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Using pretrained graph neural networks with token mixers as geometric featurizers for conformational dynamics
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2025
|
Zihan Pengmei
Chatipat Lorpaiboon
Spencer C. Guo
Jonathan Weare
Aaron R. Dinner
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Using Explainable AI and Transfer Learning to Understand and Predict the Maintenance of Atlantic Blocking With Limited Observational Data
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2024
|
Huan Zhang
Justin Finkel
Dorian S. Abbot
Edwin P. Gerber
Jonathan Weare
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PDF
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Can AI weather models predict out-of-distribution gray swan tropical
cyclones?
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2024
|
Y. Qiang Sun
Pedram Hassanzadeh
M Lashti Zand
Ashesh Chattopadhyay
Jonathan Weare
Dorian S. Abbot
|
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PDF
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geom2vec: pretrained GNNs as geometric featurizers for conformational
dynamics
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2024
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Zihan Pengmei
Chatipat Lorpaiboon
Spencer C. Guo
Jonathan Weare
Aaron R. Dinner
|
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PDF
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Sampling parameters of ordinary differential equations with Langevin
dynamics that satisfy constraints
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2024
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Chris Chi
Jonathan Weare
Aaron R. Dinner
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PDF
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BAD-NEUS: Rapidly converging trajectory stratification
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2024
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John Strahan
Chatipat Lorpaiboon
Jonathan Weare
Aaron R. Dinner
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PDF
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Convergence of Unadjusted Langevin in High Dimensions: Delocalization of
Bias
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2024
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Yifan Chen
Xiaoou Cheng
Jonathan Niles‐Weed
Jonathan Weare
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The surprising efficiency of temporal difference learning for rare event
prediction
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2024
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Xiaoou Cheng
Jonathan Weare
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PDF
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Mercury’s Chaotic Secular Evolution as a Subdiffusive Process
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2024
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Dorian S. Abbot
Robert J. Webber
David Manuel Hernández
Sam Hadden
Jonathan Weare
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PDF
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BAD-NEUS: Rapidly converging trajectory stratification
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2024
|
John Strahan
Chatipat Lorpaiboon
Jonathan Weare
Aaron R. Dinner
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PDF
Chat
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Using Explainable AI and Transfer Learning to understand and predict the
maintenance of Atlantic blocking with limited observational data
|
2024
|
Huan Zhang
Justin Finkel
Dorian S. Abbot
Edwin P. Gerber
Jonathan Weare
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PDF
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Accurate estimates of dynamical statistics using memory
|
2024
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Chatipat Lorpaiboon
Spencer C. Guo
John Strahan
Jonathan Weare
Aaron R. Dinner
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PDF
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AI Can Identify Solar System Instability Billions of Years in Advance
|
2024
|
Dorian S. Abbot
J. D. Laurence-Chasen
Robert J. Webber
David M. Hernandez
Jonathan Weare
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Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction
|
2023
|
John Strahan
Spencer C. Guo
Chatipat Lorpaiboon
Aaron R. Dinner
Jonathan Weare
|
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PDF
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Understanding and eliminating spurious modes in variational Monte Carlo using collective variables
|
2023
|
Huan Zhang
Robert J. Webber
Michael Lindsey
Timothy C. Berkelbach
Jonathan Weare
|
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PDF
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Predicting rare events using neural networks and short-trajectory data
|
2023
|
John Strahan
Justin Finkel
Aaron R. Dinner
Jonathan Weare
|
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PDF
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Revealing the Statistics of Extreme Events Hidden in Short Weather Forecast Data
|
2023
|
