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Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language…

Biomolecules · Quantitative Biology 2025-06-11 Logan Hallee , Nikolaos Rafailidis , David B. Bichara , Jason P. Gleghorn

Since the advent of reasoning-based large language models, many have found great success from distilling reasoning capabilities into student models. Such techniques have significantly bridged the gap between reasoning and standard LLMs on…

Masked diffusion models (MDMs) have emerged as a promising alternative to autoregressive models for language modeling, yet the effective design of transformer architectures for MDMs remains underexplored. In this paper, we show that…

Machine Learning · Computer Science 2026-05-26 Sanghyun Lee , Chunsan Hong , Seungryong Kim , Jonghyun Lee , Jongho Park , Dongmin Park

Recent advances in diffusion large language models (dLLMs) have introduced a promising alternative to autoregressive (AR) LLMs for natural language generation tasks, leveraging full attention and denoising-based decoding strategies.…

Computation and Language · Computer Science 2026-03-17 Haokun Lin , Haobo Xu , Yichen Wu , Ziyu Guo , Renrui Zhang , Zhichao Lu , Ying Wei , Qingfu Zhang , Zhenan Sun

Masked diffusion language models (MDLMs) are trained to in-fill positions in randomly masked sequences, in contrast to next-token prediction models. Discussions around MDLMs focus on two benefits: (1) any-order decoding and 2) multi-token…

Machine Learning · Computer Science 2025-10-24 Zachary Horvitz , Raghav Singhal , Hao Zou , Carles Domingo-Enrich , Zhou Yu , Rajesh Ranganath , Kathleen McKeown

Fine-tuning Large Language Models (LLMs) on specific datasets is a common practice to improve performance on target tasks. However, this performance gain often leads to overfitting, where the model becomes too specialized in either the task…

Computation and Language · Computer Science 2025-02-21 Sonam Gupta , Yatin Nandwani , Asaf Yehudai , Dinesh Khandelwal , Dinesh Raghu , Sachindra Joshi

Large Language Models (LLMs) have demonstrated remarkable efficiency in tackling various tasks based on human instructions, but studies reveal that they often struggle with tasks requiring reasoning, such as math or physics. This limitation…

Computation and Language · Computer Science 2024-10-08 Ruoyu Wang , Xiaoxuan Li , Lina Yao

Memorization in large language models has been studied almost exclusively through prefix-conditioned extraction, a natural choice for autoregressive models. However, diffusion language models (DLMs) can denoise masked tokens at arbitrary…

Computation and Language · Computer Science 2026-05-26 Yihan Wang , N. Asokan

Diffusion Large Language Models (dLLMs) enable breakthroughs in reasoning and parallel decoding but suffer from prohibitive quadratic computational complexity and memory overhead during inference. Current caching techniques accelerate…

Computation and Language · Computer Science 2025-11-06 Yuerong Song , Xiaoran Liu , Ruixiao Li , Zhigeng Liu , Zengfeng Huang , Qipeng Guo , Ziwei He , Xipeng Qiu

Diffusion language models (DLMs) offer a promising path toward low-latency generation through parallel decoding, but their practical efficiency depends heavily on the decoding trajectory. In practice, this advantage often fails to fully…

Computation and Language · Computer Science 2026-04-02 Lingjie Chen , Ruizhong Qiu , Yuyu Fan , Yanjun Zhao , Hanghang Tong

Large Language Models (LLMs) have transformed the natural language processing landscape and brought to life diverse applications. Pretraining on vast web-scale data has laid the foundation for these models, yet the research community is now…

Autoregressive Models (ARMs) have long dominated the landscape of Large Language Models. Recently, a new paradigm has emerged in the form of diffusion-based Large Language Models (dLLMs), which generate text by iteratively denoising masked…

Machine Learning · Computer Science 2025-06-10 Zhiyuan Liu , Yicun Yang , Yaojie Zhang , Junjie Chen , Chang Zou , Qingyuan Wei , Shaobo Wang , Linfeng Zhang

Large language models (LLMs) have demonstrated impressive capabilities across diverse tasks, yet their ability to perform structured symbolic planning remains limited, particularly in domains requiring formal representations like the…

Artificial Intelligence · Computer Science 2025-09-18 Pulkit Verma , Ngoc La , Anthony Favier , Swaroop Mishra , Julie A. Shah

Large language models (LLMs) have become increasingly prevalent in our daily lives, leading to an expectation for LLMs to be trustworthy -- - both accurate and well-calibrated (the prediction confidence should align with its ground truth…

Computation and Language · Computer Science 2024-10-04 KaShun Shum , Minrui Xu , Jianshu Zhang , Zixin Chen , Shizhe Diao , Hanze Dong , Jipeng Zhang , Muhammad Omer Raza

Large Language Models (LLMs) have transformed natural language processing and hold growing promise for advancing science, healthcare, and decision-making. Yet their training paradigms remain dominated by affirmation-based inference, akin to…

Artificial Intelligence · Computer Science 2025-12-05 Peter B. Walker , Hannah Davidson , Aiden Foster , Matthew Lienert , Thomas Pardue , Dale Russell

Large Language Models (LLMs) have shown impressive progress in mathematical reasoning. While data augmentation is promising to enhance mathematical problem-solving ability, current approaches are predominantly limited to instance-level…

Computation and Language · Computer Science 2025-06-17 Qizhi Pei , Lijun Wu , Zhuoshi Pan , Yu Li , Honglin Lin , Chenlin Ming , Xin Gao , Conghui He , Rui Yan

Recent advances in large language models have demonstrated that Supervised Fine-Tuning (SFT) with Chain-of-Thought (CoT) reasoning data distilled from large reasoning models (e.g., DeepSeek R1) can effectively transfer reasoning…

Computation and Language · Computer Science 2025-05-22 Bin Yu , Hang Yuan , Haotian Li , Xueyin Xu , Yuliang Wei , Bailing Wang , Weizhen Qi , Kai Chen

Diffusion Large Language Models (DLLMs) are emerging as a powerful alternative to the dominant Autoregressive Large Language Models, offering efficient parallel generation and capable global context modeling. However, the practical…

Computation and Language · Computer Science 2025-08-19 Jinsong Li , Xiaoyi Dong , Yuhang Zang , Yuhang Cao , Jiaqi Wang , Dahua Lin

Large language models (LLMs) with one or more fine-tuning phases have become a necessary step to unlock various capabilities, enabling LLMs to follow natural language instructions or align with human preferences. However, it carries the…

Computation and Language · Computer Science 2024-04-30 Tingfeng Hui , Zhenyu Zhang , Shuohuan Wang , Weiran Xu , Yu Sun , Hua Wu

Communication system formulation is critical for advancing 6G and future wireless technologies, yet it remains a complex, expertise-intensive task. While Large Language Models (LLMs) offer potential, existing general-purpose models often…

Machine Learning · Computer Science 2025-06-12 Panlong Wu , Ting Wang , Yifei Zhong , Haoqi Zhang , Zitong Wang , Fangxin Wang