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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. Direct stellarator coil design using global optimization: application to a comprehensive exploration of quasi-axisymmetric devices

    arXiv:2310.19097, 2023

    A. Giuliani

  2. Discriminative calibration: Check Bayesian computation from simulations and flexible classifier

    arXiv:2305.14593, 2023

    Y. Yao and Justin Domke

  3. Solving the Transmission Problem for Open Wave-Guides, II Outgoing Estimates

    arxiv:2310.05816, 2023

  4. Solving the Transmission Problem for Open Wave-Guides, I Fundamental Solutions and Integral Equations

    arXiv:2302.04353, 2023

  5. A class of dimensionality-free metrics for the convergence of empirical measures

    Stochastic Processes and their Applications, 2023

    J. Han, Ruimeng Hu, and Jihao Long

  6. A Neural Network Warm-Start Approach for the Inverse Acoustic Obstacle Scattering Problem

    Journal of Computational Physics, arxiv:2212.08736, 2023

    Mo Zhou, J. Han, M. Rachh, and Carlos Borges

  7. Variational Inference with Gaussian Score Matching

    Conference on Neural Information Processing Systems, 2023

    C. Modi, C. Margossian, Y. Yao, R. Gower, D. Blei, and L. Saul

  8. FMM-accelerated solvers for the Laplace-Beltrami problem on complex surfaces in three dimensions

    Journal of Scientific Computing, arxiv:arXiv:2111.10743, 2023

    Dhwanit Agarwal, Michael O'Neil, and M. Rachh

  9. A Gentle Introduction to Gradient-Based Optimization and Variational Inequalities for Machine Learning

    arXiv:2309.04877, 2023

    N. Wadia, Yatin Dandi, and Michael I. Jordan

  10. Reinforcement learning with function approximation: From linear to nonlinear

    Journal of Machine Learning, 2023

    Jihao Long and J. Han

  11. An equivariant neural operator for developing nonlocal tensorial constitutive models

    Journal of Computational Physics, arxiv:2201.01287, 2023

    J. Han, Xu-Hui Zhou, and Heng Xiao

  12. Automatic, high-order, and adaptive algorithms for Brillouin zone integration

    SciPost Physics, arXiv:2211.12959, 2023

    J. Kaye, Sophie Beck, A. Barnett, Lorenzo Van Muñoz, and Olivier Parcollet

  13. DeePMD-kit v2: A software package for deep potential models

    The Journal of Chemical Physics, 2023

    Jinzhe Zeng, Duo Zhang, and J. Han

  14. Normative framework for deriving neural networks with multi-compartmental neurons and non-Hebbian plasticity

    arXiv:2302.10051, 2023

    D. Lipshutz, Y. Bahroun, S. Golkar, A. Sengupta, and D. Chklovskii

  15. A fast time domain solver for the equilibrium Dyson equation

    Advances in Computational Mathematics, 2023

    J. Kaye and Hugo U. R. Strand

  16. Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy

    Current Opinion in Structural Biology, August 1, 2023

    W. Wai Shing, Ellen D. Zhong, S. Hanson, E. Thiede, and P. Cossio

  17. On Single Index Models beyond Gaussian Data

    arXiv:2307.15804, 2023

    L. Pillaud-Vivien, Joan Bruna, Ph.D., and Aaron Zweig, Ph.D.

  18. A Model-Based Method for Minimizing CVaR and Beyond

    International Conference on Machine Learning, arXiv:2305.17498, 2023

    Si Yi Meng and R. Gower

  19. SGD with Large Step Sizes Learns Sparse Features

    Proceedings of Machine Learning Research, arXiv:2210.05337, 2023

    Maksym Andriushchenko, Aditya Varre, L. Pillaud-Vivien, and Nicolas Flammarion

  20. BridgeStan: Efficient in-memory access to the methods of a Stan model

    Journal of Open Source Software, 2023

    Edward A. Roualdes, B. Ward, B. Carpenter, Adrian Seyboldt, and Seth D. Axen

  21. Unlocking the Potential of Similarity Matching: Scalability, Supervision and Pre-training

    International Conference on Machine Learning, 2023

    Y. Bahroun, Shagesh Sridharan, Atithi Acharya, D. Chklovskii, and A. Sengupta

  22. Kernelized Diffusion Maps

    Proceedings of Machine Learning Research, arXiv:2302.06757, 2023

    L. Pillaud-Vivien and Francis Bach, Ph.D.

  23. Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles

    Nature Neuroscience, 2023

    J. Morton, et al.

  24. General adjoint-differentiated Laplace approximation

    arXiv:2306.14976, 2023

    C. Margossian

  25. Improving Gradient Computation for Differentiable Physics Simulation with Contacts

    Proceedings of Machine Learning Research, 2023

    Yaofeng Desmond Zhong, J. Han, Biswadip Dey, and Georgia Olympia Brikis

  26. riccati: an adaptive, spectral solver for oscillatory ODEs

    Journal of Open Source Software, 2023

    F. Agocs and A. Barnett

  27. Low-rank Green's function representations applied to dynamical mean-field theory

    Physical Review B, arXiv:2301.07764, June 13, 2023

    Nan Sheng, Alexander Hampel, Sophie Beck, Olivier Parcollet, Nils Wentzell, J. Kaye, et al.