Justin Finkel
Edwin P. Gerber
Dorian S. Abbot
Jonathan Weare
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PDF
Chat
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Simple Physics and Integrators Accurately Reproduce Mercury Instability Statistics
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2023
|
Dorian S. Abbot
David M. Hernandez
Sam Hadden
Robert J. Webber
Georgios P. Afentakis
Jonathan Weare
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Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction
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2023
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John Strahan
Spencer C. Guo
Chatipat Lorpaiboon
Aaron R. Dinner
Jonathan Weare
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+
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Mercury's chaotic secular evolution as a subdiffusive process
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2023
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Dorian S. Abbot
Robert J. Webber
David Manuel Hernández
Sam Hadden
Jonathan Weare
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+
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Randomly sparsified Richardson iteration is really fast
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2023
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Jonathan Weare
Robert J. Webber
|
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+
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Improved Active Learning via Dependent Leverage Score Sampling
|
2023
|
Atsushi Shimizu
Xiaoou Cheng
Christopher Musco
Jonathan Weare
|
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+
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Accurate estimates of dynamical statistics using memory
|
2023
|
Chatipat Lorpaiboon
Spencer C. Guo
John Strahan
Jonathan Weare
Aaron R. Dinner
|
|
+
PDF
Chat
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Full Configuration Interaction Excited-State Energies in Large Active Spaces from Subspace Iteration with Repeated Random Sparsification
|
2022
|
Samuel M. Greene
Robert J. Webber
James E. T. Smith
Jonathan Weare
Timothy C. Berkelbach
|
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Data-Driven Transition Path Analysis Yields a Statistical Understanding of Sudden Stratospheric Warming Events in an Idealized Model
|
2022
|
Justin Finkel
Robert J. Webber
Edwin P. Gerber
Dorian S. Abbot
Jonathan Weare
|
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PDF
Chat
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Approximating Matrix Eigenvalues by Subspace Iteration with Repeated Random Sparsification
|
2022
|
Samuel M. Greene
Robert J. Webber
Timothy C. Berkelbach
Jonathan Weare
|
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PDF
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Augmented transition path theory for sequences of events
|
2022
|
Chatipat Lorpaiboon
Jonathan Weare
Aaron R. Dinner
|
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+
PDF
Chat
|
Ensemble Markov Chain Monte Carlo with Teleporting Walkers
|
2022
|
Michael Lindsey
Jonathan Weare
Anna Zhang
|
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+
PDF
Chat
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Computing transition path theory quantities with trajectory stratification
|
2022
|
Bodhi P. Vani
Jonathan Weare
Aaron R. Dinner
|
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+
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Full Configuration Interaction Excited-State Energies in Large Active Spaces from Subspace Iteration with Repeated Random Sparsification: Active Space Orbitals
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2022
|
Samuel M. Greene
Robert J. Webber
James E. T. Smith
Jonathan Weare
Timothy C. Berkelbach
|
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+
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Full Configuration Interaction Excited-State Energies in Large Active Spaces from Subspace Iteration with Repeated Random Sparsification: Active Space Orbitals
|
2022
|
Samuel M. Greene
Robert J. Webber
James E. T. Smith
Jonathan Weare
Timothy C. Berkelbach
|
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+
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Full Configuration Interaction Excited-State Energies in Large Active Spaces from Subspace Iteration with Repeated Random Sparsification
|
2022
|
Samuel M. Greene
Robert J. Webber
James E. T. Smith
Jonathan Weare
Timothy C. Berkelbach
|
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+
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Augmented Transition Path Theory for Sequences of Events
|
2022
|
Chatipat Lorpaiboon
Jonathan Weare
Aaron R. Dinner
|
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+
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Revealing the statistics of extreme events hidden in short weather forecast data
|
2022
|
Justin Finkel
Edwin P. Gerber
Dorian S. Abbot
Jonathan Weare
|
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+
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Predicting rare events using neural networks and short-trajectory data
|
2022
|
John Strahan
