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In this work, we introduce a method to fine-tune a Transformer-based generative model for molecular de novo design. Leveraging the superior sequence learning capacity of Transformers over Recurrent Neural Networks (RNNs), our model can…

Machine Learning · Computer Science 2024-03-11 Pengcheng Xu , Tao Feng , Tianfan Fu , Siddhartha Laghuvarapu , Jimeng Sun

Deep learning has become a popular tool for medical image analysis, but the limited availability of training data remains a major challenge, particularly in the medical field where data acquisition can be costly and subject to privacy…

Image and Video Processing · Electrical Eng. & Systems 2024-06-11 Aghiles Kebaili , Jérôme Lapuyade-Lahorgue , Su Ruan

We demonstrate a machine learning approach designed to extract hidden chemistry/physics to facilitate new materials discovery. In particular, we propose a novel method for learning latent knowledge from material structure data in which…

Materials Science · Physics 2021-08-03 Tien-Cuong Nguyen , Van-Quyen Nguyen , Van-Linh Ngo , Quang-Khoat Than , Tien-Lam Pham

Although machine learning has been successfully used to propose novel molecules that satisfy desired properties, it is still challenging to explore a large chemical space efficiently. In this paper, we present a conditional molecular design…

Machine Learning · Computer Science 2019-04-02 Seokho Kang , Kyunghyun Cho

Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although current graph…

Quantitative Methods · Quantitative Biology 2018-04-24 Yibo Li , Liangren Zhang , Zhenming Liu

The design of molecules and materials with tailored properties is challenging, as candidate molecules must satisfy multiple competing requirements that are often difficult to measure or compute. While molecular structures, produced through…

Chemical Physics · Physics 2023-02-07 Julia Westermayr , Joe Gilkes , Rhyan Barrett , Reinhard J. Maurer

Language modeling has seen impressive progress over the last years, mainly prompted by the invention of the Transformer architecture, sparking a revolution in many fields of machine learning, with breakthroughs in chemistry and biology. In…

Machine Learning · Computer Science 2023-10-11 Andres M Bran , Philippe Schwaller

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…

Quantum Physics · Physics 2023-08-15 A. I. Gircha , A. S. Boev , K. Avchaciov , P. O. Fedichev , A. K. Fedorov

The drug design process currently requires considerable time and resources to develop each new compound that enters the market. This work develops an application of hybrid quantum generative models based on the integration of parametrized…

Drug discovery and development is a complex and costly process. Machine learning approaches are being investigated to help improve the effectiveness and speed of multiple stages of the drug discovery pipeline. Of these, those that use…

Artificial Intelligence · Computer Science 2022-09-27 Stephen Bonner , Ian P Barrett , Cheng Ye , Rowan Swiers , Ola Engkvist , Andreas Bender , Charles Tapley Hoyt , William L Hamilton

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

Generative models for structure-based molecular design hold significant promise for drug discovery, with the potential to speed up the hit-to-lead development cycle, while improving the quality of drug candidates and reducing costs. Data…

Machine Learning · Statistics 2022-04-25 Lucian Chan , Rajendra Kumar , Marcel Verdonk , Carl Poelking

Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called "de novo" design problem have recently been…

Machine Learning · Computer Science 2023-10-17 Adam Winnifrith , Carlos Outeiral , Brian Hie

In the scope of drug discovery, the molecular design aims to identify novel compounds from the chemical space where the potential drug-like molecules are estimated to be in the order of 10^60 - 10^100. Since this search task is…

Machine Learning · Computer Science 2022-10-25 Wenlu Wang , Ye Wang , Honggang Zhao , Simone Sciabola

Recent advances in artificial intelligence have propelled the development of innovative computational materials modeling and design techniques. Generative deep learning models have been used for molecular representation, discovery, and…

Chemical Physics · Physics 2021-02-12 Navid Shervani-Tabar , Nicholas Zabaras

Deep learning has recently been applied to various research areas of design optimization. This study presents the need and effectiveness of adopting deep learning for generative design (or design exploration) research area. This work…

Machine Learning · Computer Science 2020-05-27 Sangeun Oh , Yongsu Jung , Seongsin Kim , Ikjin Lee , Namwoo Kang

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in…

Molecule design is a fundamental problem in molecular science and has critical applications in a variety of areas, such as drug discovery, material science, etc. However, due to the large searching space, it is impossible for human experts…

Machine Learning · Computer Science 2022-03-29 Yuanqi Du , Tianfan Fu , Jimeng Sun , Shengchao Liu

Thin films are ubiquitous in modern technology and highly useful in materials discovery and design. For achieving optimal extrinsic properties their microstructure needs to be controlled in a multi-parameter space, which usually requires a…

Applied Physics · Physics 2020-03-31 Lars Banko , Yury Lysogorskiy , Dario Grochla , Dennis Naujoks , Ralf Drautz , Alfred Ludwig

Generative models aim to learn the distribution of observed data by generating new instances. With the advent of neural networks, deep generative models, including variational autoencoders (VAEs), generative adversarial networks (GANs), and…

Computer Vision and Pattern Recognition · Computer Science 2023-08-29 Zifan Shi , Sida Peng , Yinghao Xu , Andreas Geiger , Yiyi Liao , Yujun Shen