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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. Prediction error bounds for linear regression with the TREX

    Test, arxiv:1801.01394, May 8, 2018

    Jacob Bien, Irina Gaynanova, Johannes Lederer, and C. Müller

  2. An adaptive fast Gauss transform in two dimensions

    SIAM Journal on Scientific Computing, arxiv:1712.00380, May 3, 2018

    J. Wang and L. Greengard

  3. Decoupled field integral equations for electromagnetic scattering from homogeneous penetrable obstacles

    Communications in Partial Differential Equations, arxiv:1704.06741, March 13, 2018

    Felipe Vico, L. Greengard, and Miguel Ferrando

  4. APPLE Picker: Automatic Particle Picking, a Low-Effort Cryo-EM Framework

    arXiv:1802.00469, February 1, 2018

    Ayelet Heimowitz, J. Andén, and A. Singer

  5. Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing

    Bioinformatics, bioRxiv, February 1, 2018

    Tarmo Äijö, C. Müller, and R. Bonneau

  6. Non-convex Global Minimization and False Discovery Rate Control for the TREX

    Journal of Computational and Graphical Statistics, arXiv:1604.06815, January 25, 2018

    J. Bien, Irina Gaynanova, Johannes Lederer, and C. Müller

  7. Fungi stabilize connectivity in the lung and skin microbial ecosystems

    Microbiome, January 15, 2018

    Laura Tipton, C. Müller, Zachary D Kurtz, Laurence Huang, Eric Kleerup, Alison Morris, et al.

  8. Perspective Functions: Proximal Calculus and Applications in High-Dimensional Statistics

    Journal of Mathematical Analysis and Applications, Code Available on GitHub, 2018

    Patrick L Combettes and C. Müller

  9. Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets

    PLoS Computational Biolog, October 12, 2017

    Kevin Drew, C. Müller, R. Bonneau, and Edward M Marcotte

  10. Robust integral formulations for electromagnetic scattering from three-dimensional cavities

    Journal of Computational Physics, arXiv:1606.03599, September 15, 2017

    Jun Lai, L. Greengard, and Michael O'Neil

  11. A Fully Automated Approach to Spike Sorting

    Neuron, September 13, 2017

    J.E. Chung, J. Magland, A. Barnett, V.M. Tolosa, A.C. Tooker, K.Y. Lee, et al.

  12. A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity

    Nature Communications, September 11, 2017

    V Ruiz, T Battaglia, S Kurtz, L Bijnens, A Ou, I Engstrand, et al.

  13. Rapid solution of the cryo-EM reconstruction problem by frequency marching

    SIAM Journal on Imaging Sciences, August 1, 2017

    A. Barnett, L. Greengard, A. Pataki, and M. Spivak

  14. High resolution inverse scattering in two dimensions using recursive linearization

    SIAM Journal on Imaging Sciences, arxiv:1608.06871, May 9, 2017

    Carlos Borges, Adrianna Gillman, and L. Greengard

  15. Lp-Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems

    Scientific Reports, May 2, 2017

    J Asmus, C. Müller, and I Sbalzarini

  16. An integral equation formulation for rigid bodies in Stokes flow in three dimensions

    Journal of Computational Physics, arxiv:1606.07428, March 1, 2017

    Eduardo Corona, L. Greengard, M. Rachh, and Shravan Veerapaneni

  17. A fast summation method for oscillatory lattice sums

    Journal of Mathematical Physics, arxiv:1609.08523, February 28, 2017

    Ryan Denlinger, Zydrunas Gimbutas, L. Greengard, and Vladimir Rokhlin

  18. Pseudo-Spectral Methods for the Laplace-Beltrami Equation and the Hodge Decomposition on Surfaces of Genus One

    Numerical Methods for Partial Differential Equations, arxiv:1608.04436, February 9, 2017