Justin Finkel
Aaron R. Dinner
Jonathan Weare
|
|
+
|
Understanding and eliminating spurious modes in variational Monte Carlo using collective variables
|
2022
|
Huan Zhang
Robert J. Webber
Michael Lindsey
Timothy C. Berkelbach
Jonathan Weare
|
|
+
|
Simple physics and integrators accurately reproduce Mercury instability statistics
|
2022
|
Dorian S. Abbot
David Manuel Hernández
Sam Hadden
Robert J. Webber
Georgios P. Afentakis
Jonathan Weare
|
|
+
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Rare Event Sampling Improves Mercury Instability Statistics
|
2021
|
Dorian S. Abbot
Robert J. Webber
Sam Hadden
Darryl Z. Seligman
Jonathan Weare
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PDF
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Learning Forecasts of Rare Stratospheric Transitions from Short Simulations
|
2021
|
Justin Finkel
Robert J. Webber
Edwin P. Gerber
Dorian S. Abbot
Jonathan Weare
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Exploring stratospheric rare events with transition path theory and short simulations
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2021
|
Justin Finkel
Robert J. Webber
Edwin P. Gerber
Dorian S. Abbot
Jonathan Weare
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Long-Time-Scale Predictions from Short-Trajectory Data: A Benchmark Analysis of the Trp-Cage Miniprotein
|
2021
|
John Strahan
Adam Antoszewski
Chatipat Lorpaiboon
Bodhi P. Vani
Jonathan Weare
Aaron R. Dinner
|
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+
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Approximating matrix eigenvalues by randomized subspace iteration.
|
2021
|
Samuel M. Greene
Robert J. Webber
Timothy C. Berkelbach
Jonathan Weare
|
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+
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Randomized subspace iteration--data from numerical experiments
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2021
|
Samuel M. Greene
Robert J. Webber
Timothy C. Berkelbach
Jonathan Weare
|
|
+
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Randomized subspace iteration--data from numerical experiments
|
2021
|
Samuel M. Greene
Robert J. Webber
Timothy C. Berkelbach
Jonathan Weare
|
|
+
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Learning forecasts of rare stratospheric transitions from short simulations
|
2021
|
Justin Finkel
Robert J. Webber
Dorian S. Abbot
Edwin P. Gerber
Jonathan Weare
|
|
+
PDF
Chat
|
A Kinetic Monte Carlo Approach for Simulating Cascading Transmission Line Failure
|
2021
|
J. P. Roth
David A. Barajas‐Solano
Panos Stinis
Jonathan Weare
Mihai Anitescu
|
|
+
PDF
Chat
|
Error Bounds for Dynamical Spectral Estimation
|
2021
|
Robert J. Webber
Erik H. Thiede
Douglas Dow
Aaron R. Dinner
Jonathan Weare
|
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+
PDF
Chat
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A Metric on Directed Graphs and Markov Chains Based on Hitting Probabilities
|
2021
|
Zachary M. Boyd
Nicolás Fraiman
Jeremy L. Marzuola
Peter J. Mucha
Braxton Osting
Jonathan Weare
|
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+
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Data-driven transition path analysis yields a statistical understanding of sudden stratospheric warming events in an idealized model
|
2021
|
Justin Finkel
Robert J. Webber
Edwin P. Gerber
Dorian S. Abbot
Jonathan Weare
|
|
+
|
Approximating matrix eigenvalues by subspace iteration with repeated random sparsification
|
2021
|
Samuel M. Greene
Robert J. Webber
Timothy C. Berkelbach
Jonathan Weare
|
|
+
|
Ensemble Markov chain Monte Carlo with teleporting walkers
|
2021
|
Michael Lindsey
Jonathan Weare
Anna Zhang
|
|
+
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Integrated Variational Approach to Conformational Dynamics: A Robust Strategy for Identifying Eigenfunctions of Dynamical Operators
|
2020
|
Chatipat Lorpaiboon
Erik H. Thiede
Robert J. Webber
Jonathan Weare
Aaron R. Dinner
|
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+
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Long-timescale predictions from short-trajectory data: A benchmark analysis of the trp-cage miniprotein
|
2020
|
John Strahan
Adam Antoszewski
Chatipat Lorpaiboon
Bodhi P. Vani
Jonathan Weare
Aaron R. Dinner
|
|
+
PDF
Chat
|
Improved Fast Randomized Iteration Approach to Full Configuration Interaction
|
2020
|
Samuel M. Greene
Robert J. Webber
Jonathan Weare
Timothy C. Berkelbach
|
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+
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Integrated VAC: A robust strategy for identifying eigenfunctions of dynamical operators
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2020
|
Chatipat Lorpaiboon
Erik H. Thiede
Robert J. Webber
Jonathan Weare
Aaron R. Dinner
|
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A metric on directed graphs and Markov chains based on hitting probabilities
|
2020
|
Zachary M. Boyd
Nicolás Fraiman
Jeremy L. Marzuola
Peter J. Mucha
Braxton Osting
Jonathan Weare
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+
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Error bounds for dynamical spectral estimation.
