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Although generative models hold promise for discovering molecules with optimized desired properties, they often fail to suggest synthesizable molecules that improve upon the known molecules seen in training. We find that a key limitation is…

Machine Learning · Computer Science 2025-01-07 Evan R. Antoniuk , Peggy Li , Nathan Keilbart , Stephen Weitzner , Bhavya Kailkhura , Anna M. Hiszpanski

Active learning has been increasingly applied to screening functional materials from existing materials databases with desired properties. However, the number of known materials deposited in the popular materials databases such as ICSD and…

Generating novel molecules is challenging, with most representations leading to generative models producing many invalid molecules. Spanning Tree-based Graph Generation (STGG) is a promising approach to ensure the generation of valid…

Machine Learning · Computer Science 2025-07-17 Alexia Jolicoeur-Martineau , Aristide Baratin , Kisoo Kwon , Boris Knyazev , Yan Zhang

Chemical space is routinely explored by machine learning methods to discover interesting molecules, before time-consuming experimental synthesizing is attempted. However, these methods often rely on a graph representation, ignoring 3D…

Generating molecules with desired chemical properties presents a critical challenge in fields such as chemical synthesis and drug discovery. Recent advancements in artificial intelligence (AI) and deep learning have significantly…

Machine Learning · Computer Science 2025-09-25 Chen Li , Huidong Tang , Ye Zhu , Yoshihiro Yamanishi

The incredible capabilities of generative artificial intelligence models have inevitably led to their application in the domain of drug discovery. Within this domain, the vastness of chemical space motivates the development of more…

Machine Learning · Computer Science 2024-02-08 Gregory W. Kyro , Anton Morgunov , Rafael I. Brent , Victor S. Batista

Deep generative models, such as generative adversarial networks (GANs), have been employed for $de~novo$ molecular generation in drug discovery. Most prior studies have utilized reinforcement learning (RL) algorithms, particularly Monte…

Biomolecules · Quantitative Biology 2025-09-09 Huidong Tang , Chen Li , Sayaka Kamei , Yoshihiro Yamanishi , Yasuhiko Morimoto

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we…

Traditional drug discovery programs are being transformed by the advent of machine learning methods. Among these, Generative AI methods (GM) have gained attention due to their ability to design new molecules and enhance specific properties…

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a…

Computation and Language · Computer Science 2024-10-11 Peng Zhou , Jianmin Wang , Chunyan Li , Zixu Wang , Yiping Liu , Siqi Sun , Jianxin Lin , Leyi Wei , Xibao Cai , Houtim Lai , Wei Liu , Longyue Wang , Yuansheng Liu , Xiangxiang Zeng

How to accurately predict the properties of molecules is an essential problem in AI-driven drug discovery, which generally requires a large amount of annotation for training deep learning models. Annotating molecules, however, is quite…

Machine Learning · Computer Science 2022-05-24 Kuangqi Zhou , Kaixin Wang , Jiashi Feng , Jian Tang , Tingyang Xu , Xinchao Wang

Machine learning has the potential to automate molecular design and drastically accelerate the discovery of new functional compounds. Towards this goal, generative models and reinforcement learning (RL) using string and graph…

Machine Learning · Computer Science 2022-02-02 Daniel Flam-Shepherd , Alexander Zhigalin , Alán Aspuru-Guzik

Molecular property prediction (e.g., energy) is an essential problem in chemistry and biology. Unfortunately, many supervised learning methods usually suffer from the problem of scarce labeled molecules in the chemical space, where such…

Machine Learning · Computer Science 2020-07-08 Zhongkai Hao , Chengqiang Lu , Zheyuan Hu , Hao Wang , Zhenya Huang , Qi Liu , Enhong Chen , Cheekong Lee

Discovering functional crystalline materials entails navigating an immense combinatorial design space. While recent advances in generative artificial intelligence have enabled the sampling of chemically plausible compositions and…

Machine Learning · Computer Science 2025-11-11 Hyunsoo Park , Aron Walsh

Current generative models for drug discovery primarily use molecular docking as an oracle to guide the generation of active compounds. However, such models are often not useful in practice because even compounds with high docking scores do…

Machine Learning · Computer Science 2025-06-11 Peter Eckmann , Dongxia Wu , Germano Heinzelmann , Michael K. Gilson , Rose Yu

The aim of the inverse chemical design is to develop new molecules with given optimized molecular properties or objectives. Recently, generative deep learning (DL) networks are considered as the state-of-the-art in inverse chemical design…

Machine Learning · Computer Science 2019-10-10 Haoran Wei , Mariefel Olarte , Garrett B. Goh

Efficiently retrieving an enormous chemical library to design targeted molecules is crucial for accelerating drug discovery, organic chemistry, and optoelectronic materials. Despite the emergence of generative models to produce novel…

Computational Engineering, Finance, and Science · Computer Science 2024-09-13 Zijun Chen , Yu Wang , Liuzhenghao Lv , Hao Li , Zongying Lin , Li Yuan , Yonghong Tian

Recently, large-scale language-image generative models have gained widespread attention and many works have utilized generated data from these models to further enhance the performance of perception tasks. However, not all generated data…

Computer Vision and Pattern Recognition · Computer Science 2024-06-05 Muzhi Zhu , Chengxiang Fan , Hao Chen , Yang Liu , Weian Mao , Xiaogang Xu , Chunhua Shen

It is well known that Drug Design is often a costly process both in terms of time and economic effort. While good Quantitative Structure-Activity Relationship models (QSAR) can help predicting molecular properties without the need to…

Biomolecules · Quantitative Biology 2022-02-14 Dylan Savoia , Alessio Ragno , Roberto Capobianco

Active learning (AL) strategies aim to train high-performance models with minimal labeling efforts, only selecting the most informative instances for annotation. Current approaches to evaluating data informativeness predominantly focus on…

Computer Vision and Pattern Recognition · Computer Science 2026-01-23 Zhixuan Liang , Xingyu Zeng , Rui Zhao , Ping Luo
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