Changes for page SGA3 D1.5 Showcase 1

Last modified by gorkazl on 2023/11/13 14:27
From version 9.13
edited by gorkazl
on 2023/10/08 18:59
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To version 16.1
edited by fousekjan
on 2023/10/31 09:43
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1 -XWiki.gorkazl
1 +XWiki.fousekjan
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24 24  (((
25 25  Running the notebooks //**requires an EBRANS account**// with permissions to access the Lab and programmatic access to the Knowledge Graph API. In addition, to interact with the HPC infrastructure, the user needs access to an active allocation on the corresponding FENIX site. Lastly, the virtual ageing brain notebooks write data to the Bucket storage.
26 26  
27 -Please, to avoid overwriting precomputed data, //**make first a private working duplicate**// of this Collab using the notebook [[copy_showcase1_collab.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/copy_showcase1_collab.ipynb]]. If you encounter any issues running the notebooks, contact [[The Virtual Brain Facility Hub>>mailto:jan.fousek@univ-amu.fr]].
27 +Please, to avoid overwriting precomputed data, //**make first a private working duplicate**// of this Collab using the notebook [[copy_showcase1_collab.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/copy_showcase1_collab.ipynb]]. If you encounter any issues running the notebooks, contact [[The Virtual Brain Facility Hub>>mailto:jan.fousek@univ-amu.fr]].
28 28  )))
29 29  )))
30 30  
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31 31  (% class="wikigeneratedid" %)
32 32  The Showcase 1 aimed at investigations related to variability in neuroscience from two perspectives: (a) the interpersonal variability studied by the virtual ageing study, and (b) the variability across different cortical regions within an individual brain.
33 33  
34 -(% class="wikigeneratedid" %)
35 -== (a) Interpersonal variability—virtual ageing ==
34 +== a. Interpersonal variability – virtual ageing ==
36 36  
37 37  (% class="wikigeneratedid" %)
38 38  See the details of the first study in the following publication:
39 39  
40 -M. Lavanga, J. Stumme, B. H. Yalcinkaya, J. Fousek, C. Jockwitz, H. Sheheitli, N. Bittner, M. Hashemi, S. Petkoski, S. Caspers, and V. Jirsa, [[The Virtual Aging Brain: A Model-Driven Explanation for Cognitive Decline in Older Subjects>>https://doi.org/10.1101/2022.02.17.480902]].
39 +Lavanga, M., Stumme, J., Yalcinkaya, B. H., Fousek, J., Jockwitz, C., Sheheitli, H., Bittner, N., Hashemi, M., Petkoski, S., Caspers, S., & Jirsa, V. (2023)[[. The virtual aging brain: Causal inference supports interhemispheric dedifferentiation in healthy aging.>>https://doi.org/10.1016/j.neuroimage.2023.120403]] //NeuroImage//, //283//, 120403.
41 41  
42 42  === Simulation of resting-state activity ===
43 43  
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50 50  
51 51  Link to the notebook:
52 52  
53 -* [[virtual_ageing/notebooks/1_BNM_for_resting_state.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/virtual_ageing/notebooks/1_BNM_for_resting_state.ipynb]]
52 +* [[virtual_ageing/notebooks/1_BNM_for_resting_state.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/virtual_ageing/notebooks/1_BNM_for_resting_state.ipynb]]
54 54  
55 -[[image:image-20220103100841-2.png]]
54 +[[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/image-20220103100841-2.png?rev=1.1||alt="image-20220103100841-2.png"]]
56 56  
57 57  === Virtual ageing trajectories ===
58 58  
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64 64  
65 65  Link to the notebook:
66 66  
67 -* [[virtual_ageing/notebooks/2_virtual_ageing_trajectories.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/virtual_ageing/notebooks/2_virtual_ageing_trajectories.ipynb]]
66 +* [[virtual_ageing/notebooks/2_virtual_ageing_trajectories.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/virtual_ageing/notebooks/2_virtual_ageing_trajectories.ipynb]]
68 68  
69 -[[image:image-20220103101022-3.png]]
68 +[[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/image-20220103101022-3.png?rev=1.1||alt="image-20220103101022-3.png"]]
70 70  
71 71  === Inference with SBI ===
72 72  
73 73  The last step of the inter-individual variability workflow employs Simulation Based Inference for estimation of the full posterior values of the parameters. Here, a deep neural estimator is trained to provide a relationship between the parameters of a model (black box simulator) and selected descriptive statistics of the observed data.