|
2020
|
Robert J. Webber
Erik H. Thiede
Douglas Dow
Aaron R. Dinner
Jonathan Weare
|
|
+
PDF
Chat
|
Path Properties of Atmospheric Transitions: Illustration with a Low-Order Sudden Stratospheric Warming Model
|
2020
|
Justin Finkel
Dorian S. Abbot
Jonathan Weare
|
|
+
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Improved Fast Randomized Iteration Approach to Full Configuration Interaction
|
2020
|
Samuel M. Greene
Robert J. Webber
Jonathan Weare
Timothy C. Berkelbach
|
|
+
PDF
Chat
|
Stratification as a General Variance Reduction Method for Markov Chain Monte Carlo
|
2020
|
Aaron R. Dinner
Erik H. Thiede
Brian Van Koten
Jonathan Weare
|
|
+
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Integrated VAC: A robust strategy for identifying eigenfunctions of dynamical operators
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2020
|
Chatipat Lorpaiboon
Erik H. Thiede
Robert J. Webber
Jonathan Weare
Aaron R. Dinner
|
|
+
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Long-timescale predictions from short-trajectory data: A benchmark analysis of the trp-cage miniprotein
|
2020
|
John Strahan
Adam Antoszewski
Chatipat Lorpaiboon
Bodhi P. Vani
Jonathan Weare
Aaron R. Dinner
|
|
+
|
A metric on directed graphs and Markov chains based on hitting probabilities
|
2020
|
Zachary M. Boyd
Nicolás Fraiman
Jeremy L. Marzuola
Peter J. Mucha
Braxton Osting
Jonathan Weare
|
|
+
|
Error bounds for dynamical spectral estimation
|
2020
|
Robert J. Webber
Erik H. Thiede
Douglas Dow
Aaron R. Dinner
Jonathan Weare
|
|
+
|
Improved Fast Randomized Iteration Approach to Full Configuration Interaction
|
2020
|
Samuel M. Greene
Robert J. Webber
Jonathan Weare
Timothy C. Berkelbach
|
|
+
|
A Kinetic Monte Carlo Approach for Simulating Cascading Transmission Line Failure
|
2019
|
J. P. Roth
David A. Barajas‐Solano
Panos Stinis
Jonathan Weare
Mihai Anitescu
|
|
+
PDF
Chat
|
Beyond Walkers in Stochastic Quantum Chemistry: Reducing Error Using Fast Randomized Iteration
|
2019
|
Samuel M. Greene
Robert J. Webber
Jonathan Weare
Timothy C. Berkelbach
|
|
+
PDF
Chat
|
Galerkin approximation of dynamical quantities using trajectory data
|
2019
|
Erik H. Thiede
Dimitrios Giannakis
Aaron R. Dinner
Jonathan Weare
|
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+
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Beyond Walkers in Stochastic Quantum Chemistry: Reducing Error using Fast Randomized Iteration
|
2019
|
Samuel M. Greene
Robert J. Webber
Jonathan Weare
Timothy C. Berkelbach
|
|
+
PDF
Chat
|
Practical rare event sampling for extreme mesoscale weather
|
2019
|
Robert J. Webber
D. A. Plotkin
Morgan O’Neill
Dorian S. Abbot
Jonathan Weare
|
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+
PDF
Chat
|
Maximizing Simulated Tropical Cyclone Intensity With Action Minimization
|
2019
|
D. A. Plotkin
Robert J. Webber
Morgan O’Neill
Jonathan Weare
Dorian S. Abbot
|
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+
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A Kinetic Monte Carlo Approach for Simulating Cascading Transmission Line Failure
|
2019
|
Jacob S. Roth
David A. Barajas‐Solano
Panos Stinis
Jonathan Weare
Mihai Anitescu
|
|
+
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Beyond Walkers in Stochastic Quantum Chemistry: Reducing Error using Fast Randomized Iteration
