BVEP

Bayesian Virtual Epileptic Patient (BVEP): A probabilistic framework designed to invert a individualized whole-brain model of epilepsy spread by PPLs using No-U-Turn Sam- pler (NUTS), Automatic Differentiation Variational Inference (ADVI), Simulation-based Inference (SBI), and global optimization algorithms.

Installation:

For simulation using TVB:

https://www.thevirtualbrain.org/tvb/zwei

For inference using Stan:

https://mc-stan.org/

For inference using PyMC3:

https://docs.pymc.io/

For inference using Simuation-based Inference (SBI):

https://github.com/sbi-dev/sbi

Refs:

** Hashemi M, Vattikonda AN, Sip V, Guye M, Bartolomei F, Woodman MM, Jirsa VK. The Bayesian Virtual Epileptic Patient: A probabilistic framework designed to infer the spatial map of epileptogenicity in a personalized large-scale brain model of epilepsy spread. NeuroImage. 2020 Aug 15;217:116839.

** Hashemi M, Vattikonda AN, Sip V, Diaz-Pier S, Peyser A, Wang H, Guye M, Bartolomei F, Woodman MM, Jirsa VK. On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread. PLoS computational biology. 2021 Jul 14;17(7):e1009129.

** Vattikonda AN, Hashemi M, Sip V, Woodman MM, Bartolomei F, Jirsa VK. Identifying spatio-temporal seizure propagation patterns in epilepsy using Bayesian inference. Communications biology. 2021 Nov 1;4(1):1244.

** Jha J, Hashemi M, Vattikonda AN, Wang H, Jirsa V. Fully Bayesian estimation of virtual brain parameters with self-tuning Hamiltonian Monte Carlo. Machine Learning: Science and Technology. 2022 Sep 26;3(3):035016.

** Hashemi M, Vattikonda AN, Jha J, Sip V, Woodman MM, Bartolomei F, Jirsa VK. Amortized Bayesian inference on generative dynamical network models of epilepsy using deep neural density estimators. Neural Networks. 2023 Jun 1;163:178-94.

Fundings:

The French National Research Agency (ANR) as part of the second “Investissements d’Avenir” program (ANR-17-RHUS-0004, EPINOV), European Union's Horizon 2020 research and innovation programme under grant agreement No. 785907 (SGA2), and No. 945539 (SGA3) Human Brain Project, and the SATT Sud-Est (827-SA-16-UAM).