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Molecular editing and optimization are multi-step problems that require iteratively improving properties while keeping molecules chemically valid and structurally similar. We frame both tasks as sequential, tool-guided decisions and…

Artificial Intelligence · Computer Science 2025-12-25 Zhuo Yang , Yeyun Chen , Jiaqing Xie , Ben Gao , Shuaike Shen , Wanhao Liu , Liujia Yang , Beilun Wang , Tianfan Fu , Yuqiang Li

In drug discovery, molecular optimization aims to iteratively refine a lead compound to improve molecular properties while preserving structural similarity to the original molecule. However, each oracle evaluation is expensive, making…

Machine Learning · Computer Science 2026-04-15 Ziqing Wang , Yibo Wen , Abhishek Pandy , Han Liu , Kaize Ding

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

Large language models (LLMs) have large potential for molecular optimization, as they can gather external chemistry tools and enable collaborative interactions to iteratively refine molecular candidates. However, this potential remains…

Artificial Intelligence · Computer Science 2025-05-28 Hyomin Kim , Yunhui Jang , Sungsoo Ahn

In recent research advancements within the community, large language models (LLMs) have sparked great interest in creating autonomous agents. However, current prompt-based agents often heavily rely on large-scale LLMs. Meanwhile, although…

Computation and Language · Computer Science 2025-03-04 Xueyang Feng , Bo Lan , Quanyu Dai , Lei Wang , Jiakai Tang , Xu Chen , Zhenhua Dong , Ji-Rong Wen

Large Language Models (LLMs) perform well in language tasks but often lack collaborative awareness and struggle to optimize global performance in multi-agent settings. We present a reinforcement learning-augmented LLM agent framework that…

Artificial Intelligence · Computer Science 2026-01-01 Dong Qiu , Duo Xu , Limengxi Yue

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

Reinforcement Learning (RL) has emerged as a critical driver for enhancing the reasoning capabilities of Large Language Models (LLMs). While recent advancements have focused on reward engineering or data synthesis, few studies exploit the…

Machine Learning · Computer Science 2026-04-17 Bowen Ping , Zijun Chen , Tingfeng Hui , Qize Yu , Chenxuan Li , Junchi Yan , Baobao Chang

Drug discovery frequently loses momentum when data, expertise, and tools are scattered, slowing design cycles. To shorten this loop we built a hierarchical, tool using agent framework that automates molecular optimisation. A Principal…

Machine Learning · Computer Science 2025-08-06 Atabey Ünlü , Phil Rohr , Ahmet Celebi

While reinforcement learning (RL) has achieved notable success in various domains, training effective policies for complex tasks remains challenging. Agents often converge to local optima and fail to maximize long-term rewards. Existing…

Artificial Intelligence · Computer Science 2025-05-28 Heng Tan , Hua Yan , Yu Yang

Lead optimization in drug discovery requires efficiently navigating vast chemical space through iterative cycles to enhance molecular properties while preserving structural similarity to the original lead compound. Despite recent advances,…

Machine Learning · Computer Science 2025-09-29 Ziqing Wang , Yibo Wen , William Pattie , Xiao Luo , Weimin Wu , Jerry Yao-Chieh Hu , Abhishek Pandey , Han Liu , Kaize Ding

Optimizing the structure of molecules to achieve desired properties is a central bottleneck across the chemical sciences, particularly in the pharmaceutical industry where it underlies the discovery of new drugs. Since molecular property…

Artificial Intelligence · Computer Science 2026-02-19 Fabian P. Krüger , Andrea Hunklinger , Adrian Wolny , Tim J. Adler , Igor Tetko , Santiago David Villalba

Recent progress in Large Language Models (LLMs) has drawn attention to their potential for accelerating drug discovery. However, a central problem remains: translating theoretical ideas into robust implementations in the highly specialized…

Machine Learning · Computer Science 2025-03-06 Sizhe Liu , Yizhou Lu , Siyu Chen , Xiyang Hu , Jieyu Zhao , Yingzhou Lu , Yue Zhao

Drug discovery is a lengthy and resource-intensive process composed of multiple stages. Among these stages, lead optimization plays a critical role in transforming early hit compounds into viable drug candidates. This stage requires…

Machine Learning · Computer Science 2026-05-29 Lingxiao Li , Haobo Zhang , Ruohao Fan , Bin Chen , Jiayu Zhou

Finetuning a Large Language Model (LLM) is crucial for generating results towards specific objectives. This research delves into the realm of drug optimization and introduce a novel reinforcement learning algorithm to finetune a drug…

Machine Learning · Computer Science 2025-02-12 Xuefeng Liu , Songhao Jiang , Siyu Chen , Zhuoran Yang , Yuxin Chen , Ian Foster , Rick Stevens

Code optimization is a crucial task that aims to enhance code performance. However, this process is often tedious and complex, highlighting the necessity for automatic code optimization techniques. Reinforcement Learning (RL) has emerged as…

Chemical process optimization maximizes production efficiency and economic performance, but optimization algorithms, including gradient-based solvers, numerical methods, and parameter grid searches, become impractical when operating…

Machine Learning · Computer Science 2025-10-17 Tong Zeng , Srivathsan Badrinarayanan , Janghoon Ock , Cheng-Kai Lai , Amir Barati Farimani

Grounding the reasoning ability of large language models (LLMs) for embodied tasks is challenging due to the complexity of the physical world. Especially, LLM planning for multi-agent collaboration requires communication of agents or credit…

Artificial Intelligence · Computer Science 2025-09-30 Yang Zhang , Shixin Yang , Chenjia Bai , Fei Wu , Xiu Li , Zhen Wang , Xuelong Li

Large Language Models (LLMs) can generate code from natural language, but their performance is highly sensitive to prompt formulation. We propose a reinforcement-learning-based framework that models prompt refinement as a sequential…

Software Engineering · Computer Science 2026-05-20 Ali Mohammadi Esfahani , Nafiseh Kahani , Samuel A. Ajila

Large language models (LLMs) gained immense popularity due to their impressive capabilities in unstructured conversations. Empowering LLMs with advanced prompting strategies such as reasoning and acting (ReAct) (Yao et al., 2022) has shown…

Computation and Language · Computer Science 2025-03-18 Michelle Elizabeth , Morgan Veyret , Miguel Couceiro , Ondrej Dusek , Lina M. Rojas-Barahona
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