Our seminar focuses on efficient computational methods for numerical
problems, mostly phrased in a mathematical language, arising in areas
of science throughout the Institute and beyond. Topics include
signal processing and data analysis (neural spike sorting,
cryo-EM, imaging); computational statistics
(Bayesian, MCMC, variational, robust inference, microbiome); deep learning (equivariant networks);
PDEs (fluid flow, wave scattering), integral equations, spectral methods,
fast algorithms (i.e., close to optimal complexity);
software libraries and programming.
We discuss research topics as well as review classical topics in numerical
analysis and statistics.
As of Fall 2020, the new time is 10am-11:30am on Wednesdays, unless as announced. We (used to) meet in person at CCM in the 3rd-floor classroom (unless otherwise announced; sometimes round-table meetings are in 4th-floor conference room). Since 3/25/20 we meet on zoom. All from Flatiron are welcome, and guests from outside must arrange a visitor's pass. Other events of interest are also listed in [square brackets]. |

This page is maintained by Alex Barnett but may be edited in raw HTML from any cluster account. External potential speakers should please contact someone at CCM working in a relevant research area. Cindy Rampersad-Phillips can help CCM staff with booking and speaker logistics.

- Jan 15: regular group meeting (short-format show & tell): David Barmherzig on MLE for holographic CDI, Jeremy Magland on SpikeForest release, Aditya Mishra on robust regression.
- Jan 22: Dhairya Malhotra (NYU).
*Integral equation methods for computing equilibria in magnetically confined plasmas*. [host: Manas] - Jan 29: Jeremy Hoskins (Yale).
*Multi-wave and multi-frequency inverse problems*. [host: Manas] - Feb 5: Jack Poulson (HodgeStar).
*High-performance sampling of generic determinantal point processes*. [host: Risi] - Feb 12: Chongliang (Jason) Luo (UPenn, biostats).
*ODAC: learning from local to global - an efficient algorithm for integrating time to event healthcare system data*. [host: Aditya] - Feb 19: Kathryn Smetana (Twente).
*Randomized local model order reduction*. [host: Alex] - Feb 26: Dan Simpson.
*The fine art of putting a bunch of straight lines through things*[host: Leslie] - Mar 4: Tingran Gao.
*Manifold Learning on Fibre Bundles*[host: Leslie] - Mar 9 [postponed until the summer: Yu Feng (Berkeley)]
- Mar 11: regular group meeting show & tell: Alex on lap3dkernel speeds, Manas Rachh on surface quadrature optimization.
- Mar 18: [postponed due to COVID-19: Karsten Urban (Ulm). Reduced Basis Methods - Prospects and Challenges. host: Alex]
- Mar 25 [note: remotely via zoom]: Sonya Hanson (MPI Frankfurt).
*Elucidating mechanisms of biological temperature sensing*. [host: Leslie] - Mar 30 [note: Monday, special seminar. Postponed.]: Yaroslav Halchenko (Dartmouth). [host: Jeremy].
- Apr 1: regular group meeting on zoom: reports in alphabetical order.
- Apr 8: group meeting open discussion (including Alex reviewing Fourier matrix results). [postponed: John Urschel, host: Leslie]. Group meetings now all on zoom, each Wed 10am in April.
- Apr 15: Risi Kondor & Erik Thiede:
*Permutation equivariant neural network architectures for generating molecules*. - Apr 22: Hannah Lawrence: overview of two recent deep learning cryo-EM preprints.
- Apr 29: Andreas Buja on reproducibility and COVID trials; Leslie on epidemiology; Alex on nonlinear Volterra integral equation for CCQ.
- May 7 [note new summer weekly slot: Thursday 10:30am]: Bob Carpenter (CCM):
*Rejecting Dawid and Skene's model of data annotation and fixing it with item difficulty*. - May 14: regular group meeting on zoom: updates & FWAM-II.
- May 21: regular group meeting on zoom: updates.
- May 26, 4pm, phase-retrieval zoom meeting: Ju Sun (UMinn).