  28. Ensemble Reweighting Using Cryo-EM Particle Images

    The Journal of Physical Chemistry B, 2023

    W. Wai Shing, David Silva-Sánchez, Julian Giraldo-Barreto, B. Carpenter, S. Hanson, A. Barnett, et al.

  29. Algebraically rigorous quaternion framework for the neural network pose estimation problem

    IEEE Explore, 2023

    C. Lin, Andrew J. Hanson, and S. Hanson

  30. Conditionally Strongly Log-Concave Generative Models

    International Conference on Machine Learning, 2023

    Florentin Guth, Etienne Lempereur, Joan Bruna, and S. Mallat

  31. A Stochastic Proximal Polyak Step Size

    Transactions on Machine Learning Research, arXiv:2301.04935, 2023

    Fabian Schaipp, R. Gower, and Michael Ulbrich

  32. Learning multi-scale local conditional probability models of images

    International Conference on Learning Representations, 2023

    Zahra Kadkhodaie, Florentin Guth, S. Mallat, and Eero P Simoncelli

  33. Complex-to-Real Sketches for Tensor Products with Applications to the Polynomial Kernel

    International Conference on Artificial Intelligence and Statistics, arXiv:2202.02031, 2023

    Jonas Wacker, R. Ohana, and Maurizio Filippone

  34. A Cheat Sheet for Bayesian Prediction

    arXiv:2304.12218, 2023

    Bertrand Clarke and Y. Yao

  35. Simulation-based inference of single-molecule force spectroscopy

    Machine Learning: Science and Technology, 2023

    Lars Dingeldein, P. Cossio, and Roberto Covino

  36. Simulation-based inference of single-molecule force spectroscopy

    Machine Learning: Science and Technology, arxiv.org/abs/2209.10392, 2023

    Lars Dingeldein, P. Cossio, and Roberto Covino

  37. A fast, accurate and easy to implement Kapur -- Rokhlin quadrature scheme for singular integrals in axisymmetric geometries

    Journal of Plasma Physics, arXiv:2211.00493, April 14, 2023

    Evan Toler, A.J. Cerfon, and D. Malhotra

  38. Folding and modulation of the helical conformation of Glycophorin A by point mutations

    Physical Chemistry Chemical Physics, March 27, 2023

    Pei-Yin Lee, A. Sahoo, and Silvina Matysiak

  39. A Bregman-Kaczmarz method for nonlinear systems of equations

    arXiv:2303.08549, March 15, 2023

    R. Gower, Dirk A. Lorenz, and Maximilian Winkler

  40. Quantum electrodynamics of chiral and antichiral waveguide arrays

    Optics Letters, arXiv:2210.04082, March 1, 2023

    Jeremy G. Hoskins, M. Rachh, and John C. Schotland

  41. Linear Convergence of Natural Policy Gradient Methods with Log-Linear Policies

    International Conference on Learning Representations, arXiv:2210.01400, 2023

    Rui Yuan, Rui Yuan, R. Gower, Alessandro Lazaric, and Lin Xiao

  42. Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study

    Computational and Structural Biotechnology Journal, February 18, 2023

    Rodrigo Ochoa, Thyago R Cardim-Pires, Ricardo Sant'Anna, P. Cossio, and Debora Foguel

  43. Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study

    Computational and Structural Biotechnology Journal, February 18, 2023

    Rodrigo Ochoa, Thyago R Cardim-Pires, Ricardo Sant'Anna, P. Cossio, and Debora Foguel

  44. Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike

    iScience, February 17, 2023

    Miłosz Wieczór, P. Tang, Modesto Orozco, and P. Cossio

  45. The Shrinkage-Delinkage Trade-off: An Analysis of Factorized Gaussian Approximations for Variational Inference

    Uncertainty in Artificial Intelligence, arXiv:2302.09163, February 17, 2023

    C. Margossian and L. Saul

  46. Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike

    iScience, February 17, 2023

    Miłosz Wieczór, P. Tang, Modesto Orozco, and P. Cossio

  47. PETSc/TAO Users Manual Revision 3.18

    Argonne National Laboratory, February 7, 2023

    B. Smith

  48. SP2 : A Second Order Stochastic Polyak Method

    International Conference on Learning Representations, arXiv:2207.08171, February 1, 2023

    Shuang Li, William Joseph Swartworth, Martin Takáč, Deanna Needell, and R. Gower

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