Jonathan
Weare Warren Weaver Hall, Room 1103 251 Mercer Street New York, NY 10012-1185 [my last name]@nyu.edu |
Our group is primarily
focused on the design, mathematical analysis, and
application of stochastic algorithms and models. Our
work draws on tools from probability theory, numerical
analysis, and statistical and machine learning. Research
in the group is informed by our long term collaborations
with applications experts in areas such as astrophysics,
biophysics, computational chemistry, and weather and
climate science.
I am a professor of
mathematics in the Courant Institute of Mathematical
Sciences at New York University. Previously I was an
associate professor in the statistics department and in
the James Franck Institute at the University of Chicago
and, before that, an assistant professor in the
mathematics department there. Before moving to Chicago,
I was a Courant Instructor of mathematics at NYU and a
PhD student in mathematics at the University of
California at Berkeley.
Research areas Monte
Carlo sampling
multiscale analysis and simulation randomized numerical linear algebra rare event analysis and simulation statistical and machine learning for scientific computing People High school
students
Anna
Zhang, Stuyvesant High School 2020-2021
Undergraduate
students
James
Butler, mathematics, University of Chicago (co-mentored
with D. Abbot) 2020-2021
Runxin Ni, mathematics, New York University (co-mentored with D. Abbot) Summer 2020 Charlie Marshall, mathematics, University of Chicago (co-mentored with D. Abbot) 2019-2020 Douglas Dow, mathematics, University of Chicago 2019-2020 Bradley Stadie, mathematics, University of Chicago 2013-2014 Masters students Bixing
Qiao, mathematics, New York University 2019-2020
Eileen Li, statistics, University of Chicago (co-mentored with A. Dinner) 2016-2017 Doctoral students Xiaoou
Cheng, New York University 2020-
Huan Zhang, mathematics, New York University 2019- Zhengqu Wan, mathematics, New York University 2018- Chatipat Lorpaiboon, chemistry, University of Chicago (co-mentored with A. Dinner) 2018- John Strahan, chemistry, University of Chicago (co-mentored with A. Dinner) 2018- Anya Katsevich, mathematics, New York University 2017-2022 Justin Finkel, applied math, University of Chicago (co-mentored with D. Abbot) 2017-2022 Adam Antoszewski, chemistry, University of Chicago (co-mentored with A. Dinner) 2017-2022 Sam Greene, chemistry, Columbia (co-mentored with T. Berkelbach) 2017-2022 Robert Webber, mathematics, New York University 2015-2021 Bodhi Vani, chemistry, University of Chicago (co-mentored with A. Dinner) 2015-2021 Erik Thiede, chemistry, University of Chicago (co-mentored with A. Dinner) 2013-2019 David Plotkin, geoscience, University of Chicago (co-mentored with D. Abbot) 2012-2018 Jeremy Tempkin, chemistry, University of Chicago (co-mentored with A. Dinner) 2012-2017 Instructors and postdoctoral scholars Michael Lindsey, mathematics, New
York University 2019-
Brian Van Koten, applied math, University of Chicago 2014-2018 Charles Matthews, applied math, University of Chicago 2014-2018 Seyit Kale, chemistry, University of Chicago 2012-2015 Editorial work Publications (sorted
roughly by area) Preprints can be found on arXiv Monte Carlo, Markov chains, and related Ensemble
Markov chain Monte Carlo with teleporting walkers
with M. Lindsey and A. Zhang, SIAM Journal on
Uncertainty Quantification, 10(3) [2022], 860-885A metric on directed graphs and Markov chains based on hitting probabilities with Z.M. Boyd, N. Fraiman, J.L. Marzuola, P.J. Mucha, and B. Osting, SIAM Journal on Mathematics of Data
Science, 3(2) [2021], 467-493Stratification as a general variance reduction method for Markov chain Monte Carlo with A.R. Dinner, E.H. Thiede, and B. Van Koten, SIAM/ASA
