Software
A core part of my Ph.D. is building open-source tools for analyzing neural and behavioral data. Below are the packages I develop and maintain.
StateSpaceDynamics.jl
A Julia library for fitting and analyzing state-space models. It provides efficient implementations of a range of SSMs — including the canonical Gaussian linear dynamical system (Kalman filter/smoother), the Poisson LDS, and hidden Markov models — with a unified, hierarchical interface aimed at neural data. The package is published in the Journal of Open Source Software, and I’m actively extending it with the recurrent switching linear dynamical system (rSLDS).
Documentation · GitHub · Paper (JOSS)
Senne, R., Loschinskey, Z., Fourie, J., Loughridge, C., & DePasquale, B. D. (2025). StateSpaceDynamics.jl: A Julia package for probabilistic state space models (SSMs). Journal of Open Source Software, 10(115), 8077.
ParallelMCMC.jl
A Julia package that implements MCMC algorithms parallelized across the sequence length via Newton’s method, i.e., DEER.