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%% Cell type:markdown id:b1331599 tags:
# Down-scaled multi-area model
%% Cell type:markdown id:edec8345-aec1-419e-b9e3-7f612aff8262 tags:
<img src="model_construction.png" alt="Model overview" width="1000"/>
%% Cell type:markdown id:f4a649cc-3b68-49e4-b2b6-6f29f13a6d9c tags:
The code in this notebook implements the down-scaled version of spiking network model of macaque visual cortex developed at the Institute of Neuroscience and Medicine (INM-6), Research Center Jülich. The full-scale model has been documented in the following publications:
1. Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ
Multi-scale account of the network structure of macaque visual cortex
Brain Structure and Function (2018), 223: 1409 [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
2. Schuecker J, Schmidt M, van Albada SJ, Diesmann M & Helias M (2017)
Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome.
PLOS Computational Biology, 13(2): e1005179. [https://doi.org/10.1371/journal.pcbi.1005179](https://doi.org/10.1371/journal.pcbi.1005179)
3. Schmidt M, Bakker R, Shen K, Bezgin B, Diesmann M & van Albada SJ (2018)
A multi-scale layer-resolved spiking network model of
resting-state dynamics in macaque cortex. PLOS Computational Biology, 14(9): e1006359. [https://doi.org/10.1371/journal.pcbi.1006359](https://doi.org/10.1371/journal.pcbi.1006359)
<br>
%% Cell type:markdown id:b952d0ea tags:
#### Notebook structure <a class="anchor" id="toc"></a>
* [S0. Configuration](#section_0)
* [S1. Parameterization](#section_1)
* [1.1. Parameters to tune](#section_1_1)
* [1.2. Default parameters](#section_1_2)
* [S2. Multi-Area Model Instantiation and Simulation](#section_2)
* [2.1. Instantiate a multi-area model](#section_2_1)
* [2.2. Predict firing rates from theory](#section_2_2)
* [2.3. Extract and visualize interareal connectivity](#section_2_3)
* [2.4. Run a simulation](#section_2_4)
* [S3. Simulation Results Visualization](#section_3)
* [3.1. Instantaneous and mean firing rate across all populations](#section_3_1)
* [3.2. Resting state plots](#section_3_2)
* [3.3. Time-averaged population rates](#section_3_3)
%% Cell type:markdown id:d782e527 tags:
## S0. Configuration <a class="anchor" id="section_0"></a>
%% Cell type:code id:9d6cc7d9-3110-4d96-9f9a-9ec7dee6d145 tags:
``` python
# Create config file
with open('config.py', 'w') as fp:
fp.write(
'''import os
base_path = os.path.abspath(".")
data_path = os.path.abspath("simulations")
jobscript_template = "python {base_path}/run_simulation.py {label}"
submit_cmd = "bash -c"
''')
```
%% Cell type:code id:96517739 tags:
``` python
%matplotlib inline
import numpy as np
import os
import nest
import json
import sys
from IPython.display import display, HTML
import warnings
sys.path.append('./figures/MAM2EBRAINS')
from multiarea_model import MultiAreaModel
from M2E_visualize_interareal_connectivity import visualize_interareal_connectivity
from M2E_visualize_instantaneous_and_mean_firing_rates import plot_instan_mean_firing_rate
from M2E_visualize_resting_state import plot_resting_state
from M2E_visualize_time_ave_pop_rates import plot_time_averaged_population_rates
from config import base_path, data_path
```
%% Output
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.5
Built: Jul 12 2023 06:25:27
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
%% Cell type:code id:7e07b0d0 tags:
``` python
%%capture captured
!pip install nested_dict dicthash
```
%% Cell type:code id:1d440c07-9b69-4e52-8573-26b13493bc5a tags:
``` python
# Jupyter notebook display format setting
style = """
<style>
table {float:left}
</style>
"""
display(HTML(style))
warnings.filterwarnings('ignore')
```
%% Output
%% Cell type:markdown id:27160ba8 tags:
Go back to [Notebook structure](#toc)
%% Cell type:markdown id:df83f5ea-1c4b-44d3-9926-01786aa46e14 tags:
## S1. Parameterization <a class="anchor" id="section_1"></a>
%% Cell type:markdown id:30655817 tags:
### 1.1. Parameters to tune <a class="anchor" id="section_1_1"></a>
%% Cell type:markdown id:4f67c1ba tags:
|Parameter|Default value|Value range/options|Value assigned|Description|
|:-------:|:-----------:|:-----------------:|:------------:|:---------:|
|scale_down_to|1. |(0, 1.0] |0.005 |$^1$ |
|cc_weights_factor|1. |[1.0, 2.5] |1. |$^2$ |
|areas_simulated|complete_area_list|Sublists of complete_area_list|complete_area_list|$^3$|
|replace_non_simulated_areas|None|None, 'hom_poisson_stat', 'het_poisson_stat', 'het_current_nonstat'|'het_poisson_stat'|$^4$ |
