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Protein language models have emerged as powerful tools for sequence generation, offering substantial advantages in functional optimization and denovo design. However, these models also present significant risks of generating harmful protein…

Artificial Intelligence · Computer Science 2025-07-16 Yuhao Wang , Keyan Ding , Kehua Feng , Zeyuan Wang , Ming Qin , Xiaotong Li , Qiang Zhang , Huajun Chen

Designing protein sequences with optimal energetic stability is a key challenge in protein inverse folding, as current deep learning methods are primarily trained by maximizing sequence recovery rates, often neglecting the energy of the…

Machine Learning · Computer Science 2025-06-12 Dingyi Rong , Haotian Lu , Wenzhuo Zheng , Fan Zhang , Shuangjia Zheng , Ning Liu

We introduce PEPO (Pessimistic Ensemble based Preference Optimization), a single-step Direct Preference Optimization (DPO)-like algorithm to mitigate the well-known over-optimization issue in preference learning without requiring the…

Machine Learning · Computer Science 2026-05-18 Adam Barla , Emanuele Nevali , Luca Viano , Volkan Cevher

A key challenge in reinforcement learning (RL) is managing the exploration-exploitation trade-off without sacrificing sample efficiency. Policy gradient (PG) methods excel in exploitation through fine-grained, gradient-based optimization…

Machine Learning · Computer Science 2025-04-18 Zelal Su "Lain" Mustafaoglu , Keshav Pingali , Risto Miikkulainen

Recent advances in Emotional Support Conversation (ESC) have improved emotional support generation by fine-tuning Large Language Models (LLMs) via Supervised Fine-Tuning (SFT). However, common psychological errors still persist. While…

Computation and Language · Computer Science 2026-01-19 Chao Zhang , Xin Shi , Xueqiao Zhang , Yifan Zhu , Yi Yang , Yawei Luo

On-policy reinforcement learning (RL) algorithms are widely used for their strong asymptotic performance and training stability, but they struggle to scale with larger batch sizes, as additional parallel environments yield redundant data…

Machine Learning · Computer Science 2025-11-13 Jianren Wang , Yifan Su , Abhinav Gupta , Deepak Pathak

Molecule synthesis through machine learning is one of the fundamental problems in drug discovery. Current data-driven strategies employ one-step retrosynthesis models and search algorithms to predict synthetic routes in a top-bottom manner.…

Machine Learning · Computer Science 2024-06-05 Songtao Liu , Hanjun Dai , Yue Zhao , Peng Liu

This paper proposes a novel Extended Particle Swarm Optimization model (EPSO) that potentially enhances the search process of PSO for optimization problem. Evidently, gene expression profiles are significantly important measurement factor…

Neural and Evolutionary Computing · Computer Science 2020-08-11 Ali Hakem Alsaeedi , Adil L. Albukhnefis , Dhiah Al-Shammary , Muntasir Al-Asfoor

Protein dynamics play a crucial role in protein biological functions and properties, and their traditional study typically relies on time-consuming molecular dynamics (MD) simulations conducted in silico. Recent advances in generative…

Biomolecules · Quantitative Biology 2025-06-02 Jiarui Lu , Xiaoyin Chen , Stephen Zhewen Lu , Aurélie Lozano , Vijil Chenthamarakshan , Payel Das , Jian Tang

Direct Preference Optimization (DPO) is an effective approach for aligning protein language models with experimental design goals. However, DPO faces a scalability bottleneck: the number of possible training pairs grows quadratically with…

Machine Learning · Computer Science 2025-11-27 Constance Ferragu , Jonathan D. Ziegler , Nicolas Deutschmann , Arthur Lindoulsi , Eli Bixby , Cradle ML Team

Diffusion models have achieved promising results for Structure-Based Drug Design (SBDD). Nevertheless, high-quality protein subpocket and ligand data are relatively scarce, which hinders the models' generation capabilities. Recently, Direct…

Biomolecules · Quantitative Biology 2026-02-11 Xiwei Cheng , Xiangxin Zhou , Yuwei Yang , Yu Bao , Quanquan Gu

It is challenging for reinforcement learning (RL) algorithms to succeed in real-world applications like financial trading and logistic system due to the noisy observation and environment shifting between training and evaluation. Thus, it…

Machine Learning · Computer Science 2022-05-20 Zhengyu Yang , Kan Ren , Xufang Luo , Minghuan Liu , Weiqing Liu , Jiang Bian , Weinan Zhang , Dongsheng Li

Recent advancements have established Reinforcement Learning (RL) as a pivotal paradigm for aligning generative models with human intent. However, group-based optimization frameworks (e.g., GRPO) face a critical limitation: the rapid decay…

Computer Vision and Pattern Recognition · Computer Science 2026-05-18 Sujie Hu , Chubin Chen , Jiashu Zhu , Jiahong Wu , Xiangxiang Chu , Xiu Li

DPO is an effective preference optimization algorithm. However, the DPO-tuned models tend to overfit on the dispreferred samples, manifested as overly long generations lacking diversity. While recent regularization approaches have…

Computation and Language · Computer Science 2025-08-26 Chenxu Yang , Ruipeng Jia , Naibin Gu , Zheng Lin , Siyuan Chen , Chao Pang , Weichong Yin , Yu Sun , Hua Wu , Weiping Wang

Long-horizon decision-making tasks present significant challenges for LLM-based agents due to the need for extensive planning over multiple steps. In this paper, we propose a hierarchical framework that decomposes complex tasks into…

Machine Learning · Computer Science 2024-10-07 Qi Zhao , Haotian Fu , Chen Sun , George Konidaris

Video generation techniques have achieved remarkable advancements in visual quality, yet faithfully reproducing real-world physics remains elusive. Preference-based model post-training may improve physical consistency, but requires costly…

Computer Vision and Pattern Recognition · Computer Science 2025-06-24 Wenxu Qian , Chaoyue Wang , Hou Peng , Zhiyu Tan , Hao Li , Anxiang Zeng

The remarkable performance of Large Language Models (LLMs) highly relies on crafted prompts. However, manual prompt engineering is a laborious process, creating a core bottleneck for practical application of LLMs. This phenomenon has led to…

Computation and Language · Computer Science 2025-11-21 Qing Zhang , Bing Xu , Xudong Zhang , Yifan Shi , Yang Li , Chen Zhang , Yik Chung Wu , Ngai Wong , Yijie Chen , Hong Dai , Xiansen Chen , Mian Zhang

Direct Preference Optimization (DPO) and its variants have become the de facto standards for aligning large language models (LLMs) with human preferences or specific goals. However, DPO requires high-quality preference data and suffers from…

Machine Learning · Computer Science 2024-11-12 Zhuotong Chen , Fang Liu , Jennifer Zhu , Wanyu Du , Yanjun Qi

Predicting rare extreme events such as wildfires from meteorological data requires models that remain reliable under evolving environmental conditions. This problem is inherently long-tailed: wildfire events are rare but high-impact, while…

Machine Learning · Computer Science 2026-05-13 Enyi Jiang , Wu Sun

Expectation Propagation (EP)-based Multiple-Input Multiple-Output (MIMO) detector is regarded as a state-of-the-art MIMO detector because of its exceptional performance. However, we find that the EP MIMO detector cannot guarantee to achieve…

Signal Processing · Electrical Eng. & Systems 2020-10-21 Hang Chen , Guoqiang Yao , Jianhao Hu
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