Changes for page Extension tvb-ext-xircuits
Last modified by teodoramisan on 2026/02/13 10:11
From version 75.1
edited by teodoramisan
on 2026/02/13 09:23
on 2026/02/13 09:23
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To version 77.3
edited by teodoramisan
on 2026/02/13 10:06
on 2026/02/13 10:06
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... ... @@ -157,9 +157,9 @@ 157 157 [[image:timeseries-plotly.png||alt="view3.png" height="593" width="1100"]] 158 158 159 159 160 -=== 3. Visualize posterior pairplot resultedfromaninferenceworkflow===160 +=== 3. Visualize posterior samples with a pairplot (VBI inferenece) === 161 161 162 -This functionality is available for the SamplePosterior component. Right click on the component and select the Open Viewer functionality. 162 +This functionality is available for the **SamplePosterior** component. Right click on the component and select the **Open Viewer** functionality. 163 163 164 164 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. 165 165 ... ... @@ -168,9 +168,9 @@ 168 168 [[image:plot-posteriors.png||height="593" width="1100"]] 169 169 170 170 171 -=== 4. Visualize time series resultedfrom VBI simulations ===171 +=== 4. Visualize time series from VBI simulations === 172 172 173 -This functionality is available for the SimulationRunner component. Right click on the component and select the Open Viewer functionality. 173 +This functionality is available for the **SimulationRunner** component. Right click on the component and select the **Open Viewer** functionality. 174 174 175 175 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. 176 176 ... ... @@ -193,8 +193,14 @@ 193 193 194 194 === 2. Full VBI Inference workflow === 195 195 196 -Contains all VBI components required to run an inference workflow (e.g.,inference configuration,model,simulator,trainposterior,sampleposterior).196 +Contains all VBI components required to run an inference workflow, from prior sampling and simulation to posterior training and posterior sampling. 197 197 198 +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 (for example //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 + 198 198 [[image:vbi_workflow.png||height="590" width="1100"]] 199 199 200 200 === 3. Configuring model parameters using the PhasePlaneWidget: === ... ... @@ -219,8 +219,10 @@ 219 219 220 220 === 6. Parallel simulations workflow === 221 221 222 -This example demonstrates Parameter Space Exploration (PSE) by running multiple TVB simulations in parallel for different parameter combinations. 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).228 +This example demonstrates **Parameter Space Exploration** (PSE) by running multiple TVB simulations in parallel for different parameter combinations. 223 223 230 +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 + 224 224 [[image:parallel-simulations.png||height="590" width="1100"]] 225 225 226 226