*Inverse problems, deep learning, and symmetry breaking*. - Jul 9: Pratik Chaudhari (UPenn).
*Learning from few labeled data*. [host: Manas] - Jul 16: Simon Billinge (Columbia). Open problems series:
*Solving the climate crisis one pair distribution function (PDF) at a time*. [host: Leslie] - Jul 23: Risi Kondor on
*Multilevel matrix factorizations with applications to wavelets on graphs*. - Jul 30: CCM updates?
- Aug 6: Summer intern presentations:
- Martyna Stachaczyk.
*Evaluating the performance of spike sorting algorithms using information-theoretical framework* - Di Luo.
*Quantum many-body physics using equivariant neural networks* - Henry Li.
*Applying a natural image prior to phase retrieval with deep learning* - Muawiz Chaudhary.
*Kymatio - Scattering Transforms in Python*

- Martyna Stachaczyk.
- Aug 13: Summer intern presentations:
- Michael Doppelt.
*Measuring the ill conditioning of the Fourier phase retrieval problem* - Dhwanit Agarwal.
*Fast multipole accelerated solvers for the Laplace-Beltrami problem in three dimensions* - Ryan Bernstein.
*Language improvements and formal semantics for*`stan`

- Michael Doppelt.
- Sep 3: James Stokes (CCM/CCQ) on convolutional neural networks for learning many-particle quantum ground states.
- Sep 10: Pilar Cossio (Max Planck Tandem Group / University of Antioquia).
*A path collective variable for extracting free energy profiles from cryo-electron microscopy experiments*. - [Sep 14-15: of interest to those in neuro or signal proc: SCGB spike-sorting workshop]
- Sep 17: regular group meeting and updates: Joakim, David, Alex, Marsha, Bob, Michael E.
- Sep 23 [note new time, Wed 10am]: regular group meeting and updates: Alice, Andreas, Charlie, Dan F, Marylou, Leslie.
- Sep 30: regular group meeting and updates: Gokberg, Risi, Jeremy, Dhairya.
- Oct 7: regular group meeting and updates: Dan F-M, Sara, Aditya M, Pilar, Manas, Adi R.
- Oct 14: Sangwon (Justin) Hyun (USC / CBIOMES).
*Sparse Multivariate Mixture of Regressions Modeling for Flow Cytometry Data*. [host: Aditya] - [Oct 19-20: Annual Flatiron Conference : FWAM-2!]
- Oct 21: regular group meeting and updates: Ali, Amit, Jeff, James S, Stephane, Erik, Wenda.
- Oct 28: Anne Gelb (Dartmouth).
*Empirical Bayesian Inference using Joint Sparsity*[host: Alex] - Nov 4: regular group meeting and updates: Adi on aligning to random volumes, Keaton on deep-learning closures for Navier Stokes spectral solvers, Shravan on optimization of axisymmetric Stokes swimmers.
- [Nov 10, 11am: David Donoho (Stanford),
*Neural Collapse*, kicking off the weekly deep learning math sessions organized by Mallat and Bruna] - Nov 11: Fruzsina Agocs (Cambridge).
*(py)oscode: fast solutions of oscillatory ODEs in physics*. [host: Alex] - Nov 18: general group discussion on covid and other topics.
- Dec 2: Arvind Saibaba (NCSU).
*Efficient randomized algorithms for system identification*. [host: Alex] - Dec 9: Erik Thiede (CCM).
*Umbrella Sampling: Importance Sampling for the Indecisive*. - Dec 16: Donsub Rim (NYU).
*Nonlinear model reduction of wave propagation: depth separation and the Radon transform.*. [host: Alex] - Dec 23: Leslie Greengard.
*Randomized methods for rank deficient linear systems*.

- Jan 2 (moved to 1:30pm; 4th floor conf rm): Cole Hurwitz (Institute for Adaptive and Neural Computation, Edinburgh).
*Variational auto-encoders for extracellular spike localization*. - Jan 8 (Tues, 11am): Michael Eickenberg (Neuroscience, UC Berkeley).
*Machine Learning Representations for Imaging Neuroscience and Quantum Chemistry* - Jan 9: Yuehaw Khoo (Stanford).
