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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

Read the latest papers published by our researchers.

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  1. Quantification of gas concentrations in NO/NO2/C3H8/NH3 mixtures using machine learning

    Sensors and Actuators B: Chemical, 2022

    Unab Javed, Kannan P. Ramaiyan, Cortney R. Kreller, Eric L. Brosha, Rangachary Mukundan, A. Sengupta, et al.

  2. Simple and statistically sound recommendations for analysing physical theories

    Reports on Progress in Physics, arxiv:2012.09874, April 29, 2022

    Shehu S AbdusSalam, F. Agocs, Benjamin C Allanach, Peter Athron, Csaba Balázs, Emanuele Bagnaschi, et al.

  3. Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol

    Frontiers in Immunology, April 27, 2022

    Rodrigo Ochoa, Victoria Alves Santos Lunardelli, Daniela Santoro Rosa, Alessandro Laio, and P. Cossio

  4. Vitruvion: A Generative Model of Parametric CAD Sketches

    International Conference on Learning Representations, arxiv:2109.14124, 2022

    Ari Seff, W. Zhou, Nick Richardson, and Ryan P. Adams

  5. Wavelet Moments for Cosmological Parameter Estimation

    arXiv e-prints, arxiv:2204.07646, April 15, 2022

    M. Eickenberg, Erwan Allys, Azadeh Moradinezhad Dizgah, Pablo Lemos, E. Massara, Muntazir Abidi, et al.

  6. A general sample complexity analysis of vanilla policy gradient

    inproceedings: International Conference on Artificial Intelligence and Statistics, arXiv:2107.11433, March 28, 2022

    Rui Yuan, R. Gower, and Alessandro Lazaric

  7. SAN: Stochastic Average Newton Algorithm for Minimizing Finite Sums

    Inproceedings: International Conference on Artificial Intelligence and Statistics, https://arxiv.org/abs/2106.10520, 2022

    Jiabin Chen, Rui Yuan, Guillaume Garrigos, and R. Gower

  8. Debye source representations for type-I superconductors, I: The static type I case

    arxiv:2105.12246, March 1, 2022

    M. Rachh

  9. Multi-omic analysis along the gut-brain axis points to a functional architecture of autism

    BioRxiv, 2022

    B. Carpenter, et al.

  10. Cutting Some Slack for SGD with Adaptive Polyak Stepsizes

    arxiv:2202.12328, 2022

    R. Gower, Mathieu Blondel, Nidham Gazagnadou, and Fabian Pedregosa

  11. Spatial Transformer K-Means

    arxiv:2202.07829, 2022

    Romain Cosentino, Randall Balestriero, Y. Bahroun, A. Sengupta, Richard Baraniuk, and Behnaam Aazhang

  12. Towards practical holographic coherent diffraction imaging via maximum likelihood estimation

    Optics Express, February 1, 2022

    D. Barmherzig and Ju Sun

  13. Prolonged and Pervasive Perturbations in the Composition of the Southern Hemisphere Midlatitude Lower Stratosphere From the Australian New Year’s Fires

    Geophysical Research Letters, https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021GL096270, January 28, 2022

    M. L. Santee, A. Lambert, G. L. Manney, N. J. Livesey, L. Froidevaux, J. L. Neu, et al.

  14. FMM-LU: A fast direct solver for multiscale boundary integral equations in three dimensions

    arxiv:arXiv:2201.07325, January 18, 2022

    Daria Sushnikova, L. Greengard, Michael O'Neil, and M. Rachh

  15. Neural Circuits for Dynamics-Based Segmentation of Time Series

    Neural Computation, BioRxiv:2021.04.23.441218v1, January 13, 2022

    Samaneh Nasiri, Dmitri B. Chklovskii, A. Sengupta, Tiberiu Tesileanu, and Siavash Golkar

  16. The PETSc Community Is the Infrastructure

    arxiv:2201.00967, January 4, 2022

    Mark Adams, Satish Balay, Oana Marin, Lois Curfman McInnes, Richard Tran Mills, Todd Munson, et al.

  17. Geometry of the Phase Retrieval Problem: Graveyard of Algorithms

    Book: Cambridge Monographs on Applied and Computational Mathematics, 2022

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

  18. RidgeSketch: A Fast Sketching Based Solver for Large Scale Ridge Regression

    SIAM Journal on Matrix Analysis and Applications, arxiv:2105.05565, 2022

    Nidham Gazagnadou, Mark Ibrahim, and R. Gower

  19. Pandemic Control, Game Theory, and Machine Learning

    Notices of the American Mathematical Society, arxiv:2208.08646, January 1, 2022

    Yao Xuan, Robert Balkin, J. Han, Ruimeng Hu, and Hector D Ceniceros

  20. Low-photon holographic phase retrieval with Poisson-Gaussian denoising

    Imaging and Applied Optics Congress, January 1, 2022

    David A. Barmherzig and M. Eickenberg

  21. Perturbational Complexity by Distribution Mismatch: A Systematic Analysis of Reinforcement Learning in Reproducing Kernel Hilbert Space

    Journal of Machine Learning, January 1, 2022

    Jihao Long and J. Han

  22. Economic growth and happiness in China: A Bayesian multilevel age-period-cohort analysis based on the CGSS data 2005–2015

