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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

Designing new chemical compounds with desired pharmaceutical properties is a challenging task and takes years of development and testing. Still, a majority of new drugs fail to prove efficient. Recent success of deep generative modeling…

Machine Learning · Computer Science 2021-09-15 Karina Zadorozhny , Lada Nuzhna

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

Traditional drug discovery programs are being transformed by the advent of machine learning methods. Among these, Generative AI methods (GM) have gained attention due to their ability to design new molecules and enhance specific properties…

The recent surge in Generative Artificial Intelligence (AI) has introduced exciting possibilities for computational chemistry. Generative AI methods have made significant progress in sampling molecular structures across chemical species,…

Statistical Mechanics · Physics 2024-09-06 Pratyush Tiwary , Lukas Herron , Richard John , Suemin Lee , Disha Sanwal , Ruiyu Wang

The development of novel pharmaceuticals represents a significant challenge in modern science, with substantial costs and time investments. Deep generative models have emerged as promising tools for accelerating drug discovery by…

Atomic Physics · Physics 2025-05-20 Adarsh Singh

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

"How to evaluate the de novo designs proposed by a generative model?" Despite the transformative potential of generative deep learning in drug discovery, this seemingly simple question has no clear answer. The absence of standardized…

Biomolecules · Quantitative Biology 2025-11-14 Rıza Özçelik , Francesca Grisoni

A major challenge in computational chemistry is the generation of novel molecular structures with desirable pharmacological and physiochemical properties. In this work, we investigate the potential use of autoencoder, a deep learning…

Machine Learning · Computer Science 2017-11-22 Thomas Blaschke , Marcus Olivecrona , Ola Engkvist , Jürgen Bajorath , Hongming Chen

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

Generative AI presents chemists with novel ideas for drug design and facilitates the exploration of vast chemical spaces. Diffusion models (DMs), an emerging tool, have recently attracted great attention in drug R\&D. This paper…

Biomolecules · Quantitative Biology 2025-07-14 Peining Zhang , Daniel Baker , Minghu Song , Jinbo Bi

Structure-based drug design uses three-dimensional geometric information of macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric deep learning, an emerging concept of neural-network-based machine…

Chemical Physics · Physics 2022-10-21 Clemens Isert , Kenneth Atz , Gisbert Schneider

Despite the great popularity of virtual screening of existing compound libraries, the search for new potential drug candidates also takes advantage of generative protocols, where new compound suggestions are enumerated using various…

Biomolecules · Quantitative Biology 2023-12-22 Tomasz Danel , Jan Łęski , Sabina Podlewska , Igor T. Podolak

Probabilistic generative deep learning for molecular design involves the discovery and design of new molecules and analysis of their structure, properties and activities by probabilistic generative models using the deep learning approach.…

Machine Learning · Computer Science 2019-02-15 Daniel T. Chang

In recent years the scientific community has devoted much effort in the development of deep learning models for the generation of new molecules with desirable properties (i.e. drugs). This has produced many proposals in literature. However,…

Machine Learning · Computer Science 2020-08-24 Davide Rigoni , Nicolò Navarin , Alessandro Sperduti

High throughput experimentation tools, machine learning (ML) methods, and open material databases are radically changing the way new materials are discovered. From the experimentally driven approach in the past, we are moving quickly…

Materials Science · Physics 2025-08-06 Albertus Denny Handoko , Riko I Made

Deep generative models that learn from the distribution of natural protein sequences and structures may enable the design of new proteins with valuable functions. While the majority of today's models focus on generating either sequences or…

Biomolecules · Quantitative Biology 2024-10-03 Chentong Wang , Sarah Alamdari , Carles Domingo-Enrich , Ava Amini , Kevin K. Yang

The idea of using deep-learning-based molecular generation to accelerate discovery of drug candidates has attracted extraordinary attention, and many deep generative models have been developed for automated drug design, termed molecular…

Biomolecules · Quantitative Biology 2024-05-01 Odin Zhang , Haitao Lin , Hui Zhang , Huifeng Zhao , Yufei Huang , Yuansheng Huang , Dejun Jiang , Chang-yu Hsieh , Peichen Pan , Tingjun Hou

Finding drug-like compounds with high bioactivity is essential for drug discovery, but the task is complicated by the high cost of chemical synthesis and validation. With their outstanding performance in de novo drug design, deep generative…

Quantitative Methods · Quantitative Biology 2023-01-03 Yibo Li , Jianfeng Pei , Luhua Lai

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…

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