*Multi-marginal optimal transport, density functional theory, and semidefinite programming* - Jan 16: Hugo Strand (CCQ).
*Exponentially convergent collocation method for the quantum many-body Dyson equation at finite temperature*. - Jan 30: open discussion (Alex, Jeremy, Adi).
- [Feb 6: no mtg]
- Feb 13: open discussion (Keaton, Christian).
- [Feb 25-Mar 1: SIAM CSE, Spokane]
- Mar 6: Euan Spence (Bath, UK).
*Does the Galerkin method converge for the standard second-kind integral equations for the Laplacian on Lipschitz domains?* - Mar 13, 3rd floor classrm: Mikael Slevinsky (Manitoba).
*Fast and stable computations with spherical harmonics*. - [Mar 18-22: Likelihood-Free Inference Workshop @ CCA]
- Mar 20-22: 2nd workshop on "Operator Splitting Methods in Data Analysis" @ Flatiron Institute (organizers: Christian Müller and Patrick Combettes)
- Mar 27: Marsha Berger (NYU).
*Modeling and Simulation of Asteroid-generated Tsunamis*. - Apr 3: Michael Hecht (MOSAIC group, Center for Systems Biology, Max Planck Institute, Dresden).
*Multivariate Newton interpolation* - Apr 10: Denis Zorin (NYU).
*Simulation of 3D particulate Stokesian suspensions*. - Apr 17: Alexander Vladimirsky (Cornell).
*Surveillance-evasion games under uncertainty*. - Apr 24 [7th-fl classrm]: Joshua Glaser (Columbia).
*Machine learning for neural decoding*. - [April 29-May 1: Flatiron/NYU-CDS Gotham City ML X Physics workshop.]
- May 8: open discussion (Alex, Aditya, Joakim).
- May 22: short presentations by Surya Maddu (MPI Dresden) on inferring PDEs, Jun Wang on Stokes rheology simulations, Alex on BLAS3 speed for direct summation.
- May 29 [7th-fl classrm]: William Leeb (U Minn).
*Matrix Denoising and PCA with Heteroscedastic Noise*. - Jun 5: Silvia Espinosa GĂștiez (MIT).
*Theoretical explanation of I-mode impurity removal and energy confinement in plasmas*. - [Jun 7, 3pm, 2nd fl: Flatiron seminar by David Blei, on causal inference.]
- Jun 19: Summer intern short presentations: Leo Simpson, Andrea Malleo, Dan Fortunato, Reese Pathak, Kris Pan.
- Jun 26 [3rd fl classrm]: Soumyashant Nayak (U Penn).
*An Overview of Sequence Alignment: Hidden Markov Models, Category Theory and all that jazz*. - Jul 3: Dan Fortunato on ultraspherical spectral method and hierarchical Poincare-Steklov in 2D; James Jun on drift-resistant spike sorting.
- Jul 10: open discussion: Eftychios on spectral clustering.
- Jul 17: Alex on low-rank approximation of Bessel kernel (see code, preprint); Jeremy on content-addressable
`sha1dir`

React viewer. - Jul 24 [3rd fl classrm]: Leo Simpson (summer intern) on optimization package for stats; Geoffrey Vasil (U. Sydney) on Hahn discrete orthogonal basis functions and applications to data.
- Jul 31: Summer intern final presentations: Andrea Malleo, Reese Pathak.
- Aug 7: Summer intern final presentations: Kris Pan, Dan Fortunato.
- Aug 8-10: Computational Cryo EM Summer Workshop @ Flatiron Institute, including Saturday am software show-and-tell.
- Sep 4: General show and tell; Libin Lu on SIMD vectorization.
- Sep 11: Manas talking about "box codes" (volume FMMs); general discussion.
- Sep 24 11am [9th fl classrm; joint seminar w/ CCQ]: Jianfeng Lu (Duke).
*Coordinate-descent full configuration interaction*. - Sep 25 [7th fl classrm]: Ayelet Heimowitz (Princeton).
