Last modified by teodoramisan on 2026/02/13 10:11
From version 67.1
edited by teodoramisan
on 2026/02/12 11:27
Change comment: There is no comment for this version
To version 81.1
edited by teodoramisan
on 2026/02/13 10:11
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -8,7 +8,7 @@
8 8  
9 9  == Purpose ==
10 10  
11 -This is a Jupyter Lab extension that offers graphical support for TVB and VBI workflows. It is already available in the EBRAINS Lab and it allows users to configure and execute TVB simulations and VBI inference workflows directly from a GUI, while drastically reducing the complexity of configuring them inside a Jupyter Lab notebook. Try edit
11 +This is a Jupyter Lab extension that offers graphical support for TVB and VBI workflows. It is already available in the EBRAINS Lab and it allows users to configure and execute TVB simulations and VBI inference workflows directly from a GUI, while drastically reducing the complexity of configuring them inside a Jupyter Lab notebook.
12 12  
13 13  {{html}}
14 14  <iframe width="1200" height="450" src="https://www.youtube.com/embed/-cjZOsU6PBg" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
... ... @@ -61,13 +61,13 @@
61 61  
62 62  The components that are provided in this extensions are configurable, meaning you can set some parameters on almost every component. Some of the parameters are literals, while some parameters are results of other components.
63 63  
64 -Parameters marked with a star (*) are mandatory, the workflow will not run until all required parameters have values assigned.
64 +Parameters marked with a star (★) are mandatory, the workflow will not run until all required parameters have values assigned.
65 65  
66 66  In case of primitives you need to open the //General// tab from the components tray and drag the appropriate //literal//: float, int, string, dict, etc.
67 67  
68 68  The parameters need to be linked to the inputs of the component by dragging and dropping a connection from the output port of a literal/component towards the corresponding input port of the other component (e.g. the gray connections in the screenshot below).
69 69  
70 -Components and parameters include info buttons (i) that explain their purpose and how they are used (e.g. the simulator info panel below).
70 +Components and parameters include info buttons (**i**) that explain their purpose and how they are used (e.g. the simulator info panel below).
71 71  
72 72  [[image:Screenshot 2026-02-12 115445.png||alt="diagr.png" height="592" width="1100"]]
73 73  
... ... @@ -142,7 +142,7 @@
142 142  [[image:export-model-configuration.png||alt="image-20221116130425-1.png" data-xwiki-image-style-alignment="center" height="763" width="1000"]]
143 143  
144 144  
145 -=== 2. Visualize time series resulted from simulations ===
145 +=== 2. Visualize time series resulted from TVB simulations ===
146 146  
147 147  This functionality is available for the **StoreResultsToDrive** component. Right click on the **StoreResultsToDrive** and select the **Open Viewer** option:
148 148  
... ... @@ -156,6 +156,27 @@
156 156  
157 157  [[image:timeseries-plotly.png||alt="view3.png" height="593" width="1100"]]
158 158  
159 +
160 +=== 3. Visualize posterior samples with a pairplot (VBI inferenece) ===
161 +
162 +This functionality is available for the **SamplePosterior** component. Right click on the component and select the **Open Viewer** functionality.
163 +
164 +This opens a new JupyterLab tab with an editable notebook. After following the instructions in the notebook, you will generate a pairplot of the posterior samples, showing the distribution of each parameter (uncertainty) and the relationships between parameters.
165 +
166 +*Make sure the workflow has been executed so the viewer has data to load.
167 +
168 +[[image:plot-posteriors.png||height="593" width="1100"]]
169 +
170 +
171 +=== 4. Visualize time series from VBI simulations ===
172 +
173 +This functionality is available for the **SimulationRunner** component. Right click on the component and select the **Open Viewer** functionality.
174 +
175 +This opens a new JupyterLab tab with an editable notebook. After following the instructions in the notebook, you will see a simple time-series plot of the simulated model signal over time.
176 +
177 +*Make sure the workflow has been executed so the viewer has data to load.
