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Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…

Biomolecules · Quantitative Biology 2023-02-02 Masatsugu Yamada , Mahito Sugiyama

Deep learning has proven to yield fast and accurate predictions of quantum-chemical properties to accelerate the discovery of novel molecules and materials. As an exhaustive exploration of the vast chemical space is still infeasible, we…

Machine Learning · Statistics 2020-01-10 Niklas W. A. Gebauer , Michael Gastegger , Kristof T. Schütt

In the field of computational molecule generation, an essential task in the discovery of new chemical compounds, fragment-based deep generative models are a leading approach, consistently achieving state-of-the-art results in molecular…

Biomolecules · Quantitative Biology 2024-05-10 Sergei Voloboev

In recent years, AI models that mine intrinsic patterns from molecular structures and protein sequences have shown promise in accelerating drug discovery. However, these methods partly lag behind real-world pharmaceutical approaches of…

Machine Learning · Computer Science 2023-10-17 Yizhen Luo , Xing Yi Liu , Kai Yang , Kui Huang , Massimo Hong , Jiahuan Zhang , Yushuai Wu , Zaiqing Nie

Topology design optimization offers tremendous opportunity in design and manufacturing freedoms by designing and producing a part from the ground-up without a meaningful initial design as required by conventional shape design optimization…

Machine Learning · Statistics 2019-01-10 Sharad Rawat , M. H. Herman Shen

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

The challenge of discovering new molecules with desired properties is crucial in domains like drug discovery and material design. Recent advances in deep learning-based generative methods have shown promise but face the issue of sample…

Biomolecules · Quantitative Biology 2024-12-31 Hyeonah Kim , Minsu Kim , Sanghyeok Choi , Jinkyoo Park

Automated design synthesis has the potential to revolutionize the modern engineering design process and improve access to highly optimized and customized products across countless industries. Successfully adapting generative Machine…

Machine Learning · Computer Science 2022-03-18 Lyle Regenwetter , Amin Heyrani Nobari , Faez Ahmed

Sparked by innovations in generative artificial intelligence (AI), the field of protein design has undergone a paradigm shift with an explosion of new models for optimizing existing enzymes or creating them from scratch. After more than one…

Biomolecules · Quantitative Biology 2026-02-04 Lasse Middendorf , Noelia Ferruz

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

Deep learning-based approaches for generating novel drug molecules with specific properties have gained a lot of interest in the last few years. Recent studies have demonstrated promising performance for string-based generation of novel…

Biomolecules · Quantitative Biology 2025-02-18 Hampus Gummesson Svensson , Christian Tyrchan , Ola Engkvist , Morteza Haghir Chehreghani

Advances in generative artificial intelligence are transforming how metal-organic frameworks (MOFs) are designed and discovered. This Perspective introduces the shift from laborious enumeration of MOF candidates to generative approaches…

Molecular representation learning has shown great success in advancing AI-based drug discovery. The core of many recent works is based on the fact that the 3D geometric structure of molecules provides essential information about their…

Machine Learning · Computer Science 2024-10-23 Jiying Zhang , Zijing Liu , Yu Wang , Yu Li

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

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

Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a…

Machine Learning · Computer Science 2020-09-03 Jaechang Lim , Sang-Yeon Hwang , Seungsu Kim , Seokhyun Moon , Woo Youn Kim

The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to…

Quantitative Methods · Quantitative Biology 2022-01-27 Matthew Ragoza , Tomohide Masuda , David Ryan Koes

Drug discovery using deep learning has attracted a lot of attention of late as it has obvious advantages like higher efficiency, less manual guessing and faster process time. In this paper, we present a novel neural network for generating…

Biomolecules · Quantitative Biology 2021-10-08 Abhinav Sagar

Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, offer a high potential for…

Molecular optimization, aimed at improving binding affinity or other molecular properties, is a crucial task in drug discovery that often relies on the expertise of medicinal chemists. Recently, deep learning-based 3D generative models…

Machine Learning · Computer Science 2025-05-01 Anjie Qiao , Junjie Xie , Weifeng Huang , Hao Zhang , Jiahua Rao , Shuangjia Zheng , Yuedong Yang , Zhen Wang , Guo-Bo Li , Jinping Lei
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