*From raw data to particle stacks: data-driven methods for processing of low SNR experimental data in cryo-electron microscopy*. - Oct 2: David Barmherzig (CCM).
*Holographic Phase Retrieval and Optimal Reference Design*. - Oct 9: open discussion; bring your updates and questions.
- [Oct 14-15: Alex Townsend (Cornell) visit CCM; hosts Leslie, Manas, Alex.]
- Oct 16: Kirill Serkh.
*On the solution of elliptic PDEs on three-dimensional regions with corners and conical points*. [host: Manas] - Oct 23:
Maria Lopez Fernandez (Sapienza U., Rome). [host: Leslie]:
*Efficient algorithms for time convolutions tailored to applications: fractional differential equations and Schrodinger problems with concentrated potentials*. - Oct 30-Nov 1 (2.5 days): Internal conference: Flatiron-Wide Algorithms and Mathematics (FWAM!)
- Nov 6: Bob Carpenter (Columbia)
*Taking Uncertainty Seriously for Calibrated Forecasting and Decision Making*[host: Leslie] - Nov 13: Melvin Leok (UCSD).
*The Connections Between Discrete Geometric Mechanics, Information Geometry and Machine Learning*. [host: Risi] - Nov 20: Robert Webber (CIMS)
*The role of lag time in spectral estimation for Markov processes*[host: Erik] - Nov 21 [special seminar, Thurs]: Robert Kalb (neurology, Northwestern).
- Dec 4: Amir Sagiv (Columbia, APAM).
*An optimal transport perspective on uncertainty quantification*[host: Alex] - Dec 11: Jason Kaye (Flatiron, CCM/CCQ).
*An integral equation-based solver for the time-dependent Schrodinger equation*. - Dec 18: Thomas Anderson (Caltech).
*Hybrid frequency/time methods for efficient and parallel high-order solution of wave scattering problems*[host: Alex]

- Jan 10: open discussion (Victor, Aaditya, Shidong).
- Jan 17: Logan Grosenick (Columbia).
*Wave optics theory and 3-D deconvolution for the light field microscope* - Jan 24: open discussion (Jeremy, Marina)
- Jan 26 (Friday): Manas Rachh (Yale).
*Fast algorithms for dimensionality reduction and data visualization using t-distributed Stochastic Neighborhood Embedding (t-SNE)* - Jan 31: Adrianna Gillman (Rice).
*Introduction to Fast Direct Solvers* - Feb 7: Joakim Andén (CCB).
*Particle picking in cryo-EM via the APPLE picker* - Feb 14: Aaditya Mishra and Christian Müller (CCB).
- Mar 28: Kamiar Rahnama Rad (Statistics, Baruch College, CUNY).
*A scalable estimate of the extra-sample prediction error via approximate leave-one-out* - Apr 11: open discussion (Jeremy).
- Apr 18: Adi Rangan (NYU).
*Heterogeneity problem in cryo-EM via residuals* - Apr 25: Jun Wang (CCB).
- May 2: Ludvig af Klinteberg (SFU),
*Quadrature for layer potentials with near singularities* - May 9: open discussion (Jun, Christian, Joakim, Charlie).
- May 16: Marina Spivak (CCB).
*Resolution results in cryo-EM* - [May 17: MountainSort users workshop]
- May 23: Dan Foreman-Mackey (CCA).
*Hunting for exoplanets: periodic dips in noisy light curves* - May 30: Eric Lifshin (SUNY).
*Modeling and imaging in scanning electron microscopy (SEM)*. - Jun 13: Roy Lederman (Princeton).
*Inverse Problems and Unsupervised Learning with applications to Cryo-Electron Microscopy* - Jun 20: Alex Barnett (CCB).
*Error analysis of the non-uniform FFT algorithm* - Jun 27: James Jun (CCB/Columbia).
*Spike sorting with IronClust with preliminary results on handling drift* - [July 9-13: ICOSAHOM conference, UK]
- July 26 (relocated due to steam pipe explosion): Hau-Tieng Wu (Duke).
