerating the sampling speed of diffusion models remains a significant challenge. Recent score distillation methods distill a heavy teacher model into a student generator to achieve one-step generation, which is optimized by calculating…

Denoising diffusion models, a class of generative models, have garnered immense interest lately in various deep-learning problems. A diffusion probabilistic model defines a forward diffusion stage where the input data is gradually perturbed…

Diffusion models (DMs), lauded for their generative performance, are computationally prohibitive due to their billion-scale parameters and iterative denoising dynamics. Existing efficiency techniques, such as quantization, timestep…

Diffusion-based generative models have recently emerged as powerful solutions for high-quality synthesis in multiple domains. Leveraging the bidirectional Markov chains, diffusion probabilistic models generate samples by inferring the…

Denoising Diffusion Probabilistic Models (DDPM) have recently gained significant attention. DDPMs compose a Markovian process that begins in the data domain and gradually adds noise until reaching pure white noise. DDPMs generate…

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…

Recent advancements in solving Bayesian inverse problems have spotlighted denoising diffusion models (DDMs) as effective priors. Although these have great potential, DDM priors yield complex posterior distributions that are challenging to…

Many interesting tasks in image restoration can be cast as linear inverse problems. A recent family of approaches for solving these problems uses stochastic algorithms that sample from the posterior distribution of natural images given the…

We derive a minimalist but powerful deterministic denoising-diffusion model. While denoising diffusion has shown great success in many domains, its underlying theory remains largely inaccessible to non-expert users. Indeed, an understanding…

Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…

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…

We propose a novel approach based on Denoising Diffusion Probabilistic Models (DDPMs) to control nonlinear dynamical systems. DDPMs are the state-of-art of generative models that have achieved success in a wide variety of sampling tasks. In…

In medical imaging, the diffusion models have shown great potential for synthetic image generation tasks. However, these approaches often lack the interpretable connections between the generated and real images and can create anatomically…

Normative modeling estimates reference distributions of biological measures conditional on covariates, enabling centiles and clinically interpretable deviation scores to be derived. Most neuroimaging pipelines fit one model per…

Diffusion policies, widely adopted in decision-making scenarios such as robotics, gaming and autonomous driving, are capable of learning diverse skills from demonstration data due to their high representation power. However, the sub-optimal…

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…

Diffusion models have recently gained unprecedented attention in the field of image synthesis due to their remarkable generative capabilities. Notwithstanding their prowess, these models often incur substantial computational costs,…

Denoising Diffusion Models (DDMs) have become a popular tool for generating high-quality samples from complex data distributions. These models are able to capture sophisticated patterns and structures in the data, and can generate samples…