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Journal Articles

The fast committor machine: Interpretable prediction with kernels

David Aristoff, Mats Johnson, Gideon Simpson, Robert J. Webber
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 084113 (2024)
https://doi.org/10.1063/5.0222798
Published: August 2024
View article titled, The fast committor machine: Interpretable prediction with kernels
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Journal Articles

Featurizing Koopman mode decomposition for robust forecasting

David Aristoff, Jeremy Copperman, Nathan Mankovich, Alexander Davies
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 064103 (2024)
https://doi.org/10.1063/5.0220277
Published: August 2024
View article titled, Featurizing Koopman mode decomposition for robust forecasting
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Journal Articles

Efficient, nonparametric removal of noise and recovery of probability distributions from time series using nonlinear-correlation functions: Photon and photon-counting noise

Mainak Dhar, Mark A. Berg
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 034116 (2024)
https://doi.org/10.1063/5.0212157
Published: July 2024
View article titled, Efficient, nonparametric removal of noise and recovery of probability distributions from time series using nonlinear-correlation functions: Photon and photon-counting noise
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Journal Articles

Multitask methods for predicting molecular properties from heterogeneous data

K. E. Fisher, M. F. Herbst, Y. M. Marzouk
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 014114 (2024)
https://doi.org/10.1063/5.0201681
Published: July 2024
View article titled, Multitask methods for predicting molecular properties from heterogeneous data
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Journal Articles

Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration

Amey P. Pasarkar, Gianluca M. Bencomo, Simon Olsson, Adji Bousso Dieng
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 144108 (2023)
https://doi.org/10.1063/5.0166172
Published: October 2023
View article titled, Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration
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Includes: Supplementary data
Journal Articles

Molecular dynamics-driven global potential energy surfaces: Application to the AlF dimer

Xiangyue Liu, Weiqi Wang, Jesús Pérez-Ríos
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 144103 (2023)
https://doi.org/10.1063/5.0169080
Published: October 2023
View article titled, Molecular dynamics-driven global potential energy surfaces: Application to the AlF dimer
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Journal Articles

Efficient, nonparametric removal of noise and recovery of probability distributions from time series using nonlinear-correlation functions: Additive noise

Mainak Dhar, Joseph A. Dickinson, Mark A. Berg
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 054110 (2023)
https://doi.org/10.1063/5.0158199
Published: August 2023
View article titled, Efficient, nonparametric removal of noise and recovery of probability distributions from time series using nonlinear-correlation functions: Additive noise
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Includes: Supplementary data
Journal Articles

q-pac : A Python package for machine learned charge equilibration models

Martin Vondrák, Karsten Reuter, Johannes T. Margraf
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 054109 (2023)
https://doi.org/10.1063/5.0156290
Published: August 2023
View article titled, q-pac : A Python package for machine learned charge equilibration models
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Includes: Supplementary data
Journal Articles

Kernel based quantum machine learning at record rate: Many-body distribution functionals as compact representations

Danish Khan, Stefan Heinen, O. Anatole von Lilienfeld
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 034106 (2023)
https://doi.org/10.1063/5.0152215
Published: July 2023
View article titled, Kernel based quantum machine learning at record rate: Many-body distribution functionals as compact representations
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Includes: Supplementary data
Journal Articles

State of charge estimation for lithium-ion battery based on whale optimization algorithm and multi-kernel relevance vector machine

Kui Chen, Shuyuan Zhou, Kai Liu, Guoqiang Gao, Guangning Wu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 104110 (2023)
https://doi.org/10.1063/5.0139376
Published: March 2023
View article titled, State of charge estimation for lithium-ion battery based on whale optimization algorithm and multi-kernel relevance vector machine
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Journal Articles

How protein topology controls allosteric regulations

Juan Xie, Gaoxiang Pan, Yibo Li, Luhua Lai
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 105102 (2023)
https://doi.org/10.1063/5.0138279
Published: March 2023
View article titled, How protein topology controls allosteric regulations
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Includes: Supplementary data
Journal Articles

A spur to molecular geometry optimization: Gradient-enhanced universal kriging with on-the-fly adaptive ab initio prior mean functions in curvilinear coordinates

Chong Teng, Daniel Huang, Junwei Lucas Bao
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 024112 (2023)
https://doi.org/10.1063/5.0133675
Published: January 2023
View article titled, A spur to molecular geometry optimization: Gradient-enhanced universal kriging with on-the-fly adaptive <em>ab initio</em> prior mean functions in curvilinear coordinates
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Includes: Supplementary data
Journal Articles

Reliable emulation of complex functionals by active learning with error control

Xinyi Fang, Mengyang Gu, Jianzhong Wu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 214109 (2022)
https://doi.org/10.1063/5.0121805
Published: December 2022
View article titled, Reliable emulation of complex functionals by active learning with error control
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Includes: Supplementary data
Journal Articles

Computing committors via Mahalanobis diffusion maps with enhanced sampling data

L. Evans, M. K. Cameron, P. Tiwary
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 214107 (2022)
https://doi.org/10.1063/5.0122990
Published: December 2022
View article titled, Computing committors via Mahalanobis diffusion maps with enhanced sampling data
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Journal Articles

Efficient force field and energy emulation through partition of permutationally equivalent atoms

Hao Li, Musen Zhou, Jessalyn Sebastian, Jianzhong Wu, Mengyang Gu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 184304 (2022)
https://doi.org/10.1063/5.0088017
Published: May 2022
View article titled, Efficient force field and energy emulation through partition of permutationally equivalent atoms
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Includes: Supplementary data
Journal Articles

Geometry meta-optimization

Daniel Huang, Junwei Lucas Bao, Jean-Baptiste Tristan
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 134109 (2022)
https://doi.org/10.1063/5.0087165
Published: April 2022
View article titled, Geometry meta-optimization
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Journal Articles

An orbital-based representation for accurate quantum machine learning

Konstantin Karandashev, O. Anatole von Lilienfeld
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 114101 (2022)
https://doi.org/10.1063/5.0083301
Published: March 2022
View article titled, An orbital-based representation for accurate quantum machine learning
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Includes: Supplementary data
Journal Articles

Bayesian optimization for inverse problems in time-dependent quantum dynamics

Z. Deng, I. Tutunnikov, I. Sh. Averbukh, M. Thachuk, R. V. Krems
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 164111 (2020)
https://doi.org/10.1063/5.0015896
Published: October 2020
View article titled, Bayesian optimization for inverse problems in time-dependent quantum dynamics
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Includes: Supplementary data
Journal Articles

A Bayesian inference framework for compression and prediction of quantum states

Yannic Rath, Aldo Glielmo, George H. Booth
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 124108 (2020)
https://doi.org/10.1063/5.0024570
Published: September 2020
View article titled, A Bayesian inference framework for compression and prediction of quantum states
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Journal Articles

Gaussian process model of 51-dimensional potential energy surface for protonated imidazole dimer

Hiroki Sugisawa, Tomonori Ida, R. V. Krems
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 114101 (2020)
https://doi.org/10.1063/5.0023492
Published: September 2020
View article titled, Gaussian process model of 51-dimensional potential energy surface for protonated imidazole dimer
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Includes: Supplementary data