    International Review of Economics & Finance, January 1, 2022

    Yu-Sung Su, Donald Lien, and Y. Yao

  23. Solving Fredholm second-kind integral equations with singular right-hand sides on non-smooth boundaries

    Journal of Computational Physics, arxiv:2102.03504, January 1, 2022

    Johan Helsing and S. Jiang

  24. Robust regression with compositional covariates

    Computational Statistics & Data Analysis, arxiv:1909.04990, January 1, 2022

    A. Mishra and C. Müller

  25. How exponentially ill-conditioned are contiguous submatrices of the Fourier matrix?

    SIAM Review, arxiv:2004.09643, 2022

    A. Barnett

  26. DeepHAM: A Global Solution Method for Heterogeneous Agent Models with Aggregate Shocks

    arxiv:2112.14377, December 29, 2021

    J. Han, Yucheng Yang, and Weinan E

  27. Multifrequency inverse obstacle scattering with unknown impedance boundary conditions using recursive linearization

    Advances in Computational Mathematics, arxiv:2104.13489, December 23, 2021

    Carlos Borges and M. Rachh

  28. Algorithms for solving high dimensional PDEs: from nonlinear Monte Carlo to machine learning

    Nonlinearity, arxiv:2008.13333, December 9, 2021

    Weinan E, J. Han, and Arnulf Jentzen

  29. Neural optimal feedback control with local learning rules

    NeurIPS, 2021

    D. Chklovskii, S. Golkar, S. Farashahi, J. Friedrich, A. Genkin, and A. Sengupta

  30. Gauge equivariant neural networks for quantum lattice gauge theories

    PRL, arxiv:2012.05232, 2021

    Di Luo, G. Carleo, Bryan K. Clark, and J. Stokes

  31. A Normative and Biologically Plausible Algorithm for Independent Component Analysis

    NeurIPS, 2021

    D. Chklovskii, Y. Bahroun, and A. Sengupta

  32. Shadow tomography based on informationally complete positive operator-valued measure

    Physical Review A, arxiv:2105.05992, November 16, 2021

    Atithi Acharya, Siddhartha Saha, and A. Sengupta

  33. Encoding Priors with Group Sparsity for Model Learning From Limited and Noisy Biological Data

    14th WCCM & ECCOMAS Congress 2020, November 3, 2021

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

  34. Discriminating Data: Correlation, Neighborhoods, and the New Politics of Recognition

    MIT Press, November 2, 2021

    Wendy Hui Kyong Chun and A. Barnett

  35. c-lasso - a Python package for constrained sparse and robust regression and classification

    Journal of Open Source Software, arxiv:2011.00898, November 2, 2021

    Léo Simpson, Patrick L Combettes, and C. Müller

  36. Analysis of single-excitation states in quantum optics

    arxiv:2110.07049, October 13, 2021

    Jeremy Hoskins, J. Kaye, M. Rachh, and John Schotland

  37. Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models

    FEBS Letters, October 11, 2021

    Cristian Rocha-Roa, Juan David Orjuela, Chad Leidy, P. Cossio, and Camilo Aponte-Santamaría

  38. Bayesian Hierarchical Stacking: Some Models Are (Somewhere) Useful

    Bayesian Anal., September 27, 2021

    Y. Yao, Gregor Pirš, Aki Vehtari, and Andrew Gelman

  39. Toward performance-portable PETSc for GPU-based exascale systems

    Parallel Computing, arxiv:2011.00715, August 28, 2021

    Richard Tran Mills, Mark F. Adams, Satish Balay, Jed Brown, Alp Dener, Matthew Knepley, et al.

  40. latentcor: An R Package for estimating latent correlations from mixed data types

    arxiv:2108.09180, August 20, 2021

    Mingze Huang, C. Müller, and Irina Gaynanova

  41. A Biologically Plausible Neural Network for Multichannel Canonical Correlation Analysis

    Neural Computation, arXiv:2010.00525, 2021

    David Lipshutz, Y. Bahroun, Siavash Golkar, A. Sengupta, and Dmitri B. Chklovskii

  42. Phase Retrieval with Holography and Untrained Priors: Tackling the Challenges of Low-Photon Nanoscale Imaging

    Proceedings of Machine Learning Research, arxiv:2012.07386, August 16, 2021

    D. Barmherzig, Henry Li, M. Eickenberg, and M. Gabrié

  43. Application of ensemble pharmacophore-based virtual screening to the discovery of novel antimitotic tubulin inhibitors

    Computational and Structural Biotechnology Journal, August 3, 2021

    Laura Gallego-Yerga, Rodrigo Ochoa, Isaías Lans, Carlos Peña-Varas, Melissa Alegría-Arcos, P. Cossio, et al.

  44. COP-E-CAT: Cleaning and Organization Pipeline for EHR Computational and Analytic Tasks

    Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 1, 2021

    Aishwarya Mandyam, Elizabeth C. Yoo, J. Soules, Krzysztof Laudanski, and Barbara E. Engelhardt

  45. AI-assisted superresolution cosmological simulations – II. Halo substructures, velocities, and higher order statistics

    MNRAS, arXiv:2105.01016, July 24, 2021

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

  46. Low-Photon Holographic Phase Retrieval via a Deep Decoder Neural Network

    Optical Society of America, July 23, 2021

    Hannah Lawrence, D. Barmherzig, M. Eickenberg, and M. Gabrié

  47. Tree-aggregated predictive modeling of microbiome data

    Scientific Reports, July 15, 2021

    Jacob Bien, Xiaohan Yan, Léo Simpson, and C. Müller

  48. Inverse-Dirichlet Weighting Enables Reliable Training of Physics Informed Neural Networks

    arxiv:2107.00940, July 2, 2021

    Suryanarayana Maddu, Dominik Sturm, Ivo F. Sbalzarin, and C. Müller

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