Journal on Uncertainty Quantification (JUQ), 8(3)
[2020], 1139-1188 Langevin Markov chain Monte Carlo with stochastic gradients with C. Matthews [2018] Umbrella sampling: a powerful method to sample tails of distributions with C. Matthews, A. Kravstov, and E. Jennings, Monthly
Notices of the Royal Astronomical Society, 480(3)
[2018], 4069-4079 Ensemble preconditioning for Markov chain Monte Carlo simulation with B. Leimkuhler and C. Matthews, Statistics and
Computing, 28(2) [2017], 277-290Eigenvector method for umbrella sampling enables error analysis with E. Thiede, B. Van Koten, and A. Dinner, Journal
of Chemical Physics, 145(8) [2016], 084115 Sharp entrywise perturbation bounds for Markov chains with E. Thiede and B. Van Koten, SIAM Journal on
Matrix Analysis and Applications, 36(3) [2015],
917-941 On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method with B. Roux, Journal of Chemical Physics,
138(8) [2013], 084107 An affine-invariant sampler for exoplanet fitting and discovery in radial velocity data with F. Hou, J. Goodman, D. Hogg, and C. Schwab, The
Astrophysical Journal, 75 [2012], 198 Ensemble samplers with affine invariance with J. Goodman, Communications in Applied
Mathematics and Computational Science, 5 [2010],
65-80Efficient Monte Carlo sampling by parallel marginalization Proceedings of the National Academy of Science,
104(31) [2007], 12657-12662 Multiscale analysis and simulation A Kinetic
Monte Carlo approach for simulating cascading
transmission line failure
with J. Roth, D.A. Barajas-Solano, P. Stinis, and Mihai Anitescu, SIAM Multiscale Modeling and
Simulation, 19(1) [2021], 208-241 Multiple time-step dual-Hamiltonian hybrid molecular dynamics Monte Carlo canonical propagation algorithm with Y. Chen, S. Kale, A. Dinner, and B. Roux, Journal
of Chemical Theory and Computation, 12(4)
[2016], 1449-1458 Finding chemical reaction paths with a multilevel preconditioning protocol with S. Kale, S. Olaseni, and A. Dinner, Journal
of Chemical Theory and Simulation, 10(12)
[2014], 5467-5475 Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations with J. Tempkin, B. Qui, M. Saunders, B. Roux, and A. Dinner, Journal of Chemical Physics, 140(18)
[2014], 184114Nucleotide regulation of the structure and dynamics of G-actin with M. Saunders, J. Tempkin, A. Dinner, B. Roux, and G. Voth, Biophysical Journal, 106(8) [2014],
1710-1720The relaxation of a family of broken bond crystal surface models with J. Marzuola, Physical Review E, 88
[2013], 032403 The theory of ultra coarse graining I, general principles with J. Dama, A. Sinitskiy, M. McCullagh, B. Roux, A. Dinner, and G. Voth, Journal of Chemical Theory
and Computation, 9(5) [2013], 2466-2480 Minimizing memory as an objective for coarse-graining with N. Guttenberg, J. Dama, M. Saunders, A. Dinner, and G. Voth, Journal of Chemical Physics,
138(9) [2013], 094111 Extending molecular simulation time scales: Parallel-in-time integration for high-level quantum chemistry and complex force representations with E. Bylaska and J.H. Weare, Journal of
Chemical Physics, 139 [2013], 074114 The evolution of a crystal surface: analysis of a 1D step train connecting two facets in the ADL regime with H. Al Hajj Shehadeh and R.V. Kohn, Physica D,
240 [2011], 1771-1784Variance reduction for particle filters of systems with time-scale separation with D. Givon and P. Stinis, IEEE Transactions on
Signal Processing, 57(2) [2009], 424-435 Randomized numerical linear algebra Full Configuration
Interaction Excited-State Energies in Large Active
Spaces from Subspace Iteration with Repeated Random
Sparsification
with S.M. Greene, R.J. Webber, J.E.T. Smith, and T.C. Berkelbach, Journal of Chemical Theory and
