CCM’s mission is to create new mathematical approaches, algorithms and software to advance scientific research in multiple disciplines, often in collaboration with other Flatiron Centers.
Applied and computational mathematics play a critical role in many aspects of modern science and engineering, with new opportunities for discovery in virtually every discipline. CCM will focus on developing new tools and software libraries that bring large-scale modeling, simulation and data analysis within practical reach.
Many high-throughput sequencing data sets in biology are compositional in nature. A prominent example is microbiome profiling data, including targeted…Computational Statistics & Data Analysis
Numerical methods for approximately solving partial differential equations (PDE) are at the core of scientific computing. Often, this requires high-resolution…14th WCCM & ECCOMAS Congress 2020
We introduce c-lasso, a Python package that enables sparse and robust linear regression and classification with linear equality constraints. The…Journal of Open Source Software
SpikeForest is a continuously-updating web-facing performance comparison of popular neural spike sorting codes, using a massive (1.3 TB) database of ground-truth recordings collected from over a dozen participating laboratories.
FMM3D is a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine.
IronClust is a fast and drift-resistant spike sorting pipeline. The accuracy of spike sorting is validated by multiple ground-truth datasets from a number of contributing labs.
MountainSort is a plugin package to MountainLab, a general framework for scientific data analysis, sharing, and visualization.
FINUFFT is a set of libraries to compute efficiently three types of nonuniform fast Fourier transform (NUFFT) to a specified precision, in one, two, or three dimensions, on a multi-core shared-memory machine.
A GPU implementation of the 2- and 3-dimensional non-uniform FFT of types 1 and 2, in single and double precisions, based on the CPU code FINUFFT
ISO-SPLIT is an efficient clustering algorithm that handles an unknown number of unimodal clusters in low to moderate dimension, without any user-adjustable parameters.
Fast sinc transform library
Fast sinc transform libraries which compute sums of the sinc and sinc2 kernels between N arbitrary points in 1, 2, or 3 dimensions.
FFT-accelerated Interpolation-based t-SNE
FFT-accelerated interpolation-based t-SNE (FIt-SNE) is an efficient implementation of t-SNE (stochastic neighborhood embedding) for dimensionality reduction and visualization of high dimensional datasets.
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
Complete Matlab pipeline for large scale calcium imaging data analysis.