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In machine learning and molecular design, there exist two approaches: discriminative and generative. In the discriminative approach dubbed forward design, the goal is to map a set of features/molecules to their respective electronics…

Chemical Physics · Physics 2019-04-24 Alain Tchagang , Julio Valdés

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally…

Machine Learning · Computer Science 2020-11-06 Mario Krenn , Florian Häse , AkshatKumar Nigam , Pascal Friederich , Alán Aspuru-Guzik

Deep generative models have recently been applied to molecule design. If the molecules are encoded in linear SMILES strings, modeling becomes convenient. However, models relying on string representations tend to generate invalid samples and…

Machine Learning · Computer Science 2020-10-20 Bo Pang , Tian Han , Ying Nian Wu

We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended…

Based on the traditional VAE, a novel neural network model is presented, with the latest molecular representation, SELFIES, to improve the effect of generating new molecules. In this model, multi-layer convolutional network and Fisher…

Biomolecules · Quantitative Biology 2023-05-03 Li Kai , Li Ning , Zhang Wei , Gao Ming

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

In the scope of "AI for Science", solving inverse problems is a longstanding challenge in materials and drug discovery, where the goal is to determine the hidden structures given a set of desirable properties. Deep generative models are…

Machine Learning · Computer Science 2022-12-05 Jiaxin Zhang , Sirui Bi , Victor Fung

Computer-driven molecular design combines the principles of chemistry, physics, and artificial intelligence to identify novel chemical compounds and materials with desired properties for a specific application. In particular,…

Chemical Physics · Physics 2023-09-04 Alessio Fallani , Leonardo Medrano Sandonas , Alexandre Tkatchenko

Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to…

Machine Learning · Computer Science 2020-06-09 Daniel Schwalbe-Koda , Rafael Gómez-Bombarelli

We examine the optical properties of a system of nano and micro particles of varying size, shape, and material (including metals and dielectrics, and sub-wavelength and super-wavelength regimes). Training data is generated by numerically…

Molecular generative models often assume meaningful latent geometry, but apparent property predictability can reflect sequence-level shortcuts rather than chemical organization. We study this issue in an unsupervised autoregressive…

Machine Learning · Computer Science 2026-05-08 Zakaria Elabid , Jan Andrzejewski , Bartosz Brzoza , Attila Cangi

Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…

Machine Learning · Computer Science 2020-02-10 Paul Maragakis , Hunter Nisonoff , Brian Cole , David E. Shaw

In the space of only a few years, deep generative modeling has revolutionized how we think of artificial creativity, yielding autonomous systems which produce original images, music, and text. Inspired by these successes, researchers are…

Machine Learning · Computer Science 2019-05-24 Daniel C. Elton , Zois Boukouvalas , Mark D. Fuge , Peter W. Chung

Chemical representation learning has gained increasing interest due to the limited availability of supervised data in fields such as drug and materials design. This interest particularly extends to chemical language representation learning,…

Chemical Physics · Physics 2024-08-06 Jun-Hyung Park , Yeachan Kim , Mingyu Lee , Hyuntae Park , SangKeun Lee

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

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

Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…

Quantitative Methods · Quantitative Biology 2020-11-17 Matthew Ragoza , Tomohide Masuda , David Ryan Koes

We propose a novel computational strategy for de novo design of molecules with desired properties termed ReLeaSE (Reinforcement Learning for Structural Evolution). Based on deep and reinforcement learning approaches, ReLeaSE integrates two…

Artificial Intelligence · Computer Science 2018-07-30 Mariya Popova , Olexandr Isayev , Alexander Tropsha

Machine learning is revolutionizing chemistry. Beyond the value of predictive models accelerating virtual screening, generative AI aims at enabling inverse design, reversing the compound-to-property prediction paradigm into…

We report a series of deep learning models to solve complex forward and inverse design problems in molecular modeling and design. Using both diffusion models inspired by nonequilibrium thermodynamics and attention-based transformer…

Materials Science · Physics 2023-06-21 Rachel K. Luu , Marcin Wysokowski , Markus J. Buehler
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