|
2019
|
Samuel M. Greene
Robert J. Webber
Jonathan Weare
Timothy C. Berkelbach
|
|
+
PDF
Chat
|
Umbrella sampling: a powerful method to sample tails of distributions
|
2018
|
Charles H. Matthews
Jonathan Weare
Andrey V. Kravtsov
Elise Jennings
|
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+
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Langevin Markov Chain Monte Carlo with stochastic gradients
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2018
|
Charles H. Matthews
Jonathan Weare
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Simulating the stochastic dynamics and cascade failure of power networks
|
2018
|
Charles H. Matthews
Bradly C. Stadie
Jonathan Weare
Mihai Anitescu
Christopher L. DeMarco
|
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+
PDF
Chat
|
Trajectory Stratification of Stochastic Dynamics
|
2018
|
Aaron R. Dinner
Jonathan C. Mattingly
Jeremy O. B. Tempkin
Brian Van Koten
Jonathan Weare
|
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+
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Stratification of Markov Chain Monte Carlo
|
2017
|
Aaron R. Dinner
Erik H. Thiede
Brian Van Koten
Jonathan Weare
|
|
+
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Stratification as a general variance reduction method for Markov chain Monte Carlo
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2017
|
Aaron R. Dinner
Erik H. Thiede
Brian Van Koten
Jonathan Weare
|
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+
PDF
Chat
|
Ensemble preconditioning for Markov chain Monte Carlo simulation
|
2017
|
Benedict Leimkuhler
Charles H. Matthews
Jonathan Weare
|
|
+
PDF
Chat
|
Fast Randomized Iteration: Diffusion Monte Carlo through the Lens of Numerical Linear Algebra
|
2017
|
Lek-Heng Lim
Jonathan Weare
|
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+
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Stratification as a general variance reduction method for Markov chain Monte Carlo
|
2017
|
Aaron R. Dinner
Erik H. Thiede
Brian Van Koten
Jonathan Weare
|
|
+
PDF
Chat
|
Eigenvector method for umbrella sampling enables error analysis
|
2016
|
Erik H. Thiede
Brian Van Koten
Jonathan Weare
Aaron R. Dinner
|
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+
|
Ensemble preconditioning for Markov chain Monte Carlo simulation
|
2016
|
Charles H. Matthews
Jonathan Weare
Benedict Leimkuhler
|
|
+
PDF
Chat
|
Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics – Monte Carlo Canonical Propagation Algorithm
|
2016
|
Yunjie Chen
Seyit Kale
Jonathan Weare
Aaron R. Dinner
Benoı̂t Roux
|
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+
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Ensemble preconditioning for Markov chain Monte Carlo simulation
|
2016
|
Charles E. Matthews
Jonathan Weare
Benedict Leimkuhler
|
|
+
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Trajectory stratification of stochastic dynamics
|
2016
|
Aaron R. Dinner
Jonathan C. Mattingly
Jeremy O. B. Tempkin
Brian Van Koten
Jonathan Weare
|
|
+
PDF
Chat
|
Sharp Entrywise Perturbation Bounds for Markov Chains
|
2015
|
Erik H. Thiede
Brian Van Koten
Jonathan Weare
|
|
+
PDF
Chat
|
The Brownian Fan
|
2014
|
Martin Hairer
