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Generating desirable molecular structures in 3D is a fundamental problem for drug discovery. Despite the considerable progress we have achieved, existing methods usually generate molecules in atom resolution and ignore intrinsic local…

Biomolecules · Quantitative Biology 2023-05-29 Bo Qiang , Yuxuan Song , Minkai Xu , Jingjing Gong , Bowen Gao , Hao Zhou , Weiying Ma , Yanyan Lan

We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports conditional generation of molecules over twelve properties, enabling flexible control across…

Machine Learning · Computer Science 2025-05-27 Raul Ortega-Ochoa , Tejs Vegge , Jes Frellsen

Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular…

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…

Machine Learning · Computer Science 2022-09-14 Lei Huang , Hengtong Zhang , Tingyang Xu , Ka-Chun Wong

Recent advances in auto-regressive transformers have revolutionized generative modeling across different domains, from language processing to visual generation, demonstrating remarkable capabilities. However, applying these advances to 3D…

Computer Vision and Pattern Recognition · Computer Science 2025-04-22 Jinnan Chen , Lingting Zhu , Zeyu Hu , Shengju Qian , Yugang Chen , Xin Wang , Gim Hee Lee

Visual autoregressive (AR) generation offers a promising path toward unifying vision and language models, yet its performance remains suboptimal against diffusion models. Prior work often attributes this gap to tokenizer limitations and…

Computer Vision and Pattern Recognition · Computer Science 2025-10-07 Qiyuan He , Yicong Li , Haotian Ye , Jinghao Wang , Xinyao Liao , Pheng-Ann Heng , Stefano Ermon , James Zou , Angela Yao

Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free…

Biomolecules · Quantitative Biology 2023-03-08 Jiaqi Guan , Wesley Wei Qian , Xingang Peng , Yufeng Su , Jian Peng , Jianzhu Ma

Autoregressive (AR) models for image generation typically adopt a two-stage paradigm of vector quantization and raster-scan ``next-token prediction", inspired by its great success in language modeling. However, due to the huge modality gap,…

Computer Vision and Pattern Recognition · Computer Science 2026-03-19 Hu Yu , Hao Luo , Hangjie Yuan , Yu Rong , Jie Huang , Feng Zhao

The raster-ordered image token sequence exhibits a significant Euclidean distance between index-adjacent tokens at line breaks, making it unsuitable for autoregressive generation. To address this issue, this paper proposes Direction-Aware…

Computer Vision and Pattern Recognition · Computer Science 2025-04-17 Yijia Xu , Jianzhong Ju , Jian Luan , Jinshi Cui

Autoregressive models have emerged as a powerful paradigm for visual content creation, but often overlook the intrinsic structural properties of visual data. Our prior work, IAR, initiated a direction to address this by reorganizing the…

Computer Vision and Pattern Recognition · Computer Science 2026-05-28 Ran Yi , Teng Hu , Zihan Su , Jiangning Zhang , Lizhuang Ma

Discovery of atomistic systems with desirable properties is a major challenge in chemistry and material science. Here we introduce a novel, autoregressive, convolutional deep neural network architecture that generates molecular equilibrium…

Machine Learning · Statistics 2018-10-29 Niklas W. A. Gebauer , Michael Gastegger , Kristof T. Schütt

Deep learning has proven to yield fast and accurate predictions of quantum-chemical properties to accelerate the discovery of novel molecules and materials. As an exhaustive exploration of the vast chemical space is still infeasible, we…

Machine Learning · Statistics 2020-01-10 Niklas W. A. Gebauer , Michael Gastegger , Kristof T. Schütt

Object 6D pose estimation, a crucial task for robotics and augmented reality applications, becomes particularly challenging when dealing with novel objects whose 3D models are not readily available. To reduce dependency on 3D models, recent…

Computer Vision and Pattern Recognition · Computer Science 2025-12-16 Dexin Zuo , Ang Li , Wei Wang , Wenxian Yu , Danping Zou

Autoregressive image modeling relies on visual tokenizers to compress images into compact latent representations. We design an end-to-end training pipeline that jointly optimizes reconstruction and generation, enabling direct supervision…

Computer Vision and Pattern Recognition · Computer Science 2026-05-05 Wenda Chu , Bingliang Zhang , Jiaqi Han , Yizhuo Li , Linjie Yang , Yisong Yue , Qiushan Guo

Recent progress in controllable image generation and editing is largely driven by diffusion-based methods. Although diffusion models perform exceptionally well in specific tasks with tailored designs, establishing a unified model is still…

Computer Vision and Pattern Recognition · Computer Science 2025-01-09 Jiteng Mu , Nuno Vasconcelos , Xiaolong Wang

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…

We present LTM3D, a Latent Token space Modeling framework for conditional 3D shape generation that integrates the strengths of diffusion and auto-regressive (AR) models. While diffusion-based methods effectively model continuous latent…

Computer Vision and Pattern Recognition · Computer Science 2025-06-02 Xin Kang , Zihan Zheng , Lei Chu , Yue Gao , Jiahao Li , Hao Pan , Xuejin Chen , Yan Lu

We present Infinity, a Bitwise Visual AutoRegressive Modeling capable of generating high-resolution, photorealistic images following language instruction. Infinity redefines visual autoregressive model under a bitwise token prediction…

Computer Vision and Pattern Recognition · Computer Science 2025-06-18 Jian Han , Jinlai Liu , Yi Jiang , Bin Yan , Yuqi Zhang , Zehuan Yuan , Bingyue Peng , Xiaobing Liu

Existing autoregressive (AR) image generative models use a token-by-token generation schema. That is, they predict a per-token probability distribution and sample the next token from that distribution. The main challenge is how to model the…

Computer Vision and Pattern Recognition · Computer Science 2025-03-05 Qinyu Zhao , Stephen Gould , Liang Zheng

Disordered molecular systems such as amorphous catalysts, organic thin films, electrolyte solutions, and water are at the cutting edge of computational exploration today. Traditional simulations of such systems at length-scales relevant to…

Mesoscale and Nanoscale Physics · Physics 2023-09-06 Ata Madanchi , Michael Kilgour , Frederik Zysk , Thomas D. Kühne , Lena Simine