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Protein Language Models (PLMs), pre-trained on extensive evolutionary data from natural proteins, have emerged as indispensable tools for protein design. While powerful, PLMs often struggle to produce proteins with precisely specified…

Biomolecules · Quantitative Biology 2025-09-15 Long-Kai Huang , Rongyi Zhu , Bing He , Jianhua Yao

Knowledge distillation improves large language model (LLM) reasoning by compressing the knowledge of a teacher LLM to train smaller LLMs. On-policy distillation advances this approach by having the student sample its own trajectories while…

Machine Learning · Computer Science 2026-03-23 Siyan Zhao , Zhihui Xie , Mengchen Liu , Jing Huang , Guan Pang , Feiyu Chen , Aditya Grover

Multi-Objective Alignment aims to align Large Language Models (LLMs) with diverse and often conflicting human values by optimizing multiple objectives simultaneously. Existing methods predominantly rely on static preference weight…

Machine Learning · Computer Science 2026-04-28 Wenzhe Xu , Biao Liu , Yiyang Sun , Xin Geng , Ning Xu

Learning from preference labels plays a crucial role in fine-tuning large language models. There are several distinct approaches for preference fine-tuning, including supervised learning, on-policy reinforcement learning (RL), and…

Preference learning in Large Language Models (LLMs) has advanced significantly, yet existing methods remain limited by modest performance gains, high computational costs, hyperparameter sensitivity, and insufficient modeling of global…

Computation and Language · Computer Science 2026-04-03 Liang Zhu , Yuelin Bai , Xiankun Ren , Jiaxi Yang , Lei Zhang , Feiteng Fang , Hamid Alinejad-Rokny , Minghuan Tan , Min Yang

The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…

Quantum Physics · Physics 2024-07-11 Veronica Panizza , Philipp Hauke , Cristian Micheletti , Pietro Faccioli

The landscape of high-performance image generation models is currently shifting from the inefficient multi-step ones to the efficient few-step counterparts (e.g, Z-Image-Turbo and FLUX.2-klein). However, these models present significant…

Computer Vision and Pattern Recognition · Computer Science 2026-05-27 Dengyang Jiang , Xin Jin , Dongyang Liu , Zanyi Wang , Mingzhe Zheng , Ruoyi Du , Xiangpeng Yang , Qilong Wu , Zhen Li , Peng Gao , Harry Yang , Steven Hoi

On-policy distillation (OPD) trains a student on its own trajectories with token-level teacher feedback and often outperforms off-policy distillation and standard reinforcement learning. However, we find that its standard advantage weighted…

Machine Learning · Computer Science 2026-05-14 Nan Jia , Haojin Yang , Xing Ma , Jiesong Lian , Shuailiang Zhang , Weipeng Zhang , Ke Zeng , Xunliang Cai , Zequn Sun

Aligning large language models (LLMs) with human preferences has gained significant attention, with Proximal Policy Optimization (PPO) as a standard yet computationally expensive method and Direct Preference Optimization (DPO) as a more…

Artificial Intelligence · Computer Science 2025-02-10 Yuzi Yan , Yibo Miao , Jialian Li , Yipin Zhang , Jian Xie , Zhijie Deng , Dong Yan

Training-time privileged information (PI) can enable language models to succeed on tasks they would otherwise fail, making it a powerful tool for reinforcement learning in hard, long-horizon settings. However, transferring capabilities…

Machine Learning · Computer Science 2026-02-17 Emiliano Penaloza , Dheeraj Vattikonda , Nicolas Gontier , Alexandre Lacoste , Laurent Charlin , Massimo Caccia

Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into…

Machine Learning · Computer Science 2025-06-13 Cheng-Yen Hsieh , Xinyou Wang , Daiheng Zhang , Dongyu Xue , Fei Ye , Shujian Huang , Zaixiang Zheng , Quanquan Gu

Alignment plays a crucial role in Large Language Models (LLMs) in aligning with human preferences on a specific task/domain. Traditional alignment methods suffer from catastrophic forgetting, where models lose previously acquired knowledge…

Computation and Language · Computer Science 2026-04-09 Junsong Li , Jie Zhou , Bihao Zhan , Yutao Yang , Qianjun Pan , Shilian Chen , Tianyu Huai , Xin Li , Qin Chen , Liang He

Recently, enhancing the numerical and logical reasoning capability of Large Language Models (LLMs) has emerged as a research hotspot. Existing methods face several limitations: inference-phase techniques (e.g., Chain of Thoughts) rely on…

Artificial Intelligence · Computer Science 2025-02-20 Hao Yi , Qingyang Li , Yulan Hu , Fuzheng Zhang , Di Zhang , Yong Liu

Preference optimization is widely used to align Large Language Models (LLMs) with preference feedback. However, most existing methods train on a single positive-negative pair per prompt, discarding additional supervision available in…

Computation and Language · Computer Science 2026-04-20 Jixuan Leng , Si Si , Hsiang-Fu Yu , Vinod Raman , Inderjit S. Dhillon

For efficiency, preference alignment is often performed on compact, knowledge-distilled (KD) models. We argue this common practice introduces a significant limitation by overlooking a key property of the alignment's reference model: its…

Machine Learning · Computer Science 2025-09-30 Sungmin Cha , Kyunghyun Cho

On-policy distillation (OPD) is a powerful paradigm for model alignment, yet its reliance on teacher logits restricts its application to white-box scenarios. We contend that structured semantic rubrics can serve as a scalable alternative to…

Machine Learning · Computer Science 2026-05-11 Junfeng Fang , Zhepei Hong , Mao Zheng , Mingyang Song , Gengsheng Li , Houcheng Jiang , Dan Zhang , Haiyun Guo , Xiang Wang , Tat-Seng Chua

Advanced reasoning typically requires Chain-of-Thought prompting, which is accurate but incurs prohibitive latency and substantial test-time inference costs. The standard alternative, fine-tuning smaller models, often sacrifices…

Computation and Language · Computer Science 2026-02-25 Sanket Badhe , Deep Shah

Resource-efficient training optimization techniques are becoming increasingly important as the size of large language models (LLMs) continues to grow. In particular, batch packing is commonly used in pre-training and supervised fine-tuning…

Computation and Language · Computer Science 2026-03-02 Jaekyung Cho

Preference learning is critical for aligning large language models (LLMs) with human values, with the quality of preference datasets playing a crucial role in this process. While existing metrics primarily assess data quality based on…

Machine Learning · Computer Science 2025-03-05 Kexin Huang , Junkang Wu , Ziqian Chen , Xue Wang , Jinyang Gao , Bolin Ding , Jiancan Wu , Xiangnan He , Xiang Wang

Inverse folding models play an important role in structure-based design by predicting amino acid sequences that fold into desired reference structures. Models like ProteinMPNN, a message-passing encoder-decoder model, are trained to…

Machine Learning · Computer Science 2026-05-12 Ryan Park , Darren J. Hsu , C. Brian Roland , Maria Korshunova , Chen Tessler , Shie Mannor , Olivia Viessmann , Bruno Trentini