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Protein structure prediction has been a grand challenge for over 50 years, owing to its broad scientific and application interests. There are two primary types of modeling algorithms, template-free modeling and template-based modeling. The…

Biological Physics · Physics 2021-06-01 Liangzhen Zheng , Haidong Lan , Tao Shen , Jiaxiang Wu , Sheng Wang , Wei Liu , Junzhou Huang

Modern machine learning systems based on neural networks have shown great success in learning complex data patterns while being able to make good predictions on unseen data points. However, the limited interpretability of these systems…

Machine Learning · Computer Science 2020-07-22 Sarath Shekkizhar , Antonio Ortega

Machine learning offers an exciting opportunity to improve the calibration of nearly all reconstructed objects in high-energy physics detectors. However, machine learning approaches often depend on the spectra of examples used during…

High Energy Physics - Phenomenology · Physics 2022-09-02 Rikab Gambhir , Benjamin Nachman , Jesse Thaler

Accurately calibrated effective field theories are used to compute atomic parity non-conserving (APNC) observables. Although accurately calibrated, these effective field theories predict a large spread in the neutron skin of heavy nuclei.…

Nuclear Theory · Physics 2010-12-23 Tapas Sil , M. Centelles , X. Vinas , J. Piekarewicz

The widespread adoption of machine learning surrogate models has significantly improved the scale and complexity of systems and processes that can be explored accurately and efficiently using atomistic modeling. However, the inherently…

Chemical Physics · Physics 2025-03-13 Federico Grasselli , Sanggyu Chong , Venkat Kapil , Silvia Bonfanti , Kevin Rossi

Ab initio computations of atomic nuclei, based on Hamiltonians from effective field theories of quantum chromodynamics, are now routinely used to predict and describe properties of medium heavy nuclei, and even the heavy nucleus $^{208}$Pb…

Nuclear Theory · Physics 2024-10-02 T. Papenbrock

Advances in statistical learning theory present the opportunity to develop statistical models of quantum many-body systems exhibiting remarkable predictive power. The potential of such ``theory-thin'' approaches is illustrated with the…

Nuclear Theory · Physics 2008-11-26 John W. Clark , Haochen Li

In this review, we present a symmetry-guided strategy that utilizes exact as well as partial symmetries for enabling a deeper understanding of and advancing ab initio studies for determining the microscopic structure of atomic nuclei. These…

Nuclear Theory · Physics 2016-12-14 Kristina D. Launey , Tomas Dytrych , Jerry P. Draayer

Deep learning models have been the subject of study from various perspectives, for example, their training process, interpretation, generalization error, robustness to adversarial attacks, etc. A trained model is defined by its decision…

Machine Learning · Computer Science 2019-08-09 Roozbeh Yousefzadeh , Dianne P O'Leary

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…

Chemical Physics · Physics 2019-11-11 Frank Noé , Alexandre Tkatchenko , Klaus-Robert Müller , Cecilia Clementi

We review, for a general audience, a variety of recent experiments on extracting structure from machine-learning mathematical data that have been compiled over the years. Focusing on supervised machine-learning on labeled data from…

Machine Learning · Computer Science 2021-04-09 Yang-Hui He

In this thesis, we develop various techniques for working with sets in machine learning. Each input or output is not an image or a sequence, but a set: an unordered collection of multiple objects, each object described by a feature vector.…

Machine Learning · Computer Science 2021-03-09 Yan Zhang

We address the approximation of entropy solutions to initial-boundary value problems for nonlinear strictly hyperbolic conservation laws using neural networks. A general and systematic framework is introduced for the design of efficient and…

Analysis of PDEs · Mathematics 2025-09-16 Igor Ciril , Khalil Haddaoui , Yohann Tendero

We study the functional task of deep learning image classification models and show that image classification requires extrapolation capabilities. This suggests that new theories have to be developed for the understanding of deep learning as…

Machine Learning · Computer Science 2021-12-08 Roozbeh Yousefzadeh , Jessica A. Mollick

Machine learning approaches have become popular for molecular modeling tasks, including molecular force fields and properties prediction. Traditional supervised learning methods suffer from scarcity of labeled data for particular tasks,…

Chemical Physics · Physics 2022-11-29 Xiang Gao , Weihao Gao , Wenzhi Xiao , Zhirui Wang , Chong Wang , Liang Xiang

MOTIVATION: Proteins fold into complex structures that are crucial for their biological functions. Experimental determination of protein structures is costly and therefore limited to a small fraction of all known proteins. Hence, different…

Biomolecules · Quantitative Biology 2018-04-18 David Menéndez Hurtado , Karolis Uziela , Arne Elofsson

We report a deep generative model for regression tasks in materials informatics. The model is introduced as a component of a data imputer, and predicts more than 20 diverse experimental properties of organic molecules. The imputer is…

Computational Physics · Physics 2021-03-02 Kan Hatakeyama-Sato , Kenichi Oyaizu

The rise of foundation models -- large, pretrained machine learning models that can be finetuned to a variety of tasks -- has revolutionized the fields of natural language processing and computer vision. In high-energy physics, the question…

High Energy Physics - Phenomenology · Physics 2026-01-12 Anna Hallin

Machine-learning models in chemistry - when based on descriptors of atoms embedded within molecules - face essential challenges in transferring the quality of predictions of local electronic structures and their associated properties across…

Chemical Physics · Physics 2024-09-27 Frederik Ø. Kjeldal , Janus J. Eriksen

Predictive modelling represents an emerging field that combines existing and novel methodologies aimed to rapidly understand physical mechanisms and concurrently develop new materials, processes and structures. In the current study,…