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Computational Mathematics

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    Biomolecular and Biophysical Inference Bridging the gap between molecular simulations and experimental data, enabling quantitative characterization of biomolecules.

    Machine Learning and Computational Statistics Using leading-edge tools and methods to push the boundaries of computational mathematics.

    Numerical Analysis and Scientific Computing Creating fast, accurate and robust high-order solvers for many equations in complicated geometries.

    COMPASS Connecting researchers working on molecular sampling, simulation and design.

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Flatiron Institute Computational Mathematics

Computational Mathematics: Publications

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  1. A Bayesian approach for extracting free energy profiles from cryo-electron microscopy experiments using a path collective variable

    Scientific Reports, arxiv:2102.02077, July 1, 2021

    Julian Giraldo-Barreto, Sebastian Ortiz, E. Thiede, Karen Palacio-Rodriguez, B. Carpenter, A. Barnett, et al.

  2. Regression models for compositional data: General log-contrast formulations, proximal optimization, and microbiome data applications

    Statistics in Biosciences, arxiv:1903.01050, July 1, 2021

    Patrik L Combettes and C. Müller

  3. A causal view on compositional data

    arxiv:2106.11234, June 21, 2021

    Elisabeth Ailer, Niki Kilbertus, and C. Müller

  4. Rank-normalization, folding, and localization: An improved \(R\) for assessing convergence of MCMC

    Bayesian Analysis, arxiv:1903.08008, 2021

    Aki Vehtari, Andrew Gelman, Daniel Simpson, B. Carpenter, and Paul-Christian Bürkner

  5. Adaptive Monte Carlo augmented with normalizing flows

    arXiv e-prints, arxiv:2105.12603, May 26, 2021

    M. Gabrié, Grant M. Rotskoff, and E. Vanden-Eijnden

  6. cuFINUFFT: a load-balanced GPU library for general-purpose nonuniform FFTs

    IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing, arxiv:2102.08463, May 21, 2021

    Yu-hsuan Shih, Garrett Wright, Joakim Andén, Johannes Blaschke, and A. Barnett

  7. AI-assisted super-resolution cosmological simulations

    Proceedings of the National Academy of Sciences, arxiv:2010.06608, May 11, 2021

    Y. Li, Yueying Ni, Rupert A. C. Croft, Tiziana Di Matteo, Simeon Bird, and Yu Feng

  8. Recovering missing data in coherent diffraction imaging

    SIAM Journal on Imaging Sciences, arxiv:2002.02874, May 10, 2021

    D. Barmherzig, A. Barnett, L. Greengard, J. Magland, and M. Rachh

  9. AI-assisted superresolution cosmological simulations

    PNAS, arXiv:2010.06608, May 4, 2021

    Y. Li, Yueying Ni, Rupert A. C. Croft, Tiziana Di Matteo, Simeon Bird, and Yu Feng

  10. AI-assisted super-resolution cosmological simulations II: Halo substructures, velocities and higher order statistics

    arXiv:2105.01016, May 3, 2021

    Yueying Ni, Y. Li, Patrick Lachance, Rupert A. C. Croft, Tiziana Di Matteo, Simeon Bird, et al.

  11. Low rank compression in the numerical solution of the nonequilibrium Dyson equation

    SciPost Physics, arxiv:2010.06511, April 26, 2021

    J. Kaye and D. Golez

  12. Fast multipole methods for evaluation of layer potentials with locally-corrected quadratures

    Journal of Computational Physics: X, arxiv:2006.02545, April 16, 2021

    L. Greengard, Michael O'Neil, M. Rachh, and Felipe Vico

  13. Learning physically consistent differential equation models from data using group sparsity

    Physical Review E, arxiv:2012.06391, April 13, 2021

    Suryanarayana Maddu, Bevan L Cheeseman, Ivo F Sbalzarini, and C. Müller

  14. deepregression: a Flexible Neural Network Framework for Semi-Structured Deep Distributional Regression

    arxiv:2104.02705, April 6, 2021

    David Rügamer, Ruolin Shen, Christina Bukas, Dominik Thalmeier, Nadja Klein, Chris Kolb, et al.

