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Denoising diffusion probabilistic models (DDPM) are a class of generative models which have recently been shown to produce excellent samples. We show that with a few simple modifications, DDPMs can also achieve competitive log-likelihoods…

Autoregressive models and their sequential factorization of the data likelihood have recently demonstrated great potential for image representation and synthesis. Nevertheless, they incorporate image context in a linear 1D order by…

Simulating large proteins using traditional molecular dynamics (MD) is computationally demanding. To address this challenge, we propose a novel tree-structured coarse-grained model that efficiently captures protein dynamics. By leveraging a…

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…

Deep generative models have emerged as promising tools for detecting arbitrary anomalies in data, dispensing with the necessity for manual labelling. Recently, autoregressive transformers have achieved state-of-the-art performance for…

In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…

Generating diverse, all-atom conformational ensembles of dynamic proteins such as G-protein-coupled receptors (GPCRs) is critical for understanding their function, yet most generative models simplify atomic detail or ignore conformational…

Generating protein sequences that fold into a intended 3D structure is a fundamental step in de novo protein design. De facto methods utilize autoregressive generation, but this eschews higher order interactions that could be exploited to…

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…

Data-driven and controllable human motion synthesis and prediction are active research areas with various applications in interactive media and social robotics. Challenges remain in these fields for generating diverse motions given past…

Real-world data often has a long-tailed distribution, where the scarcity of tail samples significantly limits the model's generalization ability. Denoising Diffusion Probabilistic Models (DDPM) are generative models based on stochastic…

We present protein autoregressive modeling (PAR), the first multi-scale autoregressive framework for protein backbone generation via coarse-to-fine next-scale prediction. Using the hierarchical nature of proteins, PAR generates structures…

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…

Recently, diffusion models (DMs) have made significant strides in high-quality image generation. However, the multi-step denoising process often results in considerable computational overhead, impeding deployment on resource-constrained…

By reducing resolution, coarse-grained models greatly accelerate molecular simulations, unlocking access to long-timescale phenomena, though at the expense of microscopic information. Recovering this fine-grained detail is essential for…

Peptide de novo sequencing is a method used to reconstruct amino acid sequences from tandem mass spectrometry data without relying on existing protein sequence databases. Traditional deep learning approaches, such as Casanovo, mainly…

Diffusion Probabilistic Models (DPMs) have achieved great success in image generation but suffer from high inference latency due to their iterative denoising nature. Motivated by the evolving feature dynamics across the denoising…

Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…

Diffusion models have recently gained traction as a powerful class of deep generative priors, excelling in a wide range of image restoration tasks due to their exceptional ability to model data distributions. To solve image restoration…

Understanding protein dynamics is critical for elucidating their biological functions. The increasing availability of molecular dynamics (MD) data enables the training of deep generative models to efficiently explore the conformational…