Computation, 18(12) [2022], 7218-7232Approximating matrix eigenvalues by subspace iteration with repeated random sparsification with S.M. Greene, R.J. Webber, and T.C. Berkelbach, SIAM
Journal on Scientific Computing, 44(5) [2022],
A3067-A3097Improved Fast Randomized Iteration approach to Full Configuration Interaction with S.M. Greene, R.J. Webber, and T.C. Berkelbach, Journal
of Chemical Theory and Computation, 16(9)
[2020], 5572–5585Beyond walkers in stochastic quantum chemistry: reducing error using Fast Randomized Iteration with S.M. Greene, R.J. Webber, and T.C. Berkelbach, Journal
of Chemical Theory and Computation, 15(9)
[2019], 4834-4850 Fast randomized iteration: diffusion Monte Carlo through the lens of numerical linear algebra with L.H. Lim, SIAM Reviews: Research Spotlight,
59(3) [2017], 547-587Rare event analysis and simulation Revealing the statistics
of extreme events hidden in short weather
forecast data
Statistical and machine
learning for scientific computing
with J. Finkel, E.P. Gerber, and D.S. Abbot, AGU Advances, 4 [2023], e2023AV000881(Featured as an Editor's Highlight) Simple physics and integrators accurately reproduce Mercury instability statistics with D.S. Abbot, D.M. Hernandez, S. Hadden, R.J. Webber, and G.P. Afentakis, The Astrophysical Journal, 944(2) [2023], 190Data-driven transition path analysis yields a statistical understanding of sudden stratospheric warming events in an idealized model with J. Finkel, R.J. Webber, E.P. Gerber, and D.S. Abbot, Journal of the Atmospheric Sciences,
80 [2023], 519-534Augmented transition path theory for sequences of events with C. Lorpaiboon and A.R. Dinner, Journal of
Chemical Physics, 157(9) [2022], 094115Computing transition path theory quantities with trajectory stratification with B.P. Vani and A.R. Dinner, Journal of
Chemical Physics, 157(3) [2022], 034106Rare event sampling improves Mercury instability statistics with D.S. Abott, R.J. Webber, and S. Hadden, Astrophysical
Journal, 923(2) [2021], 236Insulin dissociates by diverse mechanisms of coupled unfolding and unbinding with A. Antoszewski, C.-J. Feng, B.P. Vani, E.H. Thiede, L. Hong, A. Tokmakoff, and A.R. Dinner, Journal
of Physical Chemistry B, 124(27) [2020],
5571-5587 Path properties of atmospheric transitions: illustration with a low-order sudden stratospheric warming model with J. Finkel, and D.S. Abbot, Journal of
Atmospheric Science, 77(7) [2020], 2327-2347Practical rare event simulation for extreme mesoscale weather with R.J. Webber, D.A. Plotkin, M.E O'Neill, and D.S. Abbot, Chaos, 29 [2019], 053109 (Featured in SIAM News) Maximizing simulated tropical cyclone intensity with action minimization with D.A. Plotkin, R.J. Webber, M.E O'Neill, and D.S. Abbot, Journal of Advances in Modeling Earth
Systems (JAMES), 11(4) [2019], 863-891Trajectory stratification of stochastic dynamics with A.R. Dinner, J.C. Mattingly, J. Tempkin, and B. Van Koten, SIAM Reviews: Research Spotlight,
60(4) [2018], 909–938 Simulating the stochastic dynamics and cascade failure of power networks with C. Matthews, B. Stadie, M. Anitescu, and C. Demarco, [2017] The Brownian fan with M. Hairer, Communications in Pure and Applied
Mathematics, 68(1) [2015], 1-60Improved diffusion Monte Carlo with M. Hairer, Communications in Pure and Applied
Mathematics, 67(12) [2014], 1995-2021 Data assimilation in the low noise regime with applications to the Kuroshio with E. Vanden-Eijnden, Monthly Weather Review,
141 [2013], 1822-1841Steered transition path sampling with N. Guttenberg and A. Dinner, Journal of
Chemical Physics, 136 [2012], 234103 Rare event simulation for small noise diffusions with E. Vanden-Eijnden, Communications in Pure and