74 74  
75 -[[image:image-20220103104332-4.png||height="418" width="418"]]
74 +[[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/image-20220103104332-4.png?width=418&height=418&rev=1.1||alt="image-20220103104332-4.png"]]
76 76  
77 77  Link to the notebook:
78 78  
79 -* [[virtual_ageing/notebooks/3_inference_with_SBI.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/virtual_ageing/notebooks/3_inference_with_SBI.ipynb]]
78 +* [[virtual_ageing/notebooks/3_inference_with_SBI.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/virtual_ageing/notebooks/3_inference_with_SBI.ipynb]]
80 80  
81 -(% class="wikigeneratedid" %)
82 -== (b) Regional variability ==
80 +== b. Regional variability – Receptor density maps ==
83 83  
84 -Aims at demonstrating the construction of whole-brain network models of the brain's activity accounting for differences in receptor densities across cortical regions.
82 +Aims at demonstrating the construction of whole-brain network models of the brain's activity, accounting for differences in receptor densities across cortical regions.
85 85  
86 86  === Loading the data from EBRAINS ===
87 87  
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89 89  
90 90  1. Structural connectivity matrices,
91 91  1. GABAa and AMPA receptor densities for each brain region, and
92 -1. empirical resting-state fMRI data for fitting and validation of the simulations. The three datasets shall be characterised in the same parcellation.
90 +1. empirical resting-state fMRI data for fitting and validation of the simulations.
93 93  
94 -Link to the notebook:
92 +The three datasets are characterised in the same parcellation. Link to the notebook:
95 95  
96 -* [[regional_variability/notebooks/1_load_data.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/1_load_data.ipynb]]
94 +* [[regional_variability/notebooks/1_load_data.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/notebooks/1_load_data.ipynb]]
97 97  
98 -(% style="text-align:center" %)
99 -[[image:download - 2022-02-10T130815.902.png||alt="region-wise gene expression heterogeneity"]]
96 +[[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/download%20-%202022-02-10T130815.902.png?rev=1.1||alt="region-wise gene expression heterogeneity"]]
100 100  
101 -== Fitting model parameters for models with regional bias ==
98 +=== Fitting model parameters with regional bias ===
102 102  
103 -A series of simulations of the whole-brain network model are launched in the EBRAINS HPC facilities in order to identify the optimal model parameters leading to simulated resting-state brain activity that best resembles the empirically observed activity. In this branch of the showcase, brain regions are simulated using the Balanced Excitation-Inhibition model which allows to tune the E-I balance for every region individually, according to the empirically observed GABA and AMPA neuroreceptor densities.
100 +A series of simulations of the whole-brain network model are launched in the EBRAINS HPC facilities in order to identify the optimal model parameters leading to simulated resting-state brain activity that best resembles the empirically observed activity. In this branch of the showcase, brain regions are simulated using the mean-field AdEx population model; specifically modified to account for the regional densities of GABAa and AMPA neuroreceptors. See the details in the following document.
104 104  
105 105  Link to the notebook:
106 106  
107 -* [[regional_variability/notebooks/2_parameter_swep.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/2_parameter_swep.ipynb]]
104 +* [[regional_variability/notebooks/2_parameter_swep.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/notebooks/2_parameter_swep.ipynb]]
108 108  
109 -[[image:download - 2022-02-10T131102.033.png||alt="regional bias vs goodness of fit"]]
106 +[[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/download%20-%202022-02-10T131102.033.png?rev=1.1||alt="regional bias vs goodness of fit"]]
110 110  )))
111 111  
112 112