  15. Comment on “Stepped pressure profile equilibria in cylindrical plasmas via partial Taylor relaxation” [J. Plasma Physics (2006), vol. 72, part 6, pp. 1167–1171]

    Journal of Plasma Physics, 2021

    Yuanfan Wang, D. Malhotra, and Antoine J. Cerfon

  16. Fast computation of latent correlations

    Journal of Computational and Graphical Statistics, arxiv:2006.13875, March 29, 2021

    Grace Yoon, C. Müller, and Irina Gaynanova

  17. More data or more parameters? Investigating the effect of data structure on generalization

    arxiv:2103.05524, March 9, 2021

    Stéphane d'Ascoli, M. Gabrié, Levent Sagun, and G. Biroli

  18. Autobahn: Automorphism-based Graph Neural Nets

    arXiv e-prints, arxiv:2103.01710, March 2, 2021

    E. Thiede, W. Zhou, and . Kondor

  19. Aliasing error of the exp \(β\sqrt{1-z^2}\) kernel in the nonuniform fast Fourier transform

    Applied and Computational Harmonic Analysis, arxiv:2001.09405, 2021

    A. Barnett

  20. A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota

    bioRxiv:2021.02.24.432662, February 24, 2021

    Alice J Sommer, Annette Peters, Martina Rommel, Josef Cyrys, Harald Grallert, Dirk Haller, et al.

  21. STENCIL-NET: Data-driven solution-adaptive discretization of partial differential equations

    arxiv:2101.06182, January 18, 2021

    Suryanarayana Maddu, Dominik Sturm, Bevan L Cheeseman, C. Müller, and Ivo F Sbalzarini

  22. A fast spectral method for electrostatics in doubly-periodic slit channels

    The Journal of Chemical Physics, arxiv:2101.07088, 2021

    Ondrej Maxian, Raul P. Peláez, L. Greengard, and Aleksandar Donev

  23. Efficient high-order accurate Fresnel diffraction via areal quadrature and the nonuniform FFT

    Journal of Astronomical Telescopes, Instruments, and Systems, arxiv:2010.05978, January 11, 2021

    A. Barnett

  24. Continuous-variable neural-network quantum states and the quantum rotor model

    arxiv:2107.07105, 2021

    J. Stokes, Saibal De, and G. Carleo

  25. Overcoming barriers to scalability in variational quantum Monte Carlo

    arxiv:2106.13308, 2021

    Tianchen Zhao, Saibal De, Brian Chen, and J. Stokes

  26. Fermionic Wave Functions from Neural-Network Constrained Hidden States

    arxiv:2111.10420, 2021

    Javier Robledo Moreno, G. Carleo, A. Georges, and J. Stokes

  27. An integral equation method for the simulation of doubly-periodic suspensions of rigid bodies in a shearing viscous flow

    Journal of Computational Physics, arXiv:1912.04501, 2021

    J. Wang, Ehssan Nazockdast, and A. Barnett

  28. Learning the Evolution of the Universe in N-body Simulations

    arXiv e-prints, arxiv:2012.05472, December 10, 2020

    Chang Chen, Y. Li, Francisco Villaescua-Navarro, S. Ho, and Anthony Pullen

  29. Fast and Accurate Non-Linear Predictions of Universes with Deep Learning

    arXiv e-prints, arxiv:2012.00240, December 1, 2020

    Renan Alves Oliveira, Y. Li, Fracisco Villaescusa-Navarro, S. Ho, and D. Spergel

  30. Meta Variational Monte Carlo

    arXiv e-print, arxiv:2011.10614, November 20, 2020

    Tianchen Zhao, J. Stokes, Oliver Knitter, and Brian Chen

  31. Bayesian Workflow

    arXiv e-prints, arxiv:2011.01808, November 3, 2020

    Andrew Gelman, Aki Vehtari, Daniel Simpson, Charles C. Margossian, B. Carpenter, Yuling Yao, et al.

