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Welcome to the nm-bridge documentation!

General information

nm-bridge is a C++ library interfaced with R and Python for generating and estimating Hawkes-type (or other) interaction networks to model neural data (spike trains).

This library consists in two modules.

  • A spike train data generation module called nm-spikes, using the algorithms developed in the two following articles

Mascart, Cyrille; Hill, David; Muzy, Alexandre; Reynaud-Bouret, Patricia. Efficient Simulation of Sparse Graphs of Point Processes, ACM Transactions on Modeling and Computer Simulation, 33(1-2), 1-27 (2023) (arXiv)

Mascart, Cyrille; Scarella, Gilles; Reynaud-Bouret, Patricia; Muzy, Alexandre. Scalability of Large Neural Network Simulations via Activity Tracking with Time Asynchrony and Procedural Connectivity, Neural Computation, 34(9), 1915-1943 (2022) (bioRxiv)

  • A module which reconstructs the parameters of the underlying model in view of the observations (reconstruction of the network from trains of spikes), called nm-reconstruction, which is based on these two articles:

Hansen, Niels R.; Reynaud-Bouret, Patricia; Rivoirard, Vincent. Lasso and probabilistic inequalities for multivariate point processes, Bernoulli, 21(1), 83-143 (2015) (arXiv)

Lambert, Régis; Tuleau-Malot, Christine; Bessaih, Thomas; Rivoirard, Vincent; Bouret, Yann; Leresche, Nathalie; Reynaud-Bouret, Patricia. Reconstructing the functional connectivity of multiple spike trains using Hawkes models, Journal of Neuroscience Methods, 297, 9-21 (2018) (HAL)

The two blocks communicate and we can simulate a network of Hawkes processes using the estimated parameters, for example, or check that we have enough observations in a simulation to find the underlying graph. The modules have been designed to easily take into account the heterogeneity of data and to group together similar portions of records.

It is one of the core codes developed at the NeuroMod Institute of Université Côté d'Azur.

Contents

Here, you will find documentation on:

  • Installation instructions for Linux, Windows and macOS
  • Tutorials and demos on how to use nm-bridge in Python and R