Jonathan Weare
|
|
+
|
Sharp entrywise perturbation bounds for Markov chains
|
2014
|
Erik H. Thiede
Brian Van Koten
Jonathan Weare
|
|
+
PDF
Chat
|
Improved Diffusion Monte Carlo
|
2014
|
Martin Hairer
Jonathan Weare
|
|
+
|
The Brownian fan
|
2014
|
Martin Hairer
Jonathan Weare
|
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+
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Sharp entrywise perturbation bounds for Markov chains
|
2014
|
Erik H. Thiede
Brian Van Koten
Jonathan Weare
|
|
+
|
The Brownian fan
|
2014
|
Martin Hairer
Jonathan Weare
|
|
+
PDF
Chat
|
Relaxation of a family of broken-bond crystal-surface models
|
2013
|
Jeremy L. Marzuola
Jonathan Weare
|
|
+
PDF
Chat
|
Relaxation of a family of broken-bond crystal-surface models
|
2013
|
Jeremy L. Marzuola
Jonathan Weare
|
|
+
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Improved diffusion Monte Carlo and the Brownian fan
|
2012
|
Jonathan Weare
Martin Hairer
|
|
+
PDF
Chat
|
Data Assimilation in the Low Noise Regime with Application to the Kuroshio
|
2012
|
Eric Vanden‐Eijnden
Jonathan Weare
|
|
+
|
Improved diffusion Monte Carlo and the Brownian fan
|
2012
|
Martin Hairer
Jonathan Weare
|
|
+
|
Improved diffusion Monte Carlo
|
2012
|
Martin Hairer
Jonathan Weare
|
|
+
PDF
Chat
|
Steered transition path sampling
|
2012
|
Nicholas Guttenberg
Aaron R. Dinner
Jonathan Weare
|
|
+
|
DATA ASSIMILATION IN THE LOW NOISE, ACCURATE OBSERVATION REGIME WITH APPLICATION TO THE KUROSHIO CURRENT
|
2012
|
Eric Vanden‐Eijnden
Jonathan Weare
|
|
+
PDF
Chat
|
AN AFFINE-INVARIANT SAMPLER FOR EXOPLANET FITTING AND DISCOVERY IN RADIAL VELOCITY DATA
|
2012
|
Fengji Hou
Jonathan Goodman
David W. Hogg
Jonathan Weare
Christian Schwab
|
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+
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Improved diffusion Monte Carlo
|
2012
|
Martin Hairer
Jonathan Weare
|
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+
|
The evolution of a crystal surface: Analysis of a one-dimensional step train connecting two facets in the ADL regime
|
2011
|
Hala Al Hajj Shehadeh
Robert V. Kohn
Jonathan Weare
|
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+
PDF
Chat
|
Ensemble samplers with affine invariance
|
2010
|
Jonathan Goodman
Jonathan Weare
|
|
+
PDF
Chat
|
Variance Reduction for Particle Filters of Systems With Time Scale Separation
|
2008
|
Dror Givon
Panos Stinis
Jonathan Weare
|
|
+
PDF
Chat
|
Efficient Monte Carlo sampling by parallel marginalization
|
2007
|
Jonathan Weare
|
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+
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Dimensional reduction for particle filters of systems with time-scale separation
|
2007
|
Dror Givon
Panagiotis Stinis
Jonathan Weare
|
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+
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Parallel marginalization Monte Carlo with applications to conditional path sampling
|
2007
|
Jonathan Weare
|
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+
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Variance reduction for particle filters of systems with time-scale separation
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2007
|
Dror Givon
Panagiotis Stinis
Jonathan Weare
|