%% Cell type:markdown id:a2161477 tags:
1. `scale_down_to` is the down-scaling factor that defines the ratio by which the full-scale multi-area model is reduced to a model with fewer neurons and indegrees. This reduction is essential to enable simulation on machines with limited computational power, ensuring that simulation results can be obtained in a relatively shorter timeframe. <br> If the value is `scale_down_to = 1.`, the full-scale network will be simulated. <br> In the pre-set downscale version, it is set to `scale_down_to = 0.005`, This setting reduces both the number of neurons and indegrees to 0.5 % of their full-scale counterparts, facilitating simulation on a typical local machine. <br> **Warning**: This will not yield reasonable dynamical results from the network and is only meant to demonstrate the simulation workflow <br>
2. `cc_weights_factor` is the scaling factor that controls the cortico-cortical synaptic strength. <br> By default it's set as `1.0`, where the inter-area synaptic strength is the same as the intra-areal. <br> **Important**: This factor changes the network activity from ground state to metastable state. <br>
3. `areas_simulated` specifies the cortical areas to be included in the simulation process. Its default value is `complete_area_list` meaning all the areas in the complete_area_list will be simulated. The value assigned to `areas_simulated` can be any sublist of the list below:
```python
complete_area_list = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']
```
<br>
4. `replace_non_simulated_areas` defines how non-simulated areas will be replaced. <br> When all areas are included, it is set as `None` by default. <br> Other options are: `'hom_poisson_stat'`, `'het_poisson_stat'`, and `'het_current_nonstat'`.<br> `'hom_poisson_stat'` replaces the non-simulated areas by Poisson sources with the same global rate `rate_ext`. The `'het_poisson_stat'` and `'het_current_nonstat'` options use the loaded specific rates from `'replace_cc_input_source'`, which contains the area-specific firing rates of our full scale simulation results. The difference between them is that `'het_poisson_stat'` replaces the non-simulated areas by Poisson spike trains and `'het_current_nonstat'` replaces it by a time-varying current input.
%% Cell type:code id:60265d52 tags:
``` python
# Downscaling factor
# Value range/options: (0, 1.]
# Value assigned: 0.005
scale_down_to = 0.005 # Change it to 1. for running the fullscale network
# Scaling factor for cortico-cortical connections (chi)
# Value range/options: [1., 2.5]
# Value assigned: 1.0
cc_weights_factor = 1.0
# Cortical areas included in the simulation
# Value range/options: any sublist of complete_area_list
# where complete_area_list = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']
# Value assigned: complete_area_list
# Note: at this pre-released multi-area model v2.0.0, the areas_similated has to contain at leat three areas in order to plot the 3 raster plots
# areas_simulated = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']
areas_simulated = ['V1', 'V2', 'VP']
# Firing rates used to replace the non-simulated areas
# Value range/options: None, 'hom_poisson_stat', 'het_poisson_stat', 'het_current_nonstat'
# Value assigned: 'het_poisson_stat'
replace_non_simulated_areas = 'het_poisson_stat'
```
%% Cell type:markdown id:de11b07f tags:
### 1.2. Default parameters <a class="anchor" id="section_1_2"></a>
We try our best not to confuse users with too many parameters. However, if you want to change more parameters and explore the model, you can do so by passing a dictionary to the `default_params` argument of the `MultiAreaModel` class. (*NOTE: it should may be moved to the default parameters file in the future.*)
%% Cell type:code id:6e4bed8d tags:
``` python
# Decide the parameter replace_cc_input_source
complete_area_list = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']
if areas_simulated != complete_area_list and replace_non_simulated_areas == None:
raise Exception("When not all areas are simulated, a not None value should be assigned to replace_non_simulated_areas!")
elif replace_non_simulated_areas == 'hom_poisson_stat':
replace_cc_input_source = None
else:
replace_cc_input_source = 'tests/fullscale_rates.json'
# Connection parameters
conn_params = {
'replace_non_simulated_areas': replace_non_simulated_areas, # Whether to replace non-simulated areas by Poisson sources with the same global rate, by default: None
'g': -11., # It sets the relative inhibitory synaptic strength, by default: -16.