  32. Generalized co-sparse factor regression

    Computational Statistics & Data Analysis, November 3, 2020

    A. Mishra, Dipak K. Dey, Yong Chen, and Kun Chen

  33. Constraining the Halo Mass of Damped Lyα Absorption Systems (DLAs) at z=2-3.5 using the Quasar-CMB Lensing Cross-correlation

    arXiv e-prints, arxiv:2011.01234, November 2, 2020

    Xiaojing Lin, Zheng Cai, Y. Li, Alex Krolewski, and Simone Ferraro

  34. The CAMELS project: Cosmology and Astrophysics with MachinE Learning Simulations

    arXiv e-prints, arxiv:2010.00619, October 1, 2020

    F. Villaescusa-Navarro, D. Angles-Alcazar, S. Genel, D. Spergel, Rachel S. Somerville, Romeel Dave, et al.

  35. Integrated VAC: A robust strategy for identifying eigenfunctions of dynamical operators

    The Journal of Physical Chemistry B, arxiv:, September 21, 2020

    Chatipat Lorpaiboon, E. Thiede, Robert Webber, Jonathan Weare, and Aaron Dinner

  36. Multitaper estimation on arbitrary domains

    SIIMS, arXiv:1812.03225, September 15, 2020

    J. Andén and José Luis Romero

  37. On the discretization of Laplace’s equation with Neumann boundary conditions on polygonal domains

    JCOPX, arXiv:2001.05434, September 1, 2020

    Jeremy Hoskins and M. Rachh

  38. Geometry of the Phase Retrieval Problem

    Inverse Problems, arXiv:1808.10747, 2020

    A. Barnett, L. Greengard, and J. Magland

  39. Bayesian analysis of tests with unknown specificity and sensitivity

    Royal Statistical Society, medRxiv:2020.05.22.20108944v2, August 13, 2020

    Andrew Gelman and B. Carpenter

  40. The Quijote Simulations

    The Astrophysical Journal Supplement Series, arxiv:1909.05273, 2020

    Govind Menon, ChangHoon Hahn, Elena Massara, Arka Banerjee, Ana Maria Delgado, Doogesh Kodi Ramanah, et al.

  41. High-density Neural Recordings from Feline Sacral Dorsal Root Ganglia with Thin-film Array

    bioRxiv: 2020.07.14.199653, 2020

    Zachariah J. Sperry, Kyounghwan Na, J. Jun, Lauren R. Madden, Alec Socha, Eusik Yoon, et al.

  42. Accurate quadrature of nearly singular line integrals in two and three dimensions by singularity swapping

    BIT, arXiv:1910.09899, July 3, 2020

    L. af Klinteberg and A. Barnett

  43. Low-Photon Holographie Phase Retrieval

    Imaging and Applied Optics Congress, June 26, 2020

    D. Barmherzig and Ju Sun

  44. Lorentz Group Equivariant Neural Network for Particle Physics

    Proceedings of Machine Learning and Systems 2020, arxiv:2006.04780, June 8, 2020

    Alexander Bogatskiy, Brandon Anderson, Jan Offermann, Marwah Roussi, David Miller, and . Kondor

  45. Solution of Stokes flow in complex nonsmooth 2D geometries via a linear-scaling high-order adaptive integral equation scheme

    JCOP, arXiv:1909.00049, June 1, 2020

    B. Wu, H. Zhu, A. Barnett, and S. Veerapaneni

  46. On the solution of Laplace’s equation in the vicinity of triple junctions

    Pure and Applied Analysis, arxiv:1907.10718, May 22, 2020

    Jeremy Hoskins and M. Rachh

  47. SpikeForest, reproducible web-facing ground-truth validation of automated neural spike sorters

    eLife, May 19, 2020

    J. Magland, J. Jun, E. Lovero, A. J. Morley, C. L. Hurwitz, A. P. Buccino, et al.

  48. Low-Rank Toeplitz Matrix Estimation Via Random Ultra-Sparse Rulers

    ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing, arxiv:1911.08015, May 14, 2020

    Jerry Li, Cameron Musco, and Christopher Musco

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