    Lise-Marie Imbert-Gérard and L. Greengard

  19. Compressed sensing and optimal denoising of monotone signals

    ICASSP, arxiv:1701.00056, December 31, 2016

    E. Pnevmatikakis

  20. Fused regression for multi-source gene regulatory network inference

    PLoS computational biology, December 6, 2016

    K Lam, Z Westrick, C. Müller, L Christiaen, and R. Bonneau

  21. Fast convolution with free-space Green’s functions

    Journal of Computational Physics, arXiv: 1604.03155, October 15, 2016

    Felipe Vico, L. Greengard, and Miguel Ferrando

  22. Integral Equation Methods for Elastance and Mobility Problems in Two Dimensions

    SIAM Journal on Numerical Analysis, arxiv:1507.05925, September 22, 2016

    M. Rachh and L. Greengard

  23. On the stability of time-domain integral equations for acoustic wave propagation

    Discrete & Continuous Dynamical Systems - A, arXiv: 1504.04047, August 1, 2016

    Charles L. Epstein, L. Greengard, and Thomas Hagstrom

  24. Fast, adaptive, high order accurate discretization of the Lippmann-Schwinger equation in two dimension

    SIAM Journal on Scientific Computing, arxiv:1505.07157, June 9, 2016

    Sivaram Ambikasaran, Carlos Borges, Lise-Marie Imbert-Gerard, and L. Greengard

  25. Generalized Stability Approach for Regularized Graphical Models

    arXiv preprint arXiv:1605.07072, May 23, 2016

    C. Müller, R. Bonneau, and Z Kurtz

  26. Population-Level Representation of a Temporal Sequence Underlying Song Production in the Zebra Finch

    Neuron, May 18, 2016

    Michel A. Picardo, Josh Merel, Kalman A. Katlowitz, Daniela Vallentin, Daniel E. Okobi, Sam E. Benezra, et al.

  27. Validation of neural spike sorting algorithms without ground-truth information

    Journal of Neuroscience Methods, May 1, 2016

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

  28. 4C-ker: a method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments

    PLoS Computational Biology, March 3, 2016

    R Raviram, P Rocha, C. Müller, E. Miraldi, S Badri, Y Fu, et al.

  29. Robust classification of protein variation using structural modelling and large-scale data integration

    Nucleic Acids Research, February 28, 2016

    E Baugh, R Simmons-Edler, C. Müller, R Alford, N. Volfovsky, and R. Bonneau

  30. Inferring causal molecular networks: empirical assessment through a community-based effort

    Nature Methods, February 22, 2016

    Steven M Hill, et al.

  31. Fast Direct Methods for Gaussian Processes

    IEEE Transactions on Pattern Analysis and Machine Intelligence, arxiv:1403.6015, February 1, 2016

    Sivaram Ambikasaran, Daniel Foreman-Mackey, L. Greengard, David W. Hogg, and Michael O'Neil

  32. Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data

    Neuron, January 20, 2016

    E. Pnevmatikakis, Daniel Soudry, Yuanjun Gao, Timothy A Machado, Josh Merel, David Pfau, et al.

  33. Unimodal clustering using isotonic regression: ISO-SPLIT

    arXiv:1508.04841, August 20, 2015

    J. Magland and A. Barnett

  34. Primacy of Flexor Locomotor Pattern Revealed by Ancestral Reversion of Motor Neuron Identity

    Cell, July 16, 2015

    Timonty A Machado, E. Pnevmatikakis, Liam Paninski, Thomas M Jessell, and Andrew Miri

  35. Simple and efficient representations for the fundamental solutions of Stokes flow in a half-space

    Journal of Fluid Mechanics, arxiv:1504.00102, July 2, 2015

    Zydrunas Gimbutas, L. Greengard, and Shravan Veerapaneni

  36. Variable metric random pursuit

    Mathematical Programming, arXiv: 1210.5114, May 24, 2015

    Sebastian U Stich, C. Müller, and Bernd Gärtner

  37. Inverse Obstacle Scattering in Two Dimensions with Multiple Frequency Data and Multiple Angles of Incidence

    SIAM Journal on Imaging Sciences, arxiv:1408.5436, January 27, 2015

    Carlos Borges and L. Greengard

  38. A Fast Direct Solver for High Frequency Scattering from a Large Cavity in Two Dimensions

    SIAM Journal on Scientific Computing, arxiv:1404.3451, November 4, 2014

    Jun Lai, Sivaram Ambikasaran, and L. Greengard

  39. A fast solver for multi-particle scattering in a layered medium

    Optics Express, arxiv:1407.3868, 2014

    Jun Lai, Motoki Kobayashi, and L. Greengard

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