Applied Mathematics, 65(12) [2012], 1770-1803 Particle filtering with path sampling and an application to a bimodal ocean current model Journal of Computational Physics, 228 [2009],
4312-4331 Efficient Conditional Path Sampling of
Stochastic Differential EquationsThesis (Ph.D.) - University of California, Berkeley, ProQuest,
[2007], ISBN: 978-0549-73732-2
Inexact
iterative numerical linear algebra for neural
network-based spectral estimation and rare-event
prediction
with J. Strahan, S.C. Guo, C. Lorpaiboon, and A.R. Dinner, Journal
of Chemical Physics, acceptedPredicting rare events using neural networks and short-trajectory data with J. Strahan, J. Finkel, and A.R. Dinner, Journal
of Computational Physics, 488 [2023],
112152Understanding and eliminating spurious modes in variational Monte Carlo using collective variables with H. Zhang, R.J. Webber, M. Lindsey, and T.C. Berkelbach, Physical Review Research, 5
[2023], 023101
Learning forecasts of rare stratospheric transitions from short simulations with J. Finkel, R.J. Webber, D.S. Abbot, and E.P. Gerber, Monthly Weather Review,
149(11) [2021], 3649-3669Long-timescale predictions from short-trajectory data: A benchmark analysis of the trp-cage miniprotein with J. Strahan, A. Antoszewski, C. Lorpaiboon, B. Vani, and A.R. Dinner, Journal of Chemical Theory
and Computation, 17(5) [2021], 2948-2963Error bounds for dynamical spectral estimation with R.J. Webber, E.H. Thiede, D. Dow, and A.R. Dinner, SIAM Journal on Mathematics of Data
Science, 3(1) [2021], 225-252Integrated VAC: A robust strategy for identifying eigenfunctions of dynamical operators with C. Lorpaiboon, E.H. Thiede, R.J. Webber, and A.R. Dinner, Journal of Physical Chemistry B,
124(42) [2020], 9354-9364Galerkin approximation of dynamical quantities using trajectory data with E.H. Thiede, D. Giannakis, and A.R. Dinner, Journal
of Chemical Physics, 150 [2019], 24111 Distinguishing meanders of the Kuroshio using machine learning with D. Plotkin and D. Abbot, Journal of
Geophysical Research - Oceans, 119(10) [2014],
6593-6604 Software Fast Randomized Iteration for Electronic Structure (FRIES) S.M. Greene (I am not an author) C++ implementations of various methods within the Fast Randomized Iteration (FRI) framework for performing Full Configuration Interaction calculations on molecular systems and the Hubbard model. pyEDGAR E.H. Thiede (I am not an author) Python implementation of Dynamic Galerkin Approximation (DGA) which builds predictions of long-timescale phenomena from short trajectory data. Eigenvector Method for Umbrella Sampling (EMUS) E.H. Thiede (I am not an author) Python implementation of a stratification approach to MCMC Umbrella Sampling for Data Science Applications C. Matthews (I am not an author) Lightweight Python implementation of EMUS for data science applications A very nice EMUS tutorial in Python G.J. Gilbert (I am not an author) Ensemble QuasiNewton MCMC (EQN) C. Matthews (I am not an author) Python implementation of an emsemble preconditioning approach to MCMC Fast Randomized Iteration (FRI) with J. Dama Demonstration C++ implementation of randomized power iteration. Enhanced Sampling Toolkit J. Tempkin (I am not an author) The Enhanced Sampling Toolkit provides a flexible and extensible toolkit for rapidly prototyping rare event simulation algorithms. The code is written entirely in Python and acts as a wrapper to various well-established molecular dynamics codes. Ticketed Diffusion Monte Carlo (TDMC) J. Dama (I am not an author) Demonstration C++ implementation of an improved diffusion Monte Carlo method. emcee: The MCMC Hammer D. Foreman-Mackey, D. Hogg, D. Lang, and J. Goodman (I am not an author) Python implementation of an affine invariant ensemble MCMC scheme. |