Last modified by mhashemi on 2022/06/21 12:37
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1 = Bayesian Virtual Epileptic Patient (BVEP) =
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4 Bayesian Virtual Epileptic Patient (BVEP): a probabilistic framework designed to infer the spatial map of epileptogenicity in a personalized large-scale brain model of epilepsy spread by PPLs using No-U-Turn Sampler (NUTS) and Automatic Differentiation Variational Inference (ADVI), and also now using the state-of-the-art deep learning algorithms for conditional density estimation in simulation-based-inference (SBI) framework.
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7 Installation:
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9 For simulation using TVB:
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11 [[https:~~/~~/www.thevirtualbrain.org/tvb/zwei>>url:https://www.thevirtualbrain.org/tvb/zwei]]
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13 For inference using Stan:
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15 [[https:~~/~~/mc-stan.org/>>url:https://mc-stan.org/]]
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17 For inference using PyMC3:
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19 [[https:~~/~~/docs.pymc.io/>>url:https://docs.pymc.io/]]
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22 For inference using SBI:
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24 [[https:~~/~~/www.mackelab.org/sbi/>>https://www.mackelab.org/sbi/]]
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27 Notebooks:
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29 Bayesian inference of 2D Epileptor model:
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31 [[https:~~/~~/lab.ebrains.eu/user/user-redirect/lab/tree/drive/Shared%20with%20all/Bayesian%20Virtual%20Epileptic%20Patient/BVEP_noncen_pymc3_patient1.ipynb>>url:https://lab.ebrains.eu/user/user-redirect/lab/tree/drive/Shared with all/Bayesian Virtual Epileptic Patient/BVEP_noncen_pymc3_patient1.ipynb]]
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34 Cross-validation and hypothesis inference in 2D Epileptor model:
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36 [[https:~~/~~/lab.ebrains.eu/user/user-redirectm/lab/tree/drive/Shared%20with%20all/Bayesian%20Virtual%20Epileptic%20Patient/EpileptorInferHyposPrior.ipynb>>url:https://lab.ebrains.eu/user/user-redirectm/lab/tree/drive/Shared with all/Bayesian Virtual Epileptic Patient/EpileptorInferHyposPrior.ipynb]]
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39 Bayesian inference of whole-brain network model in PPLs:
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41 [[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Bayesian%20Virtual%20Epileptic%20Patient/BVEP_noncen_stan_patient1.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Bayesian%20Virtual%20Epileptic%20Patient/BVEP_noncen_stan_patient1.ipynb]]
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44 [[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Bayesian%20Virtual%20Epileptic%20Patient/BVEP_noncen_pymc3_patient1.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Bayesian%20Virtual%20Epileptic%20Patient/BVEP_noncen_pymc3_patient1.ipynb]]
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47 SBI-VEP:
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50 [[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Bayesian%20Virtual%20Epileptic%20Patient/BVEP_sde_sbi_maf_seeg_GrExp_patient1.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Bayesian%20Virtual%20Epileptic%20Patient/BVEP_sde_sbi_maf_seeg_GrExp_patient1.ipynb]]