*Can applied harmonic analysis turn a fetus into a radar of maternal stress?* - Aug 1: open discussion (Jeremy, Eftychios, Marina).
- Aug 8: Jeremy Magland (CCB).
*The spikeforest spike sorting validation framework*. - Aug 15: Yu-Hsuan "Melody" Shih (NYU).
*A GPU implementation of FINUFFT in 2D*. - Aug 29: Johan Helsing (Lund).
*Solving integral equations on boundaries with singular points* - Sept 5: Joakim Andén (CCB).
*Review of the Wiener filter*. - Sept 12: Caroline Moore-Kochlacs (MIT, Northeastern).
*Bursting spike detection*. - Sept 19: open discussion (James, Joakim)
- [Sept 25, 4:30 pm, conf rm: Nick Trefethen and Abi Gopal, PDE corners]
- Sept 26 (11am, 7th fl classroom): Tamir Bendory (Princeton).
*Estimation below the detection limit with application to cryo-EM* - Oct 3: Alex Barnett on numerical steepest descent; open discussion (Jeremy).
- Oct 10, 10:30am, 3rd fl classroom: Xinyi Deng (Columbia, neuroscience).
*Clusterless methods for understanding internally generated hippocampal sequences*. - [cancelled: Oct 16, 4:30pm, 7th fl classroom, Greengard gp mtg: Mahadevan Ganesh (Colorado School of Mines).
*A coercive Helmholtz model: Formulation, wavenumber-explicit analysis, and preconditioned high-order FEM*.] - Oct 17, 10am 7th fl classroom: Ari Pakman (Columbia).
*Sampling with Velocities* - [Oct 18, 11:15am, 3rd fl classroom: StĂ©phane Mallat (Collège de France).
*Learning in High Dimension: Is There an Architecture of Complexity?*] - [Oct 22, 7th fl classroom, BPM seminar: Yoichiro Mori (U. Minn.).
*Mathematical Justification of Slender Body Theory*] - Oct 23, 10:30am, 5rd fl classroom: Gabi Pragier (Tel-Aviv University).
*A common-lines approach for three-dimensional modeling of molecules in cryo-electron microscopy* - [Oct 24-26: FI Software Revue]
- Oct 31: Christian Müller (CCM).
*Overview of statistical learning of PDE coefficients* - Nov 5, 5th fl classroom: Yariv Aizenbud (Tel-Aviv University).
*Randomized algorithms for matrix decomposition*. - [Nov 6, 10am, 7th fl classroom: Dhairya Malhotra (CIMS).
*Overview of PVFMM: a parallel kernel-independent FMM library for particle and volume potentials)*. ] - Nov 7: Eftychios Pnevmatikakis (CCM).
*Convex clustering* - Nov 14, 7th fl classroom: Bill Press (UT Austin).
*Indel-tolerant error-correcting codes and algorithms for DNA*. - Nov 20, 2pm, 7th fl classrm: Risi Kondor (CS and Stats, U. Chicago).
*Covariant neural network architectures for learning physics*. - Nov 28: Leo Zepeda-Núñez (Lawrence Berkeley Labs).
*Accelerating ab-initio molecular dynamics via multi-scale neural networks*. - Dec 12, 7th fl classroom: David Schneider (CNS, NYU).
*Concepts and technologies for studying neural circuits in behaving mice* - Dec 13: Ozan Öktem (KTH).
*Recent advances in using machine learning for image reconstruction* - Dec 19, 2pm, 4th fl conf: Redux of Cryo-ET conference (Manas, Joakim); open discussion.

- Apr 5: Patrick Combettes (NCSU).
*Perspective functions: construction, proximal calculus, and applications in data analysis* - Oct 4: open discussion (Aaditya, Joakim, Marina)
- Oct 11: open discussion (Victor, Christian, Marina)
- Oct 25: Aaditya Mishra (CCB).
*Robust sparse regression for compositional data* - Nov 15: Jun Wang (CCB).
*Fast integral-equation based solvers for the heat equation with moving boundary* - Nov 29: Jeremy Magland (CCB).
*Spike sorting with drift via dynamic programming*