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In this review, we highlight recent developments in the application of machine learning for molecular modeling and simulation. After giving a brief overview of the foundations, components, and workflow of a typical supervised learning…

数据分析、统计与概率 · 物理学 2019-02-21 Mojtaba Haghighatlari , Johannes Hachmann

Predicting molecular properties is essential for drug discovery, and computational methods can greatly enhance this process. Molecular graphs have become a focus for representation learning, with Graph Neural Networks (GNNs) widely used.…

机器学习 · 计算机科学 2025-01-31 Yan Sun , Yutong Lu , Yan Yi Li , Zihao Jing , Carson K. Leung , Pingzhao Hu

Neural methods of molecule property prediction require efficient encoding of structure and property relationship to be accurate. Recent work using graph algorithms shows limited generalization in the latent molecule encoding space. We build…

定量方法 · 定量生物学 2020-11-26 Prateeth Nayak , Andrew Silberfarb , Ran Chen , Tulay Muezzinoglu , John Byrnes

Machine-learning of atomic-scale properties amounts to extracting correlations between structure, composition and the quantity that one wants to predict. Representing the input structure in a way that best reflects such correlations makes…

化学物理 · 物理学 2021-02-02 Michael J. Willatt , Félix Musil , Michele Ceriotti

Designing a neural network architecture for molecular representation is crucial for AI-driven drug discovery and molecule design. In this work, we propose a new framework for molecular representation learning. Our contribution is threefold:…

机器学习 · 计算机科学 2022-10-18 Jiye Kim , Seungbeom Lee , Dongwoo Kim , Sungsoo Ahn , Jaesik Park

Deep neural networks are a powerful technique that have found ample applications in several branches of Physics. In this work, we apply machine learning algorithms to a specific problem of Cosmic Ray Physics: the estimation of the muon…

天体物理仪器与方法 · 物理学 2019-04-10 A. Guillen , A. Bueno , J. M. Carceller , J. C. Martinez-Velazquez , G. Rubio , C. J. Todero Peixoto , P. Sanchez-Lucas

Accurate prediction of physical properties is critical for discovering and designing novel materials. Machine learning technologies have attracted significant attention in the materials science community for their potential for large-scale…

材料科学 · 物理学 2021-11-24 Boyu Zhang , Mushen Zhou , Jianzhong Wu , Fuchang Gao

The prediction of physicochemical properties from molecular structures is a crucial task for artificial intelligence aided molecular design. A growing number of Graph Neural Networks (GNNs) have been proposed to address this challenge.…

机器学习 · 计算机科学 2020-11-17 Shuo Zhang , Yang Liu , Lei Xie

This paper studies the usefulness of incorporating path information in predicting chemical properties from molecular graphs, in the domain of QSAR (Quantitative Structure-Activity Relationship). Towards this, we developed a GNN-style model…

生物大分子 · 定量生物学 2024-07-22 Abdulrahman Ibraheem , Narsis Kiani , Jesper Tegner

The validity of the dissipative quantum model of olfaction has not been examined yet and therefore the model suffers from the lack of experimental support. Here, we generalize the model and propose a numerical analysis of the dissipative…

化学物理 · 物理学 2017-01-05 Arash Tirandaz , Farhad Taher Ghahramani , Vahid Salari

Progress in the application of machine learning techniques to the prediction of solid-state and molecular materials properties has been greatly facilitated by the development state-of-the-art feature representations and novel deep learning…

材料科学 · 物理学 2022-03-21 David E. Sommer , Scott T. Dunham

The nexus of quantum computing and machine learning - quantum machine learning - offers the potential for significant advancements in chemistry. This review specifically explores the potential of quantum neural networks on gate-based…

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…

机器学习 · 计算机科学 2022-06-08 Zhaoning Yu , Hongyang Gao

The insect olfactory system, which includes the antennal lobe (AL), mushroom body (MB), and ancillary structures, is a relatively simple neural system capable of learning. Its structural features, which are widespread in biological neural…

神经元与认知 · 定量生物学 2018-02-09 Charles B. Delahunt , Jeffrey A. Riffell , J. Nathan Kutz

Glasses offer a broad range of tunable thermophysical properties that are linked to their compositions. However, it is challenging to establish a universal composition-property relation of glasses due to their enormous composition and…

软凝聚态物质 · 物理学 2023-08-23 Kumar Ayush , Pooja Sahu , Sk Musharaf Ali , Tarak K Patra

Machine learning (ML) can be used to construct surrogate models for the fast prediction of a property of interest. ML can thus be applied to chemical projects, where the usual experimentation or calculation techniques can take hours or days…

Despite the rapid and significant advancements in deep learning for Quantitative Structure-Activity Relationship (QSAR) models, the challenge of learning robust molecular representations that effectively generalize in real-world scenarios…

机器学习 · 计算机科学 2024-05-28 Jose Arjona-Medina , Ramil Nugmanov

Machine Learning is a rapidly expanding field with a wide range of applications in science. In the field of physics, the Large Hadron Collider, the world's largest particle accelerator, utilizes Neural Networks for various tasks, including…

高能物理 - 实验 · 物理学 2024-01-19 Greta Brianti , Roberto Iuppa , Marco Cristoforetti

Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which amino-acid residues are in close spatial proximity given the amino-acid sequence…

Molecules have seemed like a natural fit to deep learning's tendency to handle a complex structure through representation learning, given enough data. However, this often continuous representation is not natural for understanding chemical…

机器学习 · 计算机科学 2021-03-12 Austin Clyde , Arvind Ramanathan , Rick Stevens