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Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of…

Biomolecules · Quantitative Biology 2019-05-22 Sean M. Colby , Jamie R. Nuñez , Nathan O. Hodas , Courtney D. Corley , Ryan R. Renslow

Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in…

Computational Physics · Physics 2021-03-19 Jun Zhang , Yao-Kun Lei , Zhen Zhang , Junhan Chang , Maodong Li , Xu Han , Lijiang Yang , Yi Isaac Yang , Yi Qin Gao

The discovery of new materials has been the essential force which brings a discontinuous improvement to industrial products' performance. However, the extra-vast combinatorial design space of material structures exceeds human experts'…

The rational design of molecules with desired properties is a long-standing challenge in chemistry. Generative neural networks have emerged as a powerful approach to sample novel molecules from a learned distribution. Here, we propose a…

Molecular representation learning plays an essential role in cheminformatics. Recently, language model-based approaches have gained popularity as an alternative to traditional expert-designed features to encode molecules. However, these…

Machine Learning · Computer Science 2022-04-19 Zhihui Guo , Pramod Sharma , Andy Martinez , Liang Du , Robin Abraham

Molecular generation and molecular property prediction are both crucial for drug discovery, but they are often developed independently. Inspired by recent studies, which demonstrate that diffusion model, a prominent generative approach, can…

Machine Learning · Computer Science 2025-04-07 Shikun Feng , Yuyan Ni , Yan Lu , Zhi-Ming Ma , Wei-Ying Ma , Yanyan Lan

A proof-of-concept framework for identifying molecules of unknown elemental composition and structure using experimental rotational data and probabilistic deep learning is presented. Using a minimal set of input data determined…

Chemical Physics · Physics 2020-07-01 Michael C. McCarthy , Kin Long Kelvin Lee

Optimizing molecular design and discovering novel chemical structures to meet certain objectives, such as quantitative estimates of the drug-likeness score (QEDs), is NP-hard due to the vast combinatorial design space of discrete molecular…

Machine Learning · Computer Science 2023-02-23 Mohammad Sajjad Ghaemi , Hang Hu , Anguang Hu , Hsu Kiang Ooi

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as…

Recently, molecule generation using deep learning has been actively investigated in drug discovery. In this field, Transformer and VAE are widely used as powerful models, but they are rarely used in combination due to structural and…

Biomolecules · Quantitative Biology 2024-04-08 Yasuhiro Yoshikai , Tadahaya Mizuno , Shumpei Nemoto , Hiroyuki Kusuhara

Machine learning has transformed material discovery for inorganic compounds and small molecules, yet polymers remain largely inaccessible to these methods. While data scarcity is often cited as the primary bottleneck, we demonstrate that…

Machine Learning · Computer Science 2025-12-09 Jihun Ahn , Gabriella Pasya Irianti , Vikram Thapar , Su-Mi Hur

Molecular property prediction is an increasingly critical task within drug discovery and development. Typically, neural networks can learn molecular properties using graph-based, language-based or feature-based methods. Recent advances in…

Machine Learning · Computer Science 2025-07-31 Philip Spence , Brooks Paige , Anne Osbourn

The research of metamaterials has achieved enormous success in the manipulation of light in an artificially prescribed manner using delicately designed sub-wavelength structures, so-called meta-atoms. Even though modern numerical methods…

Optics · Physics 2019-01-31 Wei Ma , Feng Cheng , Yihao Xu , Qinlong Wen , Yongmin Liu

Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction…

Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with…

Machine Learning · Computer Science 2019-09-09 Bidisha Samanta , Abir De , Gourhari Jana , Pratim Kumar Chattaraj , Niloy Ganguly , Manuel Gomez-Rodriguez

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

Machine learning has enabled the prediction of quantum chemical properties with high accuracy and efficiency, allowing to bypass computationally costly ab initio calculations. Instead of training on a fixed set of properties, more recent…

Singlet fission has emerged as one of the most exciting phenomena known to improve the efficiencies of different types of solar cells and has found uses in diverse optoelectronic applications. The range of available singlet fission…

The next generation of force fields for molecular dynamics will be developed using a wealth of data. Training systematically with experimental data remains a challenge, however, especially for machine learning potentials. Differentiable…

Biomolecules · Quantitative Biology 2025-04-16 Joe G Greener

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