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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

Autoregressive visual generation has garnered increasing attention due to its scalability and compatibility with other modalities compared with diffusion models. Most existing methods construct visual sequences as spatial patches for…

Computer Vision and Pattern Recognition · Computer Science 2025-06-13 Yuanhui Huang , Weiliang Chen , Wenzhao Zheng , Yueqi Duan , Jie Zhou , Jiwen Lu

Graph generation generally aims to create new graphs that closely align with a specific graph distribution. Existing works often implicitly capture this distribution through the optimization of generators, potentially overlooking the…

Machine Learning · Computer Science 2024-07-19 Song Wang , Zhen Tan , Xinyu Zhao , Tianlong Chen , Huan Liu , Jundong Li

Nowadays, scene text recognition has attracted more and more attention due to its various applications. Most state-of-the-art methods adopt an encoder-decoder framework with attention mechanism, which generates text autoregressively from…

Computer Vision and Pattern Recognition · Computer Science 2021-09-10 Zhi Qiao , Yu Zhou , Jin Wei , Wei Wang , Yuan Zhang , Ning Jiang , Hongbin Wang , Weiping Wang

As text generation has become a core capability of modern Large Language Models (LLMs), it underpins a wide range of downstream applications. However, most existing LLMs rely on autoregressive (AR) generation, producing one token at a time…

Computation and Language · Computer Science 2026-02-11 Lingzhe Zhang , Liancheng Fang , Chiming Duan , Minghua He , Leyi Pan , Pei Xiao , Shiyu Huang , Yunpeng Zhai , Xuming Hu , Philip S. Yu , Aiwei Liu

Decoding-based regression, which reformulates regression as a sequence generation task, has emerged as a promising paradigm of applying large language models for numerical prediction. However, its progress is hindered by the misalignment…

Machine Learning · Computer Science 2025-12-09 Ming Chen , Sheng Tang , Rong-Xi Tan , Ziniu Li , Jiacheng Chen , Ke Xue , Chao Qian

Modeling the time-dependent evolution of electron density is essential for understanding quantum mechanical behaviors of condensed matter and enabling predictive simulations in spectroscopy, photochemistry, and ultrafast science. Yet, while…

Computational Physics · Physics 2025-09-03 Yuan Chiang , Youngsoo Choi , Daniel Osei-Kuffuor

In this paper, we propose Continuous Graph Flow, a generative continuous flow based method that aims to model complex distributions of graph-structured data. Once learned, the model can be applied to an arbitrary graph, defining a…

Machine Learning · Computer Science 2019-10-01 Zhiwei Deng , Megha Nawhal , Lili Meng , Greg Mori

Directed graphs naturally model systems with asymmetric, ordered relationships, essential to applications in biology, transportation, social networks, and visual understanding. Generating such graphs enables tasks such as simulation, data…

Machine Learning · Computer Science 2026-02-20 Alba Carballo-Castro , Manuel Madeira , Yiming Qin , Dorina Thanou , Pascal Frossard

To mitigate the high inference latency stemming from autoregressive decoding in Large Language Models (LLMs), Speculative Decoding has emerged as a novel decoding paradigm for LLM inference. In each decoding step, this method first drafts…

Computation and Language · Computer Science 2024-06-05 Heming Xia , Zhe Yang , Qingxiu Dong , Peiyi Wang , Yongqi Li , Tao Ge , Tianyu Liu , Wenjie Li , Zhifang Sui

Statistical generative models for molecular graphs attract attention from many researchers from the fields of bio- and chemo-informatics. Among these models, invertible flow-based approaches are not fully explored yet. In this paper, we…

Machine Learning · Computer Science 2019-10-01 Shion Honda , Hirotaka Akita , Katsuhiko Ishiguro , Toshiki Nakanishi , Kenta Oono

Code completion tools are frequently used by software developers to accelerate software development by suggesting the following code elements. Completing a sequence of code tokens (e.g., a full line of code) has been proved more efficient…

Software Engineering · Computer Science 2022-04-22 Fang Liu , Zhiyi Fu , Ge Li , Zhi Jin , Hui Liu , Yiyang Hao

Diffusion language models have recently emerged as a competitive alternative to autoregressive language models. Beyond next-token generation, they are more efficient and flexible by enabling parallel and any-order token generation. However,…

Machine Learning · Computer Science 2025-11-18 Chenxiao Yang , Cai Zhou , David Wipf , Zhiyuan Li

Transformers can generate predictions in two approaches: 1. auto-regressively by conditioning each sequence element on the previous ones, or 2. directly produce an output sequences in parallel. While research has mostly explored upon this…

Computer Vision and Pattern Recognition · Computer Science 2021-08-18 Andrea Alfieri , Yancong Lin , Jan C. van Gemert

Vision-Language Latent Diffusion Models (LDMs) (Rombach et al., 2022) provide powerful generative priors for inverse problems. However, existing LDM-based inverse solvers typically require a large number of neural function evaluations…

Machine Learning · Statistics 2026-05-11 Alessio Spagnoletti , Tim Y. J. Wang , Marcelo Pereyra , O. Deniz Akyildiz

Non-autoregressive (NAR) language models offer notable efficiency in text generation by circumventing the sequential bottleneck of autoregressive decoding. However, accurately modeling dependencies in discrete sequences remains challenging…

Computation and Language · Computer Science 2026-05-05 Egor Sevriugov , Nikita Dragunov , Anton Razzhigaev , Andrey Kuznetsov , Ivan Oseledets

Autoregressive models have recently shown great promise in visual generation by leveraging discrete token sequences akin to language modeling. However, existing approaches often suffer from inefficiency, either due to token-by-token…

Computer Vision and Pattern Recognition · Computer Science 2025-11-20 Ruiqing Yang , Kaixin Zhang , Zheng Zhang , Shan You , Tao Huang

Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…

Machine Learning · Computer Science 2022-03-02 Yuanqi Du , Xiaojie Guo , Amarda Shehu , Liang Zhao

We present an extension of our Molecular Transformer architecture combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state…

The stochastic reaction network in which chemical species evolve through a set of reactions is widely used to model stochastic processes in physics, chemistry and biology. To characterize the evolving joint probability distribution in the…

Molecular Networks · Quantitative Biology 2023-02-08 Ying Tang , Jiayu Weng , Pan Zhang
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