Related papers: Protein Design with Guided Discrete Diffusion

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…

Diffusion Probabilistic Models (DPMs) are powerful generative models that have achieved unparalleled success in a number of generative tasks. In this work, we aim to build inductive biases into the training and sampling of diffusion models…

Due to the high complexity and technical requirements of industrial production processes, surface defects will inevitably appear, which seriously affects the quality of products. Although existing lightweight detection networks are highly…

Deep generative models have achieved tremendous success in structure-based drug design in recent years, especially for generating 3D ligand molecules that bind to specific protein pocket. Notably, diffusion models have transformed ligand…

Diffusion models have shown remarkable success across a wide range of generative tasks. However, they often suffer from spatially inconsistent generation, arguably due to the inherent locality of their denoising mechanisms. This can yield…

The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…

Masked diffusion language models (MDLMs) have recently emerged as a new paradigm in language modeling, offering flexible generation dynamics and enabling efficient parallel decoding. However, existing decoding strategies for pre-trained…

Tandem mass spectrometry (MS/MS) is a high-throughput technology used toidentify the proteins in a complex biological sample, such as a drop of blood. A collection of spectra is generated at the output of the process, each spectrum of which…

Diffusion Models (DMs) have demonstrated state-of-the-art performance in content generation without requiring adversarial training. These models are trained using a two-step process. First, a forward - diffusion - process gradually adds…

The de novo design of ligand-binding proteins with tailored functions is essential for advancing biotechnology and molecular medicine, yet existing AI approaches are limited by scarce protein-ligand complex data. To circumvent this data…

RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…

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 models have made substantial advances in image generation, yet models trained on large, unfiltered datasets often yield outputs misaligned with human preferences. Numerous methods have been proposed to fine-tune pre-trained…

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 Language Models (DLMs) have recently emerged as a promising alternative to autoregressive language models, offering stronger global awareness and highly parallel generation. However, post-training DLMs with standard Negative…

Diffusion models have demonstrated remarkable success in various visual generation tasks, including image, video, and 3D content generation. Preference optimization (PO) is a prominent and growing area of research that aims to align these…

The performance of pre-trained masked diffusion models is often constrained by their sampling procedure, which makes decisions irreversible and struggles in low-step generation regimes. We introduce a novel sampling algorithm that works…

Diffusion-based generative models (DBGMs) perturb data to a target noise distribution and reverse this process to generate samples. The choice of noising process, or inference diffusion process, affects both likelihoods and sample quality.…

Diffusion models are powerful generative models that map noise to data using stochastic processes. However, for many applications such as image editing, the model input comes from a distribution that is not random noise. As such, diffusion…

Inverse design refers to the problem of optimizing the input of an objective function in order to enact a target outcome. For many real-world engineering problems, the objective function takes the form of a simulator that predicts how the…