Wiki source code of Bayesian Virtual Epileptic Patient
Last modified by mhashemi on 2022/06/21 12:37
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9.1 | 1 | = Bayesian Virtual Epileptic Patient (BVEP) = |
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25.1 | 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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9.2 | 6 | |
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9.1 | 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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25.1 | 22 | For inference using SBI: |
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9.2 | 23 | |
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25.1 | 24 | [[https:~~/~~/www.mackelab.org/sbi/>>https://www.mackelab.org/sbi/]] |
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9.1 | 27 | Notebooks: |
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11.1 | 29 | Bayesian inference of 2D Epileptor model: |
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16.1 | 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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9.1 | 32 | |
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11.1 | 34 | Cross-validation and hypothesis inference in 2D Epileptor model: |
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17.1 | 35 | |
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16.1 | 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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26.1 | 39 | Bayesian inference of whole-brain network model in PPLs: |
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26.1 | 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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26.1 | 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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25.1 | 45 | |
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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]] |