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Recently, the impressive performance of large language models (LLMs) on a wide range of tasks has attracted an increasing number of attempts to apply LLMs in drug discovery. However, molecule optimization, a critical task in the drug…

Quantitative Methods · Quantitative Biology 2024-01-22 Geyan Ye , Xibao Cai , Houtim Lai , Xing Wang , Junhong Huang , Longyue Wang , Wei Liu , Xiangxiang Zeng

The high cost and data scarcity in scientific exploration have motivated the use of large language models (LLMs) as knowledge-driven components in Bayesian optimization (BO). However, existing approaches typically embed LLMs directly into…

Evolutionary prompt optimization has demonstrated effectiveness in refining prompts for LLMs. However, existing approaches lack robust operators and efficient evaluation mechanisms. In this work, we propose several key improvements to…

Computation and Language · Computer Science 2025-11-10 Daniel Grießhaber , Maximilian Kimmich , Johannes Maucher , Ngoc Thang Vu

The remarkable performance of Large Language Models (LLMs) has inspired many applications, which often necessitate edge-cloud collaboration due to connectivity, privacy, and cost considerations. Traditional methods primarily focus on…

Databases · Computer Science 2025-07-15 Prasoon Patidar , Alex Crown , Kevin Hsieh , Yifei Xu , Tusher Chakraborty , Ranveer Chandra , Yuvraj Agarwal

Goal-oriented de novo molecule design, namely generating molecules with specific property or substructure constraints, is a crucial yet challenging task in drug discovery. Existing methods, such as Bayesian optimization and reinforcement…

Computational Engineering, Finance, and Science · Computer Science 2025-02-28 Chuanliu Fan , Ziqiang Cao , Zicheng Ma , Nan Yu , Yimin Peng , Jun Zhang , Yiqin Gao , Guohong Fu

Designing optimization approaches, whether heuristic or meta-heuristic, usually demands extensive manual intervention and has difficulty generalizing across diverse problem domains. The combination of Large Language Models (LLMs) and…

Neural and Evolutionary Computing · Computer Science 2024-10-29 He Yu , Jing Liu

Evolutionary algorithms excel in solving complex optimization problems, especially those with multiple objectives. However, their stochastic nature can sometimes hinder rapid convergence to the global optima, particularly in scenarios…

Neural and Evolutionary Computing · Computer Science 2024-05-10 Zeyi Wang , Songbai Liu , Jianyong Chen , Kay Chen Tan

Automatic performance tuning (auto-tuning) is essential for optimizing high-performance applications, where vast and irregular search spaces make manual exploration infeasible. While auto-tuners traditionally rely on classical approaches…

Machine Learning · Computer Science 2026-04-01 Floris-Jan Willemsen , Niki van Stein , Ben van Werkhoven

Prompt optimization aims to find the best prompt to a large language model (LLM) for a given task. LLMs have been successfully used to help find and improve prompt candidates for single-step tasks. However, realistic tasks for agents are…

Computation and Language · Computer Science 2024-10-04 Yongchao Chen , Jacob Arkin , Yilun Hao , Yang Zhang , Nicholas Roy , Chuchu Fan

Molecule generation and optimization is a fundamental task in chemical domain. The rapid development of intelligent tools, especially large language models (LLMs) with powerful knowledge reserves and interactive capabilities, has provided…

Machine Learning · Computer Science 2026-02-10 Haoran Liu , Zheni Zeng , Yukun Yan , Yuxuan Chen , Yunduo Xiao

Existing memory systems enable Large Language Models (LLMs) to support long-horizon human-LLM interactions by persisting historical interactions beyond limited context windows. However, while recent approaches have succeeded in constructing…

Computation and Language · Computer Science 2026-04-21 Haidong Xin , Xinze Li , Zhenghao Liu , Yukun Yan , Shuo Wang , Cheng Yang , Yu Gu , Ge Yu , Maosong Sun

Multi-objective discrete optimization problems, such as molecular design, pose significant challenges due to their vast and unstructured combinatorial spaces. Traditional evolutionary algorithms often get trapped in local optima, while…

Machine Learning · Computer Science 2025-10-09 Nian Ran , Zhongzheng Li , Yue Wang , Qingsong Ran , Xiaoyuan Zhang , Shikun Feng , Richard Allmendinger , Xiaoguang Zhao

Large Language Models (LLMs) possess substantial reasoning capabilities and are increasingly applied to optimization tasks, particularly in synergy with evolutionary computation. However, while recent surveys have explored specific aspects…

Neural and Evolutionary Computing · Computer Science 2026-01-08 Yisong Zhang , Ran Cheng , Guoxing Yi , Kay Chen Tan

Many real-world optimization problems are guided by complex, subjective preferences that are difficult to express as explicit closed-form objectives. In response, we introduce Language-in-the-Loop Optimization (LILO), a Bayesian…

Machine Learning · Computer Science 2026-05-12 Katarzyna Kobalczyk , Zhiyuan Jerry Lin , Benjamin Letham , Zhuokai Zhao , Maximilian Balandat , Eytan Bakshy

Discovering efficient algorithms for solving complex problems has been an outstanding challenge in mathematics and computer science, requiring substantial human expertise over the years. Recent advancements in evolutionary search with large…

Artificial Intelligence · Computer Science 2026-05-26 Anja Surina , Amin Mansouri , Lars Quaedvlieg , Amal Seddas , Maryna Viazovska , Emmanuel Abbe , Caglar Gulcehre

Designing functional transition metal complexes (TMCs) faces challenges due to the vast search space of metals and ligands, requiring efficient optimization strategies. Traditional genetic algorithms (GAs) are commonly used, employing…

Chemical Physics · Physics 2024-10-25 Jieyu Lu , Zhangde Song , Qiyuan Zhao , Yuanqi Du , Yirui Cao , Haojun Jia , Chenru Duan

Optimization problems seek to find the best solution to an objective under a set of constraints, and have been widely investigated in real-world applications. Modeling and solving optimization problems in a specific domain typically require…

Optimization and Control · Mathematics 2024-07-12 Jihai Zhang , Wei Wang , Siyan Guo , Li Wang , Fangquan Lin , Cheng Yang , Wotao Yin

Prompt optimization has become crucial for enhancing the performance of large language models (LLMs) across a broad range of tasks. Although many research papers demonstrate its effectiveness, practical adoption is hindered because existing…

Computation and Language · Computer Science 2026-02-24 Tom Zehle , Timo Heiß , Moritz Schlager , Matthias Aßenmacher , Matthias Feurer

Recent advancements in explainable recommendation have greatly bolstered user experience by elucidating the decision-making rationale. However, the existing methods actually fail to provide effective feedback signals for potentially better…

Information Retrieval · Computer Science 2025-08-08 Jiakai Tang , Jingsen Zhang , Zihang Tian , Xueyang Feng , Lei Wang , Xu Chen

Molecular optimization is a fundamental goal in the chemical sciences and is of central interest to drug and material design. In recent years, significant progress has been made in solving challenging problems across various aspects of…

Computational Engineering, Finance, and Science · Computer Science 2022-10-11 Wenhao Gao , Tianfan Fu , Jimeng Sun , Connor W. Coley