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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…

Chemical Physics · Physics 2020-12-17 Julien Horwood , Emmanuel Noutahi

De novo molecular design has facilitated the exploration of large chemical space to accelerate drug discovery. Structure-based de novo method can overcome the data scarcity of active ligands by incorporating drug-target interaction into…

Biomolecules · Quantitative Biology 2022-09-16 Yaqin Li , Lingli Li , Yongjin Xu , Yi Yu

De novo drug design is a crucial component of modern drug development, yet navigating the vast chemical space to find synthetically accessible, high-affinity candidates remains a significant challenge. Reinforcement Learning (RL) enhances…

Machine Learning · Computer Science 2025-12-25 R Yadunandan , Nimisha Ghosh

Discovering new drug molecules is a pivotal yet challenging process due to the near-infinitely large chemical space and notorious demands on time and resources. Numerous generative models have recently been introduced to accelerate the drug…

Computational Engineering, Finance, and Science · Computer Science 2025-12-23 Shitong Luo , Wenhao Gao , Zuofan Wu , Jian Peng , Connor W. Coley , Jianzhu Ma

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

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

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…

Biomolecules · Quantitative Biology 2024-01-15 Xiuyuan Hu , Guoqing Liu , Yang Zhao , Hao Zhang

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

Synthesizable molecular design (also known as synthesizable molecular optimization) is a fundamental problem in drug discovery, and involves designing novel molecular structures to improve their properties according to drug-relevant oracle…

Machine Learning · Computer Science 2026-05-07 Dannong Wang , Jintai Chen , Yingzhou Lu , Minjie Shen , Lulu Chen , Zhiding Liang , Tianfan Fu , Xiao-Yang Liu

Generative models see increasing use in computer-aided drug design. However, while performing well at capturing distributions of molecular motifs, they often produce synthetically inaccessible molecules. To address this, we introduce…

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

The discovery of functional molecules is an expensive and time-consuming process, exemplified by the rising costs of small molecule therapeutic discovery. One class of techniques of growing interest for early-stage drug discovery is de novo…

Quantitative Methods · Quantitative Biology 2020-02-18 Wenhao Gao , Connor W. Coley

Recently, deep reinforcement learning (DRL) methods have achieved impressive performance on tasks in a variety of domains. However, neural network policies produced with DRL methods are not human-interpretable and often have difficulty…

Machine Learning · Computer Science 2022-02-02 Dweep Trivedi , Jesse Zhang , Shao-Hua Sun , Joseph J. Lim

A major obstacle to the realization of novel inorganic materials with desirable properties is the inability to perform efficient optimization across both materials properties and synthesis of those materials. In this work, we propose a…

Materials Science · Physics 2022-10-24 Elton Pan , Christopher Karpovich , Elsa Olivetti

Developing new drugs is laborious and costly, demanding extensive time investment. In this paper, we introduce a de-novo drug design strategy, which harnesses the capabilities of language models to devise targeted drugs for specific…

Biomolecules · Quantitative Biology 2025-05-20 Salma J. Ahmed , Emad A. Mohammed

Advancements in additive manufacturing have enabled design and fabrication of materials and structures not previously realizable. In particular, the design space of composite materials and structures has vastly expanded, and the resulting…

Drug discovery is a complex, resource-intensive process requiring significant time and cost to bring new medicines to patients. Many generative models aim to accelerate drug discovery, but few produce synthetically accessible molecules.…

Machine Learning · Computer Science 2025-01-30 Zygimantas Jocys , Zhanxing Zhu , Henriette M. G. Willems , Katayoun Farrahi

Automating molecular design using deep reinforcement learning (RL) holds the promise of accelerating the discovery of new chemical compounds. Existing approaches work with molecular graphs and thus ignore the location of atoms in space,…

Machine Learning · Statistics 2021-03-02 Gregor N. C. Simm , Robert Pinsler , José Miguel Hernández-Lobato

Reinforcement learning (RL) is a goal-oriented learning solution that has proven to be successful for Neural Architecture Search (NAS) on the CIFAR and ImageNet datasets. However, a limitation of this approach is its high computational…

Neural and Evolutionary Computing · Computer Science 2019-12-04 J. Gomez Robles , J. Vanschoren

We introduce SynFormer, a generative modeling framework designed to efficiently explore and navigate synthesizable chemical space. Unlike traditional molecular generation approaches, we generate synthetic pathways for molecules to ensure…

Machine Learning · Computer Science 2024-10-07 Wenhao Gao , Shitong Luo , Connor W. Coley
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