'K_stable': 'K_stable.npy', # Whether to apply the stabilization method of Schuecker, Schmidt et al. (2017), by default: None
'fac_nu_ext_TH': 1.2, # Increase the external input to 2/3E and 5E in area TH
'fac_nu_ext_5E': 1.125, # Increase the external Poisson indegree onto 5E
'fac_nu_ext_6E': 1.41666667, # Increase the external Poisson indegree onto 6E
'av_indegree_V1': 3950. # Adjust the average indegree in V1 based on monkey data
'av_indegree_V1': 3950., # Adjust the average indegree in V1 based on monkey data
'replace_cc_input_source': replace_cc_input_source
}
# Input parameters
input_params = {
'rate_ext': 10. # Rate of the Poissonian spike generator (in spikes/s)
}
# Neuron parameters
neuron_params = {
'V0_mean': -150., # Mean for the distribution of initial membrane potentials, by default: -100.
'V0_sd': 50. # Standard deviation for the distribution of initial membrane potentials, by default: 50.
}
# Network parameters
network_params = {
'N_scaling': scale_down_to, # Scaling of population sizes, by default: 1.
'K_scaling': scale_down_to, # Scaling of indegrees, by default: 1.
'fullscale_rates': 'tests/fullscale_rates.json', # Absolute path to the file holding full-scale rates for scaling synaptic weights, by default: None
'input_params': input_params, # Input parameters
'connection_params': conn_params, # Connection parameters
'neuron_params': neuron_params # Neuron parameters
}
# Simulation parameters
sim_params = {
'areas_simulated': areas_simulated,
't_sim': 2000., # Simulated time (in ms), by default: 10.0
'num_processes': 1, # The number of MPI processes, by default: 1
'local_num_threads': 1, # The number of threads per MPI process, by default: 1
'recording_dict': {'record_vm': False},
'rng_seed': 1 # global random seed
}
# Theory paramters (theory_params)
theory_params = {
'dt': 0.1 # The time step of the mean-field theory integration, by default: 0.01
}
```
%% Output
Cell In [6], line 20
'replace_cc_input_source': replace_cc_input_source
^
SyntaxError: invalid syntax
%% Cell type:markdown id:1472e9c5 tags:
Go back to [Notebook structure](#toc)
%% Cell type:markdown id:de4a6703 tags:
## S2. Multi-Area Model Instantiation and Simulation <a class="anchor" id="section_2"></a>
%% Cell type:markdown id:1fd58841 tags:
### 2.1. Instantiate a multi-area model <a class="anchor" id="section_2_1"></a>
%% Cell type:code id:ab25f9f8 tags:
``` python
%%capture captured
M = MultiAreaModel(network_params,
simulation=True,
sim_spec=sim_params,
theory=True,
theory_spec=theory_params)
```
%% Output
Error in library("aod") : there is no package called ‘aod’
Execution halted
%% Cell type:markdown id:91649c30 tags:
### 2.2. Predict firing rates from theory <a class="anchor" id="section_2_2"></a>
%% Cell type:code id:6a7ddf0e tags:
``` python
p, r = M.theory.integrate_siegert()
print("Mean-field theory predicts an average "
"firing rate of {0:.3f} spikes/s across all populations.".format(np.mean(r[:, -1])))
```
%% Output
Iteration: 0
Mean-field theory predicts an average firing rate of 29.588 spikes/s across all populations.
%% Cell type:markdown id:2062ddf3 tags:
### 2.3. Extract and visualize interareal connectivity <a class="anchor" id="section_2_3"></a>
%% Cell type:markdown id:8a7c09e0 tags:
The connectivity and neuron numbers are stored in the attributes of the model class. Neuron numbers are stored in `M.N` as a dictionary (and in `M.N_vec` as an array), indegrees in `M.K` as a dictionary (and in `M.K_matrix` as an array). Number of synapses can also be access via `M.synapses` (and in `M.syn_matrix` as an array). <br>
%% Cell type:code id:6316ac24 tags:
``` python
# Neuron numbers
# Dictionary of neuron numbers
# print(M.N)
# Array of neuron numbers
# (M.N_vec)
```
%% Cell type:code id:8408d463-557b-481b-afc1-5fbbbd67306d tags:
``` python
# Indegrees
# Dictionary of nodes indegrees organized as:
# {<source_area>: {<source_pop>: {<target_area>: {<target_pop>: indegree_values}}}}
# M.K
# Array of nodes indegrees
# M.K_matrix.shape
```
%% Cell type:code id:445a722a tags:
``` python
# Synapses
# Dictionary of synapses that target neurons receive, it is organized as:
# {<source_area>: {<source_pop>: {<target_area>: {<target_pop>: number_of_synapses}}}}
# M.synapses
# Array of
# M.syn_matrix
```
%% Cell type:code id:05512922-26e5-425f-90a4-0df7c2279ccf tags:
``` python
visualize_interareal_connectivity(M)
```
%% Output
Initializing network from dictionary.
RAND_DATA_LABEL 7864
Error in library("aod") : there is no package called ‘aod’
Execution halted
No R installation or IndexError, taking hard-coded SLN fit parameters.
========================================
Customized parameters
--------------------
{}
========================================
%% Cell type:markdown id:bae85d86-157c-47a2-9826-860b410a440e tags:
Comparable figure in our publications: <br>
1. Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ <br>
Multi-scale account of the network structure of macaque visual cortex
Brain Structure and Function (2018), 223: 1409 [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4) <br>
**Fig. 4 D Area-level connectivity of the model, based on data in a–c, expressed as relative indegrees for each target area**
%% Cell type:markdown id:e67f37e9-ec8d-4bb1-bd21-45e966f47ab6 tags:
Go back to [Notebook structure](#toc)
%% Cell type:markdown id:0c1cad59-81d0-4e24-ac33-13c4ca8c6dec tags:
### 2.4. Run a simulation <a class="anchor" id="section_2_4"></a>
%% Cell type:code id:15778e9c tags:
``` python
# %%capture captured
# run the simulation, depending on the model parameter and downscale ratio, the running time varies largely.
M.simulation.simulate()
```
%% Output
Prepared simulation in 0.00 seconds.
Rank 0: created area V1 with 0 local nodes
Memory after V1 : 1515.25 MB
Rank 0: created area V2 with 0 local nodes
Memory after V2 : 1541.84 MB
Rank 0: created area VP with 0 local nodes
Memory after VP : 1571.05 MB
Created areas and internal connections in 0.21 seconds.
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In [13], line 3
1 # %%capture captured
2 # run the simulation, depending on the model parameter and downscale ratio, the running time varies largely.
----> 3 M.simulation.simulate()
File ~/MAM2EBRAINS/multiarea_model/simulation.py:300, in Simulation.simulate(self)
296 self.time_network_local = t2 - t1
297 print("Created areas and internal connections in {0:.2f} seconds.".format(
298 self.time_network_local))
--> 300 self.cortico_cortical_input()
301 t3 = time.time()
302 self.network_memory = self.memory()
File ~/MAM2EBRAINS/multiarea_model/simulation.py:224, in Simulation.cortico_cortical_input(self)
222 elif replace_non_simulated_areas == 'het_poisson_stat':
223 fn = self.network.params['connection_params']['replace_cc_input_source']
--> 224 with open(fn, 'r') as f:
225 non_simulated_cc_input = json.load(f)
226 elif replace_non_simulated_areas == 'hom_poisson_stat':
TypeError: expected str, bytes or os.PathLike object, not NoneType
%% Cell type:markdown id:fd6e3232 tags:
Go back to [Notebook structure](#toc)
%% Cell type:markdown id:bb71c922 tags:
## S3. Simulation Results Visualization <a class="anchor" id="section_3"></a>
%% Cell type:markdown id:38ddd973 tags:
### 3.1. Instantaneous and mean firing rate across all populations <a class="anchor" id="section_3_1"></a>
%% Cell type:code id:bea30fc8 tags:
``` python
plot_instan_mean_firing_rate(M)
```
%% Cell type:markdown id:e91c436e-db94-4cd7-a531-29c032efeeae tags:
### 3.2 Resting state plots <a class="anchor" id="section_3_2"></a>
%% Cell type:code id:ae19bcc3 tags:
``` python
# Choose 3 areas from the complete_area_list to show their sipking activity
# By default, it's set as ['V1', 'V2', 'FEF']
# Note: at this pre-released multi-area model v2.0.0, the areas_similated has to contain at leat three areas in order to plot the 3 raster plots
raster_areas = ['V1', 'V2', 'VP']
plot_resting_state(M, data_path, raster_areas)
```
%% Cell type:markdown id:cfc2c065-491c-4a3c-bfe2-1233308aaf77 tags:
Comparable figure in our publications: <br>
1. Schmidt M, Bakker R, Shen K, Bezgin B, Diesmann M & van Albada SJ (2018)
A multi-scale layer-resolved spiking network model of
resting-state dynamics in macaque cortex. PLOS Computational Biology, 14(9): e1006359. [https://doi.org/10.1371/journal.pcbi.1006359](https://doi.org/10.1371/journal.pcbi.1006359) <br>
**Fig 3. Ground state of the model.**
%% Cell type:markdown id:473d0882-8e45-4330-bfa2-2c7e1af0dac4 tags:
### 3.3 Time-averaged population rates <a class="anchor" id="section_4_3"></a>
An overview over time-averaged population rates encoded in colors with areas along x-axis and populations along y-axis.
%% Cell type:code id:721d1f03-df25-468d-8075-a807025a9c58 tags:
``` python
plot_time_averaged_population_rates(M)
```
%% Cell type:markdown id:ef74ca3e-98dc-49c9-a4a0-2c640e29b1d9 tags:
Go back to [Notebook structure](#toc)
......
multi-area-model.ipynb
+ 22
− 102
View file @ 28ef1e61
%% Cell type:markdown id:b1331599 tags:
# Down-scaled multi-area model
%% Cell type:markdown id:edec8345-aec1-419e-b9e3-7f612aff8262 tags:
<img src="model_construction.png" alt="Model overview" width="1000"/>
%% Cell type:markdown id:f4a649cc-3b68-49e4-b2b6-6f29f13a6d9c tags:
The code in this notebook implements the down-scaled version of spiking network model of macaque visual cortex developed at the Institute of Neuroscience and Medicine (INM-6), Research Center Jülich. The full-scale model has been documented in the following publications:
1. Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ
Multi-scale account of the network structure of macaque visual cortex
Brain Structure and Function (2018), 223: 1409 [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
2. Schuecker J, Schmidt M, van Albada SJ, Diesmann M & Helias M (2017)
Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome.
PLOS Computational Biology, 13(2): e1005179. [https://doi.org/10.1371/journal.pcbi.1005179](https://doi.org/10.1371/journal.pcbi.1005179)
3. Schmidt M, Bakker R, Shen K, Bezgin B, Diesmann M & van Albada SJ (2018)
A multi-scale layer-resolved spiking network model of
resting-state dynamics in macaque cortex. PLOS Computational Biology, 14(9): e1006359. [https://doi.org/10.1371/journal.pcbi.1006359](https://doi.org/10.1371/journal.pcbi.1006359)
<br>
%% Cell type:markdown id:b952d0ea tags:
#### Notebook structure <a class="anchor" id="toc"></a>
* [S0. Configuration](#section_0)
* [S1. Parameterization](#section_1)
* [1.1. Parameters to tune](#section_1_1)
* [1.2. Default parameters](#section_1_2)
* [S2. Multi-Area Model Instantiation and Simulation](#section_2)
* [2.1. Instantiate a multi-area model](#section_2_1)
* [2.2. Predict firing rates from theory](#section_2_2)
* [2.3. Extract and visualize interareal connectivity](#section_2_3)
* [2.4. Run a simulation](#section_2_4)
* [S3. Simulation Results Visualization](#section_3)
* [3.1. Instantaneous and mean firing rate across all populations](#section_3_1)
* [3.2. Resting state plots](#section_3_2)
* [3.3. Time-averaged population rates](#section_3_3)
%% Cell type:markdown id:d782e527 tags:
## S0. Configuration <a class="anchor" id="section_0"></a>
%% Cell type:code id:9d6cc7d9-3110-4d96-9f9a-9ec7dee6d145 tags:
``` python
# Create config file
with open('config.py', 'w') as fp:
fp.write(
'''import os
base_path = os.path.abspath(".")
data_path = os.path.abspath("simulations")
jobscript_template = "python {base_path}/run_simulation.py {label}"
submit_cmd = "bash -c"
''')
```
%% Cell type:code id:96517739 tags:
``` python
%matplotlib inline
import numpy as np
import os
import nest
import json
import sys
from IPython.display import display, HTML
import warnings
sys.path.append('./figures/MAM2EBRAINS')
from multiarea_model import MultiAreaModel
from M2E_visualize_interareal_connectivity import visualize_interareal_connectivity
from M2E_visualize_instantaneous_and_mean_firing_rates import plot_instan_mean_firing_rate
from M2E_visualize_resting_state import plot_resting_state
from M2E_visualize_time_ave_pop_rates import plot_time_averaged_population_rates
from config import base_path, data_path
```
%% Output
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.5
Built: Jul 12 2023 06:25:27
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
%% Cell type:code id:7e07b0d0 tags:
``` python
%%capture captured
!pip install nested_dict dicthash
```
%% Cell type:code id:1d440c07-9b69-4e52-8573-26b13493bc5a tags:
``` python
# Jupyter notebook display format setting
style = """
<style>
table {float:left}
</style>
"""
display(HTML(style))
warnings.filterwarnings('ignore')
```
%% Output
%% Cell type:markdown id:27160ba8 tags:
Go back to [Notebook structure](#toc)
%% Cell type:markdown id:df83f5ea-1c4b-44d3-9926-01786aa46e14 tags:
## S1. Parameterization <a class="anchor" id="section_1"></a>
%% Cell type:markdown id:30655817 tags:
### 1.1. Parameters to tune <a class="anchor" id="section_1_1"></a>
%% Cell type:markdown id:4f67c1ba tags:
|Parameter|Default value|Value range/options|Value assigned|Description|
|:-------:|:-----------:|:-----------------:|:------------:|:---------:|
|scale_down_to|1. |(0, 1.0] |0.005 |$^1$ |
|cc_weights_factor|1. |[1.0, 2.5] |1. |$^2$ |
|areas_simulated|complete_area_list|Sublists of complete_area_list|complete_area_list|$^3$|
|replace_non_simulated_areas|None|None, 'hom_poisson_stat', 'het_poisson_stat', 'het_current_nonstat'|'het_poisson_stat'|$^4$ |
%% Cell type:markdown id:a2161477 tags:
1. `scale_down_to` is the down-scaling factor that defines the ratio by which the full-scale multi-area model is reduced to a model with fewer neurons and indegrees. This reduction is essential to enable simulation on machines with limited computational power, ensuring that simulation results can be obtained in a relatively shorter timeframe. <br> If the value is `scale_down_to = 1.`, the full-scale network will be simulated. <br> In the pre-set downscale version, it is set to `scale_down_to = 0.005`, This setting reduces both the number of neurons and indegrees to 0.5 % of their full-scale counterparts, facilitating simulation on a typical local machine. <br> **Warning**: This will not yield reasonable dynamical results from the network and is only meant to demonstrate the simulation workflow <br>
2. `cc_weights_factor` is the scaling factor that controls the cortico-cortical synaptic strength. <br> By default it's set as `1.0`, where the inter-area synaptic strength is the same as the intra-areal. <br> **Important**: This factor changes the network activity from ground state to metastable state. <br>
3. `areas_simulated` specifies the cortical areas to be included in the simulation process. Its default value is `complete_area_list` meaning all the areas in the complete_area_list will be simulated. The value assigned to `areas_simulated` can be any sublist of the list below:
```python
complete_area_list = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']
```
<br>
4. `replace_non_simulated_areas` defines how non-simulated areas will be replaced. <br> When all areas are included, it is set as `None` by default. <br> Other options are: `'hom_poisson_stat'`, `'het_poisson_stat'`, and `'het_current_nonstat'`.<br> `'hom_poisson_stat'` replaces the non-simulated areas by Poisson sources with the same global rate `rate_ext`. The `'het_poisson_stat'` and `'het_current_nonstat'` options use the loaded specific rates from `'replace_cc_input_source'`, which contains the area-specific firing rates of our full scale simulation results. The difference between them is that `'het_poisson_stat'` replaces the non-simulated areas by Poisson spike trains and `'het_current_nonstat'` replaces it by a time-varying current input.
%% Cell type:code id:60265d52 tags:
``` python
# Downscaling factor
# Value range/options: (0, 1.]
# Value assigned: 0.005
scale_down_to = 0.005 # Change it to 1. for running the fullscale network
# Scaling factor for cortico-cortical connections (chi)
# Value range/options: [1., 2.5]
# Value assigned: 1.0
cc_weights_factor = 1.0
# Cortical areas included in the simulation
# Value range/options: any sublist of complete_area_list
# where complete_area_list = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']
# Value assigned: complete_area_list
# Note: at this pre-released multi-area model v2.0.0, the areas_similated has to contain at leat three areas in order to plot the 3 raster plots
# areas_simulated = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']
areas_simulated = ['V1', 'V2', 'VP']
# Firing rates used to replace the non-simulated areas
# Value range/options: None, 'hom_poisson_stat', 'het_poisson_stat', 'het_current_nonstat'
# Value assigned: 'het_poisson_stat'
replace_non_simulated_areas = 'het_poisson_stat'
```
%% Cell type:markdown id:de11b07f tags:
### 1.2. Default parameters <a class="anchor" id="section_1_2"></a>
We try our best not to confuse users with too many parameters. However, if you want to change more parameters and explore the model, you can do so by passing a dictionary to the `default_params` argument of the `MultiAreaModel` class. (*NOTE: it should may be moved to the default parameters file in the future.*)
%% Cell type:code id:6e4bed8d tags:
``` python
# Decide the parameter replace_cc_input_source
complete_area_list = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']
if areas_simulated != complete_area_list and replace_non_simulated_areas == None:
raise Exception("When not all areas are simulated, a not None value should be assigned to replace_non_simulated_areas!")
elif replace_non_simulated_areas == 'hom_poisson_stat':
replace_cc_input_source = None
else:
replace_cc_input_source = 'tests/fullscale_rates.json'
# Connection parameters
conn_params = {
'replace_non_simulated_areas': replace_non_simulated_areas, # Whether to replace non-simulated areas by Poisson sources with the same global rate, by default: None
'g': -11., # It sets the relative inhibitory synaptic strength, by default: -16.
'K_stable': 'K_stable.npy', # Whether to apply the stabilization method of Schuecker, Schmidt et al. (2017), by default: None
'fac_nu_ext_TH': 1.2, # Increase the external input to 2/3E and 5E in area TH
'fac_nu_ext_5E': 1.125, # Increase the external Poisson indegree onto 5E
'fac_nu_ext_6E': 1.41666667, # Increase the external Poisson indegree onto 6E
'av_indegree_V1': 3950. # Adjust the average indegree in V1 based on monkey data
'av_indegree_V1': 3950., # Adjust the average indegree in V1 based on monkey data
'replace_cc_input_source': replace_cc_input_source
}
# Input parameters
input_params = {
'rate_ext': 10. # Rate of the Poissonian spike generator (in spikes/s)
}
# Neuron parameters
neuron_params = {
'V0_mean': -150., # Mean for the distribution of initial membrane potentials, by default: -100.
'V0_sd': 50. # Standard deviation for the distribution of initial membrane potentials, by default: 50.
}
# Network parameters
network_params = {
'N_scaling': scale_down_to, # Scaling of population sizes, by default: 1.
'K_scaling': scale_down_to, # Scaling of indegrees, by default: 1.
'fullscale_rates': 'tests/fullscale_rates.json', # Absolute path to the file holding full-scale rates for scaling synaptic weights, by default: None
'input_params': input_params, # Input parameters
'connection_params': conn_params, # Connection parameters
'neuron_params': neuron_params # Neuron parameters
}
# Simulation parameters
sim_params = {
'areas_simulated': areas_simulated,
't_sim': 2000., # Simulated time (in ms), by default: 10.0
'num_processes': 1, # The number of MPI processes, by default: 1
'local_num_threads': 1, # The number of threads per MPI process, by default: 1
'recording_dict': {'record_vm': False},
'rng_seed': 1 # global random seed
}
# Theory paramters (theory_params)
theory_params = {
'dt': 0.1 # The time step of the mean-field theory integration, by default: 0.01
}
```
%% Output
Cell In [6], line 20
'replace_cc_input_source': replace_cc_input_source
^
SyntaxError: invalid syntax
%% Cell type:markdown id:1472e9c5 tags:
Go back to [Notebook structure](#toc)
%% Cell type:markdown id:de4a6703 tags:
## S2. Multi-Area Model Instantiation and Simulation <a class="anchor" id="section_2"></a>
%% Cell type:markdown id:1fd58841 tags:
### 2.1. Instantiate a multi-area model <a class="anchor" id="section_2_1"></a>
%% Cell type:code id:ab25f9f8 tags:
``` python
%%capture captured
M = MultiAreaModel(network_params,
simulation=True,
sim_spec=sim_params,
theory=True,
theory_spec=theory_params)
```
%% Output
Error in library("aod") : there is no package called ‘aod’
Execution halted
%% Cell type:markdown id:91649c30 tags:
### 2.2. Predict firing rates from theory <a class="anchor" id="section_2_2"></a>
%% Cell type:code id:6a7ddf0e tags:
``` python
p, r = M.theory.integrate_siegert()
print("Mean-field theory predicts an average "
"firing rate of {0:.3f} spikes/s across all populations.".format(np.mean(r[:, -1])))
```
%% Output
Iteration: 0
Mean-field theory predicts an average firing rate of 29.588 spikes/s across all populations.
%% Cell type:markdown id:2062ddf3 tags:
### 2.3. Extract and visualize interareal connectivity <a class="anchor" id="section_2_3"></a>
%% Cell type:markdown id:8a7c09e0 tags:
The connectivity and neuron numbers are stored in the attributes of the model class. Neuron numbers are stored in `M.N` as a dictionary (and in `M.N_vec` as an array), indegrees in `M.K` as a dictionary (and in `M.K_matrix` as an array). Number of synapses can also be access via `M.synapses` (and in `M.syn_matrix` as an array). <br>
%% Cell type:code id:6316ac24 tags:
``` python
# Neuron numbers
# Dictionary of neuron numbers
# print(M.N)
# Array of neuron numbers
# (M.N_vec)
```
%% Cell type:code id:8408d463-557b-481b-afc1-5fbbbd67306d tags:
``` python
# Indegrees
# Dictionary of nodes indegrees organized as:
# {<source_area>: {<source_pop>: {<target_area>: {<target_pop>: indegree_values}}}}
# M.K
# Array of nodes indegrees
# M.K_matrix.shape
```
%% Cell type:code id:445a722a tags:
``` python
# Synapses
# Dictionary of synapses that target neurons receive, it is organized as:
# {<source_area>: {<source_pop>: {<target_area>: {<target_pop>: number_of_synapses}}}}
# M.synapses
# Array of
# M.syn_matrix
```
%% Cell type:code id:05512922-26e5-425f-90a4-0df7c2279ccf tags:
``` python
visualize_interareal_connectivity(M)
```
%% Output
Initializing network from dictionary.
RAND_DATA_LABEL 7864
Error in library("aod") : there is no package called ‘aod’
Execution halted
No R installation or IndexError, taking hard-coded SLN fit parameters.
========================================
Customized parameters
--------------------
{}
========================================
%% Cell type:markdown id:bae85d86-157c-47a2-9826-860b410a440e tags:
Comparable figure in our publications: <br>
1. Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ <br>
Multi-scale account of the network structure of macaque visual cortex
Brain Structure and Function (2018), 223: 1409 [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4) <br>
**Fig. 4 D Area-level connectivity of the model, based on data in a–c, expressed as relative indegrees for each target area**
%% Cell type:markdown id:e67f37e9-ec8d-4bb1-bd21-45e966f47ab6 tags:
Go back to [Notebook structure](#toc)
%% Cell type:markdown id:0c1cad59-81d0-4e24-ac33-13c4ca8c6dec tags:
### 2.4. Run a simulation <a class="anchor" id="section_2_4"></a>
%% Cell type:code id:15778e9c tags:
``` python
# %%capture captured
# run the simulation, depending on the model parameter and downscale ratio, the running time varies largely.
M.simulation.simulate()
```
%% Output
Prepared simulation in 0.00 seconds.
Rank 0: created area V1 with 0 local nodes
Memory after V1 : 1515.25 MB
Rank 0: created area V2 with 0 local nodes
Memory after V2 : 1541.84 MB
Rank 0: created area VP with 0 local nodes
Memory after VP : 1571.05 MB
Created areas and internal connections in 0.21 seconds.
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In [13], line 3
1 # %%capture captured
2 # run the simulation, depending on the model parameter and downscale ratio, the running time varies largely.
----> 3 M.simulation.simulate()
File ~/MAM2EBRAINS/multiarea_model/simulation.py:300, in Simulation.simulate(self)
296 self.time_network_local = t2 - t1
297 print("Created areas and internal connections in {0:.2f} seconds.".format(
298 self.time_network_local))
--> 300 self.cortico_cortical_input()
301 t3 = time.time()
302 self.network_memory = self.memory()
File ~/MAM2EBRAINS/multiarea_model/simulation.py:224, in Simulation.cortico_cortical_input(self)
222 elif replace_non_simulated_areas == 'het_poisson_stat':
223 fn = self.network.params['connection_params']['replace_cc_input_source']
--> 224 with open(fn, 'r') as f:
225 non_simulated_cc_input = json.load(f)
226 elif replace_non_simulated_areas == 'hom_poisson_stat':
TypeError: expected str, bytes or os.PathLike object, not NoneType
%% Cell type:markdown id:fd6e3232 tags:
Go back to [Notebook structure](#toc)
%% Cell type:markdown id:bb71c922 tags:
## S3. Simulation Results Visualization <a class="anchor" id="section_3"></a>
%% Cell type:markdown id:38ddd973 tags:
### 3.1. Instantaneous and mean firing rate across all populations <a class="anchor" id="section_3_1"></a>
%% Cell type:code id:bea30fc8 tags:
``` python
plot_instan_mean_firing_rate(M)
```
%% Cell type:markdown id:e91c436e-db94-4cd7-a531-29c032efeeae tags:
### 3.2 Resting state plots <a class="anchor" id="section_3_2"></a>
%% Cell type:code id:ae19bcc3 tags:
``` python
# Choose 3 areas from the complete_area_list to show their sipking activity
# By default, it's set as ['V1', 'V2', 'FEF']
# Note: at this pre-released multi-area model v2.0.0, the areas_similated has to contain at leat three areas in order to plot the 3 raster plots
raster_areas = ['V1', 'V2', 'VP']
plot_resting_state(M, data_path, raster_areas)
```
%% Cell type:markdown id:cfc2c065-491c-4a3c-bfe2-1233308aaf77 tags:
Comparable figure in our publications: <br>
1. Schmidt M, Bakker R, Shen K, Bezgin B, Diesmann M & van Albada SJ (2018)
A multi-scale layer-resolved spiking network model of
resting-state dynamics in macaque cortex. PLOS Computational Biology, 14(9): e1006359. [https://doi.org/10.1371/journal.pcbi.1006359](https://doi.org/10.1371/journal.pcbi.1006359) <br>
**Fig 3. Ground state of the model.**
%% Cell type:markdown id:473d0882-8e45-4330-bfa2-2c7e1af0dac4 tags:
### 3.3 Time-averaged population rates <a class="anchor" id="section_4_3"></a>
An overview over time-averaged population rates encoded in colors with areas along x-axis and populations along y-axis.
%% Cell type:code id:721d1f03-df25-468d-8075-a807025a9c58 tags:
``` python
plot_time_averaged_population_rates(M)
```
%% Cell type:markdown id:ef74ca3e-98dc-49c9-a4a0-2c640e29b1d9 tags:
Go back to [Notebook structure](#toc)
......
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