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In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…

Machine Learning · Computer Science 2026-04-16 Peter Zhiping Zhang , Jeffrey D. Varner

Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this…

The size and quality of chemical libraries to the drug discovery pipeline are crucial for developing new drugs or repurposing existing drugs. Existing techniques such as combinatorial organic synthesis and High-Throughput Screening usually…

Biomolecules · Quantitative Biology 2020-10-02 Brighter Agyemang , Wei-Ping Wu , Daniel Addo , Michael Y. Kpiebaareh , Ebenezer Nanor , Charles Roland Haruna

Chemical synthesis remains a critical bottleneck in the discovery and manufacture of functional small molecules. AI-based synthesis planning models could be a potential remedy to find effective syntheses, and have made progress in recent…

Retrosynthesis is the task of planning a series of chemical reactions to create a desired molecule from simpler, buyable molecules. While previous works have proposed algorithms to find optimal solutions for a range of metrics (e.g.…

Artificial Intelligence · Computer Science 2024-04-16 Austin Tripp , Krzysztof Maziarz , Sarah Lewis , Marwin Segler , José Miguel Hernández-Lobato

In this work, we present a learning-based approach to analysis cyberspace configuration. Unlike prior methods, our approach has the ability to learn from past experience and improve over time. In particular, as we train over a greater…

Artificial Intelligence · Computer Science 2020-07-10 Lei Zhang , Wei Bai , Shize Guo , Shiming Xia , Hongmei Li , Zhisong Pan

Optimal operation of chemical processes is vital for energy, resource, and cost savings in chemical engineering. The problem of optimal operation can be tackled with reinforcement learning, but traditional reinforcement learning methods…

Machine Learning · Computer Science 2025-11-21 Dean Brandner , Sergio Lucia

Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-step retrosynthesis models and search algorithms, taking only…

Machine Learning · Computer Science 2023-06-01 Songtao Liu , Zhengkai Tu , Minkai Xu , Zuobai Zhang , Lu Lin , Rex Ying , Jian Tang , Peilin Zhao , Dinghao Wu

In recent years, conventional chemistry techniques have faced significant challenges due to their inherent limitations, struggling to cope with the increasing complexity and volume of data generated in contemporary research endeavors.…

We propose a reinforcement learning based method to identify important configurations that connect reactant and product states along chemical reaction paths. By shooting multiple trajectories from these configurations, we can generate an…

Chemical Physics · Physics 2023-05-30 Senwei Liang , Aditya N. Singh , Yuanran Zhu , David T. Limmer , Chao Yang

Retrosynthesis is the task of breaking down a chemical compound recursively step-by-step into molecular precursors until a set of commercially available molecules is found. Consequently, the goal is to provide a valid synthesis route for a…

In retrosynthetic planning, the huge number of possible routes to synthesize a complex molecule using simple building blocks leads to a combinatorial explosion of possibilities. Even experienced chemists often have difficulty to select the…

Artificial Intelligence · Computer Science 2023-06-13 Siqi Hong , Hankz Hankui Zhuo , Kebing Jin , Guang Shao , Zhanwen Zhou

Atomic-scale modeling has advanced rapidly through integration of machine learning, yet a key bottleneck remains. Even with an accurate potential energy surface and a clear target material, we still lack a practical atomistic dynamics…

Materials Science · Physics 2026-05-18 Wonseok Jeong , Francesca Tavazza , Brian DeCost

Due to the intrinsic complexity and nonlinearity of chemical reactions, direct applications of traditional machine learning algorithms may face with many difficulties. In this study, through two concrete examples with biological background,…

Molecular Networks · Quantitative Biology 2020-06-02 Wuyue Yang , Liangrong Peng , Yi Zhu , Liu Hong

In this paper a deep reinforcement based multi-agent path planning approach is introduced. The experiments are realized in a simulation environment and in this environment different multi-agent path planning problems are produced. The…

Machine Learning · Computer Science 2021-10-05 Mert Çetinkaya

The goal of most materials discovery is to discover materials that are superior to those currently known. Fundamentally, this is close to extrapolation, which is a weak point for most machine learning models that learn the probability…

Biomolecules · Quantitative Biology 2024-05-08 Hyunseung Kim , Haeyeon Choi , Dongju Kang , Won Bo Lee , Jonggeol Na

Drug development is an expensive and time-consuming process where thousands of chemical compounds are being tested in order to find those possessing drug-like properties while being safe and effective. One of key parts of the early drug…

Quantitative Methods · Quantitative Biology 2022-02-15 Josip Mesarić

This paper aims to provide an innovative machine learning-based solution to automate security testing tasks for web applications, ensuring the correct functioning of all components while reducing project maintenance costs. Reinforcement…

Many multi-genic systemic diseases such as neurological disorders, inflammatory diseases, and the majority of cancers do not have effective treatments yet. Reinforcement learning powered systems pharmacology is a potentially effective…

Biomolecules · Quantitative Biology 2022-02-25 Ryan K. Tan , Yang Liu , Lei Xie

Additive manufacturing has enabled the fabrication of advanced reactor geometries, permitting larger, more complex design spaces. Identifying promising configurations within such spaces presents a significant challenge for current…

Computational Engineering, Finance, and Science · Computer Science 2024-06-07 Tom Savage , Nausheen Basha , Jonathan McDonough , James Krassowski , Omar K Matar , Ehecatl Antonio del Rio Chanona