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Multi-objective evolutionary algorithms (MOEAs) are widely used for searching optimal solutions in complex multi-component applications. Traditional MOEAs for multi-component deep learning (MCDL) systems face challenges in enhancing the…

Neural and Evolutionary Computing · Computer Science 2025-06-12 Haoxiang Tian , Xingshuo Han , Guoquan Wu , An Guo , Yuan Zhou. Jie Zhang , Shuo Li , Jun Wei , Tianwei Zhang

Optimizing chemical molecules for desired properties lies at the core of drug development. Despite initial successes made by deep generative models and reinforcement learning methods, these methods were mostly limited by the requirement of…

Machine Learning · Computer Science 2021-12-01 Shuangjia Zheng , Ying Song , Zhang Pan , Chengtao Li , Le Song , Yuedong Yang

Machine learning methods have been used to accelerate the molecule optimization process. However, efficient search for optimized molecules satisfying several properties with scarce labeled data remains a challenge for machine learning…

Biomolecules · Quantitative Biology 2022-12-20 Xin Xia , Yansen Su , Chunhou Zheng , Xiangxiang Zeng

Molecular optimization, which aims to discover improved molecules from a vast chemical search space, is a critical step in chemical development. Various artificial intelligence technologies have demonstrated high effectiveness and…

Chemical Physics · Physics 2024-11-26 Xin Xia , Yajie Zhang , Xiangxiang Zeng , Xingyi Zhang , Chunhou Zheng , Yansen Su

Molecular editing aims to modify a given molecule to optimize desired chemical properties while preserving structural similarity. However, current approaches typically rely on string-based or continuous representations, which fail to…

Machine Learning · Computer Science 2025-05-27 Yuanxin Zhuang , Dazhong Shen , Ying Sun

The efficient exploration of chemical space remains a central challenge, as many generative models still produce unstable or non-synthesizable compounds. To address these limitations, we present EvoMol-RL, a significant extension of the…

Machine Learning · Computer Science 2025-10-02 Gaelle Milon-Harnois , Chaimaa Touhami , Nicolas Gutowski , Benoit Da Mota , Thomas Cauchy

Machine learning (ML) is revolutionising drug discovery by expediting the prediction of small molecule properties essential for developing new drugs. These properties -- including absorption, distribution, metabolism and excretion (ADME)--…

Machine Learning · Computer Science 2024-08-02 Alex G. C. de Sá , David B. Ascher

Predicting whether a molecule can cross the blood-brain barrier (BBB) is a key step in early-stage neuro-pharmaceutical design, directly influencing the efficiency and success rate of drug development. Traditional methods based on…

Quantitative Methods · Quantitative Biology 2026-03-16 Zihan Yang , Yuchen Xiao

The integration of deep learning, particularly AI-Generated Content, with high-quality data derived from ab initio calculations has emerged as a promising avenue for transforming the landscape of scientific research. However, the challenge…

Machine Learning · Computer Science 2024-12-11 Kaiwei Zhang , Yange Lin , Guangcheng Wu , Yuxiang Ren , Xuecang Zhang , Bo wang , Xiaoyu Zhang , Weitao Du

Advances in large language models (LLMs) have recently opened new and promising avenues for small-molecule drug discovery. Yet existing LLM-based approaches for molecular generation often suffer from high rates of invalid and low-quality…

Machine Learning · Computer Science 2026-05-15 Andrew Y. Zhou , Sharvaree Vadgama , Sumanth Varambally , Peter Eckmann , Michael K. Gilson , Rose Yu

Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…

Machine Learning · Computer Science 2022-03-02 Yuanqi Du , Xiaojie Guo , Amarda Shehu , Liang Zhao

Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to molecular property prediction. However, the inherent…

Machine Learning · Computer Science 2024-09-16 Xiaohua Lu , Liangxu Xie , Lei Xu , Rongzhi Mao , Shan Chang , Xiaojun Xu

In this paper, we propose a deep evolutionary learning (DEL) process that integrates fragment-based deep generative model and multi-objective evolutionary computation for molecular design. Our approach enables (1) evolutionary operations in…

Neural and Evolutionary Computing · Computer Science 2021-02-02 Yifeng Li , Hsu Kiang Ooi , Alain Tchagang

Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…

Machine Learning · Computer Science 2020-02-10 Paul Maragakis , Hunter Nisonoff , Brian Cole , David E. Shaw

The development of Multimodal Large Language Models (MLLMs) has seen significant advancements with increasing demands in various fields (e.g., multimodal agents, embodied intelligence). While model-driven approaches attempt to enhance MLLMs…

Accurate molecular property prediction (MPP) is a critical step in modern drug development. However, the scarcity of experimental validation data poses a significant challenge to AI-driven research paradigms. Under few-shot learning…

Machine Learning · Computer Science 2025-05-20 Yifan Dai , Xuanbai Ren , Tengfei Ma , Qipeng Yan , Yiping Liu , Yuansheng Liu , Xiangxiang Zeng

Current molecular generative models primarily focus on improving drug-target binding affinity and specificity, often neglecting the system-level phenotypic effects elicited by compounds. Transcriptional profiles, as molecule-level readouts…

Chemical Physics · Physics 2025-09-29 Ran Song , Hui Liu

The rapid evolution of machine learning (ML) has led to the widespread adoption of complex "black box" models, such as deep neural networks and ensemble methods. These models exhibit exceptional predictive performance, making them…

Machine Learning · Computer Science 2025-03-28 Moncef Garouani , Josiane Mothe , Ayah Barhrhouj , Julien Aligon

Constrained multi-objective optimization problems (CMOPs) pervade real-world applications in science, engineering, and design. Constraint violation has been a building block in designing evolutionary multi-objective optimization algorithms…

Neural and Evolutionary Computing · Computer Science 2024-01-03 Shuang Li , Ke Li , Wei Li , Ming Yang

Artificial intelligence has demonstrated immense potential in scientific research. Within molecular science, it is revolutionizing the traditional computer-aided paradigm, ushering in a new era of deep learning. With recent progress in…

Biomolecules · Quantitative Biology 2024-03-22 Yi Xiao , Xiangxin Zhou , Qiang Liu , Liang Wang