178 +[[image:plot-timeseries-vbi.png||height="592" width="1100"]]
179 +
159 159  == ==
160 160  
161 161  == Workflow examples ==
... ... @@ -164,15 +164,26 @@
164 164  === 1. Full TVB Simulation workflow ===
165 165  )))
166 166  
167 -Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
188 +Contains all TVB components necessary for running a TVB simulation (e.g., connectivity, coupling, model, integrator, monitor, simulator).
168 168  
169 169  {{html}}
170 170  <iframe width="1280" height="720" src="https://www.youtube.com/embed/bmqPlIJsWLk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
171 171  {{/html}}
172 172  
194 +=== 2. Full VBI Inference workflow ===
173 173  
174 -=== 2. Configuring model parameters using the PhasePlaneWidget: ===
196 +Contains all VBI components required to run an inference workflow, from __prior sampling__ and __simulation__ to __posterior training__ and __posterior sampling__.
175 175  
198 +The workflow starts with **ConfigInference**, which builds the configuration inputs needed by the workflow. It samples parameter values from the prior distribution to generate __theta__ and prepares the feature-extraction configuration (__cfg__) used later in the pipeline.
199 +
200 +Next, **SimulationRunner** executes the selected **VBI model** for a batch of parameter samples (theta) using the chosen backend (//cpp//, //cupy// or //numba//). It selects the requested output signal from the model result and extracts the summary features defined in cfg, producing the __feature matrix__ used for training.
201 +
202 +The resulting features and parameter samples are then passed to **TrainPosterior**, which standardizes the feature matrix with //StandardScaler //and trains a posterior distribution using an SBI method (//SNPE//, //SNLE//, or //SNRE//). In the last step, **SamplePosterior** draws parameter samples from the trained posterior distribution, conditioned on the selected observed feature vector.
203 +
204 +[[image:vbi_workflow.png||height="590" width="1100"]]
205 +
206 +=== 3. Configuring model parameters using the PhasePlaneWidget: ===
207 +
176 176  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
177 177  
178 178  {{html}}
... ... @@ -179,9 +179,8 @@
179 179  <iframe width="1280" height="720" src="https://www.youtube.com/embed/jhGfYul1z9k" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
180 180  {{/html}}
181 181  
214 +=== 4. Using siibra to retrieve connectivities from the EBRAINS KG ===
182 182  
183 -=== 3. Using siibra to retrieve connectivities from the EBRAINS KG ===
184 -
185 185  A simulation workflow where **siibra **is used to retrieve a connectivity from the EBRAINS KG. That connectivity is fed into a TVB Simulator, where the rest of the parameters (coupling, model, etc.) are set to default values.
186 186  
187 187  {{html}}
... ... @@ -188,10 +188,18 @@
188 188  <iframe width="1280" height="720" src="https://www.youtube.com/embed/hnqTpFGCYMg" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
189 189  {{/html}}
190 190  
222 +=== 5. Run a workflow as an HPB job ===
191 191  
192 -=== 4. Run a workflow as an HPB job ===
193 -
194 194  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
195 195  
226 +=== 6. Parallel simulations workflow ===
227 +
228 +This example demonstrates **Parameter Space Exploration** (PSE) by running multiple TVB simulations in parallel for different parameter combinations.
229 +
230 +The workflow uses two nested ForEach components to iterate over coupling and conduction speed sets of values. For each (coupling, conduction_speed) pair, a simulation run is executed with the help of the RunParallelProcess component, which runs the workflow body in separate worker processes (using multiprocessing + dill).
231 +
232 +[[image:parallel-simulations.png||height="590" width="1100"]]
233 +
234 +
196 196  {{html}}<iframe width="1280" height="720" src="https://www.youtube.com/embed/M6rZClFgRrM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>{{/html}}
197 197  
parallel-simulations.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.teodoramisan
Size
... ... @@ -1,0 +1,1 @@
1 +325.1 KB
Content
plot-posteriors.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.teodoramisan
Size
... ... @@ -1,0 +1,1 @@
1 +442.0 KB
Content
plot-timeseries-vbi.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.teodoramisan
Size
... ... @@ -1,0 +1,1 @@
1 +579.5 KB
Content
vbi_workflow.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.teodoramisan
Size
... ... @@ -1,0 +1,1 @@
1 +465.2 KB
Content
Public

TVB Widgets