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In data-driven drug discovery, designing molecular descriptors is a very important task. Deep generative models such as variational autoencoders (VAEs) offer a potential solution by designing descriptors as probabilistic latent vectors…

机器学习 · 计算机科学 2023-08-23 Daiki Koge , Naoaki Ono , Shigehiko Kanaya

Molecular property prediction constitutes a cornerstone of drug discovery and materials science, necessitating models capable of disentangling complex structure-property relationships across diverse molecular modalities. Existing approaches…

机器学习 · 计算机科学 2026-03-24 Long Xu , Junping Guo , Jianbo Zhao , Jianbo Lu , Yuzhong Peng

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…

生物大分子 · 定量生物学 2022-12-20 Xin Xia , Yansen Su , Chunhou Zheng , Xiangxiang Zeng

Molecular discovery has brought great benefits to the chemical industry. Various molecule design techniques are developed to identify molecules with desirable properties. Traditional optimization methods, such as genetic algorithms,…

生物大分子 · 定量生物学 2025-11-05 Chris Zhuang , Debadyuti Mukherjee , Yingzhou Lu , Tianfan Fu , Ruqi Zhang

Exploration of complex high-dimensional spaces presents significant challenges in fields such as molecular discovery, process optimization, and supply chain management. Genetic Algorithms (GAs), while offering significant power for creating…

机器学习 · 计算机科学 2025-12-01 Mani Valleti , Aditya Raghavan , Sergei V. Kalinin

Recent advancements in large language models (LLMs) have demonstrated impressive performance in molecular generation, which offers potential to accelerate drug discovery. However, the current LLMs overlook a critical requirement for drug…

机器学习 · 计算机科学 2025-02-18 Hyosoon Jang , Yunhui Jang , Jaehyung Kim , Sungsoo Ahn

Deep generative chemistry models emerge as powerful tools to expedite drug discovery. However, the immense size and complexity of the structural space of all possible drug-like molecules pose significant obstacles, which could be overcome…

量子物理 · 物理学 2023-08-15 A. I. Gircha , A. S. Boev , K. Avchaciov , P. O. Fedichev , A. K. Fedorov

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…

机器学习 · 计算机科学 2026-02-10 Haoran Liu , Zheni Zeng , Yukun Yan , Yuxuan Chen , Yunduo Xiao

Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with…

The fundamental goal of generative drug design is to propose optimized molecules that meet predefined activity, selectivity, and pharmacokinetic criteria. Despite recent progress, we argue that existing generative methods are limited in…

化学物理 · 物理学 2020-12-17 Julien Horwood , Emmanuel Noutahi

Medicinal chemists often optimize drugs considering their 3D structures and designing structurally distinct molecules that retain key features, such as shapes, pharmacophores, or chemical properties. Previous deep learning approaches…

机器学习 · 计算机科学 2025-10-06 Zitao Chen , Yinjun Jia , Zitong Tian , Wei-Ying Ma , Yanyan Lan

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…

机器学习 · 计算机科学 2026-04-15 Ziqing Wang , Yibo Wen , Abhishek Pandy , Han Liu , Kaize Ding

Opioid Use Disorder (OUD) has emerged as a significant global public health issue, with complex multifaceted conditions. Due to the lack of effective treatment options for various conditions, there is a pressing need for the discovery of…

机器学习 · 计算机科学 2023-06-14 Hongsong Feng , Rui Wang , Chang-Guo Zhan , Guo-Wei Wei

Motivation: Despite its great success in various physical modeling, differential geometry (DG) has rarely been devised as a versatile tool for analyzing large, diverse and complex molecular and biomolecular datasets due to the limited…

定量方法 · 定量生物学 2018-06-12 Duc Duy Nguyen , Guo-Wei Wei

Molecular optimization is a crucial aspect of drug discovery, aimed at refining molecular structures to enhance drug efficacy and minimize side effects, ultimately accelerating the overall drug development process. Many molecular…

生物大分子 · 定量生物学 2025-05-15 Kun Li , Xiantao Cai , Jia Wu , Shirui Pan , Huiting Xu , Bo Du , Wenbin Hu

Designing molecules with desirable physiochemical properties and functionalities is a long-standing challenge in chemistry, material science, and drug discovery. Recently, machine learning-based generative models have emerged as promising…

生物大分子 · 定量生物学 2023-04-26 Zaixi Zhang , Qi Liu , Chee-Kong Lee , Chang-Yu Hsieh , Enhong Chen

Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly.…

机器学习 · 计算机科学 2020-10-28 Bonggun Shin , Sungsoo Park , JinYeong Bak , Joyce C. Ho

High-throughput approximations of quantum mechanics calculations and combinatorial experiments have been traditionally used to reduce the search space of possible molecules, drugs and materials. However, the interplay of structural and…

量子物理 · 物理学 2019-10-29 Alain Tchagang , Julio Valdés

Designing a molecule with desired properties is one of the biggest challenges in drug development, as it requires optimization of chemical compound structures with respect to many complex properties. To augment the compound design process…

机器学习 · 计算机科学 2020-01-23 Łukasz Maziarka , Agnieszka Pocha , Jan Kaczmarczyk , Krzysztof Rataj , Michał Warchoł

De novo drug design is a pivotal issue in pharmacology and a new area of focus in AI for science research. A central challenge in this field is to generate molecules with specific properties while also producing a wide range of diverse…

生物大分子 · 定量生物学 2024-01-15 Xiuyuan Hu , Guoqing Liu , Yang Zhao , Hao Zhang