Related papers: Equivariant Asynchronous Diffusion: An Adaptive De…

The vast applications of deep generative models are anchored in three core capabilities -- generating new instances, reconstructing inputs, and learning compact representations -- across various data types, such as discrete text/protein…

We present significant extensions to diffusion-based sequence generation models, blurring the line with autoregressive language models. We introduce hyperschedules, which assign distinct noise schedules to individual token positions,…

Molecule generation, especially generating 3D molecular geometries from scratch (i.e., 3D \textit{de novo} generation), has become a fundamental task in drug designs. Existing diffusion-based 3D molecule generation methods could suffer from…

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…

Discrete diffusion models have recently shown great promise for modeling complex discrete data, with masked diffusion models (MDMs) offering a compelling trade-off between quality and generation speed. MDMs denoise by progressively…

Edge-enhancing diffusion (EED) can reconstruct a close approximation of an original image from a small subset of its pixels. This makes it an attractive foundation for PDE based image compression. In this work, we generalize second-order…

Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one…

Discrete diffusion models are a class of generative models that construct sequences by progressively denoising samples from a categorical noise distribution. Beyond their rapidly growing ability to generate coherent natural language, these…

Diffusion models have recently achieved great success in the synthesis of high-quality images and videos. However, the existing denoising techniques in diffusion models are commonly based on step-by-step noise predictions, which suffers…

Extracting 3D atomic coordinates from spectroscopic data is a longstanding inverse problem. We present an equivariant diffusion model that generates site-specific 3D structures directly from near-edge spectra (ELNES/XANES). Trained on Si-O…

Diffusion Probabilistic Models (DPMs) have emerged as a powerful class of deep generative models, achieving remarkable performance in image synthesis tasks. However, these models face challenges in terms of widespread adoption due to their…

Breakthroughs in high-accuracy protein structure prediction, such as AlphaFold, have established receptor-based molecule design as a critical driver for rapid early-phase drug discovery. However, most approaches still struggle to balance…

Transformer-based autoregressive models offer an efficient alternative to diffusion- and flow-matching-based approaches for generating 3D molecules. One challenge remains: standard transformer architectures require a sequential ordering of…

Can we train a 3D molecule generator using data from dense regions to generate samples in sparse regions? This challenge can be framed as an out-of-distribution (OOD) generation problem. While prior research on OOD generation predominantly…

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…

We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new representation of protein structure, relies on a novel…

We propose SDAR, a Synergistic Diffusion-Autoregression paradigm that unifies the training efficiency of autoregressive models with the parallel inference capability of diffusion. Instead of costly end-to-end diffusion training, SDAR…

Denoising diffusion models have shown great potential in multiple research areas. Existing diffusion-based generative methods on de novo 3D molecule generation face two major challenges. Since majority heavy atoms in molecules allow…

Diffusion-based models have shown great promise in molecular generation but often require a large number of sampling steps to generate valid samples. In this paper, we introduce a novel Straight-Line Diffusion Model (SLDM) to tackle this…

The goal of point cloud assembly is to reconstruct a complete 3D shape by aligning multiple point cloud pieces. This work presents a novel equivariant solver for assembly tasks based on flow matching models. We first theoretically show that…