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The goal of protein design is to generate amino acid sequences that fold into functional structures with desired properties. Prior methods combining autoregressive language models with Monte Carlo Tree Search (MCTS) struggle with long-range…

Machine Learning · Computer Science 2026-02-25 Xuefeng Liu , Mingxuan Cao , Songhao Jiang , Xiao Luo , Xiaotian Duan , Mengdi Wang , Tobin R. Sosnick , Jinbo Xu , Rick Stevens

Designing functional protein sequences that satisfy multiple desired properties is a core research focus of protein engineering. Prior methods struggle with inability or inefficiency when dealing with numerous, often conflicting,…

Biomolecules · Quantitative Biology 2026-05-08 Zitai Kong , Yifan Dong , Yixuan Wu , Zhaokang Liang , Jian Wu , Hongxia Xu

In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…

Soft Condensed Matter · Physics 2015-06-12 G. Foffano , D. Marenduzzo , E. Orlandini

Masked diffusion models (MDM) are powerful generative models for discrete data that generate samples by progressively unmasking tokens in a sequence. Each token can take one of two states: masked or unmasked. We observe that token sequences…

Machine Learning · Computer Science 2025-10-23 Chen-Hao Chao , Wei-Fang Sun , Hanwen Liang , Chun-Yi Lee , Rahul G. Krishnan

n this work, we propose a latent molecular diffusion model that can make the generated 3D molecules rich in diversity and maintain rich geometric features. The model captures the information of the forces and local constraints between atoms…

Machine Learning · Computer Science 2024-12-06 Xiang Chen

Procedural Content Generation (PCG) is powerful in creating high-quality 3D contents, yet controlling it to produce desired shapes is difficult and often requires extensive parameter tuning. Inverse Procedural Content Generation aims to…

Computer Vision and Pattern Recognition · Computer Science 2024-12-20 Wang Zhao , Yan-Pei Cao , Jiale Xu , Yuejiang Dong , Ying Shan

In this paper, we introduce a denoising diffusion algorithm to discover microstructures with nonlinear fine-tuned properties. Denoising diffusion probabilistic models are generative models that use diffusion-based dynamics to gradually…

Machine Learning · Computer Science 2023-06-14 Nikolaos N. Vlassis , WaiChing Sun

Speculative decoding has become the standard approach for accelerating Large Language Model (LLM) inference. It exploits a lossless draft-then-verify procedure to circumvent the latency of autoregressive decoding, achieving impressive…

Computation and Language · Computer Science 2025-11-05 Jameson Sandler , Jacob K. Christopher , Thomas Hartvigsen , Ferdinando Fioretto

Existing autoregressive (AR) methods for generating artist-designed meshes struggle to balance global structural consistency with high-fidelity local details, and are susceptible to error accumulation. To address this, we propose…

Computer Vision and Pattern Recognition · Computer Science 2026-05-19 Yichen Yang , Hong Li , Haodong Zhu , Linin Yang , Guojun Lei , Sheng Xu , Baochang Zhang

The implementation of diffusion-based pansharpening task is predominantly constrained by its slow inference speed, which results from numerous sampling steps. Despite the existing techniques aiming to accelerate sampling, they often…

Computer Vision and Pattern Recognition · Computer Science 2025-01-13 Shiqi Cao , Liangjian Deng , Shangqi Deng

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,…

Computer Vision and Pattern Recognition · Computer Science 2023-12-11 Xinyin Ma , Gongfan Fang , Xinchao Wang

Denoising Diffusion Probabilistic Models (DDPMs) have emerged as a powerful family of generative models that can yield high-fidelity samples and competitive log-likelihoods across a range of domains, including image and speech synthesis.…

Machine Learning · Computer Science 2021-06-08 Daniel Watson , Jonathan Ho , Mohammad Norouzi , William Chan

We investigate methods to reduce inference time and memory footprint in stable diffusion models by introducing lightweight decoders for both image and video synthesis. Traditional latent diffusion pipelines rely on large Variational…

Computer Vision and Pattern Recognition · Computer Science 2025-03-10 Alexey Buzovkin , Evgeny Shilov

Diffusion models have emerged as the new state-of-the-art generative model with high quality samples, with intriguing properties such as mode coverage and high flexibility. They have also been shown to be effective inverse problem solvers,…

Computer Vision and Pattern Recognition · Computer Science 2025-10-06 Hyungjin Chung , Dohoon Ryu , Michael T. McCann , Marc L. Klasky , Jong Chul Ye

Diffusion Models have become a cornerstone of modern generative AI for their exceptional generation quality and controllability. However, their inherent \textit{multi-step iterations} and \textit{complex backbone networks} lead to…

Diffusion models have recently attained significant interest within the community owing to their strong performance as generative models. Furthermore, its application to inverse problems have demonstrated state-of-the-art performance.…

Image and Video Processing · Electrical Eng. & Systems 2022-03-22 Hyungjin Chung , Byeongsu Sim , Jong Chul Ye

Graph-based diffusion models have shown promising results in terms of generating high-quality solutions to NP-complete (NPC) combinatorial optimization (CO) problems. However, those models are often inefficient in inference, due to the…

Machine Learning · Computer Science 2023-08-24 Junwei Huang , Zhiqing Sun , Yiming Yang

Any order generation of discrete data using masked diffusion models (MDMs) offers a compelling alternative to traditional autoregressive models, especially in domains that lack a natural causal ordering of data. However, current popular…

Inverse-designed nanophotonic devices offer promising solutions for analog optical computation. High-density photonic integration is critical for scaling such architectures toward more complex computational tasks and large-scale…

Optics · Physics 2025-06-09 Joel Sved , Shijie Song , Liwei Li , George Li , Debin Meng , Xiaoke Yi

Biologists frequently desire protein inhibitors for a variety of reasons, including use as research tools for understanding biological processes and application to societal problems in agriculture, healthcare, etc. Immunotherapy, for…

Machine Learning · Computer Science 2024-11-04 Po-Yu Liang , Jun Bai