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Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond…

Machine Learning · Computer Science 2021-10-06 Zhao Xu , Youzhi Luo , Xuan Zhang , Xinyi Xu , Yaochen Xie , Meng Liu , Kaleb Dickerson , Cheng Deng , Maho Nakata , Shuiwang Ji

A molecule's 2D representation consists of its atoms, their attributes, and the molecule's covalent bonds. A 3D (geometric) representation of a molecule is called a conformer and consists of its atom types and Cartesian coordinates. Every…

Molecular property prediction, crucial for early drug candidate screening and optimization, has seen advancements with deep learning-based methods. While deep learning-based methods have advanced considerably, they often fall short in fully…

Biomolecules · Quantitative Biology 2024-07-01 Taojie Kuang , Yiming Ren , Zhixiang Ren

Visual autoregressive models typically adhere to a raster-order ``next-token prediction" paradigm, which overlooks the spatial and temporal locality inherent in visual content. Specifically, visual tokens exhibit significantly stronger…

Computer Vision and Pattern Recognition · Computer Science 2025-03-17 Yefei He , Yuanyu He , Shaoxuan He , Feng Chen , Hong Zhou , Kaipeng Zhang , Bohan Zhuang

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences…

Biomolecules · Quantitative Biology 2025-03-19 Shuqi Lu , Xiaohong Ji , Bohang Zhang , Lin Yao , Siyuan Liu , Zhifeng Gao , Linfeng Zhang , Guolin Ke

Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology. Previous methods usually first predict the interatomic distances,…

Artificial Intelligence · Computer Science 2023-01-02 Jinhua Zhu , Yingce Xia , Chang Liu , Lijun Wu , Shufang Xie , Yusong Wang , Tong Wang , Tao Qin , Wengang Zhou , Houqiang Li , Haiguang Liu , Tie-Yan Liu

Prevailing autoregressive (AR) models for text-to-image generation either rely on heavy, computationally-intensive diffusion models to process continuous image tokens, or employ vector quantization (VQ) to obtain discrete tokens with…

Autoregressive transformers have revolutionized generative models in language processing and shown substantial promise in image and video generation. However, these models face significant challenges when extended to 3D generation tasks due…

Computer Vision and Pattern Recognition · Computer Science 2024-09-11 Jinzhi Zhang , Feng Xiong , Mu Xu

We introduce RandAR, a decoder-only visual autoregressive (AR) model capable of generating images in arbitrary token orders. Unlike previous decoder-only AR models that rely on a predefined generation order, RandAR removes this inductive…

Computer Vision and Pattern Recognition · Computer Science 2025-07-09 Ziqi Pang , Tianyuan Zhang , Fujun Luan , Yunze Man , Hao Tan , Kai Zhang , William T. Freeman , Yu-Xiong Wang

Autoregressive image generation aims to predict the next token based on previous ones. However, this process is challenged by the bidirectional dependencies inherent in conventional image tokenizations, which creates a fundamental…

Computer Vision and Pattern Recognition · Computer Science 2026-02-17 Pingyu Wu , Kai Zhu , Yu Liu , Longxiang Tang , Jian Yang , Yansong Peng , Wei Zhai , Yang Cao , Zheng-Jun Zha

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…

Biomolecules · Quantitative Biology 2025-01-09 Bobin Yang , Jie Deng , Zhenghan Chen , Ruoxue Wu

Recent advances in video generation have been dominated by diffusion and flow-matching models, which produce high-quality results but remain computationally intensive and difficult to scale. In this work, we introduce VideoAR, the first…

Computer Vision and Pattern Recognition · Computer Science 2026-01-15 Longbin Ji , Xiaoxiong Liu , Junyuan Shang , Shuohuan Wang , Yu Sun , Hua Wu , Haifeng Wang

De novo molecule design has become a highly active research area, advanced significantly through the use of state-of-the-art generative models. Despite these advances, several fundamental questions remain unanswered as the field…

Biomolecules · Quantitative Biology 2024-09-09 Heath Arthur-Loui , Amina Mollaysa , Michael Krauthammer

We consider the conditional generation of 3D drug-like molecules with \textit{explicit control} over molecular properties such as drug-like properties (e.g., Quantitative Estimate of Druglikeness or Synthetic Accessibility score) and…

Machine Learning · Computer Science 2024-12-20 Haoran Liu , Youzhi Luo , Tianxiao Li , James Caverlee , Martin Renqiang Min

This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly…

Machine Learning · Computer Science 2022-06-17 Emiel Hoogeboom , Victor Garcia Satorras , Clément Vignac , Max Welling

Recent advancements in autoregressive and diffusion models have led to strong performance in image generation with short scene text words. However, generating coherent, long-form text in images, such as paragraphs in slides or documents,…

Computer Vision and Pattern Recognition · Computer Science 2025-03-27 Alex Jinpeng Wang , Linjie Li , Zhengyuan Yang , Lijuan Wang , Min Li

AutoRegressive (AR) models have made notable progress in image generation, with Masked AutoRegressive (MAR) models gaining attention for their efficient parallel decoding. However, MAR models have traditionally underperformed when compared…

Computer Vision and Pattern Recognition · Computer Science 2025-07-18 Yi Xin , Le Zhuo , Qi Qin , Siqi Luo , Yuewen Cao , Bin Fu , Yangfan He , Hongsheng Li , Guangtao Zhai , Xiaohong Liu , Peng Gao

Most recent advances in 3D generative modeling rely on diffusion or flow-matching formulations. We instead explore a fully autoregressive alternative and introduce GaussianGPT, a transformer-based model that directly generates 3D Gaussians…

Computer Vision and Pattern Recognition · Computer Science 2026-03-30 Nicolas von Lützow , Barbara Rössle , Katharina Schmid , Matthias Nießner

Autoregressive models for video generation typically operate frame-by-frame, extending next-token prediction from language to video's temporal dimension. We question that unlike word as token is universally agreed in language if frame is a…

Computer Vision and Pattern Recognition · Computer Science 2025-09-30 Sucheng Ren , Chen Chen , Zhenbang Wang , Liangchen Song , Xiangxin Zhu , Alan Yuille , Yinfei Yang , Jiasen Lu

Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…

Machine Learning · Computer Science 2019-09-04 Jordan Hoffmann , Louis Maestrati , Yoshihide Sawada , Jian Tang , Jean Michel Sellier , Yoshua Bengio