English
Related papers

Related papers: Electron-Informed Coarse-Graining Molecular Repres…

200 papers

Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large…

Ultrafast diffraction imaging is a powerful tool to retrieve the geometric structure of gas-phase molecules with combined picometre spatial and attosecond temporal resolution. However, structural retrieval becomes progressively difficult…

Chemical Physics · Physics 2021-10-13 Xinyao Liu , Kasra Amini , Aurelien Sanchez , Blanca Belsa , Tobias Steinle , Jens Biegert

The exponential computational cost of describing strongly correlated electrons can be mitigated by adopting a reduced density-matrix (RDM)-based description of the electronic structure. While variational two-electron RDM (v2RDM) methods can…

Chemical Physics · Physics 2026-01-06 Grier M. Jones , Run. R. Li , A. Eugene DePrince , Konstantinos D. Vogiatzis

The pretraining-finetuning paradigm has powered major advances in domains such as natural language processing and computer vision, with representative examples including masked language modeling and next-token prediction. In molecular…

Machine Learning · Computer Science 2025-10-21 Shaoheng Yan , Zian Li , Muhan Zhang

Molecular Representation Learning is essential to solving many drug discovery and computational chemistry problems. It is a challenging problem due to the complex structure of molecules and the vast chemical space. Graph representations of…

Machine Learning · Computer Science 2023-01-18 Atia Hamidizadeh , Tony Shen , Martin Ester

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular…

Machine Learning · Computer Science 2025-02-27 Liang Wang , Shaozhen Liu , Yu Rong , Deli Zhao , Qiang Liu , Shu Wu , Liang Wang

Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based…

Advancements in lithium battery technology heavily rely on the design and engineering of electrolytes. However, current schemes for molecular design and recipe optimization of electrolytes lack an effective computational-experimental closed…

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes…

Machine Learning · Computer Science 2022-03-14 Yin Fang , Qiang Zhang , Haihong Yang , Xiang Zhuang , Shumin Deng , Wen Zhang , Ming Qin , Zhuo Chen , Xiaohui Fan , Huajun Chen

Large language models (LLMs) have demonstrated broad utility across molecular domains, spanning drug discovery and materials design. Analyzing LLMs' latent representations is crucial for elucidating their underlying mechanisms, improving…

Machine Learning · Computer Science 2026-02-03 Zhuoran Li , Xu Sun , Wanyu Lin , Jiannong Cao

Molecular property prediction, crucial for early drug candidate screening and optimization, has seen advancements with deep learning-based methods. While deep learning-based methods have advanced considerably, they often fall short in fully…

Biomolecules · Quantitative Biology 2024-07-01 Taojie Kuang , Yiming Ren , Zhixiang Ren

Machine learning has emerged as a potent computational tool for expediting research and development in solid oxide fuel cell electrodes. The effective application of machine learning for performance prediction requires transforming…

Materials Science · Physics 2025-03-19 Maksym Szemer , Szymon Buchaniec , Tomasz Prokop , Grzegorz Brus

We propose a simple, but efficient and accurate machine learning (ML) model for developing high-dimensional potential energy surface. This so-called embedded atom neural network (EANN) approach is inspired by the well-known empirical…

Chemical Physics · Physics 2019-10-23 Yaolong Zhang , Ce Hu , Bin Jiang

We consider feature representation learning problem of molecular graphs. Graph Neural Networks have been widely used in feature representation learning of molecular graphs. However, most existing methods deal with molecular graphs…

Machine Learning · Computer Science 2022-06-08 Zhaoning Yu , Hongyang Gao

Impressive advances in the field of molecular spintronics allow one to study electron transport through individual magnetic molecules embedded between metallic leads in the purely quantum regime of single electron tunneling. Besides…

Strongly Correlated Electrons · Physics 2019-09-05 Alessandro Chiesa , Emilio Macaluso , Paolo Santini , Stefano Carretta , Eva Pavarini

Ab initio methods for electronic structure of molecules have reached a satisfactory accuracy for calculation of static properties, but remain too expensive for quantum dynamical calculations. We propose an efficient semiclassical method for…

Chemical Physics · Physics 2015-05-13 Baiqing Li , Cesare Mollica , Jiri Vanicek

Variational ab-initio methods in quantum chemistry stand out among other methods in providing direct access to the wave function. This allows in principle straightforward extraction of any other observable of interest, besides the energy,…

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML…

Chemical Physics · Physics 2025-02-04 Ming Han , Ge Sun , Juan J. de Pablo

Machine learning models for 3D molecular property prediction typically rely on atom-based representations, which may overlook subtle physical information. Electron density maps -- the direct output of X-ray crystallography and cryo-electron…

Machine Learning · Computer Science 2025-12-01 Patricia Suriana , Joshua A. Rackers , Ewa M. Nowara , Pedro O. Pinheiro , John M. Nicoloudis , Vishnu Sresht

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our…

Biomolecules · Quantitative Biology 2024-12-20 He Cao , Zijing Liu , Xingyu Lu , Yuan Yao , Yu Li