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Lead optimization in drug discovery requires improving therapeutic properties while ensuring that molecular modifications correspond to feasible synthetic routes. Existing approaches either prioritize property scores without enforcing…

Machine Learning · Computer Science 2026-05-04 Tao Li , Kaiyuan Hou , Tuan Vinh , Monika Raj , Zhichun Guo , Carl Yang

Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal oracle evaluations (computational prediction or wet-lab experiment).…

Biomolecules · Quantitative Biology 2023-05-26 Jeff Guo , Philippe Schwaller

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

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

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

Molecular optimization is a crucial yet complex and time-intensive process that often acts as a bottleneck for drug development. Traditional methods rely heavily on trial and error, making multi-objective optimization both time-consuming…

Biomolecules · Quantitative Biology 2025-03-06 Jiajun Yu , Yizhen Zheng , Huan Yee Koh , Shirui Pan , Tianyue Wang , Haishuai Wang

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

Although LLM agents can leverage tools for complex tasks, they still need memory to maintain cross-turn consistency and accumulate reusable information in long-horizon interactions. However, retrieval-based external memory systems incur low…

Artificial Intelligence · Computer Science 2026-04-23 Jiaquan Zhang , Chaoning Zhang , Shuxu Chen , Zhenzhen Huang , Pengcheng Zheng , Zhicheng Wang , Ping Guo , Fan Mo , Sung-Ho Bae , Jie Zou , Jiwei Wei , Yang Yang

Achieving self-evolution in intelligent agents requires the continual accumulation of new knowledge across changing task sequences without forgetting previously acquired abilities. Existing approaches either internalize knowledge by…

Machine Learning · Computer Science 2026-05-22 Dianzhi Yu , Vireo Zhang , Hongru Wang , Yanyu Chen , Minda Hu , Wanghan Xu , Siki Chen , Philip Torr , Zhenfei Yin , Irwin King

Class-Incremental Learning (CIL) [40] trains classifiers under a strict memory budget: in each incremental phase, learning is done for new data, most of which is abandoned to free space for the next phase. The preserved data are exemplars…

Computer Vision and Pattern Recognition · Computer Science 2023-01-18 Yaoyao Liu , Bernt Schiele , Qianru Sun

Memory systems often organize user-agent interactions as retrievable external memory and are crucial for long-running agents by overcoming the limited context windows of LLMs. However, existing memory systems invoke LLMs to process every…

Computation and Language · Computer Science 2026-05-18 Zijie Dai , Shiyuan Deng , Sheng Guan , Yizhou Tian , Xin Yao , Xiao Yan , James Cheng

We address the task of controlled generation of small molecules, which entails finding novel molecules with desired properties under certain constraints (e.g., similarity to a reference molecule). Here we introduce MolMIM, a probabilistic…

Machine Learning · Computer Science 2023-03-31 Danny Reidenbach , Micha Livne , Rajesh K. Ilango , Michelle Gill , Johnny Israeli

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

Equipping agents with memory is essential for solving real-world long-horizon problems. However, most existing agent memory mechanisms rely on static and hand-crafted workflows. This limits the performance and generalization ability of…

Artificial Intelligence · Computer Science 2026-03-30 Yupeng Huo , Yaxi Lu , Zhong Zhang , Haotian Chen , Yankai Lin

Large language models (LLMs) show promise for molecular optimization, but aligning them with selective and competing drug-design constraints remains challenging. We propose C-Moral, a reinforcement learning post-training framework for…

Machine Learning · Computer Science 2026-05-28 Rui Gao , Youngseung Jeon , Swastik Roy , Morteza Ziyadi , Xiang 'Anthony' Chen

Multi-Objective Reinforcement Learning (MORL) is a generalization of traditional Reinforcement Learning (RL) that aims to optimize multiple, often conflicting objectives simultaneously rather than focusing on a single reward. This approach…

Machine Learning · Computer Science 2025-08-15 Davide Guidobene , Lorenzo Benedetti , Diego Arapovic

MLLMs exhibit strong reasoning on isolated queries, yet they operate de novo -- solving each problem independently and often repeating the same mistakes. Existing memory-augmented agents mainly store past trajectories for reuse. However,…

Artificial Intelligence · Computer Science 2026-05-05 Weihao Bo , Shan Zhang , Yanpeng Sun , Jingjing Wu , Qunyi Xie , Xiao Tan , Kunbin Chen , Wei He , Xiaofan Li , Na Zhao , Jingdong Wang , Zechao Li

We present a framework, which we call Molecule Deep $Q$-Networks (MolDQN), for molecule optimization by combining domain knowledge of chemistry and state-of-the-art reinforcement learning techniques (double $Q$-learning and randomized value…

Machine Learning · Computer Science 2020-06-22 Zhenpeng Zhou , Steven Kearnes , Li Li , Richard N. Zare , Patrick Riley

Large language model (LLM) agents demonstrate strong performance in short-text contexts but often underperform in extended dialogues due to inefficient memory management. Existing approaches face a fundamental trade-off between efficiency…

Artificial Intelligence · Computer Science 2026-05-04 Xiaochen Zhao , Kaikai Wang , Xiaowen Zhang , Chen Yao , Aili Wang

Memory-augmented LLM agents store and retrieve information from prior interactions, yet the relative importance of how memories are written versus how they are retrieved remains unclear. We introduce a diagnostic framework that analyzes how…

Artificial Intelligence · Computer Science 2026-04-14 Boqin Yuan